Personal tools

Coexpression cluster:C491

From FANTOM5_SSTAR

Revision as of 11:24, 17 September 2013 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Full id: C491_Adipocyte_dura_aorta_Preadipocyte_heart_Fibroblast_epididymis



Phase1 CAGE Peaks

Hg19::chr10:22002796..22002833,+p@chr10:22002796..22002833
+
Hg19::chr10:85462978..85462980,-p@chr10:85462978..85462980
-
Hg19::chr12:15034824..15034835,+p@chr12:15034824..15034835
+
Hg19::chr12:15034857..15034886,-p@chr12:15034857..15034886
-
Hg19::chr12:15034903..15034944,-p@chr12:15034903..15034944
-
Hg19::chr12:15034956..15034967,-p@chr12:15034956..15034967
-
Hg19::chr12:15034968..15034990,-p@chr12:15034968..15034990
-
Hg19::chr12:15035012..15035043,-p@chr12:15035012..15035043
-
Hg19::chr12:15035058..15035069,+p@chr12:15035058..15035069
+
Hg19::chr12:15035074..15035085,-p@chr12:15035074..15035085
-
Hg19::chr12:15035100..15035219,-p@chr12:15035100..15035219
-
Hg19::chr12:15035939..15035972,-p@chr12:15035939..15035972
-
Hg19::chr12:15038779..15038798,-p1@MGP
Hg19::chr12:15154767..15154778,+p1@ENST00000542689
Hg19::chr1:231005253..231005263,-p15@C1orf198
Hg19::chr4:84114490..84114492,-p@chr4:84114490..84114492
-
Hg19::chr5:150407833..150407850,-p8@CU690655
Hg19::chr9:93101022..93101028,+p@chr9:93101022..93101028
+
Hg19::chrX:102757802..102757810,-p1@RAB40A


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:0008147structural constituent of bone0.012949936385265
GO:0051592response to calcium ion0.012949936385265
GO:0048306calcium-dependent protein binding0.012949936385265
GO:0001502cartilage condensation0.012949936385265
GO:0030500regulation of bone mineralization0.012949936385265
GO:0009612response to mechanical stimulus0.014713887167521
GO:0030278regulation of ossification0.014713887167521
GO:0030282bone mineralization0.014713887167521
GO:0046850regulation of bone remodeling0.0156938887077954
GO:0010038response to metal ion0.0168662108026289
GO:0051216cartilage development0.0168662108026289
GO:0007584response to nutrient0.0168662108026289
GO:0030324lung development0.0168662108026289
GO:0010035response to inorganic substance0.0168662108026289
GO:0030323respiratory tube development0.0168662108026289
GO:0031667response to nutrient levels0.0220578331918385
GO:0009991response to extracellular stimulus0.0228343265070251
GO:0009725response to hormone stimulus0.0248296325447801
GO:0031214biomineral formation0.0258705156162679
GO:0001503ossification0.0258705156162679
GO:0046849bone remodeling0.026875288854357
GO:0048771tissue remodeling0.0280549957385919
GO:0035295tube development0.0298312385764
GO:0005201extracellular matrix structural constituent0.0298312385764
GO:0050954sensory perception of mechanical stimulus0.0298312385764
GO:0007605sensory perception of sound0.0298312385764
GO:0009628response to abiotic stimulus0.0358904978638971
GO:0001501skeletal development0.0438092210678937



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
adipocyte of omentum tissue2.77e-133
fat cell2.02e-0915
adipocyte of breast2.88e-092
Uber Anatomy
Ontology termp-valuen
adult organism3.61e-17114
omentum8.56e-176
peritoneum8.56e-176
abdominal cavity8.56e-176
visceral peritoneum8.56e-176
perirenal fat2.09e-092
heart1.17e-0824
primitive heart tube1.17e-0824
primary heart field1.17e-0824
anterior lateral plate mesoderm1.17e-0824
heart tube1.17e-0824
heart primordium1.17e-0824
cardiac mesoderm1.17e-0824
cardiogenic plate1.17e-0824
heart rudiment1.17e-0824
open tracheal system trachea2.81e-082
cavity lining3.26e-0812
serous membrane3.26e-0812
body cavity6.58e-0846
subdivision of trunk7.08e-08112
body cavity precursor8.97e-0854
anatomical space1.31e-0795
primary circulatory organ1.49e-0727
compound organ1.49e-0768
body cavity or lining2.73e-0749


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)
MA0003.12.41061e-07
MA0004.10.563888
MA0006.10.0925234
MA0007.10.180248
MA0009.10.580032
MA0014.10.000501857
MA0017.10.114723
MA0019.10.305657
MA0024.12.11236
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.12.1695
MA0030.10.492344
MA0031.10.435419
MA0038.10.269828
MA0040.10.507819
MA0041.11.12415
MA0042.10.541224
MA0043.10.580321
MA0046.10.570066
MA0048.10.0472517
MA0050.10.184533
MA0051.10.266537
MA0052.10.511289
MA0055.10.0498001
MA0056.10
MA0057.10.00844127
MA0058.10.809252
MA0059.11.30909
MA0060.10.0387582
MA0061.10.029485
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.0841176
MA0069.10.566544
MA0070.11.36913
MA0071.10.240074
MA0072.10.552241
MA0073.11.28654e-06
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.129245
MA0083.10.586921
MA0084.11.06048
MA0087.10.550016
MA0088.10.0166254
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.10.974084
MA0093.10.646398
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.0959778
MA0103.10.614572
MA0105.10.00666152
MA0106.10.302526
MA0107.10.0591705
MA0108.22.88516
MA0109.10
MA0111.11.48573
MA0113.10.847356
MA0114.10.207884
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.10.119385
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.755761
MA0139.10.0257123
MA0140.10.669735
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.10.0508083
MA0145.10.00353814
MA0146.10.0059432
MA0147.10.223797
MA0148.11.14208
MA0149.10.230803
MA0062.21.19821
MA0035.20.237534
MA0039.26.91533e-06
MA0138.20.347473
MA0002.20.138689
MA0137.20.105044
MA0104.20.151208
MA0047.22.21363
MA0112.20.00303039
MA0065.20.0691929
MA0150.10.446185
MA0151.10
MA0152.11.95806
MA0153.10.67139
MA0154.10.00634321
MA0155.10.00260895
MA0156.10.345664
MA0157.10.384449
MA0158.10
MA0159.12.33438
MA0160.10.222325
MA0161.10
MA0162.10.021183
MA0163.10.000591497
MA0164.10.32594
MA0080.20.646623
MA0018.20.30364
MA0099.20.243305
MA0079.22.9547e-09
MA0102.21.09681
MA0258.10.177641
MA0259.10.0662172
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C491&oldid=3067608"