Personal tools

Coexpression cluster:C877: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.055712496781182,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.2012348043535,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0907474205905807,0.0818231540625959,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0905616389277576,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0983303062134256,0.361991832974167,0.248779474225184,0.399266295091813,0.357148882912052,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.099145253918139,0,0,0,0.0380513783661453,0,0,0,0,0,0,0,0,0,0,0.0355204411879812,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.475423511109794,0.451587260979884,0,0,0,0.0789089986057754,0,0,0,0,0,0,0,0,0,0,0,0.766908116208019,0.556001617298675,0.698298584006718,0,0,0,0,0,0,0.128639412800133,0,0.0695293501927681,0.657339442861113,0.366714411076988,0,0.323415595049963,0.526905165432348,0.364797128903212,0,0,0.0321956448428329,0.0468626006398675,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.207103666835013,0,0,0,0.832285157417554,0,0.581058702819259,0,0,0,0,0,0.640163339220937,0.0266094859650764,0,0,0,0,0,0,0,0,0,0,0,0.0699368280688007,0,0,0,0,0,0,0.279649371901492,0,0,0.524071344519698,0,0,0.0840229578243582,0,0,0,0,0,0,0,0,0,0,0,0.447353554180645,0.503856851734894,0,0,0,0,0.0896085685791025,0,0,0,0,0,0,0,0,0,0,0,0,0.529647071424384,0.520543518080814,0.121069236870266,0,0.15089156821841,0,0,0.441182340882304,0,0,0.0222033657448865,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.626553243622454,0.455036276830013,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.442814589183038,0.551761158866051,0.419539765898424,0.517675704141427,0.407051958209435,0.586185963418573,0.056275291093238,0,0,0,0,0.166825123124581,0.0587755320721174,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0443086593632396,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.506793786654791,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.157407972322813,0,0,0,0,0,0,0,0,0,0.52846435248005,0.383270498593678,0.440274871786368,0.741353330512482,0.919605162388543,0.351183562965727,0.389747261843462,1.29136939739785,0,0,0,0,0,0,0,0.031493427513643,0,0,0,0,0,0.591522728461604,0.408605602194887,0.423818170839411,0.54858992224639,0.810887371059169,0,0,0.0703597699327489,0,0.316264741738924,0.56705811648581,0,0.0890788809625826,0,0,0,0.601045625865463,0.611863486838214,0,0,0,0.322179819586062,0,0.281751001695877,0,0,0.176188474906377,0.212734643147755,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.166690235731849,0,0.0487990718960468,0,0.190248357112215,0,0,0.0858467613960337,0.28794376861681,0,0,0.906717699781024,0.444400584457849,0.75198795010627,0,0,0,0,0,0,0,0.238130540907848,0,0.618411164673733,0,0.570503198675173,0.877674230040688,0.184415109078388,0,0,0,0,0,0,0.0421771923324582,0,0,0,0.0317229404497622,0,0.776339118865335,0.566939015035841,0,0,0,0,0,0,0,0,0,0,0.0300822291072195,0,0,0,0,0,0,0,0,0,0.0796420028184954,0
|full_id=C877_optic_parietal_occipital_temporal_corpus_duodenum_brain
|full_id=C877_optic_parietal_occipital_temporal_corpus_duodenum_brain
