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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.349955496130082,

Latest revision as of 11:20, 17 September 2013


Full id: C315_Osteoblast_Preadipocyte_mesenchymal_Smooth_Cardiac_leiomyoma_Adipocyte



Phase1 CAGE Peaks

Hg19::chr11:1774382..1774391,-p@chr11:1774382..1774391
-
Hg19::chr11:61605283..61605303,+p@chr11:61605283..61605303
+
Hg19::chr11:61624925..61624946,+p10@FADS2
Hg19::chr11:61632639..61632653,+p@chr11:61632639..61632653
+
Hg19::chr15:74219788..74219809,+p@chr15:74219788..74219809
+
Hg19::chr15:74244185..74244207,+p@chr15:74244185..74244207
+
Hg19::chr16:55523576..55523615,+p@chr16:55523576..55523615
+
Hg19::chr16:57778334..57778362,+p@chr16:57778334..57778362
+
Hg19::chr17:19288479..19288518,-p@chr17:19288479..19288518
-
Hg19::chr17:41168059..41168088,-p@chr17:41168059..41168088
-
Hg19::chr17:74681202..74681205,-p@chr17:74681202..74681205
-
Hg19::chr17:76853662..76853675,-p@chr17:76853662..76853675
-
Hg19::chr18:47984183..47984184,+p1@ENST00000498296
Hg19::chr19:1105655..1105703,+p@chr19:1105655..1105703
+
Hg19::chr19:1105737..1105752,+p@chr19:1105737..1105752
+
Hg19::chr19:18652724..18652739,-p10@FKBP8
Hg19::chr19:18897406..18897417,-p6@COMP
Hg19::chr19:49119363..49119395,-p3@RPL18
Hg19::chr1:1153003..1153016,-p@chr1:1153003..1153016
-
Hg19::chr1:1164204..1164250,-p6@SDF4
Hg19::chr1:1290694..1290708,-p3@MXRA8
Hg19::chr1:150776569..150776581,-p@chr1:150776569..150776581
-
Hg19::chr1:17303641..17303660,-p@chr1:17303641..17303660
-
Hg19::chr1:19981535..19981580,+p4@NBL1
Hg19::chr1:19983866..19983874,+p@chr1:19983866..19983874
+
Hg19::chr20:35173298..35173317,+p5@MYL9
Hg19::chr20:35177518..35177532,+p@chr20:35177518..35177532
+
Hg19::chr22:31501233..31501245,-p@chr22:31501233..31501245
-
Hg19::chr2:175629374..175629385,-p5@CHRNA1
Hg19::chr2:219269059..219269083,+p@chr2:219269059..219269083
+
Hg19::chr3:52563245..52563281,-p5@NT5DC2
Hg19::chr3:8590309..8590333,+p@chr3:8590309..8590333
+
Hg19::chrX:153061882..153061933,+p4@SSR4
Hg19::chrX:47442814..47442835,+p6@TIMP1
Hg19::chrX:47444613..47444688,+p2@TIMP1
Hg19::chrX:47444935..47445039,+p@chrX:47444935..47445039
+
Hg19::chrX:47444981..47444990,-p@chrX:47444981..47444990
-
Hg19::chrX:47445910..47445992,+p@chrX:47445910..47445992
+


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:0005509calcium ion binding0.0138219499543876
GO:0051043regulation of membrane protein ectodomain proteolysis0.01680365693209
GO:0051045negative regulation of membrane protein ectodomain proteolysis0.01680365693209
GO:0048513organ development0.01680365693209
GO:0005789endoplasmic reticulum membrane0.01680365693209
GO:0042175nuclear envelope-endoplasmic reticulum network0.01680365693209
GO:0044432endoplasmic reticulum part0.0197111800970318
GO:0044446intracellular organelle part0.0207947129244736
GO:0044422organelle part0.0207947129244736
GO:0003012muscle system process0.0207947129244736
GO:0006936muscle contraction0.0207947129244736
GO:0048731system development0.0207947129244736
GO:0005784translocon complex0.0207947129244736
GO:0005796Golgi lumen0.0207947129244736
GO:0033559unsaturated fatty acid metabolic process0.0207947129244736
GO:0006636unsaturated fatty acid biosynthetic process0.0207947129244736
GO:0044444cytoplasmic part0.0218859500403191
GO:0043249erythrocyte maturation0.0218859500403191
GO:0045861negative regulation of proteolysis0.0218859500403191
GO:0031594neuromuscular junction0.0249463112312134
GO:0048821erythrocyte development0.0277140445166692
GO:0005783endoplasmic reticulum0.0310440415863154
GO:0048856anatomical structure development0.0311691245971762
GO:0007274neuromuscular synaptic transmission0.0311691245971762
GO:0007528neuromuscular junction development0.0332421739419477
GO:0030867rough endoplasmic reticulum membrane0.0348352846073642
GO:0012505endomembrane system0.0348352846073642
GO:0016717oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water0.0348352846073642
GO:0033619membrane protein proteolysis0.0348352846073642
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0348352846073642
GO:0006509membrane protein ectodomain proteolysis0.0348352846073642
GO:0007224smoothened signaling pathway0.0354739566774395
GO:0032501multicellular organismal process0.0354739566774395
GO:0007275multicellular organismal development0.0354739566774395
GO:0001708cell fate specification0.0355904200985641
GO:0030162regulation of proteolysis0.0371404727022243
GO:0008191metalloendopeptidase inhibitor activity0.0371404727022243
GO:0005791rough endoplasmic reticulum0.0371404727022243
GO:0048468cell development0.0425221972773797
GO:0015464acetylcholine receptor activity0.0435597955985175
GO:0042166acetylcholine binding0.0445144965050405
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.0454231554612994
GO:0005578proteinaceous extracellular matrix0.0467722061889542
GO:0005859muscle myosin complex0.047114905005606
GO:0016460myosin II complex0.0479035766969372



