Biology Reference
In-Depth Information
[4] Charoensawan V, Wilson D, Teichmann SA. Lineage-specific
expansion of DNA-binding transcription factor families. Trends
Genet 2010;26:388
e
93.
[5] Gamsjaeger R, Kong Liew C, Loughlin FE, Crossley M,
Mackay JP. Sticky fingers: zinc-fingers as protein-recognition
motifs. Trends Biochem Sci 2006;32:63
e
70.
[6] Tanaka Hall TM. Multiplemodes of RNA recognition by zinc finger
proteins. Curr Opin Struct Biol 2005;15:367
e
73.
[7] Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-
Jones S, et al. The Pfam protein families database. Nucleic Acids
Res 32 Database issue 2004:D138
e
41.
[8] Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T,
Schultz J, et al. SMART 4.0: towards genomic data integration.
Nucleic Acids Res 2004;32:D142
e
4.
[9] Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D,
Bateman A, et al. The InterPro Database, 2003 brings
increased coverage and new features. Nucleic Acids Res
2003;31:315
e
8.
[10] Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA,
Walhout AJM. A compendium of C. elegans regulatory tran-
scription factors: a resource for mapping transcription regulatory
networks. Genome Biol 2005;6:R110.
[11] Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.
A census of human transcription factors: function, expression and
evolution. Nat Rev Genet 2009;10:252
e
63.
[12] Kummerfeld SK, Teichmann SA. DBD: a transcription factor
prediction database. Nucleic Acids Res 2006;34:D74
e
81.
[13] Levine M, Tjian R. Transcription regulation and animal diversity.
Nature 2003;424:147
e
51.
[14] Yen K, Narasimhan SD, Tissenbaum HA. DAF-16/Forkhead box
O transcription factor: many paths to a single Fork(head) in the
road. Antioxid Redox Signal 2011;14:623
e
34.
[15] Murre C, Bain G, van Dijk MA, Engel I, Furnari BA,
Massari ME, et al. Structure and function of helix-loop-helix
proteins. Biochim Biophys Acta 1994;1218:129
e
35.
[16] Glass CK. Differential recognition of target genes by nuclear
receptor monomers, dimers and heterodimers. Endocri Rev
1994;15:391
e
407.
[17] Grove CA, Walhout AJ. Transcription factor functionality and
transcription regulatory networks. Mol Biosyst 2008;4:309
e
14.
[18] Grove CA, deMasi F, Barrasa MI, Newburger D, Alkema MJ,
Bulyk ML, et al. A multiparameter network reveals extensive
divergence between C. elegans bHLH transcription factors. Cell
2009;138:314
e
27.
[19] Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB,
Tan K, et al. An atlas of combinatorial transcriptional regulation
in mouse and man. Cell 2010;140:744
e
52.
[20] Brasch MA, Hartley JL, Vidal M. ORFeome cloning and systems
biology: standardized mass production of the parts from the parts-
list. Genome Res 2004;14:2001
e
9.
[21] Walhout AJM, Temple GF, Brasch MA, Hartley JL, Lorson MA,
van den Heuvel S, et al. GATEWAY recombinational cloning:
application to the cloning of large numbers of open reading
frames or ORFeomes. Methods Enzymol 2000;328:575
e
92.
[22] Reboul J, Vaglio P, Rual JF, Lamesch P, Martinez M,
Armstrong CM, et al. C. elegans ORFeome version 1.1: experi-
mental verification of the genome annotation and resource for
proteome-scale protein expression. Nat Genet 2003;34:35
e
41.
[23] Rual J-F, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, Dricot A,
et al. Human ORFeome version 1.1: a platform for reverse pro-
teomics. Genome Res 2004;14:2128
e
35.
[24] Gaudinier A, Zhang L, Reece-Hoyes JS, Taylor-Teeples M, Pu L,
Liu Z, et al. An automated eY1H approach to elucidate Arabi-
dopsis stele gene regulatory networks. Nat Methods 2011;
8:1053
e
5.
[25] Hu S, Xie Z, Onishi A, Jiang L, Lin J, Rho HS, et al. Profiling the
human protein-DNA interactome reveals ERK2 as a transcrip-
tional repressor of interferon signaling. Cell 2009;139:610
e
22.
[26] Reece-Hoyes JS, Barutcu AR, Patton McCord R, Jeong J, Jian L,
MacWilliams A, et al. Yeast one-hybrid assays for high-
throughput human gene regulatory network mapping. Nat
Methods 2011;8:1050
e
2.
[27] Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS,
Arda HE, Grove CA, et al. Matrix and Steiner-triple-system smart
pooling assays for high-performance transcription regulatory
network mapping. Nat Methods 2007;4:659
e
64.
[28] Arda HE, Taubert S, Conine C, Tsuda B, Van Gilst MR,
Sequerra R, et al. Functional modularity of nuclear hormone
receptors in a C. elegans gene regulatory network. Mol Syst Biol
2010;6:367.
[29] Rowan S, Siggers T, Lachke SA, Yue Y, Bulyk ML, Maas RL.
Precise temporal control of the eye regulatory gene Pax6 via
enhancer-binding site affinity. Genes Dev 2010;24:980
e
5.
[30] Bulger M, Groudine M. Functional and mechanistic diversity of
distral transcriptional enhancers. Cell 2011;144:327
e
39.
[31] Wallace JA, Felsenfeld G. We gather together: insulators and
genome organization. Curr Opin Genetic Dev 2007;17:400
e
7.
[32] Kim J, Bhinge AA, Morgan XC, Iyer VR. Mapping DNA-protein
interactions in large genomes by sequence tag analysis of
genomic enrichment. Nat Methods 2005;2:47
e
53.
[33] Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R,
Drenkow J, et al. Prominent use of distal 5
0
transcription start sites
and discovery of a large number of additional exons in ENCODE
regions. Genome Res 2007;17:746
e
59.
[34] Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H,
et al. Cap analysis gene expression for high-throughput analysis
of transcriptional starting point and identification of promoter
usage. Proc Natl Acad Sci U S A 2003;100:15776
e
81.
[35] Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.
Mapping and quantifying mammalian transcriptomes by RNA-
seq. Nat. Methods 2008;5:621
e
8.
[36] Elemento O, Tavazoie S. Fast and systematic genome-wide
discovery of conserved regulatory elements uisng a non-align-
ment based approach. Genome Biol 2005;6:R18.
[37] Huber BR, Bulyk ML. Meta-analysis discovery of tissue-specific
DNA sequence motifs from mammalian expression data. BMC
Bioinformatics 2006;7:229.
[38] Xie X, Lu J, Kulkobas EJ, Golub TR, Mootha V, Lindblad-Toh K,
et al. Systematic discovery of regulatory motifs in human
promoters and 3
0
UTRs by comparison of several mammals.
Nature 2005;434:338
e
45.
[39] Gordan R, Hartemink AJ, Bulyk ML. Distinghuishing direct
versus indirect transcription factor-DNA interacitons. Genome
Res 2009;19:2090
e
100.
[40] Hughes JD, Estep PW, Tavazoie S, Church GM. Computational
identification of cis-regulatory elements associated with groups of
