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The methods are also useful for monitoring patient therapy and for selecting a course of therapy. Genes modulated in response to FTI treatment are provided and are used in formulating the profiles. \n","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"}]},"abstract_lang":["en"],"has_abstract":true,"claim":{"en":[{"text":"1 . A method of determining whether a patient will respond to treatment with an FTI by analyzing the expression of a gene that is differentially modulated in the presence of an FTI.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"2 . The method of claim 1 wherein the differential modulation is at least 1.5 fold.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"3 . The method of claim 1 wherein the differential modulation is at least 1.7 fold.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"4 . The method of claim 1 wherein the analysis is of the expression of more than one gene.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"5 . The method of claim 1 wherein the gene correlates with one or more nucleic acid sequences identified in Tables 1-3","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"6 . The method of claim 1 used to monitor the therapy of a patient.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"7 . The method of claim 5 wherein the FTI is (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone).","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"8 . The method of claim 1 wherein the analysis is of the expression of a group of genes correlating with nucleic acid sequences identified in Tables 1-3 and wherein the FTI is (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone).","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"9 . A method of treating a patient comprising: a) analyzing the gene expression profile of said patient to determine whether the patient will respond to treatment with an FTI, and b) treating the patient with the FTI if the analysis indicates that the patient will respond.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"10 . The method of claim 9 wherein the analysis is of the expression of more than one gene.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"11 . The method of claim 9 wherein the FTI is selected from the group consisting of quinolines or quinoline derivatives.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"12 . The method of claim 11 wherein the FTI is selected from the group consisting of 7-(3-chlorophenyl)-9-(4-chlorophenyl)-1H-imidazol-1-ylmethyl-2,3-dihydro-1H,5H-benzoijquinolizin-5-one, 7-(3-chlorophenyl)-9-(4-chlorophenyl)-1H-imidazol-1-ylmethyl-1,2-dihydro-4H-pyrrolo3,2,1-ijquinoline-4-one, 8-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-6-(3-chlorophen yl)-1,2-dihydro-4H-pyrrolo3,2,1-ijquinolin-4-one, 8-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-6-(3-chloropheny l)-2,3-dihydro-1H,5H-benzoijquinolizin-5-one, and (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone).","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"13 . The method of claim 12 wherein the FTI is (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone)","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"14 . The method of claim 10 wherein the genes correlate with one or more nucleic acid sequences identified in Tables 1-3.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"15 . The method of claim 9 wherein the treatment comprises the administration of an FTI and another therapeutic composition.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"16 . The method of claim 15 wherein said another therapeutic composition modulates MAPK/ERK signaling pathways, TGF, WNT or apoptotic pathways.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"17 . The method of claim 16 wherein said another composition is selected from the group consisting of tyrosine kinase inhibitors, MEK kinase inhibitors, PI3 kinase inhibitors, MAP kinase inhibitors, apoptosis modulators, and combinations thereof.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"18 . Articles for assessing the efficacy of treatment of a patient with an FTI comprising a medium with which patient gene expression profiles indicative of FTI response are determined.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"19 . The articles of claim 18 wherein the gene expression profiles are obtained from a group of genes correlating to more than one nucleic acid sequences identified in Tables 1-3.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"20 . The articles of claim 19 wherein the nucleic acid sequences are found in Table 3.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"21 . The articles of claim 18 comprising representations of gene expression profiles fixed to a medium.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"22 . The articles of claim 18 wherein the medium is computer readable.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"23 . Kits comprising articles for obtaining gene expression profiles for determining response to FTI treatment.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"},{"text":"24 . The kits of claim 23 further comprising instructions.","lang":"en","source":"USPTO_FULLTEXT","data_format":"ORIGINAL"}]},"claim_lang":["en"],"has_claim":true,"description":{"en":{"text":"\n This application claims the benefit of the following U.S. Provisional applications: 60/340,938; 60/338,997; 60/340,081; and 60/341,012. This invention relates to diagnostics, prognostics, and treatments for leukemia based on the gene expression profiles of leukemia cells.\n\n\nBACKGROUND \n\n Some molecules, such as Ras, that are implicated in cancers must be farnesylated by the farnesyl transferase enzyme in order to interact with the inner leaflet of the plasma membrane of the cell and become involved in various signaling pathways. Ras is not the only protein implicated in cancer that has a CAAX box that is prenylated. Farnesyl transferase inhibitors (FTIs) are therapeutic agents that inhibit the covalent attachment of the carbon farnesyl moieties to the C-terminal CAAX motif of various proteins. They have utility in the treatment of cancers and proliferative disorders such as leukemia. Acute myclogenous leukemia (AML) is among the diseases that can most beneficially be addressed with FTIs. \n\n As is true in the case of many treatment regimens, some patients respond to treatment with FTIs and others do not. Prescribing the treatment to a patient who is unlikely to respond to it is not desirable. Thus, it would be useful to know how a patient could be expected to respond to such treatment before a drug is administered so that non-responders would not be unnecessarily treated and so that those with the best chance of benefiting from the drug are properly treated and monitored. Further, of those who respond to treatment, there may be varying degrees of response. Treatment with therapeutics other than FTIs or treatment with therapeutics in addition to FTIs may be beneficial for those patients who would not respond to FTIs or in whom response to FTIs alone is less than desired. \n\nSUMMARY OF THE INVENTION \n\n The invention is a method of treating a patient with leukemia with an FTI. In one such method, the patient's gene expression profile is analyzed to determine whether the patient is likely to respond to the FTI and treating a patient with the FTI if they are likely to respond. \n\n In another aspect of the invention, a patient with leukemia is monitored for treatment with an FTI in which the patient's gene expression profile is analyzed to determine whether the patient is responding to the FTI and treating a patient with the FTI if they are likely to respond in a desirable fashion. \n\n In yet another aspect of the invention, a patient is treated if the gene expression profile shows up regulation of one or more particular genes indicative of FTI responders. \n\n In yet another aspect of the invention, gene expression profiles indicative of FTI responders are those which show at least a 1.5, 1.7, or 2 fold difference relative to FTI non-responders. \n\n In yet another aspect of the invention, a patient is treated if the gene expression profile shows down regulation of one or more particular genes indicative of FTI responders In yet another aspect of the invention, a patient is treated if the gene expression profile shows modulation of a gene selected from the group of genes identified in Tables 1-3 infra. \n\n In yet another aspect of the invention, the FTI is a quinilone or quinoline derivative. \n\n In yet another aspect of the invention, the FTI is (B)-6-amino(420 chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone). \n\n Articles used in practicing the methods are also an aspect of the invention. Such articles include gene expression profiles or representations of them that are fixed in computer readable media. Other articles according to the invention include nucleic acid arrays used to determine the gene expression profiles of the invention. \n\n In another aspect of the invention, a method of treating a patient with leukemia comprises administering an FTI and a therapeutic composition that modulates the MAPK/ERK signaling pathways, TGF, WNT or apoptotic pathways. \n\n In another aspect of the invention, the patient is treated with an FTI and a therapeutic composition selected from the group consisting of tyrosine kinase inhibitors, MEK kinase inhibitors, PI3K kinase inhibitors, MAP kinase inhibitors, apoptosis modulators and combinations thereof. \n\n In yet another aspect of this invention, the gene expression profile of a patient with leukemia is analyzed to determine whether the patient is likely to respond to an FTI or if the patient would likely benefit from the combination of an FTI and another drug. The patient is then treated with such combination or, if the patient is unlikely to respond to an FTI, the patient is treated with drug selected from the group consisting of tyrosine kinase inhibitors, MEK kinase inhibitors, PI3K kinase inhibitors, MAP kinase inhibitors, apoptosis modulators and combinations thereof.