TAPPA: topological analysis of pathway phenotype association.
Extracting biological insight from microarray data is important but challenging. Here we describe TAPPA, a java-based tool, for identification of phenotype-associated genetic pathways utilizing the pathway topological measures. This is achieved by first calculating a Pathway Connectivity Index (PCI) for each pathway, followed by evaluating its correlation to the phenotypic variation. Our PCI definition not only efficiently captures the contributions from genes that show subtle but consistent changes in expression, but also naturally overweighs the hub genes that interact with a large number of other genes in the pathway. TAPPA also allows evaluation of sub-modules within a pathway and their association to phenotypes.
Gao
Shouguo
S
The Max McGee National Research Center for Juvenile Diabetes & The Human and Molecular Genetics Center, The Medical College of Wisconsin and Children's Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
Wang
Xujing
X
D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
D020543:Proteome