mESC-Specific High-Throughput Data Used to Train the Bayesian Classifier

To train the Bayesian classifier and infer functional relationships between pairs of genes, we developed a compendium of mouse embryonic stem cell (mESC) data containing more than 2.2 million data points. Using distance measures, such as Pearson Correlation and Euclidean Distance ,we integrated these data into more than 6 billion pair-wise values. The table below lists the high-throughput datasets that contribute to the predicted edge weight (how confident we are that a functional relationship exists between genes) in the mESC probabalistic network. You can download additional supporting information on this mESC network from our PLOS One paper as well as graph files on this page. Supporting information for our new hESC and updated mESC networks is also available.

High-throughput mESC Datasets

Data type Process Source PMID Array Description/Study Title Arrays Features Gene/Protein Pairs Redundancy Relevance
Protein-DNA Interaction CUR Boyer et al. 2006 16625203 Suz12 (MGI:1261758) binding ChIP array 1 15810 15810 0.000007 0.080378
Protein-DNA Interaction CUR Boyer et al. 2006 16625203 Eed (MGI:95286) binding ChIP array 1 15810 15810 0.000007 0.005359
Protein-DNA Interaction CUR Boyer et al. 2006 16625203 Phc1 (MGI:103248) binding ChIP array 1 15810 15810 0.000006 0.000000
Protein-DNA Interaction CUR Boyer et al. 2006 16625203 Rnf2 (MGI:1101759) binding ChIP array 1 15810 15810 0.000006 0.026793
Protein-DNA Interaction CALC Boyer et al. 2006 16625203 mESC polycomb complex TF binding correlations 4 15810 123787245 0.333196 0.020343
Protein-DNA Interaction CUR Boyer et a. 2005 16153702 Pou5f1 (MGI:101893) binding ChIP array 1 2530 2530 0.000007 0.080378
Protein-DNA Interaction CUR Boyer et a. 2005 16153702 Sox2 (MGI:98364) binding ChIP array 1 2530 2530 0.000006 0.003215
Protein-DNA Interaction CUR Boyer et a. 2005 16153702 Nanog (MGI:1919200) binding ChIP array 1 2530 2530 0.000007 0.089309
Protein-DNA Interaction CUR Boyer et a. 2005 16153702 E2f4 (MGI:103012) binding ChIP array 1 2530 2530 0.000011 0.000000
Protein-DNA Interaction CALC Boyer et al. 2005 16153702 mESC transcriptional regulation TF binding correlations 4 2530 3201715 0.000177 0.044837
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Nanog (MGI:1919200) ChIP-seq TF-gene associations 1 15444 15444 0.000005 0.037640
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Tcfcp2l1 (MGI:2444691) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.092595
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Zfx (MGI:99211) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.123460
Protein-DNA Interaction CUR Chen et al. 2008 18555785 E2F1 (MGI:101941) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.123460
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Suz12 (MGI:1261758) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.123460
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Ctcf (MGI:109447) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.092595
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Pou5f1 (MGI:101893) ChIP-seq TF-gene associations 1 15444 15444 0.000005 0.089095
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Sox2 (MGI:98364) ChIP-seq TF-gene associations 1 15444 15444 0.000003 0.053470
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Smad1 (MGI:109452) ChIP-seq TF-gene associations 1 15444 15444 0.000003 0.051442
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Stat3 (MGI:103038) ChIP-seq TF-gene associations 1 15444 15444 0.000005 0.039684
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Myc (MGI:97250) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.050023
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Mycn (MGI:97357) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.025721
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Klf4 (MGI:1342287) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.073948
