Personal tools

Coexpression cluster:C4768: 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=0.0724992894770213,0.0842546465117019,0.107857131651075,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.12301741567642,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0382424828832804,0,0,0,0,0,0,0,0,0.0540496261796572,0.0907474205905807,0.0428357178336246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.198416571487356,0,0,0,0,0,0,0.0983303062134256,0,0,0.0672629396841865,0,0,0,0,0,0,0,0.0820564584332857,0.351990019608733,0.168234365485179,0.287159062945695,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.107433877051114,0,0,0.0647775726819609,0,0,0,0,0,0,0,0,0,0,0,0,0.161727153872444,0.0322218878591601,0,0,0.0831811723542952,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0813768443325499,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0763454992192642,0.0521599633818348,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0749215657724743,0,0,0,0,0,0,0,0,0,0,0,0,0,0.466119888327111,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.205962528165281,0,0,0,0,0,0.299757310563537,0.429434595592722,0,0,0,0.476031239464761,0,0,0,0,0,0,0,0,0,0,0,0.294319102417383,0.241084245299456,0.476561809887893,0,0.0700082966122911,0,0,0,0,0,0,0,0.563151579795656,0.629012215584503,0.851458289343876,0.56275692344526,0.338892655961145,0.440134714936437,0,0,0.0902054036215435,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.212984640524252,0.516569655263704,0,0,0,0,0,0,0,0,0.470503523007975,0,0.421579434615254,0,0,0,0,0,0.79261837041552,0.139601892201172,0,0.181397909488661,0,0,0,0,0.10877114496491,0,0.0695052016201444,0,0,0.379815373097718,0,0,0,0,0.110915157511936,0,0,0,0,0.260796280542386,0,0,0.154395360924333,0,0,0,0,0,0,0,0,0,0,0,0,0.105104912336182,0,0,0,0.106966425460878,0.331589670039496,0,0,0,0,0,0,0,0,0,0,0,0,0.254120022070344,0.538028174525565,0.0647398703344467,0,0,0,0,0.390579998569408,0,0.0329432353726146,0.0827201683234173,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.468235691366243,0.412761378362978,0,0,0.481293658407467,0.862618625539808,0.591028234724802,0,0,0,0,0.319737900306467,0.44009468684032,0.207551203618446,0.297458016950202,0,0.563267984373557,0.206861299127516,0.273310730353101,0.647427490269002,0.647265635836658,0.374036925218422,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.114765010550142,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.191180892262599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.382565052411727,0,0.169939272094492,0.208266392091069,0.762630723308804,0.210162025788965,0.257049046425766,0,0,0,0,0,0,0,0,0.243559703503748,0,0,0,0,0,0.257786778796628,0.250682963288844,0.209531203640986,0.261121380571535,0.878734163446933,0.18984326733154,0,0,0,0.316264741738924,0,0.206006581150341,0.226080651425874,0,0,0,0.482743845799885,0.236411416052035,0,0,0.21163965958111,0.353517073244492,0,0,0,0,0.196400697720283,0,0,0,0,0,0,0,0,0,0,0,0.227197610169401,0,0,0,0,0,0,0.0424427259395948,0,0.171934336795599,0,0,0,0,0,0,0,0,0,0.0952210875623146,0,0.251695117438976,0.202513600396907,0.42985283584002,0,0,0,0,0,0,0,0,0,0.234693879865657,0,0.259091422156153,0.824292420924008,0,0,0,0,0.0516025752814806,0.0450355340939671,0,0.0421771923324582,0,0,0,0.0889635065466152,0,0.262253936867136,0.486948760621187,0.214764912010815,0.092743246865863,0,0.0508240440617333,0,0.0267975841371139,0,0.0855462791577618,0,0,0.36002503176398,0,0,0,0,0,0,0.0500863030838633,0.14826204992358,0,0.146917605400546,0
|full_id=C4768_lung_parietal_cerebellum_occipital_temporal_duodenum_medulla
|full_id=C4768_lung_parietal_cerebellum_occipital_temporal_duodenum_medulla
|id=C4768
|id=C4768

Revision as of 17:54, 12 September 2012


Full id: C4768_lung_parietal_cerebellum_occipital_temporal_duodenum_medulla



Phase1 CAGE Peaks

Hg19::chr8:69242969..69242990,+p3@C8orf34
Hg19::chr8:69243002..69243020,+p2@C8orf34
Hg19::chr8:69243028..69243043,+p4@C8orf34


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.68e-55115
neural tube4.75e-4957
neural rod4.75e-4957
future spinal cord4.75e-4957
neural keel4.75e-4957
central nervous system1.28e-4182
regional part of brain3.14e-4059
regional part of forebrain4.93e-3941
forebrain4.93e-3941
future forebrain4.93e-3941
anterior neural tube9.03e-3842
brain1.97e-3669
future brain1.97e-3669
neural plate3.43e-3686
presumptive neural plate3.43e-3686
regional part of nervous system1.58e-3494
nervous system1.58e-3494
neurectoderm1.17e-3390
gray matter7.94e-3234
brain grey matter7.94e-3234
telencephalon1.05e-3134
regional part of telencephalon1.28e-3033
cerebral hemisphere2.13e-2932
pre-chordal neural plate2.63e-2461
regional part of cerebral cortex2.69e-2422
cerebral cortex6.12e-2425
pallium6.12e-2425
neocortex4.58e-2220
anterior region of body9.67e-22129
craniocervical region9.67e-22129
ectoderm-derived structure1.51e-21169
ectoderm1.65e-20173
presumptive ectoderm1.65e-20173
head4.14e-20123
organism subdivision4.74e-14365
posterior neural tube4.39e-1215
chordal neural plate4.39e-1215
anatomical conduit8.50e-12241
tube1.25e-11194
anatomical cluster4.38e-10286
nucleus of brain2.87e-099
neural nucleus2.87e-099
basal ganglion3.90e-099
nuclear complex of neuraxis3.90e-099
aggregate regional part of brain3.90e-099
collection of basal ganglia3.90e-099
cerebral subcortex3.90e-099
segmental subdivision of hindbrain5.82e-0912
hindbrain5.82e-0912
presumptive hindbrain5.82e-0912
diencephalon1.11e-087
future diencephalon1.11e-087
brainstem1.26e-088
epithelium1.77e-08309
cell layer3.46e-08312
organ3.46e-08511
segmental subdivision of nervous system4.59e-0813
gyrus4.91e-086
multi-tissue structure5.14e-08347
multi-cellular organism5.66e-08659
temporal lobe5.90e-087
embryo7.66e-08612
organ part2.12e-07219
limbic system2.89e-075
parietal lobe4.02e-075
telencephalic nucleus6.61e-077
occipital lobe8.79e-075


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#1066435.360256373075030.0064925092527670.0281532561282846



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:C4768&oldid=2139704"