Personal tools

Coexpression cluster:C1193: 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=0,0,0,0,0,0,0,0,0,0.0954252957357428,0,0.085804637030866,0.101667003219354,0,0,0,0,0,0,0,0.080626736260243,0,0,0,0,0,0,0,0,0,0.209317792906133,0,0.114346030083907,0.136642580572897,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0869750240711818,0.0365629421359175,0.550728662215616,0.39043717557737,0.598382881914913,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.232827633528851,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0767353931304631,0,0.517781175658004,0,0.0540496261796572,0,0.0428357178336246,0.244762505171551,0,0,0,0,0,0,0.0485609657022036,0,0,0,0,0,0,0,0,0,0,0.632719621021688,0,0,0,0,0,0.136392444904183,0,0.123606948733483,0,0.114473174685065,0.0737831746122416,0,0,0,0,0,0,0,0,0.527708916447681,0.434085214600117,0,0,0,0,0.0674361974989848,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.03931493176627,0.728975740757837,1.49681607101609,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.205415661963911,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0793645050922885,0.0382548469252227,0,0,0,0,0,0,0,0,0,0,0,0,0.104127248139133,0,0,0,0,0,0,0.939194845968548,1.22387744871729,0.419442213496002,0.0425916600387234,0,0,0,0.217499801210003,0,0,0,0,0,0,0,0,0,0,0.141255358724553,0.0521599633818348,0.206001468090966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.197923300346779,0.478697316350895,0,0.0390744040629657,0.941963217028505,0,1.16868408868907,0.81380518974823,0,0,0,0,0,0,0,0,0.154514135252951,0,0.347369262034896,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0593771573651105,0,0,0.108611070985339,0.587142061456945,1.3262046984615,1.36963753544395,0,0,0,0,0,0.300212740809256,0.105947296040957,0,0.0422874684771159,0,0,0.257394189329734,0,0,0.078198198554358,0,0,0,0,0,0,0,0,0.373926877527167,0,0.808677887665138,0,0,0.0695293501927681,0,0,0,0,0,0,0,0.353110664594184,0,0,0,0,0,0.214314512399756,0,0,0,0,0,0,0,0,0,0,0,1.42533122322502,0.108127174575846,0,0,0.131564216321577,0,0,0,0,0,0.532465552525037,0,0,0.691372608761849,0,0,0,0,0.0266094859650764,0,0,0.221323945469862,0.1241754307343,0.288204218349767,0,0.195683583376492,0,0.977925947530006,0.616554983795024,0.0362531985397609,0.1301578714358,0.0689224358658181,0.0768270310165508,0.0592523085472017,0.0660391270288988,0.24942147407107,0.0367311208382308,0,0,0,0,0.143359213980427,0.453876579513652,0.0840229578243582,0.476845548864524,0.620134927826094,0,0,0,0,0.0919109500998384,0.319571067471378,0.264067254559683,0,0,0,0,0,0.155264795610224,0,0,0,0,1.11329945222997,0.269151371139379,0.0874873383132558,0.0547535628453514,0,0,0,0,0,0,0,0,0,0,0.055966461856338,0,0,0,0,0.125622652740133,0,0.0433265804049448,0,0,0,0.234186964128339,0,0.97270544667368,0,0,0,0,0,0,0,0,0,0,0,0.179913699935071,0.231677263595219,0.771750658096849,0.322308240653542,0.542256904750742,0,0,0,0,0,0,0,0,0,0,0,0,0.331795307148208,0.221564013409524,0.0508408017580101,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.182341901105911,0.204399588044458,0.330903729395183,0,0,0.0845123315265278,0,0,0,0,0,0,0.141524917346346,1.02734437222623,0.861167645012851,0.0887404631064488,0,0,0,1.52406039701759,1.35620032259193,0,1.60381046317921,0.657800522101784,0.0990731426707233,0.128861217532784,0,0,0,0,0,0,0.0954388822399226,0.15309020639035,0,0,0,0,0,0.0568589461625992,0.210071535945973,0.306029150306422,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.409994544790888,0,0.238977554911651,0.0902761624927521,0,0,0,0.312377229161241,0,0,0,0,0.240369610670926,0,0,0,0,0,0,0,0,0.0988253147420914,0,0,0,0,0.0369091684033041,0,0,0,0,0.232783494141567,0.0458045054759181,0.032817368032432,0,0,0,0.499587556233518,0,0.0299826682885844,0,0.165827456884257,0,0,0,0,0,0,0,0,0,0.689736438870357,0,0,1.03516059228781,0.0406617582988581,1.04128488180577,0,0,0,0,0,0,0,0,0,0,0,0.157492767753078,0,0,0,0,0,0,0,0,0.0271284845789754,0,0,0,0.033520804106862,0.238130540907848,0,0,0.0636228779875179,0,0,0,0,0,0,0,0,0,0,0,0,0,0.225828130386425,0.103106967823645,0,0,0.214764912010815,0,0,0.0261550693490902,0,0,0,0.0855462791577618,0.306789446764709,0.331424239491484,0.084635829807314,0,0.195850654665458,0.154396393934003,0,0.0717533208515938,0.905214360532884,0,0,0,0.302410802070244,0
|full_id=C1193_mesothelioma_Mesothelial_Retinal_clear_amniotic_serous_Urothelial
|full_id=C1193_mesothelioma_Mesothelial_Retinal_clear_amniotic_serous_Urothelial
|id=C1193
|id=C1193

