MPromDb Data Sources

MPromDb integrates information from publicly available data and currently contains information on human and mouse. In the latest version of MPromDb, we have added the alternative promoter annotation identified from 26 different RNA Pol-II ChIP-Seq datasets for human and mouse. The dataset include samples from 6 different cell types of human (CD4+TCells, HeLa S3, K562, NB4, Lymphyoblastoid, Jurkat) whereas mouse samples include five different tissues and five different celss types: brain, liver, lung, spleen, kidney, Embryonic Stem Cell (V6.5), Mouse Embryonic Fibroblasts B4, Mouse Embryonic Fibroblasts B6, Bone Marrow-derived macrophages, 3T3-L1. We have also added promoter regions of recently discovered non-coding gene class (lincRNA).

Additionally, we also provide significant enrichment profiles of various factors (Mouse - OCT4, CEBPa, CHD7, c-Myc, CTCF, ESRRB, FOXA1, FOXA2, GFP, KLF4, n-Myc, NR5A2, P300, Rbbp5, SETDB1, SIRT1, SOX2, STAT3, STAT4, STAT6, SUZ12, TBP, TBX3, TCFCP2I1, WDR5, ZFX; Human - OCT4, CBP, CTCF, ETS1, KLF4, NANOG, P300, PCAF, PHF8, PPARG, RUNX, SOX2, STAT1, TFII, Tip60, ZNF263, SUZ12, MOF, IGF1R, NFkB)


Human RNA Pol-II Chip-seq Datasets Processed


Cell TypeSourceTitle and Summary/InformationLab Name
CD4+TCells NCBI GEO: GSM393966,GSM393967,GSM393968 Genome-wide mapping of HATs and HDACs in human CD4+ T cells

Wang Z, Zang C, Cui K, Schones DE et al., Cell 2009 Sep 4;138(5):1019-31. PMID: 19698979
Keji Zhao, NHLBI
CD4+TCells NCBI GEO: GSM417829 Chromatin Poises miRNA- and Protein-coding Genes for Expression

Barski A, Jothi R, Cuddapah S, Cui K et al., Genome Res 2009 October 19(10):1742-51. PMID: 19713549
Keji Zhao, NHLBI
HeLa S3 NCBI GEO: GSE12781 Genome-wide maps of transcription factor binding using ChIP-Seq for Human ENCODE

ENCODE Project
Michael Snyder, Yale, ENCODE
K562 NCBI GEO: GSM325933 Genome-wide mapping of RNA Polymerase II binding sites

ENCODE Project
ENCODE Project
K562 NCBI GEO: GSM487431 Close Association of RNA Polymerase II and Many Transcription Factors With Pol III Genes

Mark Gerstein
ENCODE Project
NB4 NCBI GEO: GSM325935 Genome-wide mapping of RNA Polymerase II binding sites

ENCODE Project
Michael Snyder, Yale, ENCODE Project
Jurkat NCBI GEO: GSM569087 ChIP-Seq of Histone Methylation and RNAP2 in Human Jurkat cells

Lawton LN, Young RA., 2010
Richard Young Lab, MIT
Lymphoblastoid Cells NCBI GEO: GSE19484 Variation in transcription factor binding among humans

Kasowski M, Grubert F, Heffelfinger C, Hariharan M et al., Science 2010 Apr 9;328(5975):232-5. PMID: 20299548
Jan Korbel, EMBL, Heidelberg, Germany & Michael Snyder, Stanford University School of Medicine, Stanford

Mouse RNA Pol-II Chip-seq Datasets Processed

Tissue/CellTypeSourceTitle and Summary/InformationLab Name
Brain,Liver,Kidney,Spleen,Lung NCBI GEO: GSM542586 GSM542588 GSM542587 GSM542590 GSM542589 Genome-wide mapping of RNA Pol-II promoter usage in mouse tissue by ChIP-seq

H. Sun, J. Wu, P. Wickramasinghe,S. Pal, R. Gupta, A. Bhattacharyya, F. Agosto-Perez, L. Showe, T. Huang, R. Davuluri, Nucleic Acids Research, Sep., 2010
Ramana Davuluri, The Wistar Institute, Philadelphia
Embryonic Stem Cell(V6.5) NCBI GEO: SRA008242 Divergent transcription from active promoters

Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA., Science. 2008 Dec 19;322(5909):1849-51. PMID: 19056940
Phillip Sharp, MIT, Cambridge
Mouse Embryonic Fibroblasts B4 NCBI GEO: GSM555138 Unpublished

Bilodeau S, Newman JJ, Young RA
Richard Young Lab, MIT, Cambridge
Mouse Embryonic Fibroblasts B6 NCBI GEO: GSM555139 Unpublished

