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Coexpression cluster:C2599: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.81e-45!115;UBERON:0001049!3.67e-26!57;UBERON:0005068!3.67e-26!57;UBERON:0006241!3.67e-26!57;UBERON:0007135!3.67e-26!57;UBERON:0002616!3.38e-22!59;UBERON:0003080!3.49e-22!42;UBERON:0002780!9.46e-22!41;UBERON:0001890!9.46e-22!41;UBERON:0006240!9.46e-22!41;UBERON:0001017!3.23e-21!82;UBERON:0000955!3.40e-21!69;UBERON:0006238!3.40e-21!69;UBERON:0005743!2.15e-20!86;UBERON:0003075!1.83e-19!86;UBERON:0007284!1.83e-19!86;UBERON:0000073!5.58e-19!94;UBERON:0001016!5.58e-19!94;UBERON:0002346!3.10e-18!90;UBERON:0002020!2.86e-17!34;UBERON:0003528!2.86e-17!34;UBERON:0001893!3.45e-17!34;UBERON:0002791!1.28e-16!33;UBERON:0001869!6.00e-16!32;UBERON:0003056!1.44e-14!61;UBERON:0002619!6.81e-14!22;UBERON:0001950!1.28e-12!20;UBERON:0000956!9.33e-12!25;UBERON:0000203!9.33e-12!25;UBERON:0000153!1.46e-11!129;UBERON:0007811!1.46e-11!129;UBERON:0000033!7.95e-11!123;UBERON:0004121!1.26e-08!169;UBERON:0000924!3.04e-08!173;UBERON:0006601!3.04e-08!173;UBERON:0002308!3.58e-07!9;UBERON:0002420!3.58e-07!9;UBERON:0000125!3.58e-07!9;UBERON:0007245!3.58e-07!9;UBERON:0010009!3.58e-07!9;UBERON:0010011!3.58e-07!9;UBERON:0000454!3.58e-07!9
|ontology_enrichment_uberon=UBERON:0007023!3.81e-45!115;UBERON:0001049!3.67e-26!57;UBERON:0005068!3.67e-26!57;UBERON:0006241!3.67e-26!57;UBERON:0007135!3.67e-26!57;UBERON:0002616!3.38e-22!59;UBERON:0003080!3.49e-22!42;UBERON:0002780!9.46e-22!41;UBERON:0001890!9.46e-22!41;UBERON:0006240!9.46e-22!41;UBERON:0001017!3.23e-21!82;UBERON:0000955!3.40e-21!69;UBERON:0006238!3.40e-21!69;UBERON:0005743!2.15e-20!86;UBERON:0003075!1.83e-19!86;UBERON:0007284!1.83e-19!86;UBERON:0000073!5.58e-19!94;UBERON:0001016!5.58e-19!94;UBERON:0002346!3.10e-18!90;UBERON:0002020!2.86e-17!34;UBERON:0003528!2.86e-17!34;UBERON:0001893!3.45e-17!34;UBERON:0002791!1.28e-16!33;UBERON:0001869!6.00e-16!32;UBERON:0003056!1.44e-14!61;UBERON:0002619!6.81e-14!22;UBERON:0001950!1.28e-12!20;UBERON:0000956!9.33e-12!25;UBERON:0000203!9.33e-12!25;UBERON:0000153!1.46e-11!129;UBERON:0007811!1.46e-11!129;UBERON:0000033!7.95e-11!123;UBERON:0004121!1.26e-08!169;UBERON:0000924!3.04e-08!173;UBERON:0006601!3.04e-08!173;UBERON:0002308!3.58e-07!9;UBERON:0002420!3.58e-07!9;UBERON:0000125!3.58e-07!9;UBERON:0007245!3.58e-07!9;UBERON:0010009!3.58e-07!9;UBERON:0010011!3.58e-07!9;UBERON:0000454!3.58e-07!9
|tf_chipseq_enrich=BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.0436583206594117!GTF2B#2959;2:15.9719149671621:0.00563658572353722:0.0254751331305394!JUN#3725;3:9.38462189425225:0.00191899450203047:0.0112866963337028!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386999087893225!KAT2A#2648;1:154.0225:0.00647681994931104:0.0281260955794634!POLR3A#11128;1:84.7830275229358:0.0117428417771162:0.0428650048009589!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123853033765038
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}}
}}

Revision as of 12:01, 5 September 2012


Full id: C2599_pineal_pituitary_cerebellum_spinal_thalamus_parietal_hippocampus



Phase1 CAGE Peaks

Hg19::chr1:78470530..78470551,+p7@DNAJB4
Hg19::chr4:186317034..186317083,-p1@LRP2BP
Hg19::chr4:331318..331341,-p@chr4:331318..331341
-
Hg19::chr7:95174494..95174520,+p@chr7:95174494..95174520
+


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:0009408response to heat0.0137736177222909
GO:0009266response to temperature stimulus0.0153592627850831
GO:0006986response to unfolded protein0.0156171759566238
GO:0051789response to protein stimulus0.0156171759566238
GO:0031072heat shock protein binding0.0215856666907313
GO:0009628response to abiotic stimulus0.0290713032697566
GO:0051082unfolded protein binding0.030188354377766
GO:0009607response to biotic stimulus0.0381192540324227
GO:0006457protein folding0.0404160150686843



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 organism3.81e-45115
neural tube3.67e-2657
neural rod3.67e-2657
future spinal cord3.67e-2657
neural keel3.67e-2657
regional part of brain3.38e-2259
anterior neural tube3.49e-2242
regional part of forebrain9.46e-2241
forebrain9.46e-2241
future forebrain9.46e-2241
central nervous system3.23e-2182
brain3.40e-2169
future brain3.40e-2169
neural plate1.83e-1986
presumptive neural plate1.83e-1986
regional part of nervous system5.58e-1994
nervous system5.58e-1994
neurectoderm3.10e-1890
gray matter2.86e-1734
brain grey matter2.86e-1734
telencephalon3.45e-1734
regional part of telencephalon1.28e-1633
cerebral hemisphere6.00e-1632
pre-chordal neural plate1.44e-1461
regional part of cerebral cortex6.81e-1422
neocortex1.28e-1220
cerebral cortex9.33e-1225
pallium9.33e-1225
anterior region of body1.46e-11129
craniocervical region1.46e-11129
head7.95e-11123
ectoderm-derived structure1.26e-08169
ectoderm3.04e-08173
presumptive ectoderm3.04e-08173
nucleus of brain3.58e-079
basal ganglion3.58e-079
neural nucleus3.58e-079
nuclear complex of neuraxis3.58e-079
aggregate regional part of brain3.58e-079
collection of basal ganglia3.58e-079
cerebral subcortex3.58e-079


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCLAF1#9774210.82632380506090.01202203816432580.0436583206594117
GTF2B#2959215.97191496716210.005636585723537220.0254751331305394
JUN#372539.384621894252250.001918994502030470.0112866963337028
JUND#372735.245997956403270.01043432751748420.0386999087893225
KAT2A#26481154.02250.006476819949311040.0281260955794634
POLR3A#11128184.78302752293580.01174284177711620.0428650048009589
RFX5#599339.035933120396320.002144561191324070.0123853033765038



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.