Personal tools

Coexpression cluster:C309: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(5 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|full_id=C309_normal_Chondrocyte_small_Fibroblast_tenocyte_neuroepithelioma_Osteoblast
 

Latest revision as of 11:19, 17 September 2013


Full id: C309_normal_Chondrocyte_small_Fibroblast_tenocyte_neuroepithelioma_Osteoblast



Phase1 CAGE Peaks

Hg19::chr10:15760985..15760992,-p@chr10:15760985..15760992
-
Hg19::chr11:68105668..68105675,-p@chr11:68105668..68105675
-
Hg19::chr14:61119131..61119168,+p@chr14:61119131..61119168
+
Hg19::chr14:61125184..61125196,-p8@SIX1
Hg19::chr17:54893192..54893195,-p14@C17orf67
Hg19::chr17:54893196..54893207,-p9@C17orf67
Hg19::chr17:54893213..54893220,-p12@C17orf67
Hg19::chr17:54893269..54893278,-p11@C17orf67
Hg19::chr17:54893292..54893300,-p13@C17orf67
Hg19::chr8:57353655..57353662,-p@chr8:57353655..57353662
-
Hg19::chr8:57353666..57353675,-p@chr8:57353666..57353675
-
Hg19::chr8:57353745..57353754,-p@chr8:57353745..57353754
-
Hg19::chr8:57353804..57353821,-p@chr8:57353804..57353821
-
Hg19::chr8:57353888..57353898,-p@chr8:57353888..57353898
-
Hg19::chr8:57353982..57353991,-p@chr8:57353982..57353991
-
Hg19::chr8:57353995..57354004,-p@chr8:57353995..57354004
-
Hg19::chr8:57354052..57354105,+p@chr8:57354052..57354105
+
Hg19::chr8:57354119..57354137,+p@chr8:57354119..57354137
+
Hg19::chr8:57354124..57354145,-p@chr8:57354124..57354145
-
Hg19::chr8:57354143..57354152,+p@chr8:57354143..57354152
+
Hg19::chr8:57354182..57354206,+p@chr8:57354182..57354206
+
Hg19::chr8:57354186..57354207,-p@chr8:57354186..57354207
-
Hg19::chr8:57354211..57354220,+p@chr8:57354211..57354220
+
Hg19::chr8:57354215..57354233,-p@chr8:57354215..57354233
-
Hg19::chr8:57354251..57354262,-p@chr8:57354251..57354262
-
Hg19::chr8:57354262..57354270,+p@chr8:57354262..57354270
+
Hg19::chr8:57354275..57354292,-p@chr8:57354275..57354292
-
Hg19::chr8:57354278..57354286,+p@chr8:57354278..57354286
+
Hg19::chr8:57354303..57354312,-p@chr8:57354303..57354312
-
Hg19::chr8:57354324..57354335,-p@chr8:57354324..57354335
-
Hg19::chr8:57354360..57354367,+p@chr8:57354360..57354367
+
Hg19::chr8:57354463..57354473,+p@chr8:57354463..57354473
+
Hg19::chr8:57358373..57358395,+p1@ENST00000518662
p1@uc003xtb.1
Hg19::chr8:57358393..57358427,-p2@PENK
Hg19::chr8:57358432..57358446,-p3@PENK
Hg19::chr8:57359192..57359208,-p1@PENK
Hg19::chr8:57359452..57359471,-p4@PENK
Hg19::chr8:57359557..57359570,-p5@PENK


