Personal tools

Coexpression cluster:C865: 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=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0609265521758115,0,0.615468340594955,0,0.549623379597346,0,0,1.09983000967811,1.2221599860199,0,1.13258145497373,1.08120474349356,0,0.990308074612325,0.837440949082098,0,1.00370457462974,1.13223152579341,0,1.13758569661616,0.584705813192504,0,0.575699610822564,1.24338950868166,0,1.29834872865473,1.21634944446998,0,1.0886409215053,1.11753610313502,0,1.16755493693665,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.06103375120506,0.126120892680167,0,0.385774909004834,0,0.241276208236673,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0300902972430133,0,0,0,0,0,0,0,0,0.075325458416784,0.128079986932476,0.025815943111336,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.838570824561316,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0339614479152723,0,0,0.154072694012943,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0285798987072652,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0716442562813891,0,0.0227747793812,0,0,0,0,0,0,0,0,0,0,0,0,0,0.143088749596172,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0391458894650656,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0800410362214332,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.058029039552438,0,0,0,0.0250015116011063,0.0485213324954163,0.098420842023517,0.0623803991784765,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.053013279722843,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0321604437118685,0,0,0,0.0607719272619985,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0407972803666135,0,0.0947416208466275,0,0,0,0,0,0,0,0,0.018454584201652,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0389215882764182,0.112955512742184,0.15309981666883,0,0,0,0.0206847260606282,0,0,0,0,0,0.0581752393062885,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0408295247396738,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C865_CD14_Neutrophils_Dendritic_placenta_cervical_epitheloid_spinal
|full_id=C865_CD14_Neutrophils_Dendritic_placenta_cervical_epitheloid_spinal
|gostat_on_coexpression_clusters=GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.000158559827157831!1438;3563$GO:0004912!interleukin-3 receptor activity!0.00153064978927681!3563$GO:0019978!interleukin-3 binding!0.00153064978927681!3563$GO:0004907!interleukin receptor activity!0.0183575242003379!3563$GO:0019965!interleukin binding!0.0183575242003379!3563$GO:0004888!transmembrane receptor activity!0.0230388577844583!1438;3563$GO:0019838!growth factor binding!0.028372121655368!3563$GO:0019955!cytokine binding!0.028372121655368!3563$GO:0004872!receptor activity!0.035793698202971!1438;3563$GO:0005057!receptor signaling protein activity!0.0387720512564269!3563$GO:0004871!signal transducer activity!0.0387720512564269!1438;3563$GO:0060089!molecular transducer activity!0.0387720512564269!1438;3563
|gostat_on_coexpression_clusters=GO:0004896!hematopoietin/interferon-class (D200-domain) cytokine receptor activity!0.000158559827157831!1438;3563$GO:0004912!interleukin-3 receptor activity!0.00153064978927681!3563$GO:0019978!interleukin-3 binding!0.00153064978927681!3563$GO:0004907!interleukin receptor activity!0.0183575242003379!3563$GO:0019965!interleukin binding!0.0183575242003379!3563$GO:0004888!transmembrane receptor activity!0.0230388577844583!1438;3563$GO:0019838!growth factor binding!0.028372121655368!3563$GO:0019955!cytokine binding!0.028372121655368!3563$GO:0004872!receptor activity!0.035793698202971!1438;3563$GO:0005057!receptor signaling protein activity!0.0387720512564269!3563$GO:0004871!signal transducer activity!0.0387720512564269!1438;3563$GO:0060089!molecular transducer activity!0.0387720512564269!1438;3563

Revision as of 18:37, 12 September 2012


Full id: C865_CD14_Neutrophils_Dendritic_placenta_cervical_epitheloid_spinal



Phase1 CAGE Peaks

Hg19::chrX:1367460..1367489,+p@chrX:1367460..1367489
+
Hg19::chrX:1368516..1368527,-p@chrX:1368516..1368527
-
Hg19::chrX:1387700..1387717,+p1@CSF2RA
Hg19::chrX:1387721..1387738,+p2@CSF2RA
Hg19::chrX:1393727..1393755,-p@chrX:1393727..1393755
-
Hg19::chrX:1393820..1393849,-p@chrX:1393820..1393849
-
Hg19::chrX:1435460..1435487,-p@chrX:1435460..1435487
-
Hg19::chrX:1435588..1435602,-p@chrX:1435588..1435602
-
Hg19::chrX:1455478..1455515,+p2@IL3RA
Hg19::chrX:24167737..24167762,-p1@ZFX-AS1


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


p.valueFDRnGenesnPathwayName
8.58567593366187e-050.01358683216501992265Cytokine-cytokine receptor interaction (KEGG):04060
2.92938943019595e-050.006181011697713452155Jak-STAT signaling pathway (KEGG):04630
9.39564536136585e-060.00297372175687229288Hematopoietic cell lineage (KEGG):04640
0.0003198274735665560.03374179846127162511Signaling in Immune system (Reactome):REACT_6900
1.91447319275479e-060.00121186153101378240IL-3 up reg. targets (Netpath):NetPath_15
0.0002017928378747890.02554697327494832406{GRB2,414} (Static Module):NA



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


GO IDGO nameFDR corrected p-value
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.000158559827157831
GO:0004912interleukin-3 receptor activity0.00153064978927681
GO:0019978interleukin-3 binding0.00153064978927681
GO:0004907interleukin receptor activity0.0183575242003379
GO:0019965interleukin binding0.0183575242003379
GO:0004888transmembrane receptor activity0.0230388577844583
GO:0019838growth factor binding0.028372121655368
GO:0019955cytokine binding0.028372121655368
GO:0004872receptor activity0.035793698202971
GO:0005057receptor signaling protein activity0.0387720512564269
GO:0004871signal transducer activity0.0387720512564269
GO:0060089molecular transducer activity0.0387720512564269



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>


Uber Anatomy
Ontology termp-valuen
neural tube5.17e-1357
neural rod5.17e-1357
future spinal cord5.17e-1357
neural keel5.17e-1357
female organism1.48e-1041
anterior neural tube6.11e-1042
regional part of forebrain2.70e-0941
forebrain2.70e-0941
future forebrain2.70e-0941
female reproductive organ2.92e-0937
female reproductive system2.92e-0937
regional part of brain3.22e-0959
gray matter1.47e-0834
brain grey matter1.47e-0834
central nervous system6.97e-0882
brain1.27e-0769
future brain1.27e-0769
neurectoderm3.74e-0790
neural plate4.83e-0786
presumptive neural plate4.83e-0786
regional part of telencephalon5.89e-0733
nucleus of brain5.96e-079
neural nucleus5.96e-079
internal female genitalia6.17e-0722
basal ganglion6.98e-079
nuclear complex of neuraxis6.98e-079
aggregate regional part of brain6.98e-079
collection of basal ganglia6.98e-079
cerebral subcortex6.98e-079
embryonic uterus7.98e-0722


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.