323 related articles for article (PubMed ID: 19995984)
1. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells.
Ouyang Z; Zhou Q; Wong WH
Proc Natl Acad Sci U S A; 2009 Dec; 106(51):21521-6. PubMed ID: 19995984
[TBL] [Abstract][Full Text] [Related]
2. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.
Chen X; Xu H; Yuan P; Fang F; Huss M; Vega VB; Wong E; Orlov YL; Zhang W; Jiang J; Loh YH; Yeo HC; Yeo ZX; Narang V; Govindarajan KR; Leong B; Shahab A; Ruan Y; Bourque G; Sung WK; Clarke ND; Wei CL; Ng HH
Cell; 2008 Jun; 133(6):1106-17. PubMed ID: 18555785
[TBL] [Abstract][Full Text] [Related]
3. Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.
Orlov Y; Xu H; Afonnikov D; Lim B; Heng JC; Yuan P; Chen M; Yan J; Clarke N; Orlova N; Huss M; Gunbin K; Podkolodnyy N; Ng HH
J Integr Bioinform; 2012 Sep; 9(2):211. PubMed ID: 22987856
[TBL] [Abstract][Full Text] [Related]
4. Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.
Kuznetsov VA; Singh O; Jenjaroenpun P
BMC Genomics; 2010 Feb; 11 Suppl 1(Suppl 1):S12. PubMed ID: 20158869
[TBL] [Abstract][Full Text] [Related]
5. Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse embryonic stem cells.
Chen G; Zhou Q
BMC Genomics; 2011 Oct; 12():515. PubMed ID: 22011333
[TBL] [Abstract][Full Text] [Related]
6. Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells.
Kidder BL; Yang J; Palmer S
PLoS One; 2008; 3(12):e3932. PubMed ID: 19079543
[TBL] [Abstract][Full Text] [Related]
7. Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data.
Sharov AA; Masui S; Sharova LV; Piao Y; Aiba K; Matoba R; Xin L; Niwa H; Ko MS
BMC Genomics; 2008 Jun; 9():269. PubMed ID: 18522731
[TBL] [Abstract][Full Text] [Related]
8. Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors.
Nishiyama A; Xin L; Sharov AA; Thomas M; Mowrer G; Meyers E; Piao Y; Mehta S; Yee S; Nakatake Y; Stagg C; Sharova L; Correa-Cerro LS; Bassey U; Hoang H; Kim E; Tapnio R; Qian Y; Dudekula D; Zalzman M; Li M; Falco G; Yang HT; Lee SL; Monti M; Stanghellini I; Islam MN; Nagaraja R; Goldberg I; Wang W; Longo DL; Schlessinger D; Ko MS
Cell Stem Cell; 2009 Oct; 5(4):420-33. PubMed ID: 19796622
[TBL] [Abstract][Full Text] [Related]
9. A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns.
Park SJ; Nakai K
BMC Bioinformatics; 2011 Feb; 12 Suppl 1(Suppl 1):S50. PubMed ID: 21342583
[TBL] [Abstract][Full Text] [Related]
10. ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network.
Matsuda K; Mikami T; Oki S; Iida H; Andrabi M; Boss JM; Yamaguchi K; Shigenobu S; Kondoh H
Development; 2017 Jun; 144(11):1948-1958. PubMed ID: 28455373
[TBL] [Abstract][Full Text] [Related]
11. Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells.
Hutchins AP; Choo SH; Mistri TK; Rahmani M; Woon CT; Ng CK; Jauch R; Robson P
Stem Cells; 2013 Feb; 31(2):269-81. PubMed ID: 23169531
[TBL] [Abstract][Full Text] [Related]
12. CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells.
Kidder BL
J Vis Exp; 2018 May; (135):. PubMed ID: 29889205
[TBL] [Abstract][Full Text] [Related]
13. Multilayered chromatin analysis reveals E2f, Smad and Zfx as transcriptional regulators of histones.
Gokhman D; Livyatan I; Sailaja BS; Melcer S; Meshorer E
Nat Struct Mol Biol; 2013 Jan; 20(1):119-26. PubMed ID: 23222641
[TBL] [Abstract][Full Text] [Related]
14. The pluripotency regulator Zic3 is a direct activator of the Nanog promoter in ESCs.
Lim LS; Hong FH; Kunarso G; Stanton LW
Stem Cells; 2010 Nov; 28(11):1961-9. PubMed ID: 20872845
[TBL] [Abstract][Full Text] [Related]
15. Genome-wide analysis reveals Sall4 to be a major regulator of pluripotency in murine-embryonic stem cells.
Yang J; Chai L; Fowles TC; Alipio Z; Xu D; Fink LM; Ward DC; Ma Y
Proc Natl Acad Sci U S A; 2008 Dec; 105(50):19756-61. PubMed ID: 19060217
[TBL] [Abstract][Full Text] [Related]
16. Synthetic and genomic regulatory elements reveal aspects of
King DM; Hong CKY; Shepherdson JL; Granas DM; Maricque BB; Cohen BA
Elife; 2020 Feb; 9():. PubMed ID: 32043966
[TBL] [Abstract][Full Text] [Related]
17. Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells.
Sharov AA; Nakatake Y; Wang W
BMC Bioinformatics; 2022 Sep; 23(1):377. PubMed ID: 36114445
[TBL] [Abstract][Full Text] [Related]
18. Co-regulation in embryonic stem cells via context-dependent binding of transcription factors.
Lee Y; Zhou Q
Bioinformatics; 2013 Sep; 29(17):2162-8. PubMed ID: 23793746
[TBL] [Abstract][Full Text] [Related]
19. Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data.
Gong W; Koyano-Nakagawa N; Li T; Garry DJ
BMC Bioinformatics; 2015 Mar; 16():74. PubMed ID: 25887857
[TBL] [Abstract][Full Text] [Related]
20. Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET.
Mathur D; Danford TW; Boyer LA; Young RA; Gifford DK; Jaenisch R
Genome Biol; 2008; 9(8):R126. PubMed ID: 18700969
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]