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:0014812muscle cell migration0.00638704923454376
GO:0051451myoblast migration0.00638704923454376
GO:0001662behavioral fear response0.00638704923454376
GO:0002209behavioral defense response0.00638704923454376
GO:0001515opioid peptide activity0.00638704923454376
GO:0030878thyroid gland development0.00638704923454376
GO:0048538thymus development0.00638704923454376
GO:0042596fear response0.00638704923454376
GO:0048704embryonic skeletal morphogenesis0.0072992699464958
GO:0033555multicellular organismal response to stress0.00781995564380078
GO:0048706embryonic skeletal development0.00781995564380078
GO:0007600sensory perception0.00781995564380078
GO:0048705skeletal morphogenesis0.00781995564380078
GO:0019233sensory perception of pain0.00781995564380078
GO:0001657ureteric bud development0.00924438094333698
GO:0050877neurological system process0.0102140138971916
GO:0001656metanephros development0.0102140138971916
GO:0045664regulation of neuron differentiation0.0102140138971916
GO:0042472inner ear morphogenesis0.0102140138971916
GO:0042471ear morphogenesis0.0102140138971916
GO:0005184neuropeptide hormone activity0.0102140138971916
GO:0035270endocrine system development0.0102140138971916
GO:0003008system process0.0102140138971916
GO:0030855epithelial cell differentiation0.0102140138971916
GO:0001822kidney development0.0102140138971916
GO:0048839inner ear development0.0102140138971916
GO:0001655urogenital system development0.0102140138971916
GO:0048741skeletal muscle fiber development0.0102140138971916
GO:0048747muscle fiber development0.0102140138971916
GO:0043583ear development0.0102140138971916
GO:0048732gland development0.0108252756003371
GO:0002009morphogenesis of an epithelium0.014359014802047
GO:0007519skeletal muscle development0.0148070772530198
GO:0007423sensory organ development0.0182250738705893
GO:0014706striated muscle development0.0182250738705893
GO:0048598embryonic morphogenesis0.0182250738705893
GO:0009792embryonic development ending in birth or egg hatching0.0182250738705893
GO:0043009chordate embryonic development0.0182250738705893
GO:0007389pattern specification process0.0231686483691839
GO:0050954sensory perception of mechanical stimulus0.0234575397976375
GO:0007605sensory perception of sound0.0234575397976375
GO:0045595regulation of cell differentiation0.024976336011968
GO:0007218neuropeptide signaling pathway0.0279938939753307
GO:0007517muscle development0.0279938939753307
GO:0048534hemopoietic or lymphoid organ development0.0279938939753307
GO:0002520immune system development0.0288061754355248
GO:0001501skeletal development0.0309625857559595
GO:0005667transcription factor complex0.0309625857559595
GO:0030182neuron differentiation0.0309625857559595
GO:0032501multicellular organismal process0.0309625857559595
GO:0005179hormone activity0.0309625857559595
GO:0016477cell migration0.0312158469806535
GO:0005625soluble fraction0.0312158469806535
GO:0009790embryonic development0.0312158469806535
GO:0050793regulation of developmental process0.0312158469806535
GO:0048699generation of neurons0.0314350865926451
GO:0022008neurogenesis0.0334260794360214
GO:0007610behavior0.0368445245302705
GO:0009887organ morphogenesis0.0445526366657958
GO:0051674localization of cell0.0455775334293007
GO:0006928cell motility0.0455775334293007



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>

Uber Anatomy
Ontology termp-valuen
corpus striatum7.96e-194
striatum7.96e-194
ventral part of telencephalon7.96e-194
future corpus striatum7.96e-194
mouth1.71e-1329
stomodeum1.71e-1329
periodontium2.31e-136
dentition2.31e-136
cranial skeletal system1.06e-1211
dense regular connective tissue2.15e-123
tendon2.15e-123
regular connective tissue2.15e-123
caudate-putamen7.78e-123
dorsal striatum7.78e-123
skull1.57e-117
telencephalic nucleus5.20e-117
primary palate mesenchyme3.74e-101
pneumatized bone3.74e-101
subdivision of skeleton3.74e-101
intramembranous bone3.74e-101
head bone3.74e-101
dermal bone3.74e-101
irregular bone3.74e-101
mesenchyme derived from head neural crest3.74e-101
facial mesenchyme3.74e-101
head or neck bone3.74e-101
embryonic nasal process3.74e-101
cranial neural crest3.74e-101
roof of mouth3.74e-101
mesenchyme of upper jaw3.74e-101
mesenchyme from rhombencephalic neural crest3.74e-101
membrane bone3.74e-101
pharyngeal arch mesenchymal region3.74e-101
1st arch mesenchyme3.74e-101
1st arch maxillary mesenchyme3.74e-101
1st arch mesenchyme from neural crest3.74e-101
pharyngeal arch mesenchyme from neural crest3.74e-101
maxillary process mesenchyme3.74e-101
maxilla3.74e-101
dermatocranium3.74e-101
skeleton of upper jaw3.74e-101
upper jaw region3.74e-101
frontonasal prominence3.74e-101
premaxilla3.74e-101
primary palate3.74e-101
pharyngeal arch 13.74e-101
dermal skeleton3.74e-101
entire pharyngeal arch associated mesenchyme3.74e-101
maxillary prominence3.74e-101
1st arch maxillary component3.74e-101
skeleton3.74e-101
medial nasal prominence3.74e-101
maxillary process mesenchyme from neural crest3.74e-101
rhombencephalon neural crest3.74e-101
1st arch maxillary mesenchyme from neural crest3.74e-101
axial skeletal system5.17e-1014
gingiva7.15e-108
putamen1.76e-091
nucleus accumbens2.26e-091
ventral striatum2.26e-091
dura mater2.67e-091
future meninx2.67e-091
ectomeninx2.67e-091
future dura mater2.67e-091
subdivision of skeletal system8.89e-0916
basal ganglion1.12e-089
neural nucleus1.12e-089
nuclear complex of neuraxis1.12e-089
nucleus of brain1.12e-089
aggregate regional part of brain1.12e-089
collection of basal ganglia1.12e-089
cerebral subcortex1.12e-089
subdivision of head1.14e-0749
ectoderm-derived structure7.27e-07171
ectoderm7.27e-07171
presumptive ectoderm7.27e-07171


