neoplasm genes

Summary

Summary: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.

Top Publications

  1. Jiang C, Xuan Z, Zhao F, Zhang M. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 2007;35:D137-40 pubmed
    ..Such interaction data between TFs and their target genes will assist detailed functional studies and help to obtain a panoramic view of the GRNs for cancer research. ..
  2. Domazet Loso T, Tautz D. Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol. 2010;8:66 pubmed publisher
    ..The fact that we can find a strong and consistent signal for this second peak in the phylostratigraphic map implies that a complex multi-level selection process has driven the transition to multicellularity. ..
  3. Wang S, Li X, Zhang S, Gui J, Huang D. Tumor classification by combining PNN classifier ensemble with neighborhood rough set based gene reduction. Comput Biol Med. 2010;40:179-89 pubmed publisher
  4. Syed A, D Antonio M, Ciccarelli F. Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. Nucleic Acids Res. 2010;38:D670-5 pubmed publisher
    ..NCG is freely available at: http://bio.ifom-ieo-campus.it/ncg. ..
  5. Shah S, Morin R, Khattra J, Prentice L, Pugh T, Burleigh A, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009;461:809-13 pubmed publisher
    ..Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression. ..
  6. Stratton M, Campbell P, Futreal P. The cancer genome. Nature. 2009;458:719-24 pubmed publisher
    ..These studies will provide us with a detailed and comprehensive perspective on how individual cancers have developed. ..
  7. Ortega A, Sánchez Aragó M, Giner Sánchez D, Sánchez Cenizo L, Willers I, Cuezva J. Glucose avidity of carcinomas. Cancer Lett. 2009;276:125-35 pubmed publisher
    ..At the end, the repression of mitochondrial activity affords the cancer cell with a cell-death resistant phenotype making them prone to malignant growth. ..
  8. Pleasance E, Cheetham R, Stephens P, McBride D, Humphray S, Greenman C, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191-6 pubmed publisher
    ..The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic. ..
  9. Narsing S, Jelsovsky Z, Mbah A, Blanck G. Genes that contribute to cancer fusion genes are large and evolutionarily conserved. Cancer Genet Cytogenet. 2009;191:78-84 pubmed publisher
    ..These results support a basis for designing algorithms that could have a high degree of predictive value in identifying fusion genes once conventional microscopic analyses have identified the chromosomal breakpoints...

More Information

Publications62

  1. Unger K, Wienberg J, Riches A, Hieber L, Walch A, Brown A, et al. Novel gene rearrangements in transformed breast cells identified by high-resolution breakpoint analysis of chromosomal aberrations. Endocr Relat Cancer. 2010;17:87-98 pubmed publisher
    ..Initial studies indicate that these gene alterations are also found in sporadic breast cancers. ..
  2. Ignatenko N, Yerushalmi H, Pandey R, Kachel K, Stringer D, Marton L, et al. Gene expression analysis of HCT116 colon tumor-derived cells treated with the polyamine analog PG-11047. Cancer Genomics Proteomics. 2009;6:161-75 pubmed
    ..These data show that PG-11047 has a broad spectrum of anticancer activity in colon cancer cells. ..
  3. Bea S, Salaverria I, Armengol L, Pinyol M, Fernandez V, Hartmann E, et al. Uniparental disomies, homozygous deletions, amplifications, and target genes in mantle cell lymphoma revealed by integrative high-resolution whole-genome profiling. Blood. 2009;113:3059-69 pubmed publisher
    ..This integrative genomic analysis has revealed target genes that may be potentially relevant in MCL pathogenesis...
  4. Barekati Z, Radpour R, Kohler C, Zhang B, Toniolo P, Lenner P, et al. Methylation profile of TP53 regulatory pathway and mtDNA alterations in breast cancer patients lacking TP53 mutations. Hum Mol Genet. 2010;19:2936-46 pubmed publisher
    ..Additionally, release of significant aberrant methylated PTEN in matched serum samples might represent a promising biomarker for breast cancer. ..
