TY - JOUR AU - Consortium, E. P. PY - 2004 DA - 2004// TI - The ENCODE (ENCyclopedia Of DNA Elements) Project JO - Science VL - 306 UR - https://doi.org/10.1126/science.1105136 DO - 10.1126/science.1105136 ID - Consortium2004 ER - TY - JOUR AU - Lee, T. I. AU - Rinaldi, N. J. AU - Robert, F. AU - Odom, D. T. AU - Bar-Joseph, Z. AU - Gerber, G. K. AU - Hannett, N. M. AU - Harbison, C. T. AU - Thompson, C. M. AU - Simon, I. AU - Zeitlinger, J. AU - Jennings, E. G. AU - Murray, H. L. AU - Gordon, D. B. AU - Ren, B. AU - Wyrick, J. J. AU - Tagne, J. B. AU - Volkert, T. L. AU - Fraenkel, E. AU - Gifford, D. K. AU - Young, R. A. PY - 2002 DA - 2002// TI - Transcriptional regulatory networks in Saccharomyces cerevisiae JO - Science VL - 298 UR - https://doi.org/10.1126/science.1075090 DO - 10.1126/science.1075090 ID - Lee2002 ER - TY - JOUR AU - Siggia, E. D. PY - 2005 DA - 2005// TI - Computational methods for transcriptional regulation JO - Curr Opin Genet Dev VL - 15 UR - https://doi.org/10.1016/j.gde.2005.02.004 DO - 10.1016/j.gde.2005.02.004 ID - Siggia2005 ER - TY - JOUR AU - Tavazoie, S. AU - Hughes, J. D. AU - Campbell, M. J. AU - Cho, R. J. AU - Church, G. M. PY - 1999 DA - 1999// TI - Systematic determination of genetic network architecture JO - Nat Genet VL - 22 UR - https://doi.org/10.1038/10343 DO - 10.1038/10343 ID - Tavazoie1999 ER - TY - JOUR AU - Birnbaum, K. AU - Benfey, P. N. AU - Shasha, D. E. PY - 2001 DA - 2001// TI - cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.158301 DO - 10.1101/gr.158301 ID - Birnbaum2001 ER - TY - JOUR AU - Bussemaker, H. J. AU - Li, H. AU - Siggia, E. D. PY - 2001 DA - 2001// TI - Regulatory element detection using correlation with expression JO - Nat Genet VL - 27 UR - https://doi.org/10.1038/84792 DO - 10.1038/84792 ID - Bussemaker2001 ER - TY - JOUR AU - Bar-Joseph, Z. AU - Gerber, G. K. AU - Lee, T. I. AU - Rinaldi, N. J. AU - Yoo, J. Y. AU - Robert, F. AU - Gordon, D. B. AU - Fraenkel, E. AU - Jaakkola, T. S. AU - Young, R. A. AU - Gifford, D. K. PY - 2003 DA - 2003// TI - Computational discovery of gene modules and regulatory networks JO - Nat Biotechnol VL - 21 UR - https://doi.org/10.1038/nbt890 DO - 10.1038/nbt890 ID - Bar-Joseph2003 ER - TY - JOUR AU - Segal, E. AU - Shapira, M. AU - Regev, A. AU - Pe'er, D. AU - Botstein, D. AU - Koller, D. AU - Friedman, N. PY - 2003 DA - 2003// TI - Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data JO - Nat Genet VL - 34 UR - https://doi.org/10.1038/ng1165 DO - 10.1038/ng1165 ID - Segal2003 ER - TY - JOUR AU - Gao, F. AU - Foat, B. C. AU - Bussemaker, H. J. PY - 2004 DA - 2004// TI - Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-31 DO - 10.1186/1471-2105-5-31 ID - Gao2004 ER - TY - JOUR AU - Haverty, P. M. AU - Hansen, U. AU - Weng, Z. PY - 2004 DA - 2004// TI - Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh183 DO - 10.1093/nar/gkh183 ID - Haverty2004 ER - TY - JOUR AU - Ho Sui, S. J. AU - Mortimer, J. R. AU - Arenillas, D. J. AU - Brumm, J. AU - Walsh, C. J. AU - Kennedy, B. P. AU - Wasserman, W. W. PY - 2005 DA - 2005// TI - oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki624 DO - 10.1093/nar/gki624 ID - Ho Sui2005 ER - TY - JOUR AU - Beer, M. A. AU - Tavazoie, S. PY - 2004 DA - 2004// TI - Predicting gene expression from sequence JO - Cell VL - 117 UR - https://doi.org/10.1016/S0092-8674(04)00304-6 DO - 10.1016/S0092-8674(04)00304-6 ID - Beer2004 ER - TY - JOUR AU - Wasserman, W. W. AU - Palumbo, M. AU - Thompson, W. AU - Fickett, J. W. AU - Lawrence, C. E. PY - 2000 DA - 2000// TI - Human-mouse genome comparisons to locate regulatory sites JO - Nat Genet VL - 26 UR - https://doi.org/10.1038/79965 DO - 10.1038/79965 ID - Wasserman2000 ER - TY - JOUR AU - Roth, F. P. AU - Hughes, J. D. AU - Estep, P. W. AU - Church, G. M. PY - 1998 DA - 1998// TI - Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation JO - Nat Biotechnol VL - 16 UR - https://doi.org/10.1038/nbt1098-939 DO - 10.1038/nbt1098-939 ID - Roth1998 ER - TY - JOUR AU - Elkon, R. AU - Linhart, C. AU - Sharan, R. AU - Shamir, R. AU - Shiloh, Y. PY - 2003 DA - 2003// TI - Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.947203 DO - 10.1101/gr.947203 ID - Elkon2003 ER - TY - JOUR AU - Liu, R. AU - McEachin, R. C. AU - States, D. J. PY - 2003 DA - 2003// TI - Computationally identifying novel NF-kappa B-regulated immune genes in the human genome JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.911803 DO - 10.1101/gr.911803 ID - Liu2003 ER - TY - JOUR AU - Cole, S. W. AU - Yan, W. AU - Galic, Z. AU - Arevalo, J. AU - Zack, J. A. PY - 2005 DA - 2005// TI - Expression-based monitoring of transcription factor activity: the TELiS database JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti038 DO - 10.1093/bioinformatics/bti038 ID - Cole2005 ER - TY - JOUR AU - Kim, S. Y. AU - Volsky, D. J. PY - 2005 DA - 2005// TI - PAGE: Parametric Analysis of Gene set Enrichment JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-144 DO - 10.1186/1471-2105-6-144 ID - Kim2005 ER - TY - JOUR AU - Mootha, V. K. AU - Handschin, C. AU - Arlow, D. AU - Xie, X. AU - St Pierre, J. AU - Sihag, S. AU - Yang, W. AU - Altshuler, D. AU - Puigserver, P. AU - Patterson, N. AU - Willy, P. J. AU - Schulman, I. G. AU - Heyman, R. A. AU - Lander, E. S. AU - Spiegelman, B. M. PY - 2004 DA - 2004// TI - Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0401401101 DO - 10.1073/pnas.0401401101 ID - Mootha2004 ER - TY - JOUR AU - Cicala, C. AU - Arthos, J. AU - Selig, S. M. AU - Dennis, G. AU - Hosack, D. A. AU - Van Ryk, D. AU - Spangler, M. L. AU - Steenbeke, T. D. AU - Khazanie, P. AU - Gupta, N. AU - Yang, J. AU - Daucher, M. AU - Lempicki, R. A. AU - Fauci, A. S. PY - 2002 DA - 2002// TI - HIV envelope induces a cascade of cell signals in non-proliferating target cells that favor virus replication JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.142287999 DO - 10.1073/pnas.142287999 ID - Cicala2002 ER - TY - JOUR AU - Choe, W. AU - Volsky, D. J. AU - Potash, M. J. PY - 2001 DA - 2001// TI - Induction of rapid and extensive beta-chemokine synthesis in macrophages by human immunodeficiency virus type 1 and gp120, independently of their coreceptor phenotype JO - J Virol VL - 75 UR - https://doi.org/10.1128/JVI.75.22.10738-10745.2001 DO - 10.1128/JVI.75.22.10738-10745.2001 ID - Choe2001 ER - TY - JOUR AU - Choe, W. AU - Volsky, D. J. AU - Potash, M. J. PY - 2002 DA - 2002// TI - Activation of NF-kappaB by R5 and X4 human immunodeficiency virus type 1 induces macrophage inflammatory protein 1alpha and tumor necrosis factor alpha in macrophages JO - J Virol VL - 76 UR - https://doi.org/10.1128/JVI.76.10.5274-5277.2002 DO - 10.1128/JVI.76.10.5274-5277.2002 ID - Choe2002 ER - TY - JOUR AU - Hoffmann, E. AU - Dittrich-Breiholz, O. AU - Holtmann, H. AU - Kracht, M. PY - 2002 DA - 2002// TI - Multiple control of interleukin-8 gene expression JO - J Leukoc Biol VL - 72 ID - Hoffmann2002 ER - TY - JOUR AU - DeGregori, J. AU - Kowalik, T. AU - Nevins, J. R. PY - 1995 DA - 1995// TI - Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes JO - Mol Cell Biol VL - 15 UR - https://doi.org/10.1128/MCB.15.8.4215 DO - 10.1128/MCB.15.8.4215 ID - DeGregori1995 ER - TY - JOUR AU - Zhao, F. AU - Xuan, Z. AU - Liu, L. AU - Zhang, M. Q. PY - 2005 DA - 2005// TI - TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies JO - Nucleic Acids Res VL - 33 ID - Zhao2005 ER - TY - JOUR AU - Zhu, Z. AU - Pilpel, Y. AU - Church, G. M. PY - 2002 DA - 2002// TI - Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm JO - J Mol Biol VL - 318 UR - https://doi.org/10.1016/S0022-2836(02)00026-8 DO - 10.1016/S0022-2836(02)00026-8 ID - Zhu2002 ER - TY - JOUR AU - Pilpel, Y. AU - Sudarsanam, P. AU - Church, G. M. PY - 2001 DA - 2001// TI - Identifying regulatory networks by combinatorial analysis of promoter elements JO - Nat Genet VL - 29 UR - https://doi.org/10.1038/ng724 DO - 10.1038/ng724 ID - Pilpel2001 ER - TY - JOUR AU - Tanay, A. AU - Sharan, R. AU - Kupiec, M. AU - Shamir, R. PY - 2004 DA - 2004// TI - Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0308661100 DO - 10.1073/pnas.0308661100 ID - Tanay2004 ER - TY - STD TI - DBTSS[http://dbtss.hgc.jp] UR - http://dbtss.hgc.jp ID - ref29 ER - TY - JOUR AU - Suzuki, Y. AU - Yamashita, R. AU - Nakai, K. AU - Sugano, S. PY - 2002 DA - 2002// TI - DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.328 DO - 10.1093/nar/30.1.328 ID - Suzuki2002 ER - TY - JOUR AU - Quandt, K. AU - Frech, K. AU - Karas, H. AU - Wingender, E. AU - Werner, T. PY - 1995 DA - 1995// TI - MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data JO - Nucleic Acids Res VL - 23 UR - https://doi.org/10.1093/nar/23.23.4878 DO - 10.1093/nar/23.23.4878 ID - Quandt1995 ER - TY - STD TI - TRED database[http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home] UR - http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home ID - ref32 ER - TY - STD TI - GEO (Gene Expression Omnibus)[http://www.ncbi.nlm.nih.gov/projects/geo/] UR - http://www.ncbi.nlm.nih.gov/projects/geo/ ID - ref33 ER - TY - CHAP PY - 2001 DA - 2001// BT - Microarray Suite User Guide PB - Santa Clara CY - CA ID - ref34 ER - TY - CHAP AU - Bailey, N. T. J. PY - 1995 DA - 1995// BT - Statistical Methods in Biology PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9781139170840 DO - 10.1017/CBO9781139170840 ID - Bailey1995 ER - TY - JOUR AU - Saldanha, A. J. PY - 2004 DA - 2004// TI - Java Treeview – extensible visualization of microarray data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth349 DO - 10.1093/bioinformatics/bth349 ID - Saldanha2004 ER - TY - JOUR AU - Storey, J. D. AU - Tibshirani, R. PY - 2003 DA - 2003// TI - Statistical significance for genomewide studies JO - Proc Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.1530509100 DO - 10.1073/pnas.1530509100 ID - Storey2003 ER - TY - STD TI - Bioconductor[http://www.bioconductor.org] UR - http://www.bioconductor.org ID - ref38 ER -