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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.04501882188846,

Latest revision as of 11:41, 17 September 2013


Full id: C1295_Eosinophils_CD4_CD14_Neutrophils_CD8_Basophils_Mast



Phase1 CAGE Peaks

Hg19::chr10:112632685..112632730,+p6@PDCD4
Hg19::chr10:112632799..112632821,+p15@PDCD4
Hg19::chr20:18488007..18488029,-p@chr20:18488007..18488029
-
Hg19::chr22:39096925..39096954,-p1@JOSD1
Hg19::chr22:39097117..39097135,+p@chr22:39097117..39097135
+
Hg19::chr8:146127003..146127014,+p@chr8:146127003..146127014
+


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

GO IDGO nameFDR corrected p-value
GO:0043508negative regulation of JNK activity0.00359119274696809
GO:0007569cell aging0.00933710114211703
GO:0043407negative regulation of MAP kinase activity0.00933710114211703
GO:0043506regulation of JNK activity0.00933710114211703
GO:0007568aging0.00933710114211703
GO:0006469negative regulation of protein kinase activity0.0132425232544448
GO:0033673negative regulation of kinase activity0.0132425232544448
GO:0051348negative regulation of transferase activity0.0132425232544448
GO:0043086negative regulation of catalytic activity0.0166990462734016
GO:0043405regulation of MAP kinase activity0.0166990462734016
GO:0045786negative regulation of progression through cell cycle0.0316794503036114
GO:0045859regulation of protein kinase activity0.0316794503036114
GO:0043549regulation of kinase activity0.0316794503036114
GO:0051338regulation of transferase activity0.0316794503036114
GO:0016481negative regulation of transcription0.0348345696455905
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0357997026963381
GO:0000074regulation of progression through cell cycle0.0358121721155984
GO:0051726regulation of cell cycle0.0358121721155984
GO:0031324negative regulation of cellular metabolic process0.0360064325419696
GO:0009892negative regulation of metabolic process0.0391440009419522
GO:0005829cytosol0.0485666066732828
GO:0050790regulation of catalytic activity0.0487933797142403
GO:0022402cell cycle process0.0487933797142403



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
leukocyte7.56e-51136
hematopoietic stem cell2.03e-44168
angioblastic mesenchymal cell2.03e-44168
hematopoietic cell4.15e-43177
hematopoietic lineage restricted progenitor cell3.40e-41120
hematopoietic oligopotent progenitor cell9.95e-41161
hematopoietic multipotent progenitor cell9.95e-41161
nongranular leukocyte5.75e-37115
classical monocyte1.77e-3342
CD14-positive, CD16-negative classical monocyte1.77e-3342
myeloid leukocyte4.22e-3072
defensive cell6.02e-2748
phagocyte6.02e-2748
granulocyte monocyte progenitor cell1.45e-2567
myeloid cell6.67e-25108
common myeloid progenitor6.67e-25108
myeloid lineage restricted progenitor cell2.61e-2466
macrophage dendritic cell progenitor1.77e-2161
monopoietic cell4.35e-2059
monocyte4.35e-2059
monoblast4.35e-2059
promonocyte4.35e-2059
nucleate cell4.18e-1555
lymphoid lineage restricted progenitor cell7.95e-1552
lymphocyte2.75e-1453
common lymphoid progenitor2.75e-1453
stuff accumulating cell1.38e-1287
T cell1.60e-1225
pro-T cell1.60e-1225
mature alpha-beta T cell1.18e-1118
alpha-beta T cell1.18e-1118
immature T cell1.18e-1118
mature T cell1.18e-1118
immature alpha-beta T cell1.18e-1118
granulocyte7.45e-098
mesenchymal cell3.93e-08354
intermediate monocyte4.25e-089
CD14-positive, CD16-positive monocyte4.25e-089
CD4-positive, alpha-beta T cell2.27e-076
connective tissue cell2.31e-07361
blood cell3.03e-0711
motile cell7.99e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.02e-2498
blood island4.02e-2498
bone marrow4.14e-2276
hemolymphoid system2.07e-20108
immune system1.74e-1993
bone element5.42e-1982
skeletal element1.46e-1590
skeletal system8.61e-13100
connective tissue6.91e-07371


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)
MA0003.12.14318
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.85223
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
MA0059.11.15845
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.12.33031
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.120085
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
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.11.54633
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
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
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.232472
MA0147.10.87383
MA0148.11.42897
MA0149.10.612449
MA0062.22.67639
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.65596
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.10.0270301
MA0164.10.738243
MA0080.20.394469
MA0018.26.91917
MA0099.20.629739
MA0079.20.35176
MA0102.21.58513
MA0258.10.289793
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
BRCA1#672413.45615376214928.33086868922907e-050.00125135566666819
CCNT2#90555.280167980802190.0005100943974832530.00446590232029118
CEBPB#105145.314098417216540.003008047293917460.0159770864735516
CHD2#110646.896015222744570.001115391320135990.00765880039997913
CTCF#1066443.573504248716680.01316635007238510.0465971004815259
E2F6#187665.017155731697396.26776799983417e-050.00102409171172509
ELF1#199753.548414965672950.003446837775721690.0175217469193769
ELK4#2005410.8237877723120.0001950599973010460.00234861321859857
EP300#203344.515961150815470.005543980051953740.0250946011635243
GABPB1#255344.711789224121450.004730054311555960.0222824601824354
GATA1#262349.04020542920030.0003927397840144870.00384057587103829
IRF1#365945.091442502375930.003535240765893810.0179414456654445
JUN#372536.256414596168170.008486346850954870.0324024998635205
JUNB#3726315.30531632991060.0006470753298141560.00530246374032646
JUND#372744.663109294580680.004917643408260230.0229857572464774
MYC#460965.22228187160944.92821127172503e-050.000852995454106216
PAX5#507944.446377020785220.005874733519240790.0263552961347074
POLR2A#543062.147453176558070.01019570676818780.0379780804323692
RFX5#5993510.03992568932922.19894173045095e-050.000482367728180144
SIN3A#2594265.408884726815143.99207083571449e-050.000741732584969197
SMC3#912637.522466422466420.005039540716828550.0234777675495074
SP1#666743.79892091876060.01052246616798510.0389383072004462
TAF1#687263.343046285745290.0007162474284635620.00572334852190558
TAF7#687935.716534702461960.01092729379889660.040205588763888
TBP#690863.706770687096390.000385416472907960.00377390877686428
TFAP2A#7020513.76552864420414.62854247631286e-060.000143869151096321
TFAP2C#702259.007690508216863.75071472654799e-050.000723800619597091
USF1#739144.240999518138640.007005367750829420.0295968285812651
ZBTB33#10009210.55490834332710.01374250737140590.0483771648699696
ZBTB7A#5134144.901272871917260.004079628118843750.0194811522611642
ZEB1#693538.444216008771930.003623843810733590.0183323140590557



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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