  5. Bauer A, Fostel J, Degraff L, Rondini E, Walker C, Grissom S, et al. Transcriptomic analysis of pathways regulated by toll-like receptor 4 in a murine model of chronic pulmonary inflammation and carcinogenesis. Mol Cancer. 2009;8:107 pubmed publisher
    ..g. Cxcl5), chemotaxis (e.g. Ccr1) and other cell proliferation genes (e.g. Arg1, Pthlh). Future studies will determine the utility of these pathways as indicators of immune system deficiencies and tumorigenesis. ..
  6. Loriot A, Reister S, Parvizi G, Lysy P, De Smet C. DNA methylation-associated repression of cancer-germline genes in human embryonic and adult stem cells. Stem Cells. 2009;27:822-4 pubmed publisher
    ..We conclude that CG genes do not qualify as "stemness" genes, and propose that their activation in cancers results from a tumor-specific activation process. ..
  7. Lv J, Su J, Wang F, Qi Y, Liu H, Zhang Y. Detecting novel hypermethylated genes in breast cancer benefiting from feature selection. Comput Biol Med. 2010;40:159-67 pubmed publisher
    ..This paper suggests that the feature subsets could be served as discriminating genomic markers to infer novel hypermethylated genes in cancer potentially. ..
  8. Stathopoulos G, Armakolas A. Differences in gene expression between individuals with multiple primary and single primary malignancies. Int J Mol Med. 2009;24:613-22 pubmed
    ..Nine of those were confirmed by the classifier analysis. ..
  9. Nagarajan L. Chromosomal deletions in AML. Cancer Treat Res. 2010;145:59-66 pubmed publisher
    ..Future beholds promise for targeted therapy of these poorly characterized AMLs, as we uncover the mutations driving their clonal evolution. ..
  10. Kobi D, Steunou A, Dembele D, Legras S, Larue L, Nieto L, et al. Genome-wide analysis of POU3F2/BRN2 promoter occupancy in human melanoma cells reveals Kitl as a novel regulated target gene. Pigment Cell Melanoma Res. 2010;23:404-18 pubmed publisher
    ..Our results suggest that POU3F2 may regulate the properties of melanoma cells via autocrine KIT ligand signalling. ..
  11. Dietmann S, Lee W, Wong P, Rodchenkov I, Antonov A. CCancer: a bird's eye view on gene lists reported in cancer-related studies. Nucleic Acids Res. 2010;38:W118-23 pubmed publisher
    ..A report on gene pairs from the input list which were frequently reported together by other biological studies is also provided. CCancer is freely available at http://mips.helmholtz-muenchen.de/proj/ccancer. ..
  12. Bredel M, Scholtens D, Harsh G, Bredel C, Chandler J, Renfrow J, et al. A network model of a cooperative genetic landscape in brain tumors. JAMA. 2009;302:261-75 pubmed publisher
    ..These mutations, which are likely due to nonrandom selection of a distinct genetic landscape during gliomagenesis, are associated with patient prognosis. ..
  13. Udayakumar D, Tsao H. Melanoma genetics: an update on risk-associated genes. Hematol Oncol Clin North Am. 2009;23:415-29, vii pubmed publisher
    ..The goal of personalized melanoma risk prediction is within our reach, although true clinical use has yet to be established...
  14. Heinrichs S, Li C, Look A. SNP array analysis in hematologic malignancies: avoiding false discoveries. Blood. 2010;115:4157-61 pubmed publisher
    ..Comparisons between matched tumor and normal samples will continue to be critical as the field moves from high resolution array analysis to deep sequencing to detect abnormalities in the cancer genome. ..
  15. Kan Z, Jaiswal B, Stinson J, Janakiraman V, Bhatt D, Stern H, et al. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature. 2010;466:869-73 pubmed publisher
    ..Our study provides an overview of the mutational spectra across major human cancers and identifies several potential therapeutic targets. ..
  16. Strome E, Plon S. Utilizing Saccharomyces cerevisiae to identify aneuploidy and cancer susceptibility genes. Methods Mol Biol. 2010;653:73-85 pubmed publisher
    ..In this chapter, we will describe a technique that can be used to identify heterozygous mutations in dosage-sensitive genes that mediate genomic stability by performing genome-wide screens in yeast. ..
