Personal tools

Coexpression cluster:C3278: 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=0.0724992894770213,0.0842546465117019,0.153163150959913,0,0,0,0,0,0,0.0954252957357428,0.379414727891662,0.272715235743603,0.18399087321112,0,0,0,0,0,0,0,0.107262976252031,0,0,0,0.0513619522818629,0,0,0,0,0,0.00581405156842818,0,0.114346030083907,0.240426435485783,0,0,0,0,0.102676458191195,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.153055502916071,0.0837191039350518,0.0826628337153937,0.0880145622338434,0.161526918504429,0.0647295580076124,0,0.162526324769076,0.109233914788981,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.165845936799575,0.141006687969447,0,0,0,0,0,0.288997341132196,0.0869750240711818,0.183841515445592,0.182961114915842,0.237692141113291,0.240940657106499,0,0,0,0,0,0,0.145359528047628,0,0,0.430707616901028,0,0,0.151673147612848,0.249259589209913,0.315403250032236,0.222571133856035,0,0,0.346413671224125,0.135979123430744,0.257712632750166,0.385390976844963,0.410221251976804,0.371315019293667,0,0,0.073058801099379,0,0,0.157182883491893,0,0,0,0,0,0,0,0,0.407570224606658,0,0.173298677647464,0.11484936557738,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0887965527720659,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.124623335319394,0.104741781954859,0.109512603169101,0.268066612792387,0.313917424138202,0.258483456842414,0.181359100908638,0.303041197025406,0.238034735548311,0,0,0,0,0,0.0922340184907578,0.142495818029451,0.17085466812628,0.0454379822391936,0.0856043003192711,0.0266964805817745,0.0320521290399831,0.0623746104347134,0,0,0,0,0.392712270020621,0,0,0.201612826790636,0,0.0955099827348378,0.226927433325053,0.158061138485158,0,0.0795639603670563,0.106451101971206,0,0,0,0.129622621258172,0.200588822806923,0.0585651160278124,0,0.0756397051975275,0,0,0,0.166728579178217,0.0272317210104769,0,0.0674361974989848,0.108412856849701,0.21136343755771,0,0.247178875285564,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.234236259832332,0,0,0,0.132064901528981,0,0.0305339450463875,0,0.204075993750989,0,0,0,0,0,0,0.156653296834752,0,0,0,0,0,0,0.0983303062134256,0,0,0,0,0,0,0,0.0502604313716981,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.114986933642873,0.425591991369837,0.280389607000673,0,0.0620032815069762,0,0,0,0,0,0,0,0,0,0,0.134361483765049,0.0793645050922885,0.105933361766836,0,0,0,0.279301660537643,0.248010896481871,0,0,0.213068560793708,0,0.127165533945345,0.216890726837007,0,0.188054201617406,0.176580223334895,0.305244952580507,0,0.13273570999446,0,0,0,0,0,0.439600641602686,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.197713313938225,0.403352635015532,0.115102153805393,0,0,0,0,0,0,0,0,0,0,0.196422311813607,0,0,0,0,0,0.0088123228337555,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0188670457895597,0.0407008327132364,0,0,0,0,0,0,0.14141479353858,0.165673495189126,0,0.347109281048989,0.15548949326123,0,0,0.164188268760301,0,0,0,0,0,0,0,0,0,0,0.0951833797824107,0,0,0,0,0,0,0.153310840807784,0,0,0,0,0,0.126645485425697,0,0,0.154072694012943,0,0,0,0,0,0,0,0.103959518714163,0,0,0.286838656289689,0.3368729043759,0.237584735440797,0,0,0.613173307922385,0.11292814946238,0.404115598731266,0,0.152902115792725,0.125131775077837,0,0.0831891152636857,0.505132346818394,0.376835919641402,0.16633003635109,0.080820276450175,0,0,0.133370715893297,0.132913313245494,0,0.144441446549164,0,0,0.27893053810631,0.106634247942447,0,0.0491076843236937,0.1832014903135,0.389165933845057,0.119448667568995,0.098385373642144,0.213816262759104,0,0,0.065192321219526,0.275482132507796,0.204928697981331,0.402401944384513,0.191142455090553,0,0.0861409897892114,0,0.151759294076614,0.22854210410682,0,0.090104171961993,0.317455677189908,0.0853957467812278,0.214314512399756,0.0380625695285996,0,0,0,0,0,0,0,0,0.0726591550834,0.212