Protein-DNA Interaction CUR Chen et al. 2008 18555785 Esrrb (MGI:1346832) ChIP-seq TF-gene associations 1 15444 15444 0.000004 0.121256
Protein-DNA Interaction CALC Chen et al. 2008 18555785 mESC transcriptional regulation TF binding correlations 14 15444 119250846 0.159523 0.033614
Protein-DNA Interaction CUR Cole et al. 2008 18347094 Tcf3 (MGI:98510) binding ChIP array 1 19027 19027 0.000009 0.107170
Protein-DNA Interaction CUR Cole et al. 2008 18347094 Pou5f1 (MGI:101893) binding ChIP array 1 19027 19027 0.000005 0.063375
Protein-DNA Interaction CUR Cole et al. 2008 18347094 Nanog (MGI:1919200) binding ChIP array 1 19027 19027 0.000009 0.042868
Protein-DNA Interaction CALC Cole et al. 2008 18347094 Tcf3 regulatory network TF binding correlations 3 19027 181003851 0.737229 0.020765
Protein-DNA Interaction CUR Ding et al. 2009 19345177 Ctr9 (MGI:109345) binding ChIP array 1 1124 1124 0.000012 0.000000
Protein-DNA Interaction CUR Ding et al. 2009 19345177 Ctr9 (MGI:109345) expression array 1 1124 1124 0.000004 0.000000
Microarray Expression DWN GEO Dataset GDS1014 Not Specified by GEO Serum response factor SRF overexpression in embryonic stem cells 23 12654 15947128 0.003168 0.007398
Microarray Expression DWN GEO Dataset GDS1015 Not Specified by GEO Serum response factor SRF induction in embryonic stem cells: time course 15 12654 15470703 0.003109 0.007531
Microarray Expression DWN GEO Dataset GDS1593 16311515 p38 inhibitor PD169316 effect on embryonic stem derived differentiated cells 6 12654 27317136 0.008617 0.005440
Microarray Expression DWN GEO Dataset GDS1653 16377562 Linker histone H1 depletion 6 12488 28610830 0.009368 0.006756
Microarray Expression DWN GEO Dataset GDS1824 16518401 Transcription factors Nanog and Oct4 knockdown effect on embryonic stem cells 14 45101 156140956 0.080949 0.022533
Microarray Expression DWN GEO Dataset GDS2187 16390873 Triple-fusion reporter gene effect on embryonic stem cells 7 21446 42711903 0.006483 0.003211
Microarray Expression DWN GEO Dataset GDS2276 16809427 Embryonic stem cell line response to the conditional expression of neurogenin 3 16 45101 147825415 0.063375 0.012559
Microarray Expression DWN GEO Dataset GDS2294 16940178 Histone deacetylase 1 deficient embryonic stem cells 6 12488 32800950 0.012284 0.007020
Microarray Expression DWN GEO Dataset GDS2666 17394647 Embryonic R1 stem cell differentiation in vitro (MG-430A) 33 22690 63895860 0.053032 0.014528
Microarray Expression DWN GEO Dataset GDS2667 17394647 Embryonic R1 stem cell differentiation in vitro (MG-430B) 33 22575 37623475 0.004415 0.011310
Microarray Expression DWN GEO Dataset GDS2668 17394647 Embryonic J1 stem cell differentiation in vitro (MG-430A) 33 22690 61888375 0.048476 0.010878
Microarray Expression DWN GEO Dataset GDS2669 17394647 Embryonic J1 stem cell differentiation in vitro (MG-430B) 33 22575 39147976 0.004556 0.007592
Microarray Expression DWN GEO Dataset GDS2671 17394647 Embryonic R1 stem cell differentiation in vitro (MG-430B) 33 22690 60494500 0.048092 0.019504
Microarray Expression DWN GEO Dataset GDS2672 17394647 Embryonic V6.5 stem cell differentiation in vitro (MG-430A) 33 22575 38487151 0.004558 0.016114
Microarray Expression DWN GEO Dataset GDS2905 Not Specified by GEO Embryonic stem cells and embryoid bodies (MG-430A) 6 22690 64837578 0.045145 0.010385
Microarray Expression DWN GEO Dataset GDS2906 Not Specified by GEO Embryonic stem cells and embryoid bodies (MG-430B) 6 22575 36598290 0.003933 0.014709
Microarray Expression DWN GEO Dataset GDS434 14727137 Embryonic stem cell cholesterol metabolism mutants 16 12488 33730791 0.017557 0.008424
Microarray Expression CUR GEO Series GSE11523 19112179 Expression Profiling of Differentiating Mouse ES Cells 42 24791 251720703 0.081895 0.018093
Microarray Expression CUR GEO Series GSE1160 Not Specified by GEO Oct3/4 expression and notch signaling in mESC cells 5 277 5253 0.000003 0.053237
