Article thumbnail

Data Mining for Gene Networks Relevant to Poor Prognosis in Lung Cancer Via Backward-Chaining Rule Induction

By Mary E. Edgerton, Douglas H. Fisher, Lianhong Tang, Lewis J. Frey and Zhihua Chen

Abstract

We use Backward Chaining Rule Induction (BCRI), a novel data mining method for hypothesizing causative mechanisms, to mine lung cancer gene expression array data for mechanisms that could impact survival. Initially, a supervised learning system is used to generate a prediction model in the form of “IF <conditions> THEN <outcome>” style rules. Next, each antecedent (i.e. an IF condition) of a previously discovered rule becomes the outcome class for subsequent application of supervised rule induction. This step is repeated until a termination condition is satisfied. “Chains” of rules are created by working backward from an initial condition (e.g. survival status). Through this iterative process of “backward chaining,” BCRI searches for rules that describe plausible gene interactions for subsequent validation. Thus, BCRI is a semi-supervised approach that constrains the search through the vast space of plausible causal mechanisms by using a top-level outcome to kick-start the process. We demonstrate the general BCRI task sequence, how to implement it, the validation process, and how BCRI-rules discovered from lung cancer microarray data can be combined with prior knowledge to generate hypotheses about functional genomics

Topics: Original Research
Publisher: Libertas Academica
OAI identifier: oai:pubmedcentral.nih.gov:2312096
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles

