Elucidating functional context within microarray data by integrated transcription factor-focused gene-interaction and regulatory network analysis

European Cytokine Network

Volumn 24, Issue 2, 2013, Pages 75-90

  Werner, Thomas ^a,b   Dombrowski, Susan M ^a,c   Zgheib, Carlos ^d   Zouein, Fouad A ^d   Keen, Henry L ^e   Kurdi, Mazen ^d,f   Booz, George W ^d  

^a Genomatix GmbH   (Germany)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF MISSISSIPPI SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF IOWA   (United States)

^f LEBANESE UNIVERSITY   (Lebanon)

Author keywords

High throughput (HT) approaches; Microarray data analysis; Transcription factor binding sites; Transcription factor gene networking; Transcription factors

Indexed keywords

B RAF KINASE; CHEMOKINE RECEPTOR CCR5; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; EPHRIN RECEPTOR A2; GROWTH ARREST AND DNA DAMAGE INDUCIBLE PROTEIN 153; HEPATOCYTE NUCLEAR FACTOR; INTERLEUKIN 7; JANUS KINASE; LEUKEMIA INHIBITORY FACTOR; MONOCYTE CHEMOTACTIC PROTEIN 1; P21 ACTIVATED KINASE 2; PHOSPHATIDYLINOSITOL 3, 4, 5 TRISPHOSPHATE 3 PHOSPHATASE; PROTEIN BCL 2; PROTEIN C JUN; PROTEIN KINASE B; PROTEIN KINASE B BETA; PROTEIN KINASE ZAP 70; SOMATOMEDIN C RECEPTOR; STAT3 PROTEIN; STROMAL CELL DERIVED FACTOR 1; SUPPRESSOR OF CYTOKINE SIGNALING 3; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ETS; UNCLASSIFIED DRUG; VASCULOTROPIN RECEPTOR 3; VAV PROTEIN;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DOWN REGULATION; GENE CONTROL; GENE EXPRESSION; GENE INTERACTION; GENE REGULATORY NETWORK; GENE SEQUENCE; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; MICROVASCULAR ENDOTHELIAL CELL; PROMOTER REGION; PROTEIN PHOSPHORYLATION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; UPREGULATION;

HIGH-THROUGHPUT (HT) APPROACHES; MICROARRAY DATA ANALYSIS; TRANSCRIPTION FACTOR BINDING SITES; TRANSCRIPTION FACTOR-GENE NETWORKING; TRANSCRIPTION FACTORS;

BINDING SITES; CELL LINE; ENDOTHELIAL CELLS; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA INHIBITORY FACTOR; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; RNA; SIGNAL TRANSDUCTION; STAT3 TRANSCRIPTION FACTOR; TRANSCRIPTION FACTORS;

EID: 84883147423     PISSN: 11485493     EISSN: None     Source Type: Journal    
DOI: 10.1684/ecn.2013.0336     Document Type: Article

References (13)

1. Altman RB, Raychaudhuri S. Whole-genome expression analysis: challenges beyond clustering. Curr Opin Struct Biol 2001; 11: 340-7.
2. Dunham I, Kundaje A, Aldred SF, et al. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012; 489: 57-74.
3. Barrera LO, Ren B. The transcriptional regulatory code of eukaryotic cells-insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol 2006; 18: 291-8.
4. Wettenhall JM, Smyth GK. limmaGUI: a graphical user interface for linear modeling of microarray data. Bioinformatics 2004; 20: 3705-6.
5. Cartharius K, Frech K, Grote K, et al. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005; 21: 2933-42.
6. Kubota Y, Hirashima M, Kishi K, Stewart CL, Suda T. Leukemia inhibitory factor regulates microvessel density by modulating oxygen-dependent VEGF expression in mice. J Clin Invest 2008; 118: 2393-403.
7. Zhu Z, Pilpel Y, Church GM. Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J Mol Biol 2002; 318: 71-81.
8. Nie J, Stewart R, Ruan F, et al. TF-Cluster: A Pipeline For Identifying Functionally Coordinated Transcription Factors Via Network Decomposition of the Shared Coexpression Connectivity Matrix (SCCM). BMC Syst Biol 2011; 5: 53.
9. Werner T. Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol 2008; 19: 50-4.
10. Werner T, Fessele S, Maier H, Nelson PJ. Computer modeling of promoter organization as a tool to study transcriptional coregulation. Faseb J 2003; 17: 1228-37.
11. Scherf M, Epple A, Werner T. The next generation of literature analysis: integration of genomic analysis into text mining. Brief Bioinform 2005; 6: 287-97.
12. Kurdi M, Booz GW. JAK redux: a second look at the regulation and role of JAKs in the heart. Am J Physiol Heart Circ Physiol 2009; 297: H1545-H1556.
13. Forrai A, Boyle K, Hart AH, et al. Absence of suppressor of cytokine signalling 3 reduces self-renewal and promotes differentiation in murine embryonic stem cells. Stem Cells 2006; 24: 604-14.