Bilodeau S, Newman JJ, Young RA
Richard Young Lab, MIT, Cambridge
Bone Marrow-derived macrophages NCBI GEO: GSE17631 Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

De Santa F, Narang V, Yap ZH, Tusi BK et al., EMBO J 2009 Nov 4;28(21):3341-52. PMID: 19779457
Chia-Lin Wei, Genome Institute of Singapore & Gioacchino Natoli, European Institute of Oncology, Milan, Italy
3T3-L1 cells NCBI GEO: GSE13511 Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

Nielsen R, Pedersen TA, Hagenbeek D, Moulos P et al., Genes Dev 2008 Nov 1;22(21):2953-67. PMID: 18981474
Hendrik Stunnenberg, University of Southern Denmark, Odense M, Denmark

Mouse mRNA-seq Datasets Processed

Tissue/CellTypeSourceTitle and Summary/InformationLab Name
Brain NCBI GEO: SRR001356, SRR001357, SRR006488, SRR006489 Mapping and quantifying mammalian transcriptomes by RNA-Seq

A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer & B. Wold, Nat Methods. 2008 Jul;5(7):621-628.
Liver NCBI GEO: SRR001358, SRR001359, SRR001360, SRR006490, SRR006491 Mapping and quantifying mammalian transcriptomes by RNA-Seq

A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer & B. Wold, Nat Methods. 2008 Jul;5(7):621-628.
Mouse Embryonic Stem Cell NCBI GEO: GSM521650 Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

M. Guttman, M. Garber, J. Z. Levin, J. Donaghey et al., Nat Biotechnol 2010 May;28(5):503-510.

Human Transcription Factors & other factors ChIP-seq Datasets Processed

Tissue/CellTypeFactor NameNCBI GEO IDLab Name
hESCells_H1 OCT4 GSM518373
Glioblastoma T98G Cells CBP GSM525266
CD4+TCells CBP GSM393945
Jurkat CBP GSM449527
hESCells_H1 CTCF GSM518375
Jurkat CTCF GSM325899
CD4+TCells CTCF GSM325895
HeLa CTCF GSM325897
hASCells CTCF GSM534478
Jurkat ETS1 GSM449525
hESCells_H1 KLF4 GSM447584
hESCells_H1 MYC GSM447585
hESCells_H1 NANOG GSM518374
Glioblastoma T98G Cells P300 GSM525265
hESCells_H1 P300 GSM447587
CD4+TCells P300 GSM393946
CD4+TCells PCAF GSM393947
HeLa PHF8 GSM520381
293T Cells PHF8 GSM520382
hAS Cells PPARG GSM534494
Jurkat RUNX GSM449526
hESCells_H1 SOX2 GSM456570
HeLa STAT1 GSM320736
hESCells_H1 TFII GSM447586
CD4+TCells Tip60 GSM393949
K562 Cells ZNF263 GSM476650
HeLa E2F1 GSM558469
MDA-MB-231Cells ERAlpha GSM560853
hESCells_H1 SUZ12 GSM602674
DFB Malignant Melanoma Cell line IGF1R GSM586973
GM19193 NFkappaB GSE19485

Mouse Transcription Factors & other factors ChIP-seq Datasets Processed

Tissue/CellTypeFactor NameNCBI GEO ID
mESCell OCT4 GSM288346
3T3-L1 Cells CEBPa GSM427093
Liver CEBPa GSM427088
mESCell CDH7 GSM558674
mESCell c-Myc GSM288356
mESCell CTCF GSM560352
mESCell E2F1 GSM288349
3T3-L1 Cells E2F4 GSM427094
Liver E2F4 GSM427091
MEF E2F4 GSM602777
mESCell ESRRB GSM288355
Liver FOXA1 GSM427090
Liver FOXA2 GSM427089
mESCell GFP GSM288358
mESCell KLF4 GSM288354
mESCell n-Myc GSM288357
mESCell NR5A2 GSM470523
mESCell P300 GSM558675
3T3-L1 Cells P300 GSM427092
Liver P300 GSM427087
mESCell RBBP5 GSM566278
mESCell SETDB1 GSE18371
Cerebellum SIRT1 GSM427095
mESCell SOX2 GSM288347
mESCell STAT3 GSM288353
CD4+TCells STAT4 GSM550303
CD4+TCells STAT6 GSM550311
mESCell SUZ12 GSM288360
mESCell TBP GSM555162
mESCell TBX3 GSM476146
mESCell TCFCPI1 GSM288350
mESCell WDR5 GSM566280
mESCell ZDX GSM288352
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