Citations

  1. (2003). A glycosylation site, 60SGTS63, of p 67 is required for its ability to regulate the phosphorylation and activity of eukaryotic initiation factor 2alpha.
  2. (2005). A novel method for generation of signature networks as biomarkers from complex high throughput data.
  3. (2003). Aberrant expression pattern of replication-dependent histone h3 subtype genes in human tumor cell lines.
  4. (1999). Activation of the Lbc Rho exchange factor proto-oncogene by truncation of an extended C terminus that regulates transformation and targeting.
  5. (1992). An evaluation of the prognostic signifi cance of alpha-1-antitrypsin expression in adenocarcinomas of the lung: an immunohistochemical analysis.
  6. (2000). Analysis of large-scale gene expression data.
  7. (2004). Analysis of the RNA helicase A gene in human lung cancer.
  8. (2004). Annexin A5 downregulates surface expression of tissue factor: A novel mechanism of regulating the membrane receptor repertoire.
  9. (2004). Arginine and cancer
  10. (1989). Association of mRNA and eIF-2 alpha with the cytoskeleton in cells lacking vimentin.
  11. (2002). Association rules.
  12. (2006). Bootstrapping rule induction to achieve and increase rule stability.
  13. (2003). Bootstrapping rule induction.
  14. (2003). Cisplatin may induce frataxin expression.
  15. (2001). Classifi cation of human lung carcinomas by mRNA expression profi ling reveals distinct adenocarcinoma subclasses.
  16. (1998). Complete inhibition of spontaneous pulmonary metastasis of human lung carcinoma cell line EBC-1 by neutrophil elastase inhibitor.
  17. (1975). Computer-based consultations in clinical therapeutics: explanation and rule acquisition capabilities of the MYCIN system.
  18. (2004). Concerted activation of ETS protein ER81 by p160 coactivators, the acetyltransferase p300 and the receptor tyrosine kinase HER2/Neu.
  19. (2004). Correlation between histone acetylation and expression of the MYO18B gene in human lung cancer cells.
  20. (1999). Cytokeratin 15 expression in trichoepitheliomas and a subset of basal cell carcinomas suggests they originate from hair follicle stem cells.
  21. (2002). Decision tree induction to minimize process delays.
  22. (2003). Developmental and physiological circuits: dissecting complexity. A report on a talk given by Dr Leroy Hood.
  23. (2001). Differences in the uptake and nuclear localization of anti-proliferative heparin sulfate between human lung fi broblasts and human lung carcinoma cells.
  24. (2005). Discovering regulatory binding-site modules using rule-based learning.
  25. (2001). DNA methyltransferase inhibition enhances apoptosis induced by histone deacetylase inhibitors.
  26. (1995). Expression of p68 in human colon cancer.
  27. (2005). Extracting Meaning from Functional Genomics Experiments.
  28. (1995). Flexibly exploiting prior knowledge in empirical learning.
  29. (2003). Gene expression patterns defi ne pathways correlated with loss of differentiation in lung adenocarcinomas.
  30. (2002). Gene-expression profi les predict survival of patients with lung adenocarcinoma.
  31. (2004). H6D polymorphism in macrophage-inhibitory cytokine-1 gene associated with prostate cancer.
  32. (1993). Increased expression of eukaryotic translation initiation factors eIF-4E and eIF-2 alpha in response to growth induction by c-myc.
  33. (2004). Induction of proteasome expression in skeletal muscle is attenuated by inhibitors of NFkappaB activation.
  34. (1993). Induction over the unexplained: Using overly-general theories to aid concept learning.
  35. (2000). Introducing RefSeq and LocusLink: curated human genome resources at the NCBI.
  36. (2000). Levels, phosphorylation status and cellular localization of translational factor eIF2 in gastrointestinal carcinomas.
  37. (1996). Local increase in polymorphonuclear leukocute elastase is associated with tumor invasiveness in non-small cell lung cancer.
  38. (2002). Loss of retinoic acid receptor beta gene expression is linked to aberrant histone H3 acetylation in lung cancer cell lines.
  39. (2004). Mammalian thioredoxin reductase alters cytolytic activity of an antibacterial peptide.
  40. (2002). Modeling molecular networks: a systems biology approach to gene function. Genome Biol.,
  41. (2005). Molecular alterations in tumors and response to combination chemotherapy with gefi tinib for advanced colorectal cancer.
  42. (1997). Neutrophil elastase inhibitor (ONO-5046-Na) inhibits the growth of human lung cancer cell lines transplanted into severe combined immunodefi ciency (scid) mice.
  43. (1997). Neutrophil elastase inhibitor (ONO-5046-Na) inhibits the proliferation, motility and chemotaxis of a pancreatic carcinoma cell line Capan-1.
  44. (2002). Neutrophil elastase inhibitor reduce hepatic metastases induce by ischaemia-reprefusion in rats.
  45. (1994). Overcoming process delays with decision tree induction.
  46. (2000). Overexpression of M68/DcR3 in human gastrointestinal tract tumors independent of gene amplifi cation and its location in a four-gene cluster.
  47. (2003). Pathway studio – the analysis and navigation of molecular networks.
  48. (2002). Polymorphisms in the promoter region of the neutrophil elastase gene are associated with lung cancer development.
  49. (2000). Profi le of gene expression regulated by induced p 53: connection to the TGF-beta family.
  50. (2002). Role of genomics in identifying new targets for cancer therapy.
  51. (2004). Role of imbalance between neutrophil elastase and alpha-1-antitrypsin in cancer development and progression. The Lancet. Oncology.,
  52. (2005). Searching for meaningful feature interactions with backward-chaining rule induction.
  53. (2004). Statistical methods for analyzing tissue microarray data.
  54. (2004). Systems approaches to understanding cell signaling and gene regulation.
  55. (2004). Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized
  56. (2004). Targets and mechanisms for the regulation of translation in malignant transformation.
  57. (2002). The impact of protein biochips and microarrays on the drug development process.
  58. (2003). The molecular basis of lung cancer: molecular abnormalities and therapeutic implications.
  59. (2004). The role of NUP98 gene fusions in hematologic malignancy.
  60. (2004). The role of translation in neoplastic transformation from a pathologist’s point of view.
  61. (2001). Tissue microarray profi ling of cancer specimens and cell lines: opportunities and limitations.
  62. (2002). Toward a more complete recognition of immunoreactive antigens in squamous cell lung carcinoma.
  63. (2001). Transcriptional regulation and function during the human cell cycle.