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Coexpression cluster:C1348: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.97464,1.35536,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.075749,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,1.11315,0.29639,0.576478,0.387783,1.21515,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.640661,0.35719,0.316592,0.93226,0.585658,0.878269,0.248856,0.355745,0.513952,0.664116,0.390088,0.992846,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,1.59978,0.267534,0.861462,1.63815,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,0.624519,1.12235,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.717596,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,1.02023,0.32338,0.661488,0.987239,0.776336,0.962826,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.175219,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,0.510514,0.826087,0.136746,1.06652,1.07915,0.717973,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726
|tfbs_overrepresentation_for_novel_motifs=1.97464,1.35536,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.075749,0.553339,0.707204,0.635275,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.127969,1.11315,0.29639,0.576478,0.387783,1.21515,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.640661,0.35719,0.316592,0.93226,0.585658,0.878269,0.248856,0.355745,0.513952,0.664116,0.390088,0.992846,0.468392,0.66382,0.542147,0.304272,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,1.59978,0.267534,0.861462,1.63815,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.882224,1.15727,0.624519,1.12235,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.717596,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,1.02023,0.32338,0.661488,0.987239,0.776336,0.962826,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.175219,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,0.510514,0.826087,0.136746,1.06652,1.07915,0.717973,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726
|tfbs_overrepresentation_jaspar=MA0003.1;0.321379,MA0004.1;1.37419,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.491287,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;0.906394,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.213007,MA0056.1;0,MA0057.1;0.882847,MA0058.1;1.16137,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;1.53717,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,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;0.561458,MA0092.1;0.522012,MA0093.1;1.80532,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;1.68738,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;2.42384,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.811435,MA0145.1;0.107156,MA0146.1;0.441872,MA0147.1;0.87383,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;1.90691,MA0035.2;0.621793,MA0039.2;1.47843,MA0138.2;0.765223,MA0002.2;0.709311,MA0137.2;0.414885,MA0104.2;0.735746,MA0047.2;0.695777,MA0112.2;0.680553,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;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.978497,MA0163.1;0.273773,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;1.69036,MA0099.2;0.629739,MA0079.2;0.35176,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:52, 22 January 2013


Full id: C1348_Neutrophils_Natural_CD8_Mast_CD19_CD4_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:65188819..65188833,-p@chr11:65188819..65188833
-
Hg19::chr16:27325812..27325826,-p@chr16:27325812..27325826
-
Hg19::chr1:198626826..198626837,+p@chr1:198626826..198626837
+
Hg19::chr1:226250506..226250548,+p2@H3F3AP4
Hg19::chr7:130791254..130791306,+p@chr7:130791254..130791306
+
Hg19::chr7:130791323..130791333,+p@chr7:130791323..130791333
+


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><br>

Cell Type
Ontology termp-valuen
leukocyte1.70e-53136
hematopoietic lineage restricted progenitor cell1.50e-44120
nongranular leukocyte3.94e-43115
hematopoietic stem cell1.32e-41168
angioblastic mesenchymal cell1.32e-41168
hematopoietic cell1.10e-40177
classical monocyte2.54e-4042
CD14-positive, CD16-negative classical monocyte2.54e-4042
hematopoietic oligopotent progenitor cell1.77e-38161
hematopoietic multipotent progenitor cell1.77e-38161
myeloid leukocyte6.49e-3472
defensive cell4.23e-3348
phagocyte4.23e-3348
granulocyte monocyte progenitor cell1.52e-2867
macrophage dendritic cell progenitor2.85e-2661
myeloid lineage restricted progenitor cell3.14e-2666
monopoietic cell1.21e-2459
monocyte1.21e-2459
monoblast1.21e-2459
promonocyte1.21e-2459
myeloid cell6.70e-22108
common myeloid progenitor6.70e-22108
lymphoid lineage restricted progenitor cell6.86e-1652
lymphocyte2.31e-1553
common lymphoid progenitor2.31e-1553
mature alpha-beta T cell1.12e-1418
alpha-beta T cell1.12e-1418
immature T cell1.12e-1418
mature T cell1.12e-1418
immature alpha-beta T cell1.12e-1418
nucleate cell2.25e-1455
mesenchymal cell9.18e-13354
stuff accumulating cell1.22e-1287
connective tissue cell7.16e-12361
T cell3.18e-1125
pro-T cell3.18e-1125
intermediate monocyte2.41e-099
CD14-positive, CD16-positive monocyte2.41e-099
motile cell3.78e-09386
CD8-positive, alpha-beta T cell4.26e-0811
CD4-positive, alpha-beta T cell4.59e-086
granulocyte6.08e-088
multi fate stem cell1.50e-07427
stem cell1.88e-07441
somatic stem cell4.93e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.66e-3798
blood island2.66e-3798
hemolymphoid system1.62e-32108
bone marrow3.25e-2576
immune system6.36e-2393
bone element5.09e-2282
skeletal element1.80e-1890
skeletal system2.42e-16100
lateral plate mesoderm4.10e-14203
blood9.02e-1215
haemolymphatic fluid9.02e-1215
organism substance9.02e-1215
connective tissue1.12e-10371
musculoskeletal system1.91e-07167
mesoderm6.86e-07315
mesoderm-derived structure6.86e-07315
presumptive mesoderm6.86e-07315


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)
MA0003.10.321379
MA0004.11.37419
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
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
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.213007
MA0056.10
MA0057.10.882847
MA0058.11.16137
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
MA0073.11.53717
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.80532
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.11.68738
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
MA0135.12.42384
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.10.107156
MA0146.10.441872
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.21.90691
MA0035.20.621793
MA0039.21.47843
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.680553
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.21.69036
MA0099.20.629739
MA0079.20.35176
MA0102.21.58513
MA0258.10.788656
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
CEBPB#105145.314098417216540.003008047293917460.0159778990605964
FOXA1#316935.540709874692730.01192178777860280.0433772155033967
JUN#372536.256414596168170.008486346850954870.0324060540682587
PAX5#507944.446377020785220.005874733519240790.0263575605299419
STAT3#677435.259732498577120.01377662058078550.0484694787548143
TAF1#687252.785871904787740.01078636340290410.0397851671352957
TCF12#693835.317232451093210.013367345733860.0472428080639776
USF1#739144.240999518138640.007005367750829420.0296004208653507
USF2#739236.49609869253480.007634319815300560.031454975824135



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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