\n\n\nBRIEF DESCRIPTION OF THE DRAWINGS \n\n FIG. 1 is an example of a graphical display of gene expression patterns used to analyze the gene expression profiles of this invention. \n\n FIG. 2 is a schematic diagram of the MAPK/ERK pathway. \n\n FIG. 3 is a schematic diagram of the TGF and Wnt pathway. \n\n FIG. 4 is a schematic diagram of the apoptotic pathway. \n\n\nDETAILED DESCRIPTION \n\n The therapeutic agents referred to in this specification are FTIs. They take on a multitude of forms but share the essential inhibitory function of interfering with or lessening the farnesylation of proteins implicated in cancer and proliferative diseases. Preferably, the FTIs are those indicated for the treatment of leukemias such as AML. A patient who responds to an FTI is one in whom a reduction of more than 50% of blast cells is seen in bone marrow following treatment with the FTI. \n\n Numerous FTIs are within the scope of the invention and include those described in U.S. Patents: U.S. Pat. No. 5,976,851 to Brown et al; U.S. Pat. No. 5,972,984 to Anthony et al.; U.S. Pat. No. 5,972,966 to deSolms; U.S. Pat. No. 5,968,965 to Dinsmore et al.; U.S. Pat. No. 5,968,952 to Venet et al.; U.S. Pat. No. 6,187,786 to Venet et al.; U.S. Pat. No. 6,169,096 to Venet et al.; U.S. Pat. No. 6,037,350 to Venet et. al.; U.S. Pat. No. 6,177,432 to Angibaud et al.; U.S. Pat. No. 5,965,578 to Graham et al.; U.S. Pat. No. 5,965,539 to Sebti et al.; U.S. Pat. No. 5,958,939 to Afonso et al.; U.S. Pat. No. 5,939,557 to Anthony et al.; U.S. Pat. No. 5,936,097 to Commercon et al.; U.S. Pat. No. 5,891,889 to Anthony et al.; U.S. Pat. No. 5,889,053 to Baudin et al.; U.S. Pat. No. 5,880,140 to Anthony; U.S. Pat. No. 5,872,135 to deSolms; U.S. Pat. No. 5,869,682 to deSolms; U.S. Pat. No. 5,861,529 to Baudoin; U.S. Pat. No. 5,859,015 to Graham et al.; U.S. Pat. No. 5,856,439 to Clerc; U.S. Pat. No. 5,856,326 to Anthony et al.; U.S. Pat. No. 5,852,010 to Graham et al.; U.S. Pat. No. 5,843,941 to Marsters et al.; U.S. Pat. No. 5,807,852 to Doll; U.S. Pat. No. 5,780,492 to Dinsmore et al.; U.S. Pat. No. 5,773,455 to Dong et al.; U.S. Pat. No. 5,767,274 to Kim et al.; U.S. Pat. No. 5,756,528 to Anthony et al.; U.S. Pat. No. 5,750,567 to Baudoin et al.; U.S. Pat. No. 5,721,236 to Bishop et al,; U.S. Pat. No. 5,700,806 to Doll et al.; U.S. Pat. No. 5,661,161 to Anthony et al.; U.S. Pat. No. 5,602,098 to Sebti et al.; U.S. Pat. No. 5,585,359 to Breslin et al.; U.S. Pat. No. 5,578,629 to Ciccarone et al.; U.S. Pat. No. 5,534,537 to Ciccarone et al.; U.S. Pat. No. 5,532,359 to Marsters et al.; U.S. Pat. No. 5,523,430 to Patel et al.; U.S. Pat. No. 5,504,212 to de Solms et al.; U.S. Pat. No. 5,491,164 to deSolms et al.; U.S. Pat. No. 5,420,245 to Brown et al.; and U.S. Pat. No. 5,238,922 to Graham et al. each of which is incorporated herein by reference. Non-peptidal, so-called small molecule therapeutics are preferred. More preferred FTIs are quinolines or quinoline derivatives such as: \n\n 7-(3-chlorophenyl)-9-(4-chlorophenyl)-1H-imidazol-1-ylmethyl-2,3-dihydro-1H,5H-benzoijquinolizin-5-one, \n\n 7-(3-chlorophenyl)-9-(4-chlorophenyl)-1H-imidazol-1-ylmethyl-1,2-dihydro-4H-pyrrolo3,2,1-ijquinoline-4-one, \n\n 8-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-6-(3-chlorophen yl)-1,2-dihydro-4H-pyrrolo3,2,1-ijquinolin-4-one, and \n\n 8-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-6-(3-chloropheny l)-2,3-dihydro-1H,5H-benzoijquinolizin-5-one. \n\n The most preferred FTI is (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone). \n\n In the aspect of the invention comprising treating leukemia with FTIs and other therapeutic agents, The therapeutic agents referred to in this specification are those that have an effect on the biological pathway explicated through the gene expression analysis of leukemic cells subjected to treatment with quinilone-based FTIs. \n\n The mere presence of nucleic acid sequences having the potential to express proteins or peptides (genes) within the genome is not determinative of whether a protein or peptide is expressed in a given cell. Whether or not a given gene capable of expressing proteins or peptides does so and to what extent such expression occurs, if at all, is determined by a variety of complex factors. Irrespective of difficulties in understanding and assessing these factors, assaying gene expression can provide useful information about the cellular response to a given stimulus such as the introduction of a drug or other therapeutic agent. Relative indications of the degree to which genes are active or inactive can be found in gene expression profiles. The gene expression profiles of this invention are used to identify and treat patients who will likely benefit from a given therapy or exclude patients from a given therapy where the patient likely would experience little or no beneficial response to the drug or therapy. \n\n Preferred methods for establishing gene expression profiles (including those used to arrive at the explication of the relevant biological pathways) include determining the amount of RNA that is produced by a gene that can code for a protein or peptide. This is accomplished by reverse transcription PCR (RT-PCR), competitive RT-PCR, real time RT-PCR, differential display RT-PCR, Northern Blot analysis and other related tests. While it is possible to conduct these techniques using individual PCR reactions, it is best to amplify copy DNA (cDNA) or copy RNA (cRNA) produced from mRNA and analyze it via microarray. A number of different array configurations and methods for their production are known to those of skill in the art and are described in U.S. Patents such as: U.S. Pat. Nos. 5,445,934; 5,532,128; 5,556,752; 5,242,974; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,472,672; 5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,561,071; 5,571,639; 5,593,839; 5,599,695; 5,624,711; 5,658,734; and 5,700,637; the disclosures of which are herein incorporated by reference. \n\n Microarray technology allows for the measurement of the steady-state mRNA level of thousands of genes simultaneously thereby presenting a powerful tool for identifying the effect of FTIs on cell biology and the likely effect of treatment based on analysis of such effects. Two microarray technologies are currently in wide use. The first are cDNA arrays and the second are oligonucleotide arrays. Although differences exist in the construction of these chips, essentially all downstream data analysis and output are the same. The product of these analyses are typically measurements of the intensity of the signal received from a labeled probe used to detect a cDNA sequence from the sample that hybridizes to a nucleic acid sequence at a known location on the microarray. Typically, the intensity of the signal is proportional to the quantity of cDNA, and thus mRNA, expressed in the sample cells. A large number of such techniques are available and useful. Preferred methods for determining gene expression can be found in U.S. Pat. No. 6,271,002 to Linsley, et al.; U.S. Pat. No. 6,218,122 to Friend, et al.; U.S. Pat. No. 6,218,114 to Peck, et al.; and U.S. Pat. No. 6,004,755 to Wang, et al., the disclosure of each of which is incorporated herein by reference. \n\n Analysis of the expression levels is conducted by comparing such intensities. This is best done by generating a ratio matrix of the expression intensities of genes in a test sample versus those in a control sample. For instance, the gene expression intensities from a tissue that has been treated with a drug can be compared with the expression intensities generated from the same tissue that has not been treated with the drug. A ratio of these expression intensities indicates the fold-change in gene expression between the test and control samples. \n\n Gene expression profiles can also be displayed in a number of ways. The most common method is to arrange a ratio matrix into a graphical dendogram where columns indicate test samples and rows indicate genes. The data is arranged so genes that have similar expression profiles are proximal to each other (e.g., FIG. 1 ). The expression ratio for each gene is visualized as a color. For example, a ratio less than one (indicating down-regulation) may appear in the blue portion of the spectrum while a ratio greater than one (indicating up-regulation) may appear as a color in the red portion of the specrtum. Commercially available computer software programs are available to display such data including OMNIVIZ PRO software from Batelle and TREE VIEW software from Stanford The genes that are differentially expressed are either up regulated or down regulated in diseased cells following treatment with an FTI. Up regulation and down regulation are relative terms meaning that a detectable difference (beyond the contribution of noise in the system used to measure it) is found in the amount of expression of the genes relative to some baseline. In this case, the baseline is the measured gene expression of the untreated diseased cell. The genes of interest in the treated diseased cells are then either up regulated or down regulated relative to the baseline level using the same measurement method. Preferably, levels of up and down regulation are distinguished based on fold changes of the intensity measurements of hybridized microarray probes. A 1.5 fold difference is