|gostat_on_coexpression_clusters=GO:0007399!nervous system development!0.00235882184034278!57453;56896;6457$GO:0007409!axonogenesis!0.00235882184034278!57453;56896$GO:0048667!neuron morphogenesis during differentiation!0.00235882184034278!57453;56896$GO:0048812!neurite morphogenesis!0.00235882184034278!57453;56896$GO:0000904!cellular morphogenesis during differentiation!0.00235882184034278!57453;56896$GO:0031175!neurite development!0.00235882184034278!57453;56896$GO:0048666!neuron development!0.00263048050948375!57453;56896$GO:0032990!cell part morphogenesis!0.00310783649624717!57453;56896$GO:0048858!cell projection morphogenesis!0.00310783649624717!57453;56896$GO:0030030!cell projection organization and biogenesis!0.00310783649624717!57453;56896$GO:0030182!neuron differentiation!0.00310783649624717!57453;56896$GO:0007417!central nervous system development!0.00348781455915125!57453;6457$GO:0048699!generation of neurons!0.00348781455915125!57453;56896$GO:0022008!neurogenesis!0.00379284252160859!57453;56896$GO:0048731!system development!0.00594289024873574!57453;56896;6457$GO:0042802!identical protein binding!0.00637410169344523!57453;6457$GO:0048704!embryonic skeletal morphogenesis!0.00708727549592255!57453$GO:0048856!anatomical structure development!0.00832386365774856!57453;56896;6457$GO:0048706!embryonic skeletal development!0.00832386365774856!57453$GO:0000902!cell morphogenesis!0.00832386365774856!57453;56896$GO:0032989!cellular structure morphogenesis!0.00832386365774856!57453;56896$GO:0048705!skeletal morphogenesis!0.00912432801082624!57453$GO:0031901!early endosome membrane!0.00989013586888669!6457$GO:0007275!multicellular organismal development!0.0105791378658706!57453;56896;6457$GO:0009953!dorsal/ventral pattern formation!0.014914166630396!57453$GO:0001709!cell fate determination!0.014914166630396!57453$GO:0043025!cell soma!0.0173270730176464!56896$GO:0030425!dendrite!0.018137180821599!56896$GO:0005769!early endosome!0.0225663353440213!6457$GO:0016043!cellular component organization and biogenesis!0.0233626455106897!57453;56896;6457$GO:0032502!developmental process!0.0233626455106897!57453;56896;6457$GO:0007411!axon guidance!0.0233626455106897!56896$GO:0009653!anatomical structure morphogenesis!0.0245951547792637!57453;56896$GO:0045165!cell fate commitment!0.0278535056622883!57453$GO:0043005!neuron projection!0.0289834837544392!56896$GO:0032501!multicellular organismal process!0.0289834837544392!57453;56896;6457$GO:0048468!cell development!0.0289834837544392!57453;56896$GO:0010008!endosome membrane!0.0289834837544392!6457$GO:0044440!endosomal part!0.0289834837544392!6457$GO:0003002!regionalization!0.0289834837544392!57453$GO:0048598!embryonic morphogenesis!0.0294267243002979!57453$GO:0009792!embryonic development ending in birth or egg hatching!0.0294267243002979!57453$GO:0043009!chordate embryonic development!0.0294267243002979!57453$GO:0007389!pattern specification process!0.037472638517259!57453$GO:0007420!brain development!0.0410359049211885!57453$GO:0009986!cell surface!0.042720417716659!57453$GO:0042803!protein homodimerization activity!0.0446103001695871!57453$GO:0048869!cellular developmental process!0.0473024337183543!57453;56896$GO:0030154!cell differentiation!0.0473024337183543!57453;56896$GO:0016020!membrane!0.0474945320108906!57453;256472;154215;6457$GO:0016810!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds!0.0483004518974905!56896$GO:0005768!endosome!0.0483004518974905!6457$GO:0010324!membrane invagination!0.0483004518974905!6457$GO:0006897!endocytosis!0.0483004518974905!6457
