Personal tools

Coexpression cluster:C4208: 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=0.0724992894770213,0.0842546465117019,0,0,0.160456854061196,0,0,0,0,0,0,0,0,0,0.124307696593413,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0789870938765965,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.236254602210782,0.17647845120947,0.156712528252229,0,0.172204315337917,0,0,0,0.101044953091069,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.175213663176675,0.0517815087208527,0,0.269631976484861,0.131832994540557,0,0,0,0,0,0,0.162585996137491,0.197604689528463,0,0,0,0,0,0,0,0.207489627025517,0,0.209502866741781,0.340047884800798,0.508583899855267,0,0,0,0,0.10621270172856,0.273685237297737,0.207627795464294,0.398353362576112,0,0.0716573069394021,0.268163499181463,0.0834782173702644,0.204169432998994,0.235873650717719,0.180493200633673,0.192665163897168,0.177919836311715,0.111367046208093,0.30313881687167,0.105901621330139,0.29443896415916,0.131942369721337,0.147060269021119,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046155979559586,0,0,0,0,0,0.102412476390192,0,0,0,0,0,0.188259409638053,0,0,0.233195153867752,0,0,0.272197595679984,0,0,0,0,0,0,0,0.110442433690542,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0953029273486504,0,0,0,0.0713034174053426,0.119059432222927,0.287159062945695,0.114259303421121,0,0,0,0,0.0695819800362469,0,0.128122390065496,0,0,0,0,0,0,0.0962521000248044,0.0620032815069762,0.107433877051114,0.0523626705930769,0,0.0647775726819609,0,0,0,0.0956509830217012,0.181630511148827,0.0907590042666714,0,0,0,0.0472025886002021,0.0726509725142573,0.311540966384859,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.416114259418732,0.110593802369687,0,0,0,0.186702468492164,0,0,0.159915985962935,0,0,0,0,0,0.212087596895138,0,0,0,0.271826044133587,0,0,0,0,0,0,0,0.119982377365278,0,0,0,0,0,0,0,0,0.295534984847664,0,0.149064998316823,0.194686839862908,0,0,0,0,0,0,0,0,0,0,0,0,0,0.152965337431574,0.298391186510551,0,0,0,0,0,0.0749215657724743,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.273938122834731,0,0,0,0,0,0,0,0,0,0,0,0.0789089986057754,0.105947296040957,0,0,0,0,0,0,0,0.275953830919237,0,0,0,0.0739148182245154,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0455495587624001,0,0.0861409897892114,0,0,0.548924558112347,0,0,0,0,0,0,0.185552006688486,0,0,0,0,0,0,0,0,0,0,0,0,0.299999916441319,0.314181395507761,0.346755838223862,0,0,0,0.0549201943193819,0.624314134362568,0,0,0,0,0.252651317607602,0.344374029099016,0.115967372264001,0.329877359111492,0,0,0,0,0,0,0,0,0,0,0,0.31140628842589,0,0,0,0,0.199188387463198,0,0.161955095312168,0,0,0.119438670232611,0,0,0.927927238322024,0,0,0,0,0,0,0,0,0,0,0,0,0.0557243212092205,0,0,0,0.325747445195647,0.331589670039496,0,0,0,0,0.0547535628453514,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.189419004361671,0,0.0329432353726146,0.0222033657448865,0,0,0,0,0,0,0,0,0.12273585496983,0,0,0,0,0,0,0,0,0,0,0.084066558699748,0.118730395337086,0.26208976562482,0,0,0,0,0,0.0971496406207997,0.116058079104876,0.297458016950202,0,0,0.0500030232022126,0.243322253338365,0,0.0456863240084368,0.0261639379934246,0,0,0,0,0,0,0,0.16069789587836,0.166556393082458,0,0,0,0,0.089495363820231,0.205454389011787,0.117561082617775,0,0.0641946247847473,0,0,0.150666259251702,0.102379403318181,0,0,0,0,0,0.0443086593632396,0,0,0,0.128203955531532,0.126050026678357,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.191180892262599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0444710875952832,0,0,0.126931389473126,0.0837085814034122,0,0.3257803126894,0,0,0,0.231814006190654,0.116024799788948,0.0765267314685607,0,0.169939272094492,0.149290789502833,0,0.171463389605203,0.0650101077405693,0,0,0,0,0,0,0,0,0.138634732812718,0,0,0,0,0,0.10385512828298,0,0.261678447012981,0.0981808919059217,0,0,0.541710996386576,0,0,0,0,0,0.226080651425874,0.102470447803098,0,0,0.0285589446518912,0.101434673044707,0,0,0.21163965958111,0,0,0.572810769020978,0,0,0.268979913061351,0,0,0.409040712153991,0,0,0,0,0.155405081403798,0,0,0.153323010348428,0,0,0,0,0,0,1.02984755769928,0.80198416210409,0.521089531926469,0.171934336795599,0,0,0,0,0,0,0.141722741407519,0.0858467613960337,0,0.433935882190196,0,0.0778431765528363,0.112955512742184,0.15309981666883,0,0,0.0271284845789754,0,0,0,0,0,0.163974701329705,0.0581752393062885,0,0.127091007984939,0.157260487458867,0.184415109078388,0.137352534412557,0.164999540860188,0.156132999089005,0,0,0,0,0,0,0,0.114982674895531,0.103106967823645,0,0,0.600458376193772,0.385317825735311,0.0271819376754428,0.0261550693490902,0,0.0520373174384043,0.205840601244198,0.438025315062048,0.4847836737365,0.103601303525827,0.109541028439739,0.30059136907981,0,0,0,0,0,0.392151074962825,0.346487650381282,0.221611588102807,0.256500105195395,0
|full_id=C4208_skeletal_gall_throat_penis_tongue_diaphragm_smooth
|full_id=C4208_skeletal_gall_throat_penis_tongue_diaphragm_smooth
|id=C4208
|id=C4208