  17. Liang Q, Ding J, Xu R, Xu Z, Zheng S. Identification of a novel human endogenous retrovirus and promoter activity of its 5' U3. Biochem Biophys Res Commun. 2009;382:468-72 pubmed publisher
    ..Promoter activity assays indicated that replacing the 17-bp sequence with an 8-bp sequence or deleting it reduced its activity, suggesting that the 17-bp sequence is important to the expression of HERV-HX. ..
  18. Zhang H, Li Y, Lai M. The microRNA network and tumor metastasis. Oncogene. 2010;29:937-48 pubmed publisher
    ..More information on miRNAs will promote a better understanding of the molecular mechanism of metastasis. ..
  19. Rad R, Rad L, Wang W, Cadinanos J, Vassiliou G, Rice S, et al. PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice. Science. 2010;330:1104-7 pubmed publisher
    ..Mice with different transposon types, copy numbers, and chromosomal locations support wide applicability. ..
  20. Sun Y, Xun K, Wang Y, Chen X. A systematic review of the anticancer properties of berberine, a natural product from Chinese herbs. Anticancer Drugs. 2009;20:757-69 pubmed publisher
  21. Koppen I, Hermans F, Kaspers G. Folate related gene polymorphisms and susceptibility to develop childhood acute lymphoblastic leukaemia. Br J Haematol. 2010;148:3-14 pubmed publisher
    ..Further investigations on the relevance of these polymorphisms need to be performed. In general, it is clear that susceptibility to (childhood) ALL is partly related to constitutional differences in folate gene polymorphisms. ..
  22. Anand A, Suganthan P. Multiclass cancer classification by support vector machines with class-wise optimized genes and probability estimates. J Theor Biol. 2009;259:533-40 pubmed publisher
    ..This study demonstrates successful implementation of the framework of class-wise feature selection and multiclass classification for prediction of cancer subtypes on six datasets. ..
  23. Edwards P. Fusion genes and chromosome translocations in the common epithelial cancers. J Pathol. 2010;220:244-54 pubmed publisher
  24. Yang X, Zhou Y, Jin R, Chan C. Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization. Bioinformatics. 2009;25:2236-43 pubmed publisher
  25. Shin H, Song D, Baek W, Lee S, Kwon T, Lee J, et al. Anticancer activity and differentially expressed genes in head and neck cancer cells treated with a novel cyclin-dependent kinase inhibitor. Chemotherapy. 2009;55:353-62 pubmed publisher
    ..These results indicate that BAI has strong anticancer activities on head and neck cancer cells, and the DEGs induced by BAI may become involved in BAI-induced cancer cell death. ..
  26. Stone R, Sabichi A, Gill J, Lee I, Adegboyega P, Dai M, et al. Identification of genes correlated with early-stage bladder cancer progression. Cancer Prev Res (Phila). 2010;3:776-86 pubmed publisher
    ..These findings provide insight into the earliest events in the development of bladder TCC as well as identify several promising early-stage biomarkers...
  27. Suh I, Shibru D, Eisenhofer G, Pacak K, Duh Q, Clark O, et al. Candidate genes associated with malignant pheochromocytomas by genome-wide expression profiling. Ann Surg. 2009;250:983-90 pubmed publisher
    ..Our findings provide new insight into the genes and molecular pathways that may be involved in malignant pheochromocytomas. ..
  28. Tol J, Dijkstra J, Klomp M, Teerenstra S, Dommerholt M, Vink Börger M, et al. Markers for EGFR pathway activation as predictor of outcome in metastatic colorectal cancer patients treated with or without cetuximab. Eur J Cancer. 2010;46:1997-2009 pubmed publisher
    ..PIK3CA mutation, loss of PTEN expression, EGFR GCN and HER2 GCN have no predictive value for response to treatment with cetuximab, neither individually nor in combination with other markers. ..
  29. Zhu J, Xiao H, Shen X, Wang J, Zou J, Zhang L, et al. Viewing cancer genes from co-evolving gene modules. Bioinformatics. 2010;26:919-24 pubmed publisher
    ..Functional analysis further suggested that cancer proteins within and outside modules might play different roles in carcinogenesis, providing a new hint for studying the mechanism of cancer. ..
