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Coexpression cluster:C1462: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,1.11315,0.0880431,0.576478,0.387783,0.483957,0.730467,0.585619,1.40695,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.134746,0.35388,0.585658,0.329602,0.248856,0.936389,0.513952,0.323162,0.390088,0.154075,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.0481066,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,1.5087,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,4.29974,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,1.56033,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,1.11315,0.0880431,0.576478,0.387783,0.483957,0.730467,0.585619,1.40695,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.134746,0.35388,0.585658,0.329602,0.248856,0.936389,0.513952,0.323162,0.390088,0.154075,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,0.272514,1.10535,0.0481066,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,1.5087,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,4.29974,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,1.56033,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.00461978,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;2.20326,MA0055.1;0.808182,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00076337,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;5.93827,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;1.61362,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;1.22729,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;2.82381,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;1.88357,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.0270301,MA0164.1;0.738243,MA0080.2;1.02158,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;5.9246e-06,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1462_Mast_immature_CD4_Macrophage_Dendritic_CD8_CD19



Phase1 CAGE Peaks

Hg19::chr1:114414268..114414271,-p4@PTPN22
Hg19::chr1:114414288..114414310,-p2@PTPN22
Hg19::chr1:114414316..114414407,-p1@PTPN22
Hg19::chr2:225811728..225811737,-p14@DOCK10
Hg19::chr2:225811747..225811796,-p2@DOCK10
Hg19::chr2:225811803..225811825,-p5@DOCK10


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
leukocyte6.63e-74136
hematopoietic stem cell3.09e-72168
angioblastic mesenchymal cell3.09e-72168
hematopoietic oligopotent progenitor cell9.59e-68161
hematopoietic multipotent progenitor cell9.59e-68161
hematopoietic cell4.35e-65177
hematopoietic lineage restricted progenitor cell1.41e-64120
nongranular leukocyte1.39e-63115
myeloid cell6.00e-33108
common myeloid progenitor6.00e-33108
myeloid leukocyte8.56e-3372
lymphocyte1.81e-3253
common lymphoid progenitor1.81e-3253
granulocyte monocyte progenitor cell1.88e-3267
lymphoid lineage restricted progenitor cell3.88e-3252
nucleate cell2.46e-3055
myeloid lineage restricted progenitor cell9.31e-2966
macrophage dendritic cell progenitor9.58e-2961
monopoietic cell4.05e-2759
monocyte4.05e-2759
monoblast4.05e-2759
promonocyte4.05e-2759
defensive cell6.51e-2348
phagocyte6.51e-2348
classical monocyte2.21e-1942
CD14-positive, CD16-negative classical monocyte2.21e-1942
mesenchymal cell5.76e-19354
connective tissue cell1.93e-17361
T cell2.02e-1625
pro-T cell2.02e-1625
mature alpha-beta T cell4.35e-1518
alpha-beta T cell4.35e-1518
immature T cell4.35e-1518
mature T cell4.35e-1518
immature alpha-beta T cell4.35e-1518
lymphocyte of B lineage2.32e-1424
pro-B cell2.32e-1424
multi fate stem cell2.65e-13427
motile cell6.77e-13386
somatic stem cell2.61e-12433
stem cell3.07e-12441
CD8-positive, alpha-beta T cell2.85e-1011
B cell9.65e-1014
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.89e-3898
blood island5.89e-3898
hemolymphoid system3.89e-37108
immune system2.20e-3193
bone marrow1.32e-2776
bone element1.79e-2482
skeletal element7.67e-2090
skeletal system2.81e-16100
connective tissue3.20e-16371
lateral plate mesoderm5.03e-15203
mesoderm3.89e-07315
mesoderm-derived structure3.89e-07315
presumptive mesoderm3.89e-07315
musculoskeletal system5.21e-07167
Disease
Ontology termp-valuen
hematologic cancer1.41e-0851
immune system cancer1.41e-0851


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.00461978
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.12.20326
MA0055.10.808182
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.15.93827
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.11.61362
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.22.82381
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.11.88357
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.21.02158
MA0018.20.709805
MA0099.20.629739
MA0079.25.9246e-06
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538312.17890089615180.00125981487125340.00846242637888046
BCL11A#53335314.18472755180350.0008080831849424810.00616970536970596
BCLAF1#9774310.82632380506090.001772351046991060.0108903083483379
FOSL1#8061319.85678985818650.0003014027572522190.00311080171604551
GATA2#262436.3724658667770.008058821308742550.0318893357581087
IRF4#3662310.95725634337210.001711753441810940.0106909351578335
JUN#372536.256414596168170.008486346850954870.0324167213623085
MEF2A#4205618.74323090964412.30307332780908e-081.62850829575527e-06
NFKB1#479065.488063424193843.65870229532191e-050.000707482334791937
POLR2A#543062.147453176558070.01019570676818780.0380391318959299
SIN3A#2594265.408884726815143.99207083571449e-050.000742922106220929
TBP#690863.706770687096390.000385416472907960.00377851412879324
TCF12#6938610.63446490218646.9082259011154e-073.11388953339055e-05
ZNF143#770236.750438276113950.006850259204468580.0290401940678476



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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