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)
MA0003.10.00106283
MA0004.10.0566508
MA0006.10.0696281
MA0007.10.187495
MA0009.10.332084
MA0014.12.22494e-05
MA0017.10.096641
MA0019.10.122811
MA0024.10.254518
MA0025.11.11882
MA0027.11.8466
MA0028.10.967257
MA0029.10.739626
MA0030.10.720769
MA0031.10.215562
MA0038.10.673838
MA0040.10.272523
MA0041.10.063551
MA0042.10.0519308
MA0043.10.884353
MA0046.10.323723
MA0048.10.020072
MA0050.11.15437
MA0051.11.10349
MA0052.10.275327
MA0055.11.70555
MA0056.10
MA0057.10.00552249
MA0058.10.0279236
MA0059.10.0276133
MA0060.10.0557315
MA0061.10.182822
MA0063.10
MA0066.10.100184
MA0067.10.597968
MA0068.10.00495697
MA0069.10.320777
MA0070.10.312273
MA0071.10.0821719
MA0072.10.308875
MA0073.10
MA0074.10.0975962
MA0076.12.77547
MA0077.10.303076
MA0078.10.897097
MA0081.11.19471
MA0083.10.337888
MA0084.11.81181
MA0087.10.82764
MA0088.10.0876906
MA0089.10
MA0090.10.601812
MA0091.10.799469
MA0092.10.687103
MA0093.10.0154139
MA0095.10
MA0098.10
MA0100.10.106764
MA0101.10.0736699
MA0103.10.0639402
MA0105.10.00376935
MA0106.10.12076
MA0107.10.00636804
MA0108.20.213523
MA0109.10
MA0111.10.155179
MA0113.10.129524
MA0114.10.0322938
MA0115.10.530757
MA0116.10.00669574
MA0117.10.36143
MA0119.10.0239211
MA0122.10.382044
MA0124.10.494979
MA0125.10.42437
MA0130.10
MA0131.10.161082
MA0132.10
MA0133.10
MA0135.10.355725
MA0136.10.68982
MA0139.11.1261
MA0140.12.01587
MA0141.10.0271979
MA0142.10.194761
MA0143.10.129619
MA0144.10.0268501
MA0145.10.395589
MA0146.10.000399001
MA0147.10.0373801
MA0148.10.234511
MA0149.16.28785
MA0062.20.0858982
MA0035.20.980343
MA0039.27.50587e-09
MA0138.20.151138
MA0002.20.014191
MA0137.20.674267
MA0104.20.0551645
MA0047.20.114453
MA0112.20.00389731
MA0065.20.00147623
MA0150.10.0342009
MA0151.10
MA0152.11.00374
MA0153.10.41053
MA0154.10.0116128
MA0155.13.61247
MA0156.10.217366
MA0157.10.525632
MA0158.10
MA0159.10.108362
MA0160.10.0721072
MA0161.10
MA0162.17.8067e-07
MA0163.10.0218389
MA0164.10.136341
MA0080.20.907069
MA0018.20.121488
MA0099.20.285408
MA0079.20
MA0102.20.803155
MA0258.10.00405637
MA0259.10.0411886
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
CTCF#10664192.611406950985271.99136764937984e-050.000442032828764252
RAD21#5885153.982705344406281.53959477698694e-065.89852307093687e-05
SMC3#9126145.400745123822051.00027462762102e-075.87557265658668e-06



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:C309&oldid=3067426"