Personal tools

Coexpression cluster:C1832: 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=0.134609515403383,0.268672049992273,0,0,0,0,0,0,0.362845769370742,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0587472679543123,0,0,0,0,0,0.101044953091069,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.210163845666834,0,0,0,0,0,0.117986819981215,0,0.113574834469897,0.0482220752390542,0,0,0.537800219225226,0,0.601674128907142,0,0,0,0,0,0.0511982733942606,0.191486849538524,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.285272754285256,0.23600275090536,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.660539583551993,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.20855662473171,0.132938760828427,0,0,0,0,0,0,0,0,0,0,0,0,0.0502604313716981,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0620189823948138,0,0.839359462366062,0.414168093591613,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0718350632709503,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123621336231306,0,0,0,0,0,0.0390744040629657,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.594410627417267,0,0,0,0,0,0,0.299757310563537,0.231303150876184,0,0,0,0.203507185739086,0,0,0,0,0,0,0,0,0.201904988352547,0,0,0.591954359268079,0.483001875756951,0,0,0,0.501743555404659,0,0,0,0,0,0,0.275482132507796,0.236431101238142,0,0.159060734356434,0.27568969562093,0.321583308753707,0,0,0.266338220705595,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.295134395235551,0,0,0,0,0.187297612104379,0,0.0914082188667263,0,0,0,0.144444803709627,0.344374029099016,0,0.993265175086862,0,0,0,0,0,0,0,0,0,0,0,0.379815373097718,0,0,0,0,0.0402022792589852,0,0.448373273252018,0,0,0.532220447716328,0,0,0.0840229578243582,0,0,0,0,0,0,0,0,0,0,0,0.204234048342335,0.105104912336182,0,0,0,0.545745101324563,0.163853084473343,0.498809233644789,0.0790650569133411,0.155100922768919,0.36903555894755,0.0797419986649781,0,0,0,0,0,0,0,0,0.148790834525069,0,0,0,0,0,0.527531008319266,0,0.118999338599371,0.343695178315023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.428244720256707,0.313415997354821,0,0,0,0,0,0,0,0,0,0.188652303681418,0.0971496406207997,0.116058079104876,0.12315641958565,0,0.442814589183038,0.470178173693846,0.602557227482913,0.517675704141427,0.159481831587408,0.466124161623123,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.377048286893918,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0680865676909136,0.0837085814034122,0.0507414909260677,0,0,0,0,0,0,0.415929517640787,0.823986671550837,0.48787903863257,0.421757040323494,0,0.687779133549719,0.554320779817192,0,0,0,0,0,0,0,0,0.204576464877444,0.0797978929983786,0,0,0,0,0.673441826181865,0.615351553325796,0.541609388679863,0.6759187593106,0.320966228024776,0,0.174992895090299,0,0,0.316264741738924,0.125898678133584,0.206006581150341,0,0.0369091684033041,0,0,0.462869853024152,0.632319458060227,0,0,0.118586233508558,0.322179819586062,0,0,0,0,0.646489412058764,0,0,0,0,0,0,0,0,0,0,0.153323010348428,0,0,0,0,0,0,0,0.0424427259395948,0,0.171934336795599,0.421205022607865,0,0,0,0,1.08533519814116,0.284676553291204,0.218976056853198,0,0.0952210875623146,0,0.49960367058877,0.276723497112124,0.548504194982,0,0,0,0,0,0,0,0,0,0.155341731682672,0,0.593688497886127,0,0.313456698449451,0,0.284284347934395,0,0,0,0,0,0,0,0,0.0612855891386548,0,0,0.150367083334639,0.214764912010815,0,0,0.0508240440617333,0,0.0520373174384043,0.147439601056333,0.0855462791577618,0,0,0.133095135155278,0.124719478691449,0,0,0,0,0,0.094988929438441,0.14826204992358,0,0.0796420028184954,0
|full_id=C1832_small_occipital_dura_postcentral_Skeletal_retina_paracentral
|full_id=C1832_small_occipital_dura_postcentral_Skeletal_retina_paracentral
|id=C1832
|id=C1832

Revision as of 14:27, 12 September 2012


Full id: C1832_small_occipital_dura_postcentral_Skeletal_retina_paracentral



Phase1 CAGE Peaks

Hg19::chr1:14219287..14219357,+p1@C1orf196
Hg19::chr1:14219382..14219413,+p2@C1orf196
Hg19::chr1:14220052..14220081,+p@chr1:14220052..14220081
+
Hg19::chr1:14220085..14220096,+p@chr1:14220085..14220096
+
Hg19::chr7:54610331..54610338,+p12@VSTM2A


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 organism7.78e-59115
neural tube1.63e-4057
neural rod1.63e-4057
future spinal cord1.63e-4057
neural keel1.63e-4057
anterior neural tube2.71e-3442
regional part of brain5.65e-3459
regional part of forebrain2.01e-3341
forebrain2.01e-3341
future forebrain2.01e-3341
central nervous system2.07e-3382
neurectoderm2.90e-3290
regional part of nervous system1.60e-3194
nervous system1.60e-3194
neural plate4.24e-3086
presumptive neural plate4.24e-3086
brain9.16e-3069
future brain9.16e-3069
gray matter1.21e-2834
brain grey matter1.21e-2834
telencephalon1.33e-2834
regional part of telencephalon1.42e-2733
cerebral hemisphere3.44e-2732
pre-chordal neural plate1.12e-2261
regional part of cerebral cortex2.56e-2222
cerebral cortex4.10e-2125
pallium4.10e-2125
neocortex1.02e-2020
ectoderm1.46e-20173
presumptive ectoderm1.46e-20173
anterior region of body1.09e-19129
craniocervical region1.09e-19129
head1.58e-19123
ectoderm-derived structure6.76e-19169
multi-tissue structure2.63e-12347
organism subdivision1.30e-10365
organ part4.90e-09219
nucleus of brain6.04e-099
neural nucleus6.04e-099
basal ganglion7.03e-099
nuclear complex of neuraxis7.03e-099
aggregate regional part of brain7.03e-099
collection of basal ganglia7.03e-099
cerebral subcortex7.03e-099
temporal lobe1.89e-087
brainstem2.92e-088
embryo3.39e-08612
multi-cellular organism4.83e-08659
posterior neural tube9.71e-0815
chordal neural plate9.71e-0815
cell layer1.06e-07312
gyrus1.65e-076
organ1.74e-07511
epithelium1.99e-07309
embryonic structure2.66e-07605
developing anatomical structure2.66e-07605
telencephalic nucleus3.60e-077
germ layer5.00e-07604
embryonic tissue5.00e-07604
presumptive structure5.00e-07604
epiblast (generic)5.00e-07604


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

No analysis results for this cluster

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:C1832&oldid=2136441"