Personal tools

Coexpression cluster:C521: 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=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0534545700183436,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0672629396841865,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.475423511109794,0.597043007412413,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.294319102417383,0.192179422446085,0,0,0,0,0,0,0,0.128639412800133,0,0.129448189001493,0.275482132507796,0.448543479856398,0,0.191142455090553,0.112453380477913,0.0861409897892114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.14749292295537,0,0.0914082188667263,0,0,0,0,0,0.574570020807655,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0884836478019413,0,0,0.378913208241816,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.204234048342335,0.291887574016612,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.529647071424384,0.571017616680585,0.0647398703344467,0.055966461856338,0,0,0,0.222259863956614,0,0,0.0222033657448865,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.308407239003328,0.313415997354821,0,0,0,0.0634100406668813,0,0,0,0,0,0,0,0,0,0,0.442814589183038,0.295833118776159,0.588763599398668,0.196841684047034,0.300674046226905,0.137537165784479,0.056275291093238,0,0,0.109060369074458,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.662258988445571,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0522684293388448,0.0444710875952832,0,0.0450136346124787,0,0.0837085814034122,0,0,0,0,0,0,0,0.306996761979176,0.383270498593678,0.737967322411835,0.348440814002821,0.54663111263392,0.0818769814509043,0.491247276240672,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.224112249948063,0.524166813273861,0.634173736769137,0.196104937138093,0.772525108527498,0,0,0,0,0.18630690345421,0.223383639238987,0.206006581150341,0.226080651425874,0,0,0,0.207291642179277,0.123480492992954,0,0,0,0.322179819586062,0,0,0,0,0.0299826682885844,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0610613035651264,0,0,0,0,0,0.201103507940666,0.340084155963713,0.26606967772796,0,0,0,0,0,0,0,0,0,0.234693879865657,0,0.127091007984939,0.607932466634726,0,0,0,0,0,0,0,0,0,0,0,0,0.103106967823645,0.424610342996058,0.370074122374588,0,0,0,0,0,0,0.079946807131842,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C521_parietal_occipital_middle_amygdala_temporal_medial_hippocampus
|full_id=C521_parietal_occipital_middle_amygdala_temporal_medial_hippocampus
|id=C521
|id=C521

Revision as of 18:06, 12 September 2012


Full id: C521_parietal_occipital_middle_amygdala_temporal_medial_hippocampus



Phase1 CAGE Peaks

Hg19::chr10:117443073..117443076,+p@chr10:117443073..117443076
+
Hg19::chr10:117703137..117703140,+p@chr10:117703137..117703140
+
Hg19::chr10:14017810..14017839,-p@chr10:14017810..14017839
-
Hg19::chr10:14017899..14017911,-p@chr10:14017899..14017911
-
Hg19::chr10:83671380..83671394,+p@chr10:83671380..83671394
+
Hg19::chr10:84202570..84202575,+p@chr10:84202570..84202575
+
Hg19::chr10:84220744..84220762,+p@chr10:84220744..84220762
+
Hg19::chr10:84747563..84747567,+p@chr10:84747563..84747567
+
Hg19::chr10:87388190..87388201,-p@chr10:87388190..87388201
-
Hg19::chr11:84145959..84145962,-p@chr11:84145959..84145962
-
Hg19::chr11:88554509..88554513,-p@chr11:88554509..88554513
-
Hg19::chr11:88711638..88711642,-p@chr11:88711638..88711642
-
Hg19::chr12:126140345..126140356,+p5@TMEM132B
Hg19::chr22:50779073..50779082,-p@chr22:50779073..50779082
-
Hg19::chr2:80256787..80256791,+p@chr2:80256787..80256791
+
Hg19::chr4:62163400..62163404,+p@chr4:62163400..62163404
+
Hg19::chr8:133489594..133489598,-p@chr8:133489594..133489598
-


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
regional part of nervous system1.50e-3694
nervous system1.50e-3694
central nervous system7.83e-3682
neural tube1.16e-3057
neural rod1.16e-3057
future spinal cord1.16e-3057
neural keel1.16e-3057
brain7.03e-2969
future brain7.03e-2969
regional part of forebrain8.54e-2841
forebrain8.54e-2841
future forebrain8.54e-2841
anterior neural tube2.26e-2642
regional part of brain3.25e-2659
neurectoderm7.43e-2690
adult organism1.14e-25115
neural plate3.70e-2586
presumptive neural plate3.70e-2586
gray matter1.69e-2334
brain grey matter1.69e-2334
telencephalon2.05e-2334
regional part of telencephalon8.88e-2333
cerebral hemisphere3.32e-2232
pre-chordal neural plate2.78e-1961
ectoderm4.87e-19173
presumptive ectoderm4.87e-19173
ectoderm-derived structure2.78e-18169
cerebral cortex1.03e-1725
pallium1.03e-1725
regional part of cerebral cortex1.26e-1622
neocortex3.06e-1520
anterior region of body2.81e-13129
craniocervical region2.81e-13129
head3.35e-13123
basal ganglion2.46e-079
nuclear complex of neuraxis2.46e-079
aggregate regional part of brain2.46e-079
collection of basal ganglia2.46e-079
cerebral subcortex2.46e-079
tube2.67e-07194
nucleus of brain3.17e-079
neural nucleus3.17e-079
temporal lobe9.34e-077


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:C521&oldid=2139869"