preferred for making such distinctions. That is, before a gene is said to be differentially expressed in treated versus untreated diseased cells, the treated cell is found to yield at least 1.5 times more, or 1.5 times less intensity than the untreated cells. A 1.7 fold difference is more preferred and a 2 or more fold difference in gene expression measurement is most preferred. Table 3 lists genes that were commonly modulated across all cell lines and in responder samples. \n\n A portfolio of genes is a set of genes grouped so that information obtained about them provides the basis for making a clinically relevant judgment such as a diagnosis, prognosis, or treatment choice. In this case, the judgments supported by the portfolios involve the treatment of leukemias with FTIs. Portfolios of gene expression profiles can be comprised of combinations of genes shown in Tables 1-3. \n\n One method of the invention involves comparing gene expression profiles for various genes to determine whether a person is likely to respond to the use of a therapeutic agent. Having established the gene expression profiles that distinguish responder from nonresponder, the gene expression profiles of each are fixed in a medium such as a computer readable medium as described below. A patient sample is obtained that contains diseased cells (such as hematopoietic blast cells in the case of AML) is then obtained. Sample RNA is then obtained and amplified from the diseased patient cell and a gene expression profile is obtained, preferably via micro-array, for genes in the appropriate portfolios. The expression profiles of the samples are then compared to those previously determined as responder and non-responder. If the sample expression patterns are consistent with an FTI responder expression pattern then treatment with an FTI could be indicated (in the absence of countervailing medical considerations). If the sample expression patterns are consistent with an FTI non-responder expression pattern then treatment with an FTI would not be indicated. Preferably, consistency of expression patterns is determined based on intensity measurements of micro-array reading as described above. \n\n In similar fashion, gene expression profile analysis can be conducted to monitor treatment response. In one aspect of this method, gene expression analysis as described above is conducted on a patient treated with an FTI at various periods throughout the course of treatment. If the gene expression patterns are consistent with a responder then the patient's therapy is continued. If it is not, then the patient's therapy is altered as with additional therapeutics such as tyrosine kinase inhibitor, changes to the dosage, or elimination of FTI treatment. Such analysis permits intervention and therapy adjustment prior to detectable clinical indicia or in the face of otherwise ambiguous clinical indicia. \n\n It is possible to attain ambiguous results in which some gene expression profiles are recorded that are in some respects indicative of a responder and in other respects indicative of a non-responder. For example, the profiles may show that three genes are up-regulated consistent with a responder but that another gene is not up-regulated as would ordinarily be the case for a responder. In such a case, statistical algorithms can be applied to determine the probability that the patient will respond or not respond to the drug. Statistical algorithms suitable for this purpose are well known and are available. \n\n Articles of this invention are representations of the gene expression profiles useful for treating, diagnosing, prognosticating, staging, and otherwise assessing diseases that are reduced to a medium that can be automatically read such as computer readable media (magnetic, optical, and the like). The articles can also include instructions for assessing the gene expression profiles in such media. For example, the articles may comprise a CD ROM having computer instructions for comparing gene expression profiles of the portfolios of genes described above. The articles may also have gene expression profiles digitally recorded therein so that they may be compared with gene expression data from patient samples. Alternatively, the profiles can be recorded in different representational format. A graphical recordation is one such format. FIG. 1 shows an example of the graphical display of such a recordation. Clustering algorithms such as those incorporated in OMNIVIZ and TREE VIEW computer programs mentioned above can best assist in the visualization of such data. \n\n Additional articles according to the invention are nucleic acid arrays (e.g. cDNA or oligonucleotide arrays), as described above, configured to discern the gene expression profiles of the invention. \n\n Using clustering analysis (including the algorithms mentioned above) one can compare the expression levels of patient samples to establish regulatory relationships among genes with a certain statistical confidence. A dynamic map was constructed based upon such expression data. Such a genetic network map is useful for drug discovery. For example, once basic genes of interest were identified, a list of potential up-stream regulatory genes was found using such a genetic network map. The genes so identified or their expression products were then analyzed for their use as drug targets. In some embodiments, the regulatory function of the particular genes identified was used to identify therapeutics for use in treating leukemia. \n\n The regulation of transcription, RNA processing and RNA editing are all accomplished by proteins which are coded by their own genes. In addition, DNA sequences can exert long range control over the expression of other genes by positional effects. Therefore, the expression of genes is often regulated by the expression of other genes. Those regulatory genes are called upstream genes, relative to the regulated or down-stream genes. In a simple regulatory pathway: \n\n A>B>C>D \n\n where: A, B, C, D are genes \n\n up-regulates \n\n down-regulates \n\n Gene A is an up-stream gene of gene B and B is an up-stream gene of C. One of skill in the art would appreciate that the network is frequently looped and inter-connected. In some instances, the expression of a gene is regulated by its own product as either a positive or negative feedback. \n\n Cluster analysis methods were used to group genes whose expression level is correlated. Methods for cluster analysis are described in detail in Harfigan (1975) Clustering Algorithms, NY, John Wile and Sons, Inc, and Everritt, (1980) Cluster Analysis 2nd. Ed. London Heineman Educational books, Ltd., incorporated herein for all purposed by reference. Path analysis was used to decompose relations among variables and for testing causal models for the genetic networks. Multiple primary targets of a drug in leukemic cells were identified as were drugs/drug classes useful in treating such cells. According to the current invention, drugs are any compounds of any degree of complexity that perturb a biological system. \n\n The biological effect of a drug may be a consequence of drug-mediated changes in the rate of transcription or degradation of one or more species of RNA, the rate or extent of translation or post-translational processing of one or more polypeptides, the rate or extent of the degradation of one or more proteins, the inhibition or stimulation of the action or activity of one or more proteins, and so forth. In addition to the FTIs that are preferred, the preferred drugs of this invention are those that modulate the MAPK/ERK signaling pathways, TGF, WNT or apoptotic pathways. These include, without limitation, tyrosine kinase inhibitors, MEK kinase inhibitors, P13K kinase inhibitors, MAP kinase inhibitors, apoptosis modulators and combinations thereof. Exemplary drugs that are most preferred among these are the GLEEVEC tyrosine kinase inhibitor of Novartis, U-0126 MAP kinase inhibitor, PD-098059 MAP kinase inhibitor, SB-203580 MAP kinase inhibitor, and antisense, ribozyme, and DNAzyme Bcl-XL anti-apoptotics. Examples of other useful drugs include, without limitation, the calanolides of U.S. Pat. No. 6,306,897; the substituted bicyclics of U.S. Pat. No. 6,284,764; the indolines of U.S. Pat. No. 6,133,305; and the antisense oligonucleotides of U.S. Pat. No. 6,271,210. \n\n As noted, the drugs of the instant invention can be therapeutics directed to gene therapy or antisense therapy. Oligonucleotides with sequences complementary to a mRNA sequence can be introduced into cells to block the translation of the mRNA, thus blocking the function of the gene encoding the mRNA. The use of oligonucleotides to block gene expression is described, for example, in, Strachan and Read, Human Molecular Genetics, 1996, incorporated herein by reference. \n\n These antisense molecules may be DNA, stable derivatives of DNA such as phosphorothioates or methylphosphonates, RNA, stable derivatives of RNA such as 2-O-alkylRNA, or other antisense oligonucleotide mimetics. Antisense molecules may be introduced into cells by microinjection, liposome encapsulation or by expression from vectors harboring the antisense sequence. \n\n In the case of gene therapy, the gene of interest can be ligated into viral vectors that mediate transfer of the therapeutic DNA by infection of recipient host cells. Suitable viral vectors include retrovirus, adenovirus, adeno-associated virus, herpes virus, vaccinia virus, polio virus and the like. Alternatively, therapeutic DNA can be transferred into cells for gene therapy by non-viral techniques including receptor-mediated targeted DNA transfer using ligand-DNA conjugates or adenovirus-ligand-DNA conjugates, lipofection membrane fusion or direct