|gostat_on_coexpression_clusters=GO:0007399!nervous system development!0.00235882184034278!57453;56896;6457$GO:0007409!axonogenesis!0.00235882184034278!57453;56896$GO:0048667!neuron morphogenesis during differentiation!0.00235882184034278!57453;56896$GO:0048812!neurite morphogenesis!0.00235882184034278!57453;56896$GO:0000904!cellular morphogenesis during differentiation!0.00235882184034278!57453;56896$GO:0031175!neurite development!0.00235882184034278!57453;56896$GO:0048666!neuron development!0.00263048050948375!57453;56896$GO:0032990!cell part morphogenesis!0.00310783649624717!57453;56896$GO:0048858!cell projection morphogenesis!0.00310783649624717!57453;56896$GO:0030030!cell projection organization and biogenesis!0.00310783649624717!57453;56896$GO:0030182!neuron differentiation!0.00310783649624717!57453;56896$GO:0007417!central nervous system development!0.00348781455915125!57453;6457$GO:0048699!generation of neurons!0.00348781455915125!57453;56896$GO:0022008!neurogenesis!0.00379284252160859!57453;56896$GO:0048731!system development!0.00594289024873574!57453;56896;6457$GO:0042802!identical protein binding!0.00637410169344523!57453;6457$GO:0048704!embryonic skeletal morphogenesis!0.00708727549592255!57453$GO:0048856!anatomical structure development!0.00832386365774856!57453;56896;6457$GO:0048706!embryonic skeletal development!0.00832386365774856!57453$GO:0000902!cell morphogenesis!0.00832386365774856!57453;56896$GO:0032989!cellular structure morphogenesis!0.00832386365774856!57453;56896$GO:0048705!skeletal morphogenesis!0.00912432801082624!57453$GO:0031901!early endosome membrane!0.00989013586888669!6457$GO:0007275!multicellular organismal development!0.0105791378658706!57453;56896;6457$GO:0009953!dorsal/ventral pattern formation!0.014914166630396!57453$GO:0001709!cell fate determination!0.014914166630396!57453$GO:0043025!cell soma!0.0173270730176464!56896$GO:0030425!dendrite!0.018137180821599!56896$GO:0005769!early endosome!0.0225663353440213!6457$GO:0016043!cellular component organization and biogenesis!0.0233626455106897!57453;56896;6457$GO:0032502!developmental process!0.0233626455106897!57453;56896;6457$GO:0007411!axon guidance!0.0233626455106897!56896$GO:0009653!anatomical structure morphogenesis!0.0245951547792637!57453;56896$GO:0045165!cell fate commitment!0.0278535056622883!57453$GO:0043005!neuron projection!0.0289834837544392!56896$GO:0032501!multicellular organismal process!0.0289834837544392!57453;56896;6457$GO:0048468!cell development!0.0289834837544392!57453;56896$GO:0010008!endosome membrane!0.0289834837544392!6457$GO:0044440!endosomal part!0.0289834837544392!6457$GO:0003002!regionalization!0.0289834837544392!57453$GO:0048598!embryonic morphogenesis!0.0294267243002979!57453$GO:0009792!embryonic development ending in birth or egg hatching!0.0294267243002979!57453$GO:0043009!chordate embryonic development!0.0294267243002979!57453$GO:0007389!pattern specification process!0.037472638517259!57453$GO:0007420!brain development!0.0410359049211885!57453$GO:0009986!cell surface!0.042720417716659!57453$GO:0042803!protein homodimerization activity!0.0446103001695871!57453$GO:0048869!cellular developmental process!0.0473024337183543!57453;56896$GO:0030154!cell differentiation!0.0473024337183543!57453;56896$GO:0016020!membrane!0.0474945320108906!57453;256472;154215;6457$GO:0016810!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds!0.0483004518974905!56896$GO:0005768!endosome!0.0483004518974905!6457$GO:0010324!membrane invagination!0.0483004518974905!6457$GO:0006897!endocytosis!0.0483004518974905!6457

