Affordable Access

deepdyve-link
Publisher Website

BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways.

Authors
  • Warden, Charles D1
  • Kanaya, Noriko
  • Chen, Shiuan
  • Yuan, Yate-Ching
  • 1 Bioinformatics Core, Department of Molecular Medicine , Duarte, CA , United States. , (United States)
Type
Published Article
Journal
PeerJ
Publisher
PeerJ
Publication Date
Jan 01, 2013
Volume
1
Identifiers
DOI: 10.7717/peerj.159
PMID: 24058887
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

BD-Func (BiDirectional FUNCtional enrichment) is an algorithm that calculates functional enrichment by comparing lists of pre-defined genes that are known to be activated versus inhibited in a pathway or by a regulatory molecule. This paper shows that BD-Func can correctly predict cell line alternations and patient characteristics with accuracy comparable to popular algorithms, with a significantly faster run-time. BD-Func can compare scores for individual samples across multiple groups as well as provide predictive statistics and receiver operating characteristic (ROC) plots to quantify the accuracy of the signature associated with a binary phenotypic variable. BD-Func facilitates collaboration and reproducibility by encouraging users to share novel molecular signatures in the BD-Func discussion group, which is where the novel progesterone receptor and LBH589 signatures from this paper can be found. The novel LBH589 signature presented in this paper also serves as a case study showing how a custom signature using cell line data can accurately predict activity in vivo. This software is available to download at https://sourceforge.net/projects/bdfunc/.

Report this publication

Statistics

Seen <100 times