Microarray Expression CUR GEO Series GSE12753 18433507 Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells 12 7191 7934136 0.000723 0.008261
Microarray Expression CUR GEO Series GSE13127 19745813 Myc influences embryonic stem cell pluripotency by regulating miRNAs 18 25041 229526025 0.016072 0.005076
Microarray Expression CEL GEO Series GSE13805 20506533 Decoded calreticulin-deficient embryonic stem cell transcriptome resolves latent cardiophenotype 7 16395 131211900 0.154518 0.008861
Microarray Expression CEL GEO Series GSE15173 19332562 Dppa4 is dispensable for embryonic stem cell identity 6 16395 131211900 0.153678 0.005893
Microarray Expression CUR GEO Series GSE15487 19816418 Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells. 12 15149 69484366 0.041645 0.013204
Microarray Expression CEL GEO Series GSE15998 Not Specified by GEO Mouse Exon Atlas 4 20985 202819870 0.161138 0.004114
Microarray Expression CUR GEO Series GSE18503 Not Specified by GEO Effects of environmental chemicals on development of neuronal cell lineages derived from mouse ES cells 25 31508 50145105 0.011830 0.006494
Microarray Expression CEL GEO Series GSE18840 20054295 Let-7c and miR-294 target identification in mouse ES cells 9 20985 202819870 0.159990 0.015831
Microarray Expression CEL GEO Series GSE19542 20211137 Control of histone variant H3.3 localization at specific genomic regions 6 20985 202819870 0.160436 0.001779
Microarray Expression CEL GEO Series GSE2042 18437159 Gene profiling studies in mouse Embryonic Stem cells 13 7715 28807845 0.012847 0.009872
Microarray Expression CEL GEO Series GSE2972 17394647 R1 Embryonic Stem Cell and Embryoid Body Time Course 3 5801 16054611 0.004200 0.041418
Microarray Expression CEL GEO Series GSE3223 Not Specified by GEO Gene Expression Profiles of J1 ES and J1 EB Cells 6 12109 71778171 0.066557 0.008202
Microarray Expression CEL GEO Series GSE3223 Not Specified by GEO Comparison of Gene Expression Profiles of J1 ES and J1 EB Cells 6 5801 16054611 0.002376 0.021588
Microarray Expression CEL GEO Series GSE3231 17394647 V6.5 Embryonic Stem Cell and Embryoid Body Time Course 30 12109 71778171 0.079870 0.009703
Microarray Expression CUR GEO Series GSE3509 15998450 Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray 12 21939 125920515 0.049058 0.012447
Microarray Expression CUR GEO Series GSE3527 16627687 Random differentiation of mouse embryonic stem cell 12 7670 14058253 0.003139 0.004174
Microarray Expression CUR GEO Series GSE3528 16627687 Guided differentiation of mouse embryonic stem cell 12 7670 14058253 0.003102 0.007938
Microarray Expression CEL GEO Series GSE3653 16809427 Differentiation of embryonic stem cells conditionally expressing neurogenin 3 4 16395 131211900 0.150376 0.006203
Microarray Expression CEL GEO Series GSE3749 17394647 Time Course Study of Differentiating J1 Embryoid Bodies 3 12109 71778171 0.077273 0.007969
Microarray Expression CEL GEO Series GSE3774 Not Specified by GEO Gene Expression in Embryonic Stem Cells Grown in a Maintenance Serum vs. a Non-maintenance Serum 6 12109 71778171 0.067073 0.005809
Microarray Expression CEL GEO Series GSE3774 Not Specified by GEO Gene Expression in Embryonic Stem Cells Grown in a Maintenance Serum vs. a Non-maintenance Serum 6 5801 16054611 0.002536 0.014604
Microarray Expression CUR GEO Series GSE4077 16357342 Defining a developmental path to neural fate by global expression profiling of mouse embryonic stem cells 7 15124 65660070 0.033821 0.006527
Microarray Expression CUR GEO Series GSE4082 16357342 Defining a developmental path to neural fate by global expression profiling of mouse ESCs 7 15124 65660070 0.033867 0.003351
Microarray Expression CEL GEO Series GSE4189 16518401 The Oct4 and Nanog transcription network that regulates pluripotency in mouse embryonic stem cells 14 16395 131211900 0.187667 0.019727