Revision as of 18:38, 12 September 2012


Full id: C877_optic_parietal_occipital_temporal_corpus_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr11:113075052..113075072,+p@chr11:113075052..113075072
+
Hg19::chr11:117667885..117667949,-p1@DSCAML1
Hg19::chr11:131309852..131309856,+p@chr11:131309852..131309856
+
Hg19::chr11:131433495..131433499,+p@chr11:131433495..131433499
+
Hg19::chr11:66059302..66059313,+p3@TMEM151A
Hg19::chr15:84116080..84116099,+p2@SH3GL3
Hg19::chr1:147718685..147718722,-p@chr1:147718685..147718722
-
Hg19::chr2:27170707..27170718,+p6@DPYSL5
Hg19::chr6:124124993..124125015,+p6@NKAIN2


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:0007399nervous system development0.00235882184034278
GO:0007409axonogenesis0.00235882184034278
GO:0048667neuron morphogenesis during differentiation0.00235882184034278
GO:0048812neurite morphogenesis0.00235882184034278
GO:0000904cellular morphogenesis during differentiation0.00235882184034278
GO:0031175neurite development0.00235882184034278
GO:0048666neuron development0.00263048050948375
GO:0032990cell part morphogenesis0.00310783649624717
GO:0048858cell projection morphogenesis0.00310783649624717
GO:0030030cell projection organization and biogenesis0.00310783649624717
GO:0030182neuron differentiation0.00310783649624717
GO:0007417central nervous system development0.00348781455915125
GO:0048699generation of neurons0.00348781455915125
GO:0022008neurogenesis0.00379284252160859
GO:0048731system development0.00594289024873574
GO:0042802identical protein binding0.00637410169344523
GO:0048704embryonic skeletal morphogenesis0.00708727549592255
GO:0048856anatomical structure development0.00832386365774856
GO:0048706embryonic skeletal development0.00832386365774856
GO:0000902cell morphogenesis0.00832386365774856
GO:0032989cellular structure morphogenesis0.00832386365774856
GO:0048705skeletal morphogenesis0.00912432801082624
GO:0031901early endosome membrane0.00989013586888669
GO:0007275multicellular organismal development0.0105791378658706
GO:0009953dorsal/ventral pattern formation0.014914166630396
GO:0001709cell fate determination0.014914166630396
GO:0043025cell soma0.0173270730176464
GO:0030425dendrite0.018137180821599
GO:0005769early endosome0.0225663353440213
GO:0016043cellular component organization and biogenesis0.0233626455106897
GO:0032502developmental process0.0233626455106897
GO:0007411axon guidance0.0233626455106897
GO:0009653anatomical structure morphogenesis0.0245951547792637
GO:0045165cell fate commitment0.0278535056622883
GO:0043005neuron projection0.0289834837544392
GO:0032501multicellular organismal process0.0289834837544392
GO:0048468cell development0.0289834837544392
GO:0010008endosome membrane0.0289834837544392
GO:0044440endosomal part0.0289834837544392
GO:0003002regionalization0.0289834837544392
GO:0048598embryonic morphogenesis0.0294267243002979
GO:0009792embryonic development ending in birth or egg hatching0.0294267243002979
GO:0043009chordate embryonic development0.0294267243002979
GO:0007389pattern specification process0.037472638517259
GO:0007420brain development0.0410359049211885
GO:0009986cell surface0.042720417716659
GO:0042803protein homodimerization activity0.0446103001695871
GO:0048869cellular developmental process0.0473024337183543
GO:0030154cell differentiation0.0473024337183543
GO:0016020membrane0.0474945320108906
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0483004518974905
GO:0005768endosome0.0483004518974905
GO:0010324membrane invagination0.0483004518974905
GO:0006897endocytosis0.0483004518974905



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system9.79e-3894
nervous system9.79e-3894
central nervous system1.57e-3482
neural tube3.77e-3357
neural rod3.77e-3357
future spinal cord3.77e-3357
neural keel3.77e-3357
neurectoderm4.56e-3290
neural plate7.14e-3186
presumptive neural plate7.14e-3186
regional part of brain1.50e-2759
brain3.03e-2769
future brain3.03e-2769
regional part of forebrain8.89e-2741
forebrain8.89e-2741
future forebrain8.89e-2741
anterior neural tube2.83e-2642
pre-chordal neural plate1.57e-2261
telencephalon1.76e-2234
gray matter1.81e-2234
brain grey matter1.81e-2234
adult organism2.25e-22115
ectoderm5.49e-22173
presumptive ectoderm5.49e-22173
regional part of telencephalon7.71e-2233
cerebral hemisphere4.43e-2132
ectoderm-derived structure7.30e-21169
cerebral cortex1.24e-1625
pallium1.24e-1625
anterior region of body5.07e-16129
craniocervical region5.07e-16129
head7.83e-16123
regional part of cerebral cortex1.29e-1522
neocortex2.68e-1420
organ part2.95e-11219
organism subdivision5.16e-10365
multi-tissue structure6.79e-10347
tube9.87e-09194
organ3.93e-08511
epithelium4.26e-08309
posterior neural tube4.87e-0815
chordal neural plate4.87e-0815
cell layer7.73e-08312
embryo1.13e-07612
nucleus of brain2.70e-079
neural nucleus2.70e-079
basal ganglion3.50e-079
nuclear complex of neuraxis3.50e-079
aggregate regional part of brain3.50e-079
collection of basal ganglia3.50e-079
cerebral subcortex3.50e-079
segmental subdivision of nervous system8.44e-0713


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)

{{{tfbs_overrepresentation_jaspar}}}



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
SUZ12#23512211.13684020245840.01305435313902310.0463105838140772



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.