microinjection. These procedures and variations thereof are suitable for ex vivo as well as in vivo gene therapy. Protocols for molecular methodology of gene therapy suitable for use with the gene is described in Gene Therapy Protocols, edited by Paul D. Robbins, Human press, Totawa N.J., 1996. \n\n Pharmaceutically useful compositions comprising the drugs of this invention may be formulated according to known methods such as by the admixture of a pharmaceutically acceptable carrier. Examples of such carriers and methods of formulation may be found in Remington's Pharmaceutical Sciences. To form a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of the drug. The effective amount of the drug may vary according to a variety of factors such as the individual's condition, weight, sex and age. Other factors include the mode of administration. The pharmaceutical compositions may be provided to the individual by a variety of routes such as subcutaneous, topical, oral and intramuscular. \n\n The drugs of this invention include chemical derivatives of the base molecules of the drug. That is, they may contain additional chemical moieties that are not normally a part of the base molecule. Such moieties may improve the solubility, half-life, absorption, etc. of the base molecule. Alternatively the moieties may attenuate undesirable side effects of the base molecule or decrease the toxicity of the base molecule. Examples of such moieties are described in a variety of texts, such as Remington's Pharmaceutical Sciences. \n\n Compounds identified according to the methods disclosed herein may be used alone at appropriate dosages defined by routine testing in order to obtain optimal inhibition or activity while minimizing any potential toxicity. In addition, coadministration or sequential administration of other agents may be desirable. \n\n The drugs of this invention can be administered in a wide variety of therapeutic dosage forms in conventional vehicles for administration. For example, the drugs can be administered in such oral dosage forms as tablets, capsules (each including timed release and sustained release formulations), pills, powders, granules, elixirs, tinctures, solutions, suspensions, syrups and emulsions, or by injection. Likewise, they may also be administered in intravenous (both bolus and infusion), intraperitoneal, subcutaneous, topical with or without occlusion, or intramuscular form, all using forms well known to those of ordinary skill in the pharmaceutical arts. An effective but non-toxic amount of the compound desired can be employed as a modulating agent. \n\n The daily dosage of the products may be varied over a wide range from 0.01 to 1,000 mg per patient, per day. For oral administration, the compositions are preferably provided in the form of scored or unscored tablets containing 0.01, 0.05, 0.1, 0.5, 1.0, 2.5, 5.0, 10.0, 15.0, 25.0, and 50.0 milligrams of the active ingredient for the symptomatic adjustment of the dosage to the patient to be treated. An effective amount of the drug is ordinarily supplied at a dosage level of from about 0.0001 mg/kg to about 100 mg/kg of body weight per day. The range is more particularly from about 0.001 mg/kg to 10 mg/kg of body weight per day. The dosages are adjusted when combined to achieve desired effects. On the other hand, dosages of these various agents may be independently optimized and combined to achieve a synergistic result wherein the pathology is reduced more than it would be if either agent were used alone. \n\n Advantageously, compounds or modulators used in the present invention may be administered in a single daily dose, or the total daily dosage may be administered in divided doses of two, three or four times daily. Furthermore, compounds or modulators for the present invention can be administered in intranasal form via topical use of suitable intranasal vehicles, or via transdermal routes, using those forms of transdermal skin patches well known to those of ordinary skill in that art. To be administered in the form of a transdermal delivery system, the dosage administration will, of course, be continuous rather than intermittent throughout the dosage regimen., For combination treatment with more than one active agent, where the active agents are in separate dosage formulations, the active agents can be administered concurrently, or they each can be administered at separately staggered times. \n\n The dosage regimen utilizing the compounds or modulators in the present invention is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal and hepatic function of the patient; and the particular drug employed. A physician or veterinarian of ordinary skill can readily determine and prescribe the effective amount of the drug required to prevent, counter or arrest the progress of the condition. Optimal precision in achieving concentrations of drug within the range that yields efficacy without toxicity requires a regimen based on the kinetics of the drug's availability to target sites. This involves a consideration of the distribution, equilibrium, and elimination of a drug. \n\n The drugs of this invention can form the active ingredient, and are typically administered in admixture with suitable pharmaceutical diluents, excipients or carriers (collectively referred to herein as carrier materials) suitably selected with respect to the intended form of administration, that is, oral tablets, capsules, elixirs, syrups and the like, and consistent with conventional pharmaceutical practices. \n\n For instance, for oral administration in the form of a tablet or capsule, the active drug component can be combined with an oral, non-toxic pharmaceutically acceptable inert carrier such as ethanol, glycerol, water and the like. Moreover, when desired or necessary, suitable binders, lubricants, disintegrating agents and coloring agents can also be incorporated into the mixture. Suitable binders include, without limitation, starch, gelatin, natural sugars such as glucose or beta-lactose, corn sweeteners, natural and synthetic gums such as acacia, tragacanth or sodium alginate, carboxymethylcellulose, polyethylene glycol, waxes and the like. Lubricants used in these dosage forms include, without limitation, sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride and the like. Disintegrators include, without limitation, starch, methyl cellulose, agar, bentonite, xanthan gum and the like. \n\n For liquid forms the active drug component can be combined in suitably flavored suspending or dispersing agents such as the synthetic and natural gums, for example, tragacanth, acacia, methyl-cellulose and the like. Other dispersing agents that may be employed include glycerin and the like. For parenteral administration, sterile suspensions and solutions are desired. Isotonic preparations, which generally contain suitable preservatives, are employed when intravenous administration is desired. \n\n The drugs in the present invention can also be administered in the form of liposome delivery systems, such as small unilamellar vesicles, large unilamellar vesicles and multilamellar vesicles. Liposomes can be formed from a variety of phospholipids, such as cholesterol, stearylamine or phosphatidylcholines. \n\n Drugs in the present invention may also be delivered by the use of monoclonal antibodies as individual carriers to which the compound molecules are coupled. The drugs in the present invention may also be coupled with soluble polymers as targetable drug carriers. Such polymers can include polyvinylpyrrolidone, pyran copolymer, polyhydroxypropylmethacryl-amidephenol, polyhydroxy-ethylaspartamidephenol, or polyethyl-eneoxidepolylysine substituted with palmitoyl residues. Furthermore, the drugs in the present invention may be coupled to a class of biodegradable polymers useful in achieving controlled release of a drug, for example, polylactic acid, polyepsilon caprolactone, polyhydroxy butyric acid, polyorthoesters, polyacetals, polydihydro-pyrans, polycyanoacrylates and cross-linked or amphipathic block copolymers of hydrogels. \n\n For oral administration, the drugs may be administered in capsule, tablet, or bolus form or alternatively they can be mixed with feed. The capsules, tablets, and boluses are comprised of the active ingredient in combination with an appropriate carrier vehicle such as starch, talc, magnesium stearate, or di-calcium phosphate. These unit dosage forms are prepared by intimately mixing the active ingredient with suitable finely-powdered inert ingredients including diluents, fillers, disintegrating agents, and/or binders such that a uniform mixture is obtained. An inert ingredient is one that will not react with the drugs and which is non-toxic to the animal being treated. Suitable inert ingredients include starch, lactose, talc, magnesium stearate, vegetable gums and oils, and the like. These formulations may contain a widely variable amount of the active and inactive ingredients depending on numerous factors such as the size and type of the animal species to be treated and the type and severity of the infection. The active ingredient may also be administered by simply mixing the compound with the feedstuff or by applying the compound to the surface of the foodstuff. \n\n The compounds or modulators may alternatively be administered parenterally via injection of a formulation consisting of the active ingredient dissolved in an inert liquid carrier. Injection may be either intramuscular, intraruminal, intratracheal, or subcutaneous. The injectable formulation consists of the active ingredient mixed with an appropriate inert liquid carrier. Acceptable liquid carriers include the vegetable oils such as peanut oil, cotton seed oil, sesame oil and the like as well as organic