Microarray Expression CEL GEO Series GSE4309 16547197 Single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. 16 16395 131211900 0.153114 0.010457
Microarray Expression CEL GEO Series GSE5583 16940178 Wild type versus HDAC knock out mouse embryonic stem cells 6 7715 28807845 0.012877 0.006441
Microarray Expression CEL GEO Series GSE5671 18246200 Cardiac differentiation of embryonic stem cells 16 16395 131211900 0.162733 0.009954
Microarray Expression CUR GEO Series GSE5895 17515932 Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells 12 21704 123598503 0.053210 0.014900
Microarray Expression CUR GEO Series GSE5914 17560561 Global gene expression profiling of mouse pluripotent SCs 18 21194 111833490 0.045867 0.013165
Microarray Expression CUR GEO Series GSE614 14727137 Expression profiling of mouse mutations in ES cells 16 9292 35595703 0.019146 0.011536
Microarray Expression CEL GEO Series GSE7141 18311153 MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells 6 16395 131211900 0.162216 0.013075
Microarray Expression CEL GEO Series GSE7506 18371337 Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. 18 7715 28807845 0.013802 0.011251
Microarray Expression CEL GEO Series GSE7506 18371337 Novel Networks Regulating Embryonic Stem Cell Self-Renewal and Commitment 18 5752 15947128 0.001598 0.015476
Microarray Expression CUR GEO Series GSE7866 17597760 Gene expression comparison of mouse ES cells and EpiSCs 6 21609 174275115 0.089778 0.013672
Microarray Expression CEL GEO Series GSE8128 17637833 Gene Expression in E14 ES cells and Embryoid bodies 4 16395 131211900 0.150725 0.006540
Microarray Expression CEL GEO Series GSE8503 18311153 mRNA expression analysis of undifferentiated Dicer -/- (27H10) embryonic stem cells after miRNA transfection 6 16395 131211900 0.159677 0.005114
Microarray Expression CUR GEO Series GSE8574 18433312 Mouse embryonic stem cell line R1 differentiation study 36 17852 111176416 0.071790 0.011078
Microarray Expression CEL GEO Series GSE9563 18462695 Translation state array analysis of mouse embryonic stem cells 15 16395 131211900 0.159801 0.006997
Microarray Expression CEL GEO Series GSE9978 19618472 Analysis of Rex1 (Zfp42) function in embryonic stem cell differentiation 8 16395 131211900 0.150462 0.004180
Protein-DNA Interaction CUR Hu et al. 2009 19339689 Cnot3 (MGI:2385261) binding ChIP array 1 1518 1518 0.000008 0.000000
Protein-DNA Interaction CUR Hu et al. 2009 19339689 Trim28 (MGI:109274) binding ChIP array 1 1518 1518 0.000006 0.000000
Protein-DNA Interaction CALC Hu et al. 2009 19339689 Self renewal network TF binding correlations 2 1518 1231665 0.000015 0.017365
RNAi Screen CUR Hu et al. 2009 19339689 Genome-wide RNAI screen in mouse Embryonic Stem Cells 2 16981 131795730 0.171811 0.004694
Phylogenetic Profile DWN Inparanoid Database 15608241 Phylogenetic profiles (non tissue specific) 1 15703 123284253 0.147362 0.021844
Protein-DNA Interaction CUR Johnson et al. 2008 18959480 Rest (MGI:104897) binding ChIP array 1 722 722 0.000003 0.129903
Protein-DNA Interaction CUR Kidder et al. 2008 19079543 Myc (MGI:97250) binding ChIP array 1 2151 2151 0.000007 0.021921
Protein-DNA Interaction CUR Kidder et al. 2008 19079543 Stat3 (MGI:103038) binding ChIP array 1 2151 2151 0.000008 0.026793
Protein-DNA Interaction CALC Kidder et al. 2008 19079543 Stat3/Myc interaction network TF binding correlations 2 2151 2310175 0.000045 0.008901
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Nanog (MGI:1919200) binding ChIP array 1 5533 5533 0.000009 0.061566
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Sox2 (MGI:98364) binding ChIP array 1 5533 5533 0.000007 0.025575
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Dax1|Nr0b1 (MGI:1352460) binding ChIP array 1 5533 5533 0.000009 0.080378
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Nac1|Nacc1 (MGI:1914080) binding ChIP array 1 5533 5533 0.000008 0.080378
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Pou5f1 (MGI:101893) binding ChIP array 1 5533 5533 0.000008 0.030733