Revision as of 13:40, 12 September 2012


Full id: C1193_mesothelioma_Mesothelial_Retinal_clear_amniotic_serous_Urothelial



Phase1 CAGE Peaks

Hg19::chr14:100003871..100003888,-p@chr14:100003871..100003888
-
Hg19::chr7:76139713..76139729,+p3@UPK3B
Hg19::chr7:76139741..76139750,+p6@UPK3B
Hg19::chr7:76139833..76139844,+p5@UPK3B
Hg19::chr7:76139845..76139887,+p1@UPK3B
Hg19::chr7:76139896..76139907,+p4@UPK3B
Hg19::chr7:76139925..76139937,+p2@UPK3B


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
epithelial cell8.34e-22254
endo-epithelial cell1.18e-1243
mesothelial cell1.08e-0919
endodermal cell6.52e-0959
respiratory epithelial cell2.44e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.36e-20169
endoderm3.36e-20169
presumptive endoderm3.36e-20169
digestive system1.26e-15155
digestive tract1.26e-15155
primitive gut1.26e-15155
subdivision of digestive tract9.91e-15129
endodermal part of digestive tract9.91e-15129
mixed endoderm/mesoderm-derived structure6.50e-14130
anatomical space2.35e-12104
immaterial anatomical entity4.83e-11126
foregut6.14e-1198
respiratory system7.65e-1172
respiratory tract5.82e-1053
organ segment9.95e-1097
trunk region element1.03e-09107
organ part2.16e-09219
primordium6.08e-09168
organ6.91e-09511
multi-tissue structure7.63e-09347
body cavity or lining1.56e-0849
respiratory primordium2.44e-0838
endoderm of foregut2.44e-0838
endo-epithelium3.90e-0882
body cavity4.69e-0846
mesenchyme8.63e-08238
entire embryonic mesenchyme8.63e-08238
multi-cellular organism9.91e-08659
thoracic segment organ1.96e-0735
gastrointestinal system2.80e-0735
body cavity precursor4.14e-0763
segment of respiratory tract5.78e-0746
thoracic cavity element7.13e-0734
thoracic cavity7.13e-0734
anatomical cavity7.25e-0770
embryo7.51e-07612
Disease
Ontology termp-valuen
carcinoma4.65e-14106
cell type cancer4.42e-10143
adenocarcinoma1.80e-0825


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
CTCF#1066464.594505462635740.0002478392075687640.00267480407143476
EP300#203365.806235765334176.3256174139893e-050.0010320905438207
MYC#460964.476241604236630.0002883611950910820.00306401005739317
RAD21#588568.875743338962575.20411262905738e-060.00015948131422128
TFAP2C#702269.26505309416594.03752634749879e-060.000130267288911469



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:C1193&oldid=2135731"