Personal tools

Coexpression cluster:C1639: 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:0019841!retinol binding!0.00600211739638302!116362$GO:0016918!retinal binding!0.00600211739638302!116362$GO:0005501!retinoid binding!0.00600211739638302!116362$GO:0019840!isoprenoid binding!0.00600211739638302!116362$GO:0005496!steroid binding!0.0239604357212903!4250
|gostat_on_coexpression_clusters=GO:0019841!retinol binding!0.00600211739638302!116362$GO:0016918!retinal binding!0.00600211739638302!116362$GO:0005501!retinoid binding!0.00600211739638302!116362$GO:0019840!isoprenoid binding!0.00600211739638302!116362$GO:0005496!steroid binding!0.0239604357212903!4250
|id=C1639
|id=C1639
|ontology_enrichment_celltype=CL:0002057!2.12e-20!42;CL:0000860!1.65e-17!45;CL:0000766!2.41e-15!76;CL:0002194!1.62e-12!63;CL:0000576!1.62e-12!63;CL:0000040!1.62e-12!63;CL:0000559!1.62e-12!63;CL:0000839!2.15e-12!70;CL:0000557!1.62e-11!71;CL:0002009!1.82e-11!65
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.25e-45!115;UBERON:0000062!2.11e-15!511;UBERON:0003075!1.27e-12!86;UBERON:0007284!1.27e-12!86;UBERON:0000468!1.36e-12!659;UBERON:0000922!1.44e-12!612;UBERON:0001049!2.13e-12!57;UBERON:0005068!2.13e-12!57;UBERON:0006241!2.13e-12!57;UBERON:0007135!2.13e-12!57;UBERON:0002346!8.31e-12!90;UBERON:0000467!2.44e-11!625;UBERON:0000480!3.76e-11!626;UBERON:0002050!5.37e-11!605;UBERON:0005423!5.37e-11!605;UBERON:0000923!1.16e-10!604;UBERON:0005291!1.16e-10!604;UBERON:0006598!1.16e-10!604;UBERON:0002532!1.16e-10!604;UBERON:0002390!1.20e-10!102;UBERON:0003061!1.20e-10!102;UBERON:0003080!1.46e-10!42;UBERON:0002193!2.57e-10!112;UBERON:0002780!5.81e-10!41;UBERON:0001890!5.81e-10!41;UBERON:0006240!5.81e-10!41;UBERON:0005743!7.33e-10!86;UBERON:0002616!1.01e-09!59;UBERON:0000073!1.97e-09!94;UBERON:0001016!1.97e-09!94;UBERON:0003056!4.73e-09!61;UBERON:0001017!7.88e-09!82;UBERON:0001893!5.85e-08!34;UBERON:0002020!5.87e-08!34;UBERON:0003528!5.87e-08!34;UBERON:0002371!7.19e-08!80;UBERON:0000955!9.76e-08!69;UBERON:0006238!9.76e-08!69;UBERON:0002791!9.99e-08!33;UBERON:0001474!1.14e-07!86;UBERON:0000153!3.23e-07!129;UBERON:0007811!3.23e-07!129;UBERON:0001869!4.29e-07!32;UBERON:0002405!7.40e-07!115
}}
}}

Revision as of 14:14, 21 May 2012


Full id: C1639_breast_small_left_adipose_cervix_thyroid_vagina



Phase1 CAGE Peaks

Hg19::chr11:62009704..62009716,+p2@SCGB1D2
Hg19::chr11:62037622..62037637,+p1@SCGB2A2
Hg19::chr1:10057278..10057296,+p1@RBP7
Hg19::chr3:186575556..186575565,+p@chr3:186575556..186575565
+
Hg19::chr3:186575653..186575676,+p@chr3:186575653..186575676
+


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:0019841retinol binding0.00600211739638302
GO:0016918retinal binding0.00600211739638302
GO:0005501retinoid binding0.00600211739638302
GO:0019840isoprenoid binding0.00600211739638302
GO:0005496steroid binding0.0239604357212903



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
adult organism9.25e-45115
organ2.11e-15511
neural plate1.27e-1286
presumptive neural plate1.27e-1286
multi-cellular organism1.36e-12659
embryo1.44e-12612
neural tube2.13e-1257
neural rod2.13e-1257
future spinal cord2.13e-1257
neural keel2.13e-1257
neurectoderm8.31e-1290
anatomical system2.44e-11625
anatomical group3.76e-11626
embryonic structure5.37e-11605
developing anatomical structure5.37e-11605
germ layer1.16e-10604
embryonic tissue1.16e-10604
presumptive structure1.16e-10604
epiblast (generic)1.16e-10604
hematopoietic system1.20e-10102
blood island1.20e-10102
anterior neural tube1.46e-1042
hemolymphoid system2.57e-10112
regional part of forebrain5.81e-1041
forebrain5.81e-1041
future forebrain5.81e-1041
regional part of brain1.01e-0959
regional part of nervous system1.97e-0994
nervous system1.97e-0994
pre-chordal neural plate4.73e-0961
central nervous system7.88e-0982
telencephalon5.85e-0834
gray matter5.87e-0834
brain grey matter5.87e-0834
bone marrow7.19e-0880
brain9.76e-0869
future brain9.76e-0869
regional part of telencephalon9.99e-0833
bone element1.14e-0786
anterior region of body3.23e-07129
craniocervical region3.23e-07129
cerebral hemisphere4.29e-0732
immune system7.40e-07115


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.