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Klf4 (MGI:1342287) binding ChIP array 1 5533 5533 0.000008 0.089309
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Zfp281 (MGI:3029290) binding ChIP array 1 5533 5533 0.000009 0.016076
Protein-DNA Interaction CUR Kim et al. 2008 18358816 Zfp42 (MGI:99187) binding ChIP array 1 5533 5533 0.000007 0.029228
Protein-DNA Interaction CALC Kim et al. 2008 18358816 mESC pluripotency network TF binding correlations 9 5533 15100260 0.004974 0.024503
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Suz12 (MGI:1261758) binding ChIP array 1 15471 15471 0.000008 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Pou5f1 (MGI:101893) binding ChIP array 1 15471 15471 0.000007 0.038581
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Nanog (MGI:1919200) binding ChIP array 1 15471 15471 0.000008 0.035934
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Sox2 (MGI:98364) binding ChIP array 1 15471 15471 0.000008 0.043447
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Nac1|Nacc1 (MGI:1914080) binding ChIP array 1 15471 15471 0.000007 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Zfp281 (MGI:3029290) binding ChIP array 1 15471 15471 0.000007 0.051150
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Dax1|Nr0b1 (MGI:1352460) binding ChIP array 1 15471 15471 0.000008 0.160755
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Esrrb (MGI:1346832) binding ChIP array 1 15471 15471 0.000007 0.114825
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Tcfcp2l1 (MGI:2444691) binding ChIP array 1 15471 15471 0.000008 0.000000
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Ctr9 (MGI:109345) binding ChIP array 1 15471 15471 0.000009 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Gcn5l2|Kat2a (MGI:1343101) binding ChIP array 1 15471 15471 0.000009 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Eed (MGI:95286) binding ChIP array 1 15471 15471 0.000007 0.014184
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Dmap1 (MGI:1913483) binding ChIP array 1 15471 15471 0.000007 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 E2F1 (MGI:101941) binding ChIP array 1 15471 15471 0.000009 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 E2f4 (MGI:103012) binding ChIP array 1 15471 15471 0.000007 0.000000
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Myc (MGI:97250) binding ChIP array 1 15471 15471 0.000008 0.058205
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Max (MGI:96921) binding ChIP array 1 15471 15471 0.000007 0.000000
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Mycn (MGI:97357) binding ChIP array 1 15471 15471 0.000009 0.000000
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Zfx (MGI:99211) binding ChIP array 1 15471 15471 0.000008 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Zfp42 (MGI:99187) binding ChIP array 1 15471 15471 0.000007 0.013979
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Tip60|Kat5 (MGI:1932051) binding ChIP array 1 15471 15471 0.000005 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Cnot3 (MGI:2385261) binding ChIP array 1 15471 15471 0.000006 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Phc1 (MGI:103248) binding ChIP array 1 15471 15471 0.000007 0.000000
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Trim28 (MGI:109274) binding ChIP array 1 15471 15471 0.000006 0.107170
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Rnf2 (MGI:1101759) binding ChIP array 1 15471 15471 0.000007 0.026793
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Ezh1 (MGI:1097695) binding ChIP array 1 15471 15471 0.000007 0.000000
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Ctcf (MGI:109447) binding ChIP array 1 15471 15471 0.000007 0.080378
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Smad1 (MGI:109452) binding ChIP array 1 15471 15471 0.000006 0.010717
