Personal tools

Coexpression cluster:C614: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0008334!histone mRNA metabolic process!0.00309078064288237!6741$GO:0006400!tRNA modification!0.00700576945720005!6741$GO:0000049!tRNA binding!0.00700576945720005!6741$GO:0006383!transcription from RNA polymerase III promoter!0.00700576945720005!6741$GO:0003729!mRNA binding!0.00700576945720005!6741$GO:0009451!RNA modification!0.00772695160720593!6741$GO:0008033!tRNA processing!0.0135405628164371!6741$GO:0006399!tRNA metabolic process!0.0280745908395149!6741$GO:0016071!mRNA metabolic process!0.0391498881431767!6741
|gostat_on_coexpression_clusters=GO:0008334!histone mRNA metabolic process!0.00309078064288237!6741$GO:0006400!tRNA modification!0.00700576945720005!6741$GO:0000049!tRNA binding!0.00700576945720005!6741$GO:0006383!transcription from RNA polymerase III promoter!0.00700576945720005!6741$GO:0003729!mRNA binding!0.00700576945720005!6741$GO:0009451!RNA modification!0.00772695160720593!6741$GO:0008033!tRNA processing!0.0135405628164371!6741$GO:0006399!tRNA metabolic process!0.0280745908395149!6741$GO:0016071!mRNA metabolic process!0.0391498881431767!6741
|id=C614
|id=C614
|ontology_enrichment_celltype=CL:0000055!2.28e-10!180;CL:0000057!5.86e-10!75;CL:0000136!4.08e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.62e-14!57;UBERON:0005068!1.62e-14!57;UBERON:0006241!1.62e-14!57;UBERON:0007135!1.62e-14!57;UBERON:0002616!1.12e-13!59;UBERON:0003075!8.11e-13!86;UBERON:0007284!8.11e-13!86;UBERON:0000073!1.87e-12!94;UBERON:0001016!1.87e-12!94;UBERON:0005743!2.21e-12!86;UBERON:0001017!2.47e-12!82;UBERON:0002346!1.42e-11!90;UBERON:0000955!2.06e-11!69;UBERON:0006238!2.06e-11!69;UBERON:0000475!2.79e-10!365;UBERON:0000153!3.92e-10!129;UBERON:0007811!3.92e-10!129;UBERON:0000033!4.79e-10!123;UBERON:0004121!1.53e-09!169;UBERON:0003080!2.93e-09!42;UBERON:0000924!7.06e-09!173;UBERON:0006601!7.06e-09!173;UBERON:0002780!1.02e-08!41;UBERON:0001890!1.02e-08!41;UBERON:0006240!1.02e-08!41;UBERON:0000481!2.69e-08!347;UBERON:0003056!2.77e-08!61;UBERON:0002020!7.03e-08!34;UBERON:0003528!7.03e-08!34;UBERON:0001893!1.53e-07!34;UBERON:0000468!1.79e-07!659;UBERON:0002791!2.37e-07!33;UBERON:0007023!3.81e-07!115;UBERON:0003076!6.08e-07!15;UBERON:0003057!6.08e-07!15;UBERON:0001869!7.20e-07!32
}}
}}

Revision as of 14:55, 21 May 2012


Full id: C614_bone_mesenchymal_basal_mesodermal_Adipocyte_mature_Myoblast



Phase1 CAGE Peaks

Hg19::chr10:132684824..132684837,+p@chr10:132684824..132684837
+
Hg19::chr11:24518419..24518445,+p3@LUZP2
Hg19::chr14:102704788..102704801,-p10@MOK
Hg19::chr14:102704806..102704814,-p26@MOK
Hg19::chr14:102704830..102704841,-p25@MOK
Hg19::chr14:36645620..36645634,-p6@ENST00000556013
Hg19::chr14:36645880..36645891,-p7@ENST00000556013
Hg19::chr14:36645917..36645934,-p3@ENST00000556013
Hg19::chr2:170665139..170665155,+p5@SSB
Hg19::chr2:170665157..170665172,+p8@SSB
Hg19::chr2:221311010..221311014,+p@chr2:221311010..221311014
+
Hg19::chr5:121490583..121490596,-p1@ENST00000504829
Hg19::chr7:20784945..20784950,+p@chr7:20784945..20784950
+
Hg19::chr7:68782112..68782118,+p@chr7:68782112..68782118
+


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


GO IDGO nameFDR corrected p-value
GO:0008334histone mRNA metabolic process0.00309078064288237
GO:0006400tRNA modification0.00700576945720005
GO:0000049tRNA binding0.00700576945720005
GO:0006383transcription from RNA polymerase III promoter0.00700576945720005
GO:0003729mRNA binding0.00700576945720005
GO:0009451RNA modification0.00772695160720593
GO:0008033tRNA processing0.0135405628164371
GO:0006399tRNA metabolic process0.0280745908395149
GO:0016071mRNA metabolic process0.0391498881431767



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
non-terminally differentiated cell2.28e-10180
fibroblast5.86e-1075
fat cell4.08e-0715
Uber Anatomy
Ontology termp-valuen
neural tube1.62e-1457
neural rod1.62e-1457
future spinal cord1.62e-1457
neural keel1.62e-1457
regional part of brain1.12e-1359
neural plate8.11e-1386
presumptive neural plate8.11e-1386
regional part of nervous system1.87e-1294
nervous system1.87e-1294
central nervous system2.47e-1282
neurectoderm1.42e-1190
brain2.06e-1169
future brain2.06e-1169
organism subdivision2.79e-10365
anterior region of body3.92e-10129
craniocervical region3.92e-10129
head4.79e-10123
ectoderm-derived structure1.53e-09169
anterior neural tube2.93e-0942
ectoderm7.06e-09173
presumptive ectoderm7.06e-09173
regional part of forebrain1.02e-0841
forebrain1.02e-0841
future forebrain1.02e-0841
multi-tissue structure2.69e-08347
pre-chordal neural plate2.77e-0861
gray matter7.03e-0834
brain grey matter7.03e-0834
telencephalon1.53e-0734
multi-cellular organism1.79e-07659
regional part of telencephalon2.37e-0733
adult organism3.81e-07115
posterior neural tube6.08e-0715
chordal neural plate6.08e-0715
cerebral hemisphere7.20e-0732


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.