title: PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease.
abstract: Peripheral arterial disease (PAD) results from an obstruction of blood flow in the arteries other than the heart, most commonly the arteries that supply the legs. The complexity of the known signaling pathways involved in PAD, including various growth factor pathways and their cross talks, suggests that analyses of high-throughput experimental data could lead to a new level of understanding of the disease as well as novel and heretofore unanticipated potential targets. Such bioinformatic analyses have not been systematically performed for PAD. We constructed global protein-protein interaction networks of angiogenesis (Angiome), immune response (Immunome), and arteriogenesis (Arteriome) using our previously developed algorithm GeneHits. The term "PADPIN" refers to the angiome, immunome, and arteriome in PAD. Here we analyze four microarray gene expression datasets from ischemic and nonischemic gastrocnemius muscles at day 3 posthindlimb ischemia (HLI) in two genetically different C57BL/6 and BALB/c mouse strains that display differential susceptibility to HLI to identify potential targets and signaling pathways in angiogenesis, immune, and arteriogenesis networks. We hypothesize that identification of the differentially expressed genes in ischemic and nonischemic muscles between the strains that recovers better (C57BL/6) vs. the strain that recovers more poorly (BALB/c) will help for the prediction of target genes in PAD. Our bioinformatics analysis identified several genes that are differentially expressed between the two mouse strains with known functions in PAD including TLR4, THBS1, and PRKAA2 and several genes with unknown functions in PAD including EphA4, TSPAN7, SLC22A4, and EIF2a.
authors.affiliation: Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland; chulianghui@gmail.com.
authors.forename: Liang-Hui
authors.initials: LH
authors.lastname: Chu
authors.affiliation: Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and.
authors.forename: Chaitanya G
authors.initials: CG
authors.lastname: Vijay
authors.affiliation: Cardiovascular Medicine, Department of Medicine, and the Robert M. Berne Cardiovascular Research Center University of Virginia School of Medicine, Charlottesville, Virginia; and.
authors.forename: Brian H
authors.initials: BH
authors.lastname: Annex
authors.affiliation: Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland; High-Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland.
authors.forename: Joel S
authors.initials: JS
authors.lastname: Bader
authors.affiliation: Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland;
authors.forename: Aleksander S
authors.initials: AS
authors.lastname: Popel
mesh_terms: D000818:Animals; D001158:Arteries / Q000254:growth & development* / Q000473:pathology; D015153:Blotting, Western; D016923:Cell Death; D030541:Databases, Genetic; D004195:Disease Models, Animal; D015536:Down-Regulation / Q000235:genetics; D020869:Gene Expression Profiling; D006614:Hindlimb / Q000098:blood supply / Q000473:pathology; D007249:Inflammation / Q000235:genetics*; D007511:Ischemia / Q000235:genetics / Q000473:pathology; D008297:Male; D008807:Mice, Inbred BALB C; D008810:Mice, Inbred C57BL; D009132:Muscles / Q000378:metabolism; D018919:Neovascularization, Physiologic / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010477:Perfusion; D058729:Peripheral Arterial Disease / Q000235:genetics*; D060066:Protein Interaction Maps; D012984:Software; D015854:Up-Regulation / Q000235:genetics
keywords: angiogenesis; bioinformatics; microarray; systems biology; thrombospondin 1