solvents such as solketal, glycerol formal and the like. As an alternative, aqueous parenteral formulations may also be used. The vegetable oils are the preferred liquid carriers. The formulations are prepared by dissolving or suspending the active ingredient in the liquid carrier such that the final formulation contains from 0.005 to 10% by weight of the active ingredient. \n\n The invention is further illustrated by the following nonlimiting examples. \n\nEXAMPLE 1 \n\nCell Culture \n\n The AML-like cell lines HL-60 (promyelocytic) and U-937 (promonocytic) were obtained from the ATCC. AML-193 (monocytic) and THP-1 (monocytic) cells were obtained from the RW Johnson Pharmaceutical Research Center, San Diego. Cells were grown in Roswell Park Memorial Institute medium (RPMI) with 20% Fetal Bovine Serum (FBS). AML-193 was also supplemented with granulocyte-macrophage colony-stimulating factor (GM-CSF) (10 ng/ml), insulin (0.005 mg/ml), and transferrin (0.005 mg/ml). \n\nEXAMPLE 2 \n\nToxic Dose Assay \n\n The cells of Example 1 were inoculated into 6-well plates at an initial concentration of 110 ⁵ cells/ml. (B)-6-amino(4-chlorophenyl)(1-methyl-i 1H-imidazol-5-yl)methyl-4(3-chlorophenyl)-1-methyl-2(1H)-quinolinone) was added at concentrations ranging form 0.5 to 500 nM in 3 l of DMSO directly to the culture medium. Control cells from Example 1 were grown in medium alone or in medium supplemented with vehicle (0.1% DMSO). Cell numbers were counted at days four and seven in a hemocytometer and cell viability was determined by trypan blue exclusion assay. The IC ₅₀ was defined as the dose at which the number of viable cells in the treated sample was 50% of that in the control at day seven. Calculations were made based on duplicate runs of the experiment. The IC ₅₀ of the four cell lines was calculated after seven days of treatment with the FTI. AML-193 had an IC ₅₀ of 134 nM, HL-60 had an IC ₅₀ of 24 nM, THP-1 had an IC ₅₀ of 19 nM, and U-937 had an IC ₅₀ of 44 nM. This indicated that the four AML-like cell lines were sensitive to FTI treatement. \n\nEXAMPLE 3 \n\nTime Course Assay \n\n Duplicate cultures of the cells of Example 1 were inoculated into 6-well plates at an initial concentration of 110 ⁵ cells/ml. (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone) was supplemented at a concentration of 100 nM in 3 l of DMSO directly to the culture medium. The concentration of 100 nM was chosen for the subsequent time course experiments to normalize the treatment protocol based, in part, on the results of Example 2. Duplicate control cultures were grown in medium containing 0.1% DMSO. Duplicate cultures were harvested daily for a total of six days. Cells were counted, assayed for viability, and total RNA isolated according to the manufacturer's protocol (Qiagen RNeasy). The analysis showed that cells from different cell lines were effected at different times. RNA was treated with DNase1 (Qiagen DNase1 kit) to remove any residual genomic DNA. Linear amplification of RNA was conducted according to the procedure described in U.S. Pat. No. 5,545,522 to Van Gelder et. al. Aliquots of 5 g of aRNA were then prepared for hybridization to cDNA arrays. \n\nEXAMPLE 4 \n\nBone Marrow Processing \n\n Bone marrow aspirates were obtained from two patients diagnosed with AML who had been treated with FTI. These AML patients were administered 600 mg (B)-6amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1 methyl-2(1H)-quinolinone) twice daily over a 21 day period. Bone marrow aspirates were taken at baseline and once a week for the three weeks of treatment. One of these patients did not respond (RH) while the other responded (BS) to the FTI. Response was determined as a reduction of more than 50% of blast cells in bone marrow aspirates. The aspirates were diluted to 15 ml with PBS and Ficoll-density centrifuged. White blood cells were washed twice with PBS, resuspended in FBS with 10% DMSO and immediately frozen at 80 C. Cells were cryogenically preserved to maintain cell viability. Samples were thawed at 37 C. and 10 volume of RPMI with 20% FBS was added drop-wise over a period of 5 min. Cells were centrifuged at 1600 rpm for 10 min and resuspended in 10 ml PBS with 2 mM EDTA and 0.5% BSA. Samples were then passed through a 70 M filter to remove any cell clumps. Cell viability was determined by Trypan Blue assay. If sample viability was less than 50% a Miltenyi Dead Cell Removal Kit was employed to enrich for the live cell fraction. 210 ⁵ viable cells were then double labeled with CD33-FITC and CD34-PE antibodies (Pharminigen) and FACS analysis was performed. Post (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone)-treated bone marrow samples were enriched for leukemic cells by magnetic bead cell separation using either CD33 or CD34 antibodies (Miltenyi). The extracted cells had RNA extracted as described in Example 3. \n\nEXAMPLE 5 \n\nProbe Preparation \n\n RNA samples obtained in Examples 3 and 4 were prepared for hybridization to cDNA microarrays according to the following procedure. One to two rounds of linear amplification was performed on total RNA depending on the amount of starting material. Initially, 1-10 g total RNA was reverse transcribed using the Superscript cDNA transcription kit (Gibco BRL). Ten l total RNA was first mixed with 1 l of 0.5 mg/ml T7-oligodT primer, incubated at 70 C. for 10 min, and then chilled on ice. Next, 8 l of 5first-strand reaction buffer, 0.1M DTT, 10 mM dNTPs, and 1 l Rnase Block were added, and the solution incubated at 42 C. for 5 min. One l Superscript II was then added and the reaction was incubated at 42 C. for 2 hr. The reaction was heat deactivted at 70 C. for 10 min and 1 l was removed for PCR. Next, 92 l Rnase-free water, 30 l 5second-strand reaction buffer, 3 l 10 mM dNTP, 4 l DNA polymerase 1, 1 l E. Coli Rnase H, 1 l E. Coli DNA ligase were added and the mixture incubated at 16 C. for 2 hr. cDNA was linear amplified using the Ampliscribe T7-transcription kit (Epicenter). If required, a second round of RNA amplification was performed by the random hexamer approach. Fluorescently labeled cDNA probes were synthesized by priming aRNA with random hexamers and including Cy3-dCTP in the nucleotide mix. Reactions were purified using a QIAquick PCR purification kit (Qiagen), the volumes of probe normalized using relative fluoresence (Cytofluor), and resuspended in 50 l of Version 2 hybridization buffer (Amersham Pharmacia Biotech, Pistcataway, N.J.) with 50% formamide and human Cot1 DNA (Life Technologies). \n\nEXAMPLE 6 \n\nArray Hybridization and Analysis \n\n The arrays contained 7452 cDNAs from the IMAGE consortium (Integrated Molecular Analysis of Genome and their Expression: Research Genetics, Huntsville, Ala.) and Incyte libraries. Micro-arrays were generated as follows and probes hybridized as described in Example 5. cDNAs were printed on amino silane-coated slides (Corning) with a Generation III Micro-array Spotter (Molecular Dynamics). The cDNAs were PCR amplified, purified (Qiagen PCR purification kit), and mixed 1:1 with 10 M NaSCN printing buffer. Prior to hybridization micro-arrays were incubated in isopropanol at room temperature for 10 min. The probes were incubated at 95 C. for 2 min, at room temperature for 5 min, and then applied to three replicate slides. Cover slips were sealed onto the slides with DPX (Fluka) and incubated at 42 C. overnight. Slides were then washed at 55 C. for 5 min in 1SSC/0.2% SDS and 0.1SSC/0.2% SDS, dipped in 0.1SSC and dried before being scanned by a GenIII Array Scanner (Molecular Dynamics). The fluorescence intensity for each spot was analyzed with AUTOGENE software (Biodiscovery, Los Angeles). \n\n The intensity level of each micro-array was normalized so that the 75 ^{th } percentile of the expression levels was equal across micro-arrays. Clones displaying a coefficient of variance (CV) greater than 50% of the mean were excluded from the analysis. Since background intensity was a maximum of 32 units for all experiments a threshold of 32 was assigned to all clones exhibiting an expression level lower than this. A ratio matrix was then generated based on pair-wise analysis of treated and control samples and Hierarchical clustering was performed using an euclidean metric and average linkage (Omniviz Pro). \n\n Each sample was hybridized to three identical arrays and the mean signal intensity was compared by scatter-plot analysis. High correlation coefficients were also observed when control samples were compared to treated samples from the same day. This indicated there were no gross changes in gene expression due to treatment with (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone). In addition, the variation between control samples from different days was examined. Cells were mock-treated and RNA was isolated after 1, 2, 3, 4, 5, and 6 days. Following labeling and hybridization the mean intensity of duplicate samples and the coefficient of variance (CV) of each clone (3 spots per clone) were calculated. Data points which displayed a CV of more than 50% were discarded from further analysis. \n\nEXAMPLE 7 \n\nDifferential Gene Expression in Treated Cell Line Samples \n\n Hierarchical clustering was performed on the time-course data sets using the OmniViz Pro software (Battelle). Initially, fold-changes of 1.5, 1.7, and 2.0 were used as filters for the treated versus control intensity ratios for each day of the time-course. The gene expression profiles of genes modulated beyond these thresholds were analyzed to examine those genes that were commonly modulated between the three data sets and identify gene clusters that shared similar expression profiles. Results are shown in Tables 1-3 below. \n\n Genes analyzed according to this