984640524252,0.065666642656593,0.153528048226302,0,0.600513954847267,0.529988808130209,0.5370783478329,0,0,0,0.187297612104379,0.532465552525037,0.0914082188667263,0,0.296297220916032,0,0.41133978391229,0.535136699364515,0,0.119233744361939,0.060819961675157,0.117624082631732,0,0,0,0,0.268069586889531,0,0.27133006685894,0.226843861693432,0.100776255360726,0.31140628842589,0,0.0763806111580254,0.0306358713632606,0.00242189487245242,0.335230804177181,0.0705964547155333,0.161955095312168,0,0,0.159319169054904,0.250957787133853,0.235889211459974,0.315396146312343,0.079112335990984,0.156025274855562,0,0,0,0.175224742703361,0.288422760749283,0,0,0.0421808920916863,0,0.447353554180645,0.226477949138639,0,0.155264795610224,0,0.264309401882715,0.227238961653008,0.234991060098501,0.145928835269607,0.359394923119558,0.222590162111468,0.35726497947502,0,0,0,0,0,0.0780415250326843,0,0,0.148790834525069,0.293256209338438,0.29287075140178,0.425169114961006,0,0.521321948041652,0.0727088341078527,0,0.410965102427167,0.444584359974112,0,0,0.076245357210966,0,0,0,0,0,0,0,0,0,0,0.158258943052669,0.36643582506357,0.360371772858008,0.101906882599192,0,0,0.415275776944579,0.58316220231545,0.591028234724802,0,0,0,0.214404368077712,0,0.352847824178944,0.453023632528068,0.421499149496963,0.251704024154505,0,0.238587401017672,0.138483577189796,0.196841684047034,0.249566033416824,0.241834462609344,0,0,0,0,0.167474373057587,0,0,0,0,0,0,0,0,0,0,0,0,0.0641946247847473,0,0.00646547670004505,0,0,0,0,0,0,0,0.0443086593632396,0,0,0,0,0,0,0.141524917346346,0.00340951581451887,0.100713120693921,0.329098678129041,0.22905885310373,0,0,0,0.157930425411789,0,0.141709355787741,0,0.247660205308878,0.128861217532784,0,0.262344429313623,0.142927500688746,0.102340964174604,0.0800402016265547,0.05067075996182,0.173636598619994,0,0,0,0,0.330931528776898,0,0.192990400359885,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.198124344399475,0,0.120332935578059,0.149290789502833,0,0.191243604621179,0.294213484466631,0,0.201092823406828,0.164890786542706,0.190411767844756,0,0,0.063684472253816,0,0.261813089336159,0.0797978929983786,0.408753354501022,0.311250800419779,0,0.339023632415484,0.168132892145335,0.408605602194887,0.150256972842231,0.213294071460843,0,0,0.29938140626407,0,0.247131973414421,0,0,0,0.281180858030331,0.367455732503771,0,0,0.242458701419397,0.183606380760766,0.0921546695012139,0,0.167600437054528,0.353517073244492,0.107302302820485,0.451220938524739,0.216899958319399,0.169601464072093,0.316420805089006,0,0.129923174575149,0,0,0.0817850418435885,0.268014236710241,0.37703643170745,0.155405081403798,0,0,0.598101801277775,0.0895896456213401,0,0.291266468109506,0.223010908997275,0.112085514980729,0.1353724095793,0.360755756038886,0.208435132528748,0.334416438693572,0.390428660981575,0.286851029979279,0.145476586533315,0,0.0884522690358478,0,0.162232295399933,0.577292954516892,0.27282479499172,0.167411066169369,0.0952210875623146,0.167716906896504,0.251695117438976,0.112955512742184,0.548504194982,0,0.10787168088319,0.121326529566266,0,0.186295585685449,0,0.0936752181307629,0.786208549671158,0.452540368718045,0.234693879865657,0,0.207344403065639,0,0.184415109078388,0,0,0,0.274888367861794,0.342801790914369,0,0.497173755938561,1.17304940251683,0.34136204258699,0.699952190172315,0.139530721565415,0.316359676527578,0,0.18103280933514,0.267860402174185,0.234059791889601,0,0.117395125353115,0.0878749815719147,0.261836723799116,0,0.272042912634816,0.127828009549688,0.205791098134966,0.331944353047396,0.22149788379633,0.0339876779246108,0,0,0.278353870942836,0,0.20715139958257,0.14826204992358,0.367637943472982,0.0796420028184954,0
|full_id=C3278_testicular_small_colon_amniotic_seminal_Endothelial_stomach
|full_id=C3278_testicular_small_colon_amniotic_seminal_Endothelial_stomach
|id=C3278
|id=C3278