  30. Walker L, Thompson B, Waddell N, Grimmond S, Spurdle A. Use of DNA-damaging agents and RNA pooling to assess expression profiles associated with BRCA1 and BRCA2 mutation status in familial breast cancer patients. PLoS Genet. 2010;6:e1000850 pubmed publisher
  31. Sato H, Oka T, Shinnou Y, Kondo T, Washio K, Takano M, et al. Multi-step aberrant CpG island hyper-methylation is associated with the progression of adult T-cell leukemia/lymphoma. Am J Pathol. 2010;176:402-15 pubmed publisher
  32. Ksiaa F, Ziadi S, Amara K, Korbi S, Trimeche M. Biological significance of promoter hypermethylation of tumor-related genes in patients with gastric carcinoma. Clin Chim Acta. 2009;404:128-33 pubmed publisher
    ..007 and P = 0.042, respectively). Our data suggest that methylation of multiple genes may be involved in the pathogenesis and correlated with the prognosis of gastric carcinomas. ..
  33. Nasir A, Shackelford R, Anwar F, Yeatman T. Genetic risk of breast cancer. Minerva Endocrinol. 2009;34:295-309 pubmed
  34. Brierley K, Campfield D, Ducaine W, Dohany L, Donenberg T, Shannon K, et al. Errors in delivery of cancer genetics services: implications for practice. Conn Med. 2010;74:413-23 pubmed
    ..A more realistic approach is better provider education and a framework in which healthcare providers identify patients who would benefit from a referral to a certified genetic counselor or experienced cancer genetics professional. ..
  35. Rossi S, Kopetz S, Davuluri R, Hamilton S, Calin G. MicroRNAs, ultraconserved genes and colorectal cancers. Int J Biochem Cell Biol. 2010;42:1291-7 pubmed publisher
  36. Ruano Y, Mollejo M, de Lope A, Hernández Moneo J, Martinez P, Melendez B. Microarray-based comparative genomic hybridization (array-CGH) as a useful tool for identifying genes involved in Glioblastoma (GB). Methods Mol Biol. 2010;653:35-45 pubmed publisher
    ..In this way, thousands of genes can be reviewed in a high resolution analysis to define amplicons and to identify? candidate genes showing recurrent genomic copy number changes in GB tumors. ..
  37. Kato K, Takao T, Kuboyama A, Tanaka Y, Ohgami T, Yamaguchi S, et al. Endometrial cancer side-population cells show prominent migration and have a potential to differentiate into the mesenchymal cell lineage. Am J Pathol. 2010;176:381-92 pubmed publisher
    ..These findings demonstrate that SP cells have cancer stem-like cell features, including the potential to differentiate into the mesenchymal cell lineage. ..
  38. Parris T, Danielsson A, Nemes S, Kovács A, Delle U, Fallenius G, et al. Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma. Clin Cancer Res. 2010;16:3860-74 pubmed publisher
  39. Onken M, Worley L, Tuscan M, Harbour J. An accurate, clinically feasible multi-gene expression assay for predicting metastasis in uveal melanoma. J Mol Diagn. 2010;12:461-8 pubmed publisher
    ..This prognostic assay provides an important addition to the armamentarium for managing patients with uveal melanoma, and it provides a proof of principle for the development of similar assays for other cancers...
  40. Phé V, Cussenot O, Roupret M. Methylated genes as potential biomarkers in prostate cancer. BJU Int. 2010;105:1364-70 pubmed publisher
    ..Thus, preliminary results on the use of the methylation status of specific genes as potential tumour biomarkers for the early diagnosis and the risk stratification of patients with prostate cancer are promising. ..
  41. Jeffs A, Glover A, Slobbe L, Wang L, He S, Hazlett J, et al. A gene expression signature of invasive potential in metastatic melanoma cells. PLoS ONE. 2009;4:e8461 pubmed publisher
    ..The invasion signature may provide new possibilities for predicting which primary tumours are more likely to metastasize, and which metastatic tumours might show a more aggressive clinical course. ..
  42. Lee H, O Connor B, Merriman B, Funari V, Homer N, Chen Z, et al. Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. BMC Genomics. 2009;10:646 pubmed publisher
    ..Coupled with the new massively parallel sequencing technologies, this provides a powerful approach to identifying disease-causing genetic variants that can be localized within the genome by traditional methods. ..