invention are identified in the tables below by reference to Gene ID Numbers (internally generated) and accession numbers in the Genbank database where such genes have been entered in the Genbank database. The attached sequence listing, incorporated herein by reference, shows sequences corresponding to the Gene ID Number and are named with those Gene ID Numbers. In some cases, the listed sequences are to full length nucleic acid sequences that code for the production of a protein or peptide. One skilled in the art will recognize that identification of full-length sequences is not necessary from an analytical point of view. That is, portions of the sequences or ESTs can be selected according to well-known principles for which probes can be designed to assess gene expression for the corresponding gene. Further, it should be noted that some of the sequences in the listing contain the letter N in place of a nucleotide designation. One skilled in the art will recognize that the N indicates placement of any nucleotide in that portion of the sequence. \n\nEXAMPLE 8 \n\nIdentification of Gene Networks \n\n Genes that were regulated in two or more cell lines by at least 1.5-fold in drug treated cell lines (Table 1) were identified as described above. The list of these genes was employed to identify major gene pathways that were being modulated by the most preferred FTI, (B)-6-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone). If clones did not perfectly match a known gene annotations from the best BLAST result of the clone sequence were used. Since the level of regulation of these genes varied over the course of treatment of the cell lines, the gene expression profiles from the primary AML tissue that responded to this FTI were determined. \n\n It was found that many genes in the MAPK/ERK ( FIG. 2 ) signaling pathways were being down-regulated and that genes in the TGF ( FIG. 3 ) and WNT ( FIG. 3 ) signaling pathways were generally up-regulated, while apoptotic pathways were also activated ( FIG. 4 ). This allowed the identification of other gene targets sensitive to treatment with known or novel drug compounds. For example, beneficial treatment can result from FTIs used in conjunction with tyrosine kinase, MEK kinase, PI3K and/or MAP kinase inhibitors to obtain a more potent effect. In addition, given the finding that apoptotic pathways are activated in FTI treated cells, drugs that modulate apoptosis could be expected to have beneficial effect when employed in conjunction with an FTI. Examples of these types of compounds include tyrosine kinase inhibitors (eg Gleevec, Novartis), MAP kinase inhibitors (eg U-0126, PD-098059, SB-203580), and inhibitors of anti-apoptotic genes such as Bcl-XL (eg antisense, ribozymes, DNAzymes). \n\n\nTABLE 1 \n\n\nGenes (by Genbank Accession Number) modulated at least 1.5 fold \nin 2 or more of the cell lines over the 6 day time course. \nGene ID Accession No. \n\n3434105F7 AB026898 \n3881595H1 AC000134 \nAI939481 AC005155 \nAA961061 AC005670 \n3918104H1 AC006023 \nAI025519 AC008427 \n5543360F8 AC009220 \nAA744682 AC009289 \nAA932129 AC009756 \nAI148008 AC011473 \nY00052 AC013722 \nR52476 AC021078 \nAA864819 AC022087 \nAI815593 AC022150 \nAI141943 AC026448 \nAI300541 AC073585 \n2515486H1 AF161372 \n1731618H1 AJ003147 \nBE222911 AJ400879 \nR13802 AK022901 \nAI656222 AL021155 \nAI553823 AL022313 \nAA010251 AL034397 \nAA237071 AL035420 \n2445101F6 AL049824 \nAI638342 AL122004 \nAA779424 AL136980 \nH81171 AL137073 \nR77754 AL137790 \nAI209040 AL139082 \n6421806H1 AL139396 \nH61066 AL161787 \nR59209 AL355136 \nAA486141 AL355352 \nAI339252 AP001630 \nAW023438 BC009732 \n914979H1 BC013834 \nAA455969 D00015 \nT64335 D00017 \nX02308 D00596 \nX67098 D00596 \nX01023 D10493 \nD10493 D10493 \nY00396 D10493 \nX69292 D10667 \nAA736561 D11094 \nS68252 D11139 \nM25315 D12592 \nAI186110 D13118 \nH84153 D13639 \nAA598561 D14043 \nD14695 D14695 \n2206642T6 D16889 \nAI878943 D17004 \nU38846 D17080 \nJ03801 D21235 \nAI762926 D23660 \nD25215 D25215 \nU41078 D26512 \nAA485961 D30648 \nAA456408 D38441 \nAI311090 D38616 \n1869911H1 D42084 \nD43950 D43950 \nAW006368 D44467 \nU29092 D45050 \nD45887 D45887 \nW68193 D49489 \n3633286H1 D63874 \nN76967 D66904 \nAA985407 D82326 \nAI962797 D83260 \nM59829 D85730 \n3107995H1 D86322 \nAA279906 D86550 \nAI016874 D86586 \n556963H1 D86955 \nAI810687 D86997 \nAF045581 D87462 \nU41070 D89078 \nD90209 D90209 \nAA812265 D90767 \n2135769H1 J02763 \n1876511H1 J03072 \nJ04088 J04088 \nAI590075 J04973 \nH30357 J05451 \nK00558 K03460 \nL10413 L00634 \nL01087 L01087 \nAI027898 L02426 \nL06139 L06139 \nU28936 L07914 \nM86400 L07955 \nAA428915 L08634 \nAA464627 L09604 \nM94859 L10284 \nR78541 L10717 \nL15189 L11066 \nL11284 L11284 \nT87908 L12387 \nT80827 L13802 \nL08044 L15203 \nAI278029 L16862 \nM60278 L17032 \nM60278 L17032 \nM65128 L18980 \nW49672 L20861 \nL22005 L22005 \nAI380522 L23822 \nAA988469 L25591 \nL26336 L26336 \nAI074564 L32866 \nM63175 L35233 \n2470939H1 L35848 \nAA190648 L36055 \nAI243166 L38716 \nL39833 L39833 \nM97347 L41415 \n2005142H1 L42324 \nM11723 L43615 \nU04045 L47574 \nAA284067 L76938 \nM13142 M13142 \nW68291 M15395 \n5560880H1 M19483 \n3171275H1 M20199 \nM22489 M22489 \nAA070627 M22810 \nH39560 M24736 \nM25897 M25897 \nM27492 M27492 \nAA570304 M29366 \n205581R6 M29696 \nM84739 M32294 \nM84739 M32294 \nM35857 M32315 \n3801801H1 M33680 \nM63904 M63904 \nAI091579 M63971 \nM69215 M69215 \nM74782 M74782 \nM80254 M80254 \nM80647 M80647 \nM84526 M84526 \n6805226H1 M84526 \nS93414 M86553 \nM91556 M91556 \nM95678 M95678 \n2017923F6 M96326 \nH73054 NM_000551 \nAA488324 NM_001211 \nN73242 NM_001274 \nAF013611 NM_001335 \nAW163686 NM_001524 \nAI921879 NM_002287 \nAI652785 NM_002333 \nAI423526 NM_003332 \n3028719F6 NM_003600 \nAB010882 NM_003601 \nAF030424 NM_003642 \nAW194791 NM_003668 \nAF075599 NM_003969 \nAF031141 NM_004223 \n2676931T6 NM_004412 \nAF053304 NM_004725 \nAF119815 NM_004885 \nAI816398 NM_004888 \n2185556H1 NM_004917 \n3357511H1 NM_004917 \nAA047585 NM_005109 \nAA448972 NM_005592 \nAW629084 NM_005817 \nAJ001015 NM_005854 \nAJ001016 NM_005856 \nU85055 NM_006480 \n3618886F6 NM_006536 \nAA906714 NM_006573 \nAF060153 NM_007037 \n1467864F6 NM_012089 \nAI097079 NM_012100 \nAF204944 NM_012105 \nW44673 NM_012428 \nAI522316 NM_013386 \nAI700673 NM_013439 \nAA057781 NM_014172 \nAI299795 NM_014251 \n1931159F6 NM_014397 \nAW630208 NM_014413 \n2821685T6 NM_014967 \n1539060H1 NM_015343 \nAI762738 NM_015449 \nAA401397 NM_015596 \nAW243944 NM_015596 \nAI436551 NM_016141 \nAI651159 NM_016440 \nAA527334 NM_016625 \ng922698 NM_017555 \n1693028H1 NM_017636 \n002783H1 NM_017860 \nAI368583 NM_017874 \nAW170305 NM_017903 \nH62827 NM_018321 \nM78706 NM_019020 \nBE048230 NM_020216 \nAI214466 NM_020334 \nAA452802 NM_021196 \nAI808824 NM_022082 \nW77977 NM_022336 \nAA535015 NM_022570 \nAA861140 NM_022829 \nAW078834 NM_023080 \n5122087H1 NM_024056 \nAF017182 NM_024101 \nAA449040 NM_024116 \n2792728F6 NM_024902 \nBE218593 NM_025230 \nAA669885 NM_030763 \nAI339565 NM_030908 \nAF038564 NM_031483 \nAI126706 NM_032038 \n1961084H1 NM_032188 \n4609810F6 NM_032554 \nAA745592 NM_032844 \nAW612141 NM_033050 \nAI740538 NM_033280 \nU58522 S51016 \nM57703 S63697 \nAA873257 S73591 \nAA521213 S77359 \nN77754 S79873 \nAA984230 S80071 \nR79935 S81439 \nT71391 T71391 \nAA598776 U05340 \nU11053 U11053 \nT55353 U12597 \nAA456616 U14970 \nU18300 U18300 \nAF017306 U20657 \nAA459663 U25182 \nU27699 U27699 \nAI884916 U29171 \nU29171 U29171 \n1671033F6 U33429 \nAA017042 U40989 \nAI126520 U48405 \nU48807 U48807 \nU49395 U49395 \nAA186542 U50078 \nU51586 U51586 \nAW150605 U54558 \nAA455800 U55206 \nAF029777 U57316 \nI19355 U58913 \n319095H1 U58913 \nAF027964 U59911 \nU60519 U60519 \nAI371158 U65378 \nU69883 U69883 \nH30148 U73641 \nR80718 U75283 \nU77180 U77180 \nU78180 U78180 \nU83115 U83115 \nAA938905 U86218 \nAI401546 U88844 \n2526581H1 U90904 \nAA773114 U95740 \nAA176596 U96781 \nX13274 V00543 \nI16618 V00595 \nR91899 X00226 \nAW519155 X00318 \nX87344 X00369 \nX02910 X01394 \nM15840 X02532 \nAA401046 X02592 \nX02812 X02812 \nX87344 X03066 \nX03084 X03084 \nM10901 X03225 \nX03225 X03225 \nR81823 X03742 \nX04011 X04011 \nK02400 X04076 \nX07036 X04408 \nX07036 X04408 \nY00816 X05309 \nN20475 X05344 \nM11233 X05344 \nX02544 X05784 \nX52192 X06292 \nR33755 X06547 \nX06989 X06989 \nX07979 X07979 \nX14723 X08004 \nM20566 X12830 \nM20566 X12830 \nX13197 X13197 \nM21304 X13709 \nX00351 X13839 \nX60236 X14008 \nH57180 X14034 \nM33011 X14758 \nX14768 X14768 \nM31625 X14768 \nM31626 X14768 \nM30816 X14768 \nX52882 X14983 \nAA598758 X15187 \nX15606 X15606 \nK03515 X16539 \nAA868186 X17093 \nX51416 X51416 \nM23699 X51439 \nAA455222 X51675 \nX51757 X51757 \nX52195 X52195 \nU06434 X53682 \nJ03198 X54048 \nM32304 X54533 \nAA487812 X56134 \nX56134 X56134 \nM16985 X56257 \nN31660 X56257 \nH27379 X57198 \nX57522 X57522 \nX57830 X57830 \nM57765 X58377 \nX58528 X58528 \nM81182 X58528 \nS60489 X60111 \nAI739095 X61157 \nR76314 X61587 \nM83665 X62534 \nX65921 X65921 \nM37722 X66945 \nAA453816 X69516 \nAA187162 X69654 \nX69819 X69711 \nX70070 X70070 \nX70697 X70697 \nS40706 X71427 \nT53775 X71874 \nX71877 X71877 \nX73458 X73458 \nX74801 X74801 \nAA454585 X75755 \nR43734 X76939 \nAI189206 X77303 \n2496221H1 X77303 \nH17504 X80692 \nR26434 X80910 \nX83688 X83688 \nU24231 X84709 \n3576337H1 X85030 \nX87212 X87212 \nT56477 X87212 \nAA464034 X89401 \nX89576 X89576 \nAA187458 X92396 \nM15887 X94565 \nX94991 X94991 \nX96427 X96427 \nX97058 X97058 \nAA425120 X98262 \n3283686H1 XM_005825 \nAW027188 XM_005958 \n1525902F6 XM_006646 \nR48796 XM_008099 \nAK000599 XM_027140 \nAA044653 XM_031608 \nAW665954 XM_035574 \nH86407 XM_037453 \nR00285 XM_038150 \nX57447 XM_039395 \n778372H1 XM_040459 \nR82530 XM_041024 \nAI580830 XM_042041 \n3097063H1 