Format

Send to:

Choose Destination
See comment in PubMed Commons below
Cancer Inform. 2007 Feb 10;3:93-114.

Data mining for gene networks relevant to poor prognosis in lung cancer via backward-chaining rule induction.

Author information

  • 1Department of Pathology and Department of Biomedical Informatics, Vanderbilt University, USA. medgerton@mdanderson.org

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.

KEYWORDS:

C4.5; class discovery; data analysis; decision trees; microarray; molecular mechanisms; non-small cell lung cancer; semi-supervised methods; systems biology

PMID:
19455237
[PubMed]
PMCID:
PMC2312096
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for PubMed Central
    Loading ...
    Write to the Help Desk