Revision as of 17:15, 12 September 2012


Full id: C4208_skeletal_gall_throat_penis_tongue_diaphragm_smooth



Phase1 CAGE Peaks

Hg19::chr2:240230851..240230861,-p12@HDAC4
Hg19::chr2:240230869..240230884,-p10@HDAC4
Hg19::chr2:240230890..240230920,-p3@HDAC4


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><br>

Cell Type
Ontology termp-valuen
fibroblast1.37e-0975
Uber Anatomy
Ontology termp-valuen
adult organism1.02e-35115
neural tube5.51e-1457
neural rod5.51e-1457
future spinal cord5.51e-1457
neural keel5.51e-1457
anterior neural tube9.17e-1442
regional part of forebrain1.84e-1341
forebrain1.84e-1341
future forebrain1.84e-1341
regional part of cerebral cortex2.82e-1322
regional part of brain4.04e-1359
neocortex1.23e-1220
telencephalon5.14e-1134
cerebral cortex9.39e-1125
pallium9.39e-1125
anterior region of body1.79e-10129
craniocervical region1.79e-10129
gray matter1.89e-1034
brain grey matter1.89e-1034
regional part of telencephalon2.05e-1033
cerebral hemisphere2.44e-1032
brain3.09e-1069
future brain3.09e-1069
organism subdivision5.59e-10365
head1.50e-09123
central nervous system1.54e-0982
multi-cellular organism1.61e-09659
neurectoderm2.51e-0990
neural plate3.31e-0986
presumptive neural plate3.31e-0986
regional part of nervous system4.39e-0994
nervous system4.39e-0994
organ3.66e-08511
tissue8.06e-08787
anatomical system1.52e-07625
anatomical group1.94e-07626
pre-chordal neural plate2.25e-0761
ectoderm2.56e-07173
presumptive ectoderm2.56e-07173
multi-tissue structure3.84e-07347
ectoderm-derived structure3.86e-07169


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
GATA2#2624312.7449317335540.0004829527704283790.0043768747301952



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:C4208&oldid=2139083"