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>

Uber Anatomy
Ontology termp-valuen
dense mesenchyme tissue3.54e-1773
somite5.99e-1771
presomitic mesoderm5.99e-1771
presumptive segmental plate5.99e-1771
dermomyotome5.99e-1771
trunk paraxial mesoderm5.99e-1771
paraxial mesoderm1.81e-1672
presumptive paraxial mesoderm1.81e-1672
muscle tissue1.70e-1564
musculature1.70e-1564
musculature of body1.70e-1564
epithelial vesicle1.74e-1578
skeletal muscle tissue5.18e-1562
striated muscle tissue5.18e-1562
myotome5.18e-1562
multilaminar epithelium1.38e-1483
trunk mesenchyme2.73e-12122
mesoderm2.66e-10315
mesoderm-derived structure2.66e-10315
presumptive mesoderm2.66e-10315
artery7.96e-1042
arterial blood vessel7.96e-1042
arterial system7.96e-1042
mesenchyme1.19e-09160
entire embryonic mesenchyme1.19e-09160
surface structure5.25e-0999
trunk4.15e-08199
adipose tissue5.15e-0814
systemic artery6.91e-0833
systemic arterial system6.91e-0833
unilaminar epithelium7.27e-08148
splanchnic layer of lateral plate mesoderm8.77e-0883
organism subdivision1.14e-07264
vasculature3.22e-0778
vascular system3.22e-0778
omentum5.99e-076
peritoneum5.99e-076
abdominal cavity5.99e-076
visceral peritoneum5.99e-076
integument6.45e-0746
integumental system6.45e-0746
cardiovascular system8.24e-07109
Disease
Ontology termp-valuen
ovarian cancer7.78e-0714


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)
MA0003.10.723937
MA0004.10.473448
MA0006.10.376693
MA0007.12.75326
MA0009.10.340234
MA0014.10.0229062
MA0017.11.11838
MA0019.10.128034
MA0024.10.261871
MA0025.10.448136
MA0027.11.8578
MA0028.10.216725
MA0029.10.275814
MA0030.10.267514
MA0031.10.222414
MA0038.10.341188
MA0040.10.280083
MA0041.10.0671563
MA0042.10.0551182
MA0043.10.34048
MA0046.10.331797
MA0048.10.187755
MA0050.10.203478
MA0051.10.335663
MA0052.10.282917
MA0055.10.0434088
MA0056.10
MA0057.10.979302
MA0058.10.29447
MA0059.10.292272
MA0060.10.263127
MA0061.10.735081
MA0063.10
MA0066.11.15073
MA0067.10.607707
MA0068.10.350743
MA0069.10.328825
MA0070.10.320241
MA0071.11.51648
MA0072.10.84963
MA0073.11.81965
MA0074.13.65336
MA0076.10.13753
MA0077.10.310955
MA0078.10.473318
MA0081.10.292548
MA0083.10.346089
MA0084.10.778769
MA0087.10.314949
MA0088.10.646938
MA0089.10
MA0090.11.87305
MA0091.11.25479
MA0092.10.403964
MA0093.10.634557
MA0095.10
MA0098.10
MA0100.10.359565
MA0101.10.391992
MA0103.11.23717
MA0105.11.61194
MA0106.10.125937
MA0107.10.108386
MA0108.20.220346
MA0109.10
MA0111.10.372993
MA0113.10.830796
MA0114.11.19703
MA0115.10.540206
MA0116.10.64523
MA0117.10.369828
MA0119.12.0458
MA0122.10.390603
MA0124.10.504249
MA0125.10.433225
MA0130.10
MA0131.10.16707
MA0132.10
MA0133.10
MA0135.10.364077
MA0136.10.108168
MA0139.10.170947
MA0140.10.288493
MA0141.11.22794
MA0142.10.201309
MA0143.10.134991
MA0144.10.0884648
MA0145.10.431123
MA0146.10.649926
MA0147.10.243119
MA0148.10.245107
MA0149.10.276655
MA0062.20.0942332
MA0035.20.287623
MA0039.20.0259269
MA0138.20.156943
MA0002.20.829038
MA0137.20.0905108
MA0104.20.428693
MA0047.20.76306
MA0112.21.59005
MA0065.21.7508
MA0150.10.1453
MA0151.10
MA0152.10.0881336
MA0153.10.419293
MA0154.11.87309
MA0155.10.814432
MA0156.10.0921754
MA0157.10.540861
MA0158.10
MA0159.12.07856
MA0160.10.945152
MA0161.10
MA0162.10.106228
MA0163.12.29611
MA0164.10.437358
MA0080.20.945206
MA0018.20.126682
MA0099.20.0882962
MA0079.20.185244
MA0102.20.813509
MA0258.13.54425
MA0259.10.451002
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

No analysis results for this cluster

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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