Revision as of 16:10, 12 September 2012


Full id: C3278_testicular_small_colon_amniotic_seminal_Endothelial_stomach



Phase1 CAGE Peaks

Hg19::chr12:32552434..32552448,+p10@FGD4
Hg19::chr12:32552451..32552508,+p2@FGD4
Hg19::chr12:32555079..32555083,+p@chr12:32555079..32555083
+


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 cell1.09e-24254
endothelial cell of vascular tree7.82e-0824
squamous epithelial cell5.33e-0762
Uber Anatomy
Ontology termp-valuen
adult organism2.73e-28115
multi-cellular organism2.48e-17659
organ3.89e-17511
embryo4.07e-17612
anatomical conduit9.79e-15241
embryonic structure2.62e-14605
developing anatomical structure2.62e-14605
anatomical system3.18e-14625
anatomical group4.41e-14626
germ layer5.54e-14604
embryonic tissue5.54e-14604
presumptive structure5.54e-14604
epiblast (generic)5.54e-14604
anatomical cluster1.27e-13286
organ part2.37e-13219
neural plate3.51e-1386
presumptive neural plate3.51e-1386
neural tube6.96e-1357
neural rod6.96e-1357
future spinal cord6.96e-1357
neural keel6.96e-1357
regional part of brain7.19e-1259
neurectoderm1.25e-1190
tube1.75e-11194
central nervous system1.94e-1082
head2.16e-10123
anterior region of body2.75e-10129
craniocervical region2.75e-10129
ectoderm-derived structure3.38e-10169
brain5.73e-1069
future brain5.73e-1069
multi-tissue structure6.67e-10347
epithelium1.32e-09309
endoderm-derived structure1.43e-09169
endoderm1.43e-09169
presumptive endoderm1.43e-09169
immaterial anatomical entity1.73e-09126
cell layer2.00e-09312
anterior neural tube2.47e-0942
ectoderm2.59e-09173
presumptive ectoderm2.59e-09173
regional part of forebrain7.73e-0941
forebrain7.73e-0941
future forebrain7.73e-0941
pre-chordal neural plate9.30e-0961
gray matter1.28e-0834
brain grey matter1.28e-0834
telencephalon2.51e-0834
subdivision of digestive tract3.13e-08129
endodermal part of digestive tract3.13e-08129
anatomical space3.37e-08104
regional part of nervous system3.49e-0894
nervous system3.49e-0894
regional part of telencephalon4.54e-0833
digestive system7.73e-08155
digestive tract7.73e-08155
primitive gut7.73e-08155
cerebral hemisphere9.25e-0832
trunk region element9.69e-08107
mixed endoderm/mesoderm-derived structure5.02e-07130
Disease
Ontology termp-valuen
carcinoma5.97e-10106


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
ESR1#2099220.51240219743630.003099741577095180.016303263865148
NR3C1#290829.982015554115360.01278474365547170.0460200538579241
SMARCB1#6598212.16847718743830.008675002221921740.0329721434258419
SMC3#9126210.02995522995520.0126656379767470.0457173762581558



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:C3278&oldid=2138049"