  43. Copeland N, Jenkins N. Harnessing transposons for cancer gene discovery. Nat Rev Cancer. 2010;10:696-706 pubmed publisher
    ..SB mutagenesis has already identified a large collection of known cancer genes in addition to a plethora of new candidate cancer genes and potential drug targets. ..
  44. McLellan J, O Neil N, Tarailo S, Stoepel J, Bryan J, Rose A, et al. Synthetic lethal genetic interactions that decrease somatic cell proliferation in Caenorhabditis elegans identify the alternative RFC CTF18 as a candidate cancer drug target. Mol Biol Cell. 2009;20:5306-13 pubmed publisher
    ..elegans. Furthermore, the C. elegans assay system will contribute to our knowledge of genetic interactions in a multicellular animal and is a powerful approach to identify new cancer therapeutic targets. ..
  45. Kubo T, Kuroda Y, Shimizu H, Kokubu A, Okada N, Hosoda F, et al. Resequencing and copy number analysis of the human tyrosine kinase gene family in poorly differentiated gastric cancer. Carcinogenesis. 2009;30:1857-64 pubmed publisher
    ..Our focused and integrated analyses of systemic resequencing and gene copy number have revealed the novel onco-kinome profile of GC and pave the way to a comprehensive understanding of the GC genome. ..
  46. Verhaak R, Valk P. Genes predictive of outcome and novel molecular classification schemes in adult acute myeloid leukemia. Cancer Treat Res. 2010;145:67-83 pubmed publisher
    ..The current advances made in molecular understanding of AML will ultimately lead to a further refinement of prognostics of AML. ..
  47. Lee S, Xu X, Chng W, Watson M, Lim Y, Wong C, et al. Post-treatment tumor gene expression signatures are more predictive of treatment outcomes than baseline signatures in breast cancer. Pharmacogenet Genomics. 2009;19:833-42 pubmed publisher
    ..These findings challenge the current practice of relying only on the baseline tumor to predict outcome, which overlooks the contributions of therapeutic interventions. ..
  48. Dunwell T, Hesson L, Rauch T, Wang L, Clark R, Dallol A, et al. A genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers. Mol Cancer. 2010;9:44 pubmed publisher
    ..In addition a subset of these genes may act as epigenetic markers across hematological malignancies as well as common epithelial cancers. ..
  49. Murchison E, Tovar C, Hsu A, Bender H, Kheradpour P, Rebbeck C, et al. The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science. 2010;327:84-7 pubmed publisher
    ..We provide a genomic data set for the Tasmanian devil that is applicable to cancer diagnosis, disease evolution, and conservation biology...
  50. Pai R, Samuel P, Nehru A, Manipadam M, Thomas S. Comparison of 11 endogenous control genes for normalization of mRNA obtained from paraffin-embedded tissues. APMIS. 2009;117:886-92 pubmed publisher
    ..However, betaA had greater accuracy (2 x SD) than beta2M and therefore may be a better choice of an endogenous control for experiments that require normalization while using FFPE tissues. ..
  51. Herraiz M, Munoz Navas M. Recognition and management of hereditary colorectal cancer syndromes. Rev Esp Enferm Dig. 2009;101:125-32 pubmed
    ..Extracolonic tumors are frequent in these syndromes, so specific surveillance strategies should be offered. ..
  52. Leunen K, Gevaert O, Daemen A, Vanspauwen V, Michils G, De Moor B, et al. Recurrent copy number alterations in BRCA1-mutated ovarian tumors alter biological pathways. Hum Mutat. 2009;30:1693-702 pubmed publisher
    ..Moreover, important biological pathways are altered differentially when compared to the sporadic group. ..
  53. Marsh D, Howell V. The use of denaturing high performance liquid chromatography (DHPLC) for mutation scanning of hereditary cancer genes. Methods Mol Biol. 2010;653:133-45 pubmed publisher
    ..Omaha, NE, USA) and highlights the use of Navigator software (Transgenomic Inc.), including data analysis with scatter graphs. ..