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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.17253482691446,

Latest revision as of 11:47, 17 September 2013


Full id: C1580_acute_Neutrophils_Mallassezderived_migratory_Smooth_Preadipocyte_small



Phase1 CAGE Peaks

Hg19::chr10:44101729..44101736,-p1@CAP1P2
Hg19::chr1:40506327..40506338,+p5@CAP1
Hg19::chr1:40506344..40506355,+p3@CAP1
Hg19::chr1:40506371..40506382,+p2@CAP1
Hg19::chr1:40506393..40506453,+p1@CAP1


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:0007190adenylate cyclase activation0.00508261705718434
GO:0031281positive regulation of cyclase activity0.00508261705718434
GO:0045762positive regulation of adenylate cyclase activity0.00508261705718434
GO:0051349positive regulation of lyase activity0.00508261705718434
GO:0007163establishment and/or maintenance of cell polarity0.00508261705718434
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.00508261705718434
GO:0045761regulation of adenylate cyclase activity0.00508261705718434
GO:0031279regulation of cyclase activity0.00508261705718434
GO:0051339regulation of lyase activity0.00508261705718434
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.00861404579172152
GO:0019933cAMP-mediated signaling0.00861404579172152
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.010221087049063
GO:0019935cyclic-nucleotide-mediated signaling0.010221087049063
GO:0043085positive regulation of catalytic activity0.0194591624475058
GO:0019932second-messenger-mediated signaling0.0194591624475058
GO:0003779actin binding0.0289225113492157
GO:0032989cellular structure morphogenesis0.0289225113492157
GO:0000902cell morphogenesis0.0289225113492157
GO:0008092cytoskeletal protein binding0.03294624985282
GO:0050790regulation of catalytic activity0.03294624985282
GO:0065009regulation of a molecular function0.0339611230639136
GO:0007010cytoskeleton organization and biogenesis0.0339611230639136
GO:0009653anatomical structure morphogenesis0.0495791930950809



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
myeloid leukocyte7.56e-2772
monopoietic cell8.45e-2359
monocyte8.45e-2359
monoblast8.45e-2359
promonocyte8.45e-2359
macrophage dendritic cell progenitor9.82e-2361
granulocyte monocyte progenitor cell1.58e-2167
myeloid lineage restricted progenitor cell9.19e-2166
defensive cell1.78e-1948
phagocyte1.78e-1948
somatic cell8.82e-19588
classical monocyte1.02e-1642
CD14-positive, CD16-negative classical monocyte1.02e-1642
somatic stem cell7.33e-15433
multi fate stem cell1.58e-14427
stuff accumulating cell1.80e-1487
myeloid cell2.70e-14108
common myeloid progenitor2.70e-14108
stem cell1.95e-13441
native cell5.44e-12722
animal cell1.32e-11679
eukaryotic cell1.32e-11679
vascular associated smooth muscle cell2.58e-1032
mesenchymal cell2.81e-08354
smooth muscle cell2.98e-0843
smooth muscle myoblast2.98e-0843
connective tissue cell1.58e-07361
muscle precursor cell4.34e-0758
myoblast4.34e-0758
multi-potent skeletal muscle stem cell4.34e-0758
Uber Anatomy
Ontology termp-valuen
mesoderm1.06e-25315
mesoderm-derived structure1.06e-25315
presumptive mesoderm1.06e-25315
lateral plate mesoderm3.53e-23203
musculoskeletal system4.35e-22167
bone marrow7.29e-2076
hemolymphoid system9.71e-20108
hematopoietic system9.85e-2098
blood island9.85e-2098
immune system1.49e-1793
skeletal element2.02e-1790
bone element2.11e-1782
skeletal system7.24e-17100
anatomical system2.72e-11624
anatomical group4.99e-11625
artery2.21e-1042
arterial blood vessel2.21e-1042
arterial system2.21e-1042
cardiovascular system2.90e-10109
circulatory system2.14e-09112
embryonic structure7.27e-09564
epithelial tube open at both ends8.42e-0959
blood vessel8.42e-0959
blood vasculature8.42e-0959
vascular cord8.42e-0959
multi-cellular organism8.69e-09656
vessel1.82e-0868
systemic artery2.20e-0833
systemic arterial system2.20e-0833
splanchnic layer of lateral plate mesoderm2.21e-0883
developing anatomical structure2.36e-08581
vasculature2.92e-0878
vascular system2.92e-0878
germ layer4.34e-08560
germ layer / neural crest4.34e-08560
embryonic tissue4.34e-08560
presumptive structure4.34e-08560
germ layer / neural crest derived structure4.34e-08560
epiblast (generic)4.34e-08560
connective tissue2.96e-07371
embryo7.02e-07592


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)
MA0003.11.40197
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.13.71305
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.16.54751
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.111.3869
MA0077.11.07324
MA0078.10.836493
MA0081.12.23491
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.13.51336
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.213.1374
MA0035.20.691506
MA0039.26.53669
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.11.35623
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.16.62634
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.11.49262
MA0164.10.810347
MA0080.22.01584
MA0018.20.781393
MA0099.20.699641
MA0079.20.146371
MA0102.21.66336
MA0258.10.345771
MA0259.11.80881
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
BCLAF1#9774417.32211808809752.18923511079637e-050.000481350580497816
CCNT2#90545.068961261570110.002709998091280770.0148884529539859
CEBPB#105146.376918100659850.001113944176677320.00765238544155773
E2F1#186943.925911371903460.007214984547106360.0298650775282486
E2F6#187644.013724585357910.006632118233933880.0282853559389832
EGR1#195843.990543275848110.0067800983001440.0287544337841606
ELF1#199754.258097958807540.0007142416939776840.00572440244626931
ELK4#2005516.2356816584688.85705446514576e-073.82082573847731e-05
GABPB1#255357.067683836182175.6685482528729e-050.000947682905365443
GATA1#2623410.84824651504040.0001390956917094380.00181519616974159
GTF2F1#2962410.19172870140610.000177833889427640.00215812149406615
HEY1#2346254.040111043105710.0009288852205177990.00673506272880161
HMGN3#932458.178547723350592.73180911341838e-050.000581192528002245
IRF1#365946.109731002851120.001315525264767990.00880549529751358
MAX#414956.452555509007128.93743970843928e-050.00130511362655158
NANOG#79923423.39582278481016.64263001833934e-060.000194382078028955
NFKB1#479055.488063424193840.0002008162847462320.00238764252761973
PAX5#507945.335652424942260.002223389586187790.0127727494494976
POU2F2#545259.106124057742521.59639992500654e-050.000369681622544919
SIN3A#2594255.408884726815140.0002159522671657270.00247708279302816
SIX5#147912517.0867153554596.86007756253503e-073.09753411393686e-05
SP1#666744.558705102512720.00407573565781680.0194750311738449
STAT3#677448.415571997723390.0003771527211598630.00374139941538896
TAF1#687253.343046285745290.002394600090870310.0135103256923129
TAF7#687949.146455523939130.0002720662872412990.00290208670954898
TBP#690853.706770687096390.001428755106721120.00917641932174204
TFAP2C#702248.647382887888180.0003390518878174050.00344759420813572
USF1#739156.361499277207969.59569864925045e-050.00136665099035738
USF2#7392410.39375790805570.0001646179728687530.00202574955442909
YY1#752854.911170749853860.00034993140821360.0035239115169627
ZEB1#6935413.51074561403515.85221769500384e-050.000966782290174796
ZNF143#7702513.50087655222792.22790360787208e-067.97122387470201e-05



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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