XM_044784 \n3038910H1 XM_046691 \nH53340 XM_048213 \n1654210F6 XM_048530 \nL42856 XM_054964 \n2707270F6 XM_056259 \nM23468 Y00062 \nY00649 Y00649 \nY00757 Y00757 \nM17017 Y00787 \nM28130 Y00787 \nL02932 Y07619 \nY10256 Y10256 \nAA454813 Y12395 \nAA149850 Y12670 \n704183H1 Y13710 \n059476H1 Y13829 \nY13834 Y13834 \nL11016 Y14768 \n3141315H1 Y17803 \nAI341167 Y18391 \nAI707852 Z12962 \nU51278 Z23115 \nAI686653 Z26876 \nAA043102 Z35102 \nAA136533 Z35481 \nU49083 Z49148 \nR70234 Z56852 \n257274R6 Z58168 \nU62027 Z73157 \n391237F1 Z73157 \n510997F1 Z73157 \nAI808621 Z82214 \nAA460801 Z98749 \n2673259F6 Z98752 \nR22977 Z98946 \nL03380 Z99995 \nAA425422 \nAA460392 \nAA508510 \nAA552028 \nAA576785 \nAA663307 \nAI015248 \nAI024468 \nAI086865 \nAI190605 \nAI203269 \nAI264420 \nAI333013 \nAI435052 \nAI671268 \nAI796718 \nAI990816 \nAW027164 \nAW167520 \nH24679 \nH66015 \nH91370 \nW07570 \n1274737F6 \n195337H1 \n2398102H1 \n2531082H1 \n264639H1 \n2794246F6 \n3290073H1 \n335737H1 \n4539942F8 \n6300669H1 \n938765H1 \n\n\n \n\n \n\n\nTABLE 2 \n\n\nGenes (by GenBank Accession Number) modulated \nat least 1.7 fold in primary AML Sample. \nGene ID Accession No. \n\nT94331 AB026898 \n3881595H1 AC000134 \n1329021F6 AC002073 \n2858615H1 AC002325 \nAI791539 AC002428 \nAI821217 AC004258 \nAA774798 AC004671 \nH29666 AC004845 \nT95173 AC005071 \nAA814523 AC005160 \n5905620T9 AC005212 \n5986963H1 AC005280 \n5825251H1 AC005306 \nN36113 AC005670 \n1700438H1 AC005682 \nR48756 AC005757 \n5538589F6 AC005839 \n3918104H1 AC006023 \nAA443719 AC007240 \nAI867297 AC007883 \nR63067 AC008073 \nAW022174 AC008382 \n5537789F6 AC008525 \nH00249 AC008733 \n1436240H1 AC008860 \n2668191F6 AC008949 \n5543360F8 AC009220 \nAA737674 AC009892 \n5104579H1 AC009892 \n3335217F6 AC010311 \nBE326380 AC010521 \n3746214H1 AC011088 \n1671315F6 AC011500 \nH60969 AC012351 \nAA926944 AC012377 \n3100089H1 AC012454 \nY00052 AC013722 \nR52476 AC021078 \nN45149 AC021106 \nAI742120 AC022137 \n4177228F6 AC022224 \n2676312H1 AC022415 \nH73476 AC022740 \nAA652121 AC046170 \nAI308320 AC046170 \n1956982H1 AC046170 \n1428534F6 AC051619 \n2914934H1 AC055707 \nAA621370 AC064807 \n5514511R6 AC073333 \nAI698737 AC074331 \n3406131H1 AC079118 \nN20072 AC096579 \n5911413H1 AC096667 \nAI458182 AF042782 \n2291436H1 AF074333 \nW32067 AF136745 \n6755801J1 AF157623 \n2397317F6 AF235100 \nR53190 AF384819 \n1731618H1 AJ003147 \n2959801H1 AJ003147 \n3123232H1 AJ003147 \n2760110H1 AJ006345 \nX64073 AJ239325 \n3986782F7 AJ249275 \nAI366098 AJ276674 \nAI695385 AJ289236 \nBE222911 AJ400879 \nAI400473 AK017738 \nAI299633 AK021499 \nR13802 AK022901 \n1489075H1 AK025775 \nAI656222 AL021155 \nW96144 AL021155 \n2459540H1 AL031282 \n3461693F6 AL031588 \n4333034H1 AL031726 \n3332309H1 AL031728 \nR61661 AL032821 \nU71321 AL033519 \nAA935151 AL034374 \nAA010251 AL034397 \nU43431 AL035367 \nAA237071 AL035420 \nAA609779 AL049610 \nAA167461 AL049612 \n4228729H2 AL049742 \n6712339H1 AL049766 \nAI051176 AL049872 \n1747028H1 AL078600 \n5164454H1 AL109840 \n7007735H1 AL117382 \nAA526337 AL121601 \nAI638342 AL122004 \n4835576H1 AL122035 \nW01596 AL133243 \nU64205 AL133367 \n4820983H1 AL135786 \n5594552H1 AL136381 \nH12102 AL136979 \nH81171 AL137073 \nAA151374 AL137790 \nAA578089 AL138787 \nAI209040 AL139082 \n6421806H1 AL139396 \nH60498 AL157776 \n3721604H1 AL160271 \nH61066 AL161787 \n2798009H1 AL162252 \n2225447F6 AL162430 \nAI885557 AL162729 \n2918417F6 AL163279 \nAA489975 AL355151 \nU77456 AL355794 \n5375277T9 AL356266 \nAI051860 AL356489 \n4019605F6 AL356489 \nU29607 AL356801 \nAA861429 AL359512 \nAA767859 AL359915 \n1362587H1 AL391122 \nR09122 AL391194 \nR93094 AP000173 \nAA954331 AP000432 \nR10535 AP000555 \n5327443H1 AP000936 \n1569726H1 AP001347 \nR92422 AP001672 \n3422674H1 AP002800 \nAI310451 AP002812 \n3568042H1 AP003900 \nAA455969 D00015 \nAF030575 D00015 \nT64335 D00017 \nD12614 D00102 \nX67098 D00596 \nR27585 D00759 \nAA465593 D00762 \nM80436 D10202 \nM80436 D10202 \nM80436 D10202 \nM80436 D10202 \nAA464600 D10493 \nAI147046 D10653 \nS68252 D11139 \nM25315 D12592 \nAI186110 D13118 \nS57708 D13515 \nD13626 D13626 \nAA682625 D13641 \nAA598561 D14043 \nD14695 D14695 \nD14825 D14825 \n855326R1 D16234 \nL20046 D16305 \nV00496 D17206 \nAA629808 D17554 \nM57285 D21214 \nJ03801 D21235 \nAI700360 D21878 \nD25216 D25216 \nU41078 D26512 \nAF245447 D28468 \nAF245447 D28468 \nAA070997 D29012 \n2134847H1 D30756 \nAI147295 D30756 \nAA455067 D31839 \nAI311090 D38616 \nAW629690 D42084 \n1869911H1 D42084 \n5122374H1 D43701 \nD43950 D43950 \nD45887 D45887 \nW68193 D49489 \nX72498 D50326 \nL11667 D63861 \nD63874 D63874 \n3633286H1 D63874 \nX61598 D83174 \nAA279906 D86550 \nAA729988 D86550 \nD86956 D86956 \nL36719 D87116 \nD89078 D89078 \nU41070 D89078 \nAI821897 D89675 \nD90209 D90209 \n2135769H1 J02763 \nJ03040 J03040 \n1876511H1 J03072 \nJ03258 J03258 \nJ03571 J03571 \nJ04111 J04111 \nAI125073 J04132 \n1634342H1 J04794 \nH30357 J05451 \nK02054 K02054 \nX02415 K02569 \nK03000 K03000 \nH58873 K03195 \nAI791949 K03474 \nL10413 L00634 \nH22919 L03558 \nL04288 L04288 \nAA405769 L05144 \nH62473 L07594 \nL08177 L08177 \nL08177 L08177 \nAA234897 L08895 \nAA464627 L09604 \nM94859 L10284 \nR78541 L10717 \nL15189 L11066 \nM15400 L11910 \nL12168 L12168 \nL12350 L12350 \nL12350 L12350 \nT87908 L12387 \nL09600 L13974 \nM14221 L16510 \nM60278 L17032 \nM60278 L17032 \nM60278 L17032 \nM60278 L17032 \n2745317H1 L17411 \nM65128 L18980 \nW49672 L20861 \nAI380522 L23822 \nAA988469 L25591 \nNM_001168 L26245 \nR20939 L31848 \n2470939H1 L35848 \nAA442810 L36034 \nL36148 L36148 \nM11723 L43615 \nM14745 M14745 \nW68291 M15395 \nM16038 M16038 \n339598H1 M16038 \nM17783 M17783 \n3171275H1 M20199 \n5189380H1 M21121 \n4130807F7 M22440 \nM22612 M22612 \nAA070627 M22810 \n1445982H1 M23254 \nM28638 M24906 \nR45525 M28215 \nAI051962 M28983 \n736837R6 M29696 \nM29870 M29870 \nAI264247 M30309 \n1512407F6 M30310 \nM30471 M30471 \nM30704 M30703 \nAW467649 M31158 \nM84739 M32294 \nM84739 M32294 \nU52165 M32315 \nM35857 M32315 \n5077322H1 M32315 \nN72918 M34175 \nM63193 M58602 \nM59465 M59465 \n2294719H1 M60858 \n2992331H1 M63005 \nAA069596 M63582 \nM63904 M63904 \nAI091579 M63971 \nM74782 M74782 \nAA410680 M77016 \nM80647 M80647 \nM84526 M84526 \nS93414 M86553 \nAI310138 M91463 \nM95678 M95678 \n2017923F6 M96326 \nR60624 NM_000702 \nAA488324 NM_001211 \nAA488341 NM_001336 \nAF006823 NM_002246 \n1322305T6 NM_002250 \nAI921879 NM_002287 \nAW129770 NM_002349 \nAJ004977 NM_002873 \nAI423526 NM_003332 \n4516963H1 NM_003576 \n3028719F6 NM_003600 \nAB010882 NM_003601 \nAF030424 NM_003642 \nAF029899 NM_003814 \nAF055993 NM_003864 \nAI220935 NM_004142 \nAW665782 NM_004142 \nAI191941 NM_004226 \n1392516T6 NM_004621 \nAA449579 NM_004769 \n1810447H1 NM_004917 \nAA047585 NM_005109 \n4181072F6 NM_005468 \nAA448972 NM_005592 \nAA742351 NM_005739 \n3406436F6 NM_005845 \nAJ001015 NM_005854 \n3118530H1 NM_005880 \nAA906714 NM_006573 \nAI016020 NM_006672 \nAW770551 NM_006770 \nAW009940 NM_006871 \n864164H1 NM_007194 \n1467864F6 NM_012089 \nAF204944 NM_012105 \nW23427 NM_012115 \n3363678H2 NM_012226 \nAI652076 NM_012243 \n346874T6 NM_013308 \nAI522316 NM_013386 \nAI338030 NM_013439 \nAI700673 NM_013439 \n4540025H1 NM_014322 \nW00842 NM_014331 \nAW511388 NM_014358 \nAW630208 NM_014413 \nH63640 NM_014834 \nAI743175 NM_014959 \n2821685T6 NM_014967 \nW38474 NM_015542 \nAW243944 NM_015596 \nW07181 NM_015701 \n2997457H1 NM_015938 \nAA631149 NM_016205 \nAA527334 NM_016625 \n5543749F6 NM_017414 \nAW170305 NM_017903 \nAA160974 NM_018155 \nAA625433 NM_018404 \nAA074666 NM_018834 \n767295H1 NM_018983 \nM78706 NM_019020 \nAF245447 NM_020126 \nAF245447 NM_020126 \n4294821H1 NM_020344 \n2490994H1 NM_021624 \n3556218H1 NM_021634 \n2435705R6 NM_022048 \n3092423H1 NM_022054 \nW77977 NM_022336 \nAA429219 NM_023930 \n1001514R6 NM_024022 \nAI031531 NM_024083 \nAA449040 NM_024116 \n2803571H1 NM_024586 \n1390130H1 NM_024671 \n3241088H1 NM_024850 \nH96170 NM_030779 \n1540906H1 NM_030779 \nAI824146 NM_030811 \nW90438 NM_032127 \nAA430653 NM_032177 \n3495438F6 NM_032294 \nAW612141 NM_033050 \nAA417237 NM_033225 \nAI740538 NM_033280 \nM57703 S63697 \n780099H1 S63912 \nAA714835 S67156 \nAA777347 S76736 \nAA521213 S77359 \nU39231 S79852 \nN77754 S79873 \nAA984230 S80071 \nU00672 U00672 \nU02478 U02478 \nAA019459 U02680 \n3401107H1 U03019 \nAI580044 U04816 \n3041874H1 U07563 \n2457652H1 U12465 \nU39318 U13175 \nU13666 U13666 \nU13695 U13695 \nAA056652 U14176 \nAA456616 U14970 \nU18242 U18242 \nU18300 U18300 \nAA465444 U18422 \nU20537 U20536 \nU25128 U25128 \nU35237 U26174 \nAI884916 U29171 \nAA481076 U31278 \nNM_002411 U33147 \n1671033F6 U33429 \nAA664389 U35048 \n6313632H1 U43030 \nR09288 U43522 \nAA488645 U47007 \nU47077 U47077 \n5801413H1 U48449 \n2405358R6 U48729 \nAA186542 U50078 \nU51586 U51586 \n1355140F1 U51586 \nAA455800 U55206 \nU56390 U56390 \nU83410 U58088 \nAA121261 U58675 \nAF027964 U59911 \nU60519 U60519 \n2836805T6 U62293 \nU62433 U62433 \n3188135H1 U66673 \n3188135H1 U66673 \n3188135H1 U66673 \n3188135H1 U66673 \n1360938T6 U66679 \n809631T6 U66684 \nAA454652 U67058 \nAI214335 U68755 \nU69883 U69883 \nR98589 U81375 \n5695322H1 U82671 \nAA745989 U82979 \nAA188256 U83661 \n2526581H1 U90904 \nAA434064 U95000 \nAA773114 U95740 \nAA514978 U96776 \nY07503 V00510 \nX96754 V00557 \nN67917 V01512 \nV01514 V01514 \nX87344 X00369 \nN53169 X00567 \nX02910 X01394 \nX01451 X01451 \nX01451 X01451 \nX01451 X01451 \nX01451 X01451 \nAA401046 X02592 \n5537736F6 X02592 \nX87344 X03066 \nM10901 X03225 \nM54894 X04403 \nM54894 X04403 \nM54894 X04403 \nM54894 X04403 \nX07036 X04408 \nX07036 X04408 \nN75719 X04744 \nM19507 X04876 \nY00816 X05309 \nM11233 X05344 \nAA479102 X05972 \nN24824 X06182 \nR33755 X06547 \nN41062 X06820 \nM86511 X06882 \nX07549 X07549 \n1686702H1 X07730 \nX07979 X07979 \nX14723 X08004 \nJ03561 X12510 \nJ03561 X12510 \nJ03561 X12510 \nJ03561 X12510 \nM20566 X12830 \nM20566 X12830 \nM20566 X12830 \nM20566 X12830 \nU76549 X12882 \nM21304 X13709 \nX00351 X13839 \nX14830 X14830 \nX52882 X14983 \nAA598758 X15187 \nH27564 X15729 \nW15277 X15940 \nAA393214 X15949 \nM23502 X16166 \nK03515 X16539 \nM28880 X166P9 \n2403512H1 X16674 \nAA868186 X17093 \nJ03236 X51345 \nX51416 X51416 \nAA411440 X51521 \nAA058828 X51602 \nAA455222 X51675 \nX51804 X51804 \nT72877 X52015 \nX52195 X52195 \nX52947 X52947 \nU06434 X53682 \n3081284F6 X53702 \nM36821 X53799 \nAA490256 X54048 \nJ03198 X54048 \nM60761 X54228 \nM11025 X55283 \nM33294 X55313 \nM33294 X55313 \nM31627 X55543 \nX55544 X55544 \nAA487812 X56134 \nX56134 X56134 \nX56777 X56777 \nH27379 X57198 \nM83652 X57748 \nX58528 X58528 \nM81182 X58528 \nS60489 X60111 \nX60592 X60592 \nR76314 X61587 \nM83665 X62534 \nR11490 X62947 \nAI436567 X63422 \nX63465 X63465 \nAA083577 X63527 \nX63547 X63546 \n2159360H1 X63692 \nX64074 X63926 \nX63926 X63926 \nX64083 X63926 \n2535659H1 X69168 \nAA187162 X69654 \nX69819 X69711 \nAI310990 X71491 \nT53775 X71874 \n3285272H1 X73568 \nU11087 X75299 \nX75299 X75299 \nAA454585 X75755 \nX75821 X75821 \nX75918 X75918 \nX76029 X76029 \nR43734 X76939 \nAI189206 X77303 \nH17504 X80692 \nR26434 X80910 \nAI521155 X81892 \nAA088861 X83228 \nU10440 X84849 \n407169H1 X84909 \n3576337H1 X85030 \nT55802 X85117 \n4407508H1 X85337 \nAA025432 X85373 \nT56477 X87212 \nAA464034 X89401 \nX89576 X89576 \nX89576 X89576 \nR83270 X89750 \n917064H1 X91249 \nX91809 X91809 \nX92106 X92106 \nAA187458 X92396 \nAJ000519 X92962 \nX94991 X94991 \nX96427 X96427 \nR85213 X98022 \nX98296 X98296 \nX99585 X99585 \nR48796 XM_008099 \nR50354 XM_009915 \nW15172 XM_016514 \nAK000599 XM_027140 \n7157414H1 XM_031246 \nAA044653 XM_031608 \nL16953 XM_032556 \n1266202T6 XM_033674 \nAA805691 XM_033788 \nAA861582 XM_036492 \nH86407 XM_037453 \n778372H1 XM_040459 \nAA016239 XM_041087 \nAI580830 XM_042041 \nAI732875 XM_042637 \nAA463411 XM_045320 \nAA648280 XM_046411 \n3038910H1 XM_046691 \nH63831 XM_047328 \n1654210F6 XM_048530 \nAA460131 XM_049228 \n5539620F6 XM_049755 \nAA682896 XM_050250 \nL42856 XM_054964 \n1483347H1 XM_056259 \nAI307255 XM_058135 \nH74265 Y00062 \nY00064 Y00064 \nM17017 Y00787 \nM28130 Y00787 \nL02932 Y07619 \nAA504415 Y09781 \nAI809036 Y12336 \nAA516206 Y12851 \n000527H1 Y13829 \n059476H1 Y13829 \nY13834 Y13834 \nL11016 Y14768 \n3141315H1 Y17803 \n551234R6 Y17803 \nAA426103 Y18000 \nH97778 Z13009 \nAA402431 Z15005 \nL07555 Z22576 \nU51278 Z23115 \nM58525 Z26491 \nAW772610 Z26652 \nZ29090 Z29090 \nH19371 Z32684 \nAA136533 Z35481 \nZ48810 Z48810 \nU49083 Z49148 \nR70234 Z56852 \n4902714H1 Z69918 \n150224T6 Z80147 \nM29871 Z82188 \nAI808621 Z82214 \nAA699919 Z83821 \n5538394H1 Z83843 \n5020377F9 Z97832 \nAA460801 Z98749 \nAI625585 Z98750 \n2673259F6 Z98752 \nR22977 Z98946 \nAA007595 \nAA188574 \nAA280754 \nAA283874 \nAA460392 \nAA508510 \nAA515469 \nAA526772 \nAA576785 \nAA634241 \nAA663307 \nAA663482 \nAA713864 \nAA714520 \nAA828809 \nAA868502 \nAI061445 \nAI086865 \nAI264420 \nAI378131 \nAI440504 \nAI567491 \nAI693066 \nAI709066 \nAI766478 \nAI821337 \nAI949694 \nAW439329 \nAW630054 \nH24679 \nH29257 \nH51856 \nH66015 \nH72339 \nN57580 \nN54592 \nW07570 \nT75463 \nR88730 \nR91509 \nT56441 \nT77711 \nW92423 \n1274737F6 \n1338107F6 \n1508571F6 \n1548205H1 \n1594182F6 \n1594701F6 \n1879290H1 \n1902928H1 \n194370H1 \n195337H1 \n198381H1 \n2021568H1 \n205203T6 \n2194064H1 \n224922R6 \n2398102H1 \n2531082H1 \n2630745F6 \n264639H1 \n2704982H1 \n2716787H1 \n2798810F6 \n2832401H1 \n2894096F6 \n2919406F6 \n2937644F6 \n2950021H1 \n3010621F6 \n3123948H1 \n3253054R6 \n3290073H1 \n3330472H1 \n335737H1 \n3674358H1 \n3749346F6 \n3820429H1 \n3978404F6 \n4031124H1 \n4056384H1 \n4097060H1 \n4288779H1 \n4301823H1 \n4558488F6 \n4570377H1 \n5058893F9 \n5541621H1 \n5546249F6 \n5546336H1 \n5771839H1 \n5804485H1 \n5849807H1 \n6530555H1 \n656258H1 \n6591535H1 \n859993H1 \n930273R6 \n938765H1 \n\n\n \n\n \n\n\nTABLE 3 \n\n\nGenes (By Genbank Accession Number) modulated at least 1.5 fold in \nall cell lines and at least 1.7 fold in patient responder sample. \nGene ID Accession No. \n\n5543360F8 AC009220 \nAA237071 AL035420 \nAA455969 D00015 \nM25315 D12592 \nU41078 D26512 \nL10413 L00634 \nAA464627 L09604 \n2470939H1 L35848 \nM84526 M84526 \nAI921879 NM_002287 \nAF204944 NM_012105 \nW77977 NM_022336 \nAA449040 NM_024116 \nAA521213 S77359 \nAA984230 S80071 \nAA456616 U14970 \nAI884916 U29171 \nU60519 U60519 \nX00351 X13839 \nAA868186 X17093 \nH27379 X57198 \nAA454585 X75755 \nX89576 X89576 \nAI580830 XM_042041 \nU49083 Z49148 \n2398102H1 \n2531082H1 \n\n\n \n\n 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fold."],"number":2,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the differential modulation is at least 1.7 fold."],"number":3,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the analysis is of the expression of more than one gene."],"number":4,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the gene correlates with one or more nucleic acid sequences identified in Tables 1-3"],"number":5,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 used to monitor the therapy of a patient."],"number":6,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 5 wherein the FTI is (B)-6-[amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone)."],"number":7,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 1 wherein the analysis is of the expression of a group of genes correlating with nucleic acid sequences identified in Tables 1-3 and wherein the FTI is (B)-6-[amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone)."],"number":8,"annotation":false,"claim":true,"title":false},{"lines":["A method of treating a patient comprising: \n
a) analyzing the gene expression profile of said patient to determine whether the patient will respond to treatment with an FTI, and\n
b) treating the patient with the FTI if the analysis indicates that the patient will respond."],"number":9,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 9 wherein the analysis is of the expression of more than one gene."],"number":10,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 9 wherein the FTI is selected from the group consisting of quinolines or quinoline derivatives."],"number":11,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 11 wherein the FTI is selected from the group consisting of \n
7-(3-chlorophenyl)-9-[(4-chlorophenyl)-1H-imidazol-1-ylmethyl]-2,3-dihydro-1H,5H-benzo[ij]quinolizin-5-one,\n
7-(3-chlorophenyl)-9-[(4-chlorophenyl)-1H-imidazol-1-ylmethyl]-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinoline-4-one,\n
8-[amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-6-(3-chlorophen yl)-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one,\n
8-[amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-6-(3-chloropheny l)-2,3-dihydro-1H,5H-benzo[ij]quinolizin-5-one, and\n
(B)-6-[amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone)."],"number":12,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 12 wherein the FTI is (B)-6-[amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-4-(3-chlorophenyl)-1-methyl-2(1H)-quinolinone)"],"number":13,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 10 wherein the genes correlate with one or more nucleic acid sequences identified in Tables 1-3."],"number":14,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 9 wherein the treatment comprises the administration of an FTI and another therapeutic composition."],"number":15,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 15 wherein said another therapeutic composition modulates MAPK/ERK signaling pathways, TGFβ, WNT or apoptotic pathways."],"number":16,"annotation":false,"claim":true,"title":false},{"lines":["The method of claim 16 wherein said another composition is selected from the group consisting of tyrosine kinase inhibitors, MEK kinase inhibitors, PI3 kinase inhibitors, MAP kinase inhibitors, apoptosis modulators, and combinations thereof."],"number":17,"annotation":false,"claim":true,"title":false},{"lines":["Articles for assessing the efficacy of treatment of a patient with an FTI comprising a medium with which patient gene expression profiles indicative of FTI response are determined."],"number":18,"annotation":false,"claim":true,"title":false},{"lines":["The articles of claim 18 wherein the gene expression profiles are obtained from a group of genes correlating to more than one nucleic acid sequences identified in Tables 1-3."],"number":19,"annotation":false,"claim":true,"title":false},{"lines":["The articles of claim 19 wherein the nucleic acid sequences are found in Table 3."],"number":20,"annotation":false,"claim":true,"title":false},{"lines":["The articles of claim 18 comprising representations of gene expression profiles fixed to a medium."],"number":21,"annotation":false,"claim":true,"title":false},{"lines":["The articles of claim 18 wherein the medium is computer readable."],"number":22,"annotation":false,"claim":true,"title":false},{"lines":["Kits comprising articles for obtaining gene expression profiles for determining response to FTI treatment."],"number":23,"annotation":false,"claim":true,"title":false},{"lines":["The kits of claim 23 further comprising instructions."],"number":24,"annotation":false,"claim":true,"title":false}]}},"filters":{"npl":[],"notNpl":[],"applicant":[],"notApplicant":[],"inventor":[],"notInventor":[],"owner":[],"notOwner":[],"tags":[],"dates":[],"types":[],"notTypes":[],"j":[],"notJ":[],"fj":[],"notFj":[],"classIpcr":[],"notClassIpcr":[],"classNat":[],"notClassNat":[],"classCpc":[],"notClassCpc":[],"so":[],"notSo":[],"sat":[]},"sequenceFilters":{"s":"SEQIDNO","d":"ASCENDING","p":0,"n":10,"sp":[],"si":[],"len":[],"t":[],"loc":[]}}