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Stat3 (MGI:103038) binding ChIP array 1 15471 15471 0.000006 0.043634
Protein-DNA Interaction CUR Kim et al. 2010 20946988 Klf4 (MGI:1342287) binding ChIP array 1 15471 15471 0.000007 0.050236
Protein-DNA Interaction CALC Kim et al. 2010 20946988 Myc interaction network TF binding correlations 34 15471 119668185 0.193701 0.041583
Protein-DNA Interaction CUR Liu et al. 2008 19030024 Sox2 (MGI:98364) binding ChIP array 1 4393 4393 0.000007 0.042993
Protein-DNA Interaction CUR Liu et al. 2008 19030024 Klf4 (MGI:1342287) binding ChIP array 1 4393 4393 0.000009 0.080378
Protein-DNA Interaction CUR Liu et al. 2008 19030024 Myc (MGI:97250) binding ChIP array 1 4393 4393 0.000008 0.023641
Protein-DNA Interaction CALC Liu et al. 2008 19030024 Yamanaka factor regulatory TF binding correlations 3 4393 9647028 0.003743 0.027111
Protein-DNA Interaction CUR Loh et al. 2006 16518401 Pou5f1 (MGI:101893) binding ChIP array 1 2135 2135 0.000007 0.002061
Protein-DNA Interaction CUR Loh et al. 2006 16518401 Nanog (MGI:1919200) binding ChIP array 1 2135 2135 0.000008 0.029770
Protein-DNA Interaction CALC Loh et al. 2006 16518401 Pou5f1/Nanog regulatory network TF binding correlations 2 2135 2275911 0.000091 0.024336
Protein-DNA Interaction CUR Marson et al. 2008 18692474 Pou5f1 (MGI:101893) binding ChIP array 1 18858 18858 0.000007 0.088106
Protein-DNA Interaction CUR Marson et al. 2008 18692474 Sox2 (MGI:98364) binding ChIP array 1 18859 18859 0.000009 0.026793
Protein-DNA Interaction CUR Marson et al. 2008 18692474 Nanog (MGI:1919200) binding ChIP array 1 18859 18859 0.000007 0.058944
Protein-DNA Interaction CUR Marson et al. 2008 18692474 Tcf3 (MGI:98510) binding ChIP array 1 18859 18859 0.000006 0.053585
Protein-DNA Interaction CUR Marson et al. 2008 18692474 Suz12 (MGI:1261758) binding ChIP array 1 18858 18858 0.000008 0.080378
Protein-DNA Interaction CALC Marson et al. 2008 18692474 mESC transcriptional regulation TF binding correlations 5 18858 177821511 0.545998 0.030880
Protein-DNA Interaction CUR Mathur et al. 2008 18700969 Pou5f1 (MGI:101893) binding ChIP-Chip array 1 17803 17803 0.000011 0.054626
Protein-DNA Interaction CUR Mathur et al. 2008 18700969 Pou5f1 (MGI:101893) binding ChIP-PET array 1 17803 17803 0.000007 0.024972
Protein-DNA Interaction CUR Mathur et al. 2008 18700969 Nanog (MGI:1919200) binding ChIP-Chip array 1 17803 17803 0.000007 0.037931
Protein-DNA Interaction CUR Mathur et al. 2008 18700969 Nanog (MGI:1919200) binding ChIP-PET array 1 17803 17803 0.000007 0.027094
Protein-DNA Interaction CALC Mathur et al. 2008 18700969 mESC pluripotency regulation TF binding correlations 4 17803 158482306 0.598176 0.012542
Protein-DNA Interaction DWN BioBase Transfac Database 8594589 Transcription factor binding predictions (non-tissue specific) 1 86320 86320 0.000004 0.043114
Protein-DNA Interaction CUR Van den Berg et al. 2010 20362541 Pou5f1 (MGI:101893) binding ChIP array 1 161 161 0.000008 0.029613
Protein-DNA Interaction CUR Van den Berg et al. 2010 20362541 Sall4 (MGI:2139360) binding ChIP array 1 161 161 0.000008 0.053585
Protein-DNA Interaction CUR Van den Berg et al. 2010 20362541 Dax1|Nr0b1 (MGI:1352460) binding ChIP array 1 161 161 0.000010 0.080378
Protein-DNA Interaction CUR Van den Berg et al. 2010 20362541 Tcfcp2l1 (MGI:2444691) binding ChIP array 1 161 161 0.000007 0.000000
Protein-DNA Interaction CUR Van den Berg et al. 2010 20362541 Dax1|Nr0b1 (MGI:1352460) binding ChIP array 1 161 161 0.000007 0.000000
Protein-DNA Interaction CALC Van den Berg et al. 2010 20362541 Pou5f1 interaction network TF binding correlations 5 161 12880 0.000008 0.138428
Protein_Protein Interaction CUR Wang et al. 2005 15860457 Nanog (MGI:1919200) binding ChIP array 1 207 207 0.000004 0.078179

Supporting Information for mESC Network

mESC Network Graph Files

Supporting Information for Comparative hESC and mESC Networks

Comparative hESC and mESC Network Graph Files