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Coexpression cluster:C1312: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.555913,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.127969,0.436569,1.03374,0.576478,0.387783,0.483957,1.73319,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.640661,1.67655,0.134746,0.35388,0.585658,1.5795,0.69481,0.355745,0.513952,0.323162,1.01199,0.636689,1.18176,0.66382,1.33909,0.304272,1.02586,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,0.192925,0.84426,0.913168,0.477584,0.240887,2.00082,0.684313,0.272514,1.10535,0.181326,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,1.23175,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.352243,0.460936,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,2.44613,0.53374,1.20639,0.692462,1.35529,0.520084,1.30187,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.8388,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,0.79772,0.661335,0.152397
|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.788761,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.05129,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;0.464411,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.450439,MA0058.1;1.16137,MA0059.1;0.457555,MA0060.1;0.737586,MA0061.1;0.671725,MA0063.1;0,MA0066.1;1.59928,MA0067.1;1.35893,MA0068.1;0.578694,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;2.07987,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;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;1.37996,MA0092.1;0.522012,MA0093.1;1.02138,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.419295,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;1.84113,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,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;0.299851,MA0145.1;0.107156,MA0146.1;0.718193,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.658749,MA0035.2;0.621793,MA0039.2;0.82735,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.718489,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;1.39622,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.248693,MA0102.2;1.58513,MA0258.1;0.788656,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 19:50, 22 January 2013


Full id: C1312_Eosinophils_Basophils_CD4_Natural_Mast_granulocyte_CD14CD16



Phase1 CAGE Peaks

Hg19::chr10:43932190..43932234,-p@chr10:43932190..43932234
-
Hg19::chr12:111028863..111028911,+p@chr12:111028863..111028911
+
Hg19::chr15:66084828..66084847,+p@chr15:66084828..66084847
+
Hg19::chr1:150980668..150980692,-p11@FAM63A
Hg19::chr2:86669343..86669357,-p@chr2:86669343..86669357
-
Hg19::chr3:53926081..53926105,+p@chr3:53926081..53926105
+


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
leukocyte6.29e-57136
hematopoietic stem cell1.68e-48168
angioblastic mesenchymal cell1.68e-48168
hematopoietic cell2.51e-45177
hematopoietic oligopotent progenitor cell5.39e-45161
hematopoietic multipotent progenitor cell5.39e-45161
nongranular leukocyte5.41e-45115
hematopoietic lineage restricted progenitor cell2.06e-43120
classical monocyte3.16e-3142
CD14-positive, CD16-negative classical monocyte3.16e-3142
myeloid leukocyte5.29e-2972
defensive cell6.36e-2548
phagocyte6.36e-2548
granulocyte monocyte progenitor cell2.30e-2467
myeloid cell2.86e-23108
common myeloid progenitor2.86e-23108
macrophage dendritic cell progenitor8.71e-2361
monopoietic cell1.19e-2159
monocyte1.19e-2159
monoblast1.19e-2159
promonocyte1.19e-2159
myeloid lineage restricted progenitor cell2.45e-2166
lymphocyte1.82e-2053
common lymphoid progenitor1.82e-2053
lymphoid lineage restricted progenitor cell5.45e-2052
nucleate cell4.42e-1955
mesenchymal cell1.22e-14354
connective tissue cell1.52e-14361
motile cell3.30e-13386
mature alpha-beta T cell6.81e-1218
alpha-beta T cell6.81e-1218
immature T cell6.81e-1218
mature T cell6.81e-1218
immature alpha-beta T cell6.81e-1218
B cell9.59e-1014
lymphocyte of B lineage1.21e-0924
pro-B cell1.21e-0924
T cell2.92e-0925
pro-T cell2.92e-0925
stuff accumulating cell8.39e-0987
intermediate monocyte1.55e-089
CD14-positive, CD16-positive monocyte1.55e-089
granulocyte1.73e-088
CD4-positive, alpha-beta T cell5.94e-076
CD8-positive, alpha-beta T cell9.60e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.54e-2998
blood island1.54e-2998
hemolymphoid system7.58e-25108
bone marrow4.96e-2276
bone element1.84e-2082
immune system1.14e-1993
skeletal element5.43e-1890
skeletal system4.51e-14100
connective tissue1.09e-13371


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)
MA0003.10.176622
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
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
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.10.457555
MA0060.10.737586
MA0061.10.671725
MA0063.10
MA0066.11.59928
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
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
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.718193
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.20.718489
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
MA0162.11.39622
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.248693
MA0102.21.58513
MA0258.10.788656
MA0259.10.893594
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
ELF1#199753.548414965672950.003446837775721690.0175225998081483
ELK4#200538.117840829234010.004056113134185760.0194061294434572
GABPB1#255344.711789224121450.004730054311555960.0222844705090488
IRF1#365945.091442502375930.003535240765893810.0179423175405376
MAX#414944.301703672671410.006644923910676370.0282914475461528
NANOG#79923314.62238924050630.000739456292883380.00582501702914824
NFE2#4778225.7347535505430.002429969709029260.0136884361618828
PAX5#507944.446377020785220.005874733519240790.0263564282836887
POLR2A#543062.147453176558070.01019570676818780.0379834992923866
RFX5#599348.03194055146340.0006204615428381410.00510923149668632
SIN3A#2594254.507403939012610.001096110061208640.00765781247458484
SMARCB1#659839.126357890578710.002900247150367020.0156747522323112
SPI1#668856.836936257102270.0001449641773974030.00188541889454638
TAF1#687252.785871904787740.01078636340290410.0397837620933711
TBP#690853.088975572580320.006645448275786930.0282786934146156
THAP1#55145210.45638153428380.01399147851103650.0491161985887582
USF1#739144.240999518138640.007005367750829420.0295980259124104
ZNF143#770236.750438276113950.006850259204468580.0290331231659563
ZNF263#1012745.481227758007120.002675609380607230.0147413994567017



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1312&oldid=2569823"