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Coexpression cluster:C1381: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.91e-48!115;UBERON:0001049!1.17e-30!57;UBERON:0005068!1.17e-30!57;UBERON:0006241!1.17e-30!57;UBERON:0007135!1.17e-30!57;UBERON:0001017!2.84e-26!82;UBERON:0002616!5.20e-26!59;UBERON:0000955!1.60e-25!69;UBERON:0006238!1.60e-25!69;UBERON:0000073!3.40e-25!94;UBERON:0001016!3.40e-25!94;UBERON:0005743!5.49e-25!86;UBERON:0003080!5.78e-24!42;UBERON:0002780!6.51e-24!41;UBERON:0001890!6.51e-24!41;UBERON:0006240!6.51e-24!41;UBERON:0002346!2.37e-20!90;UBERON:0001893!1.93e-19!34;UBERON:0002020!2.44e-19!34;UBERON:0003528!2.44e-19!34;UBERON:0003075!2.51e-19!86;UBERON:0007284!2.51e-19!86;UBERON:0002791!8.00e-19!33;UBERON:0001869!4.51e-18!32;UBERON:0003056!5.18e-15!61;UBERON:0000153!7.35e-15!129;UBERON:0007811!7.35e-15!129;UBERON:0002619!2.68e-14!22;UBERON:0000956!1.08e-13!25;UBERON:0000203!1.08e-13!25;UBERON:0000924!4.57e-13!173;UBERON:0006601!4.57e-13!173;UBERON:0001950!4.59e-13!20;UBERON:0000033!7.41e-13!123;UBERON:0004121!3.16e-12!169;UBERON:0003076!7.58e-08!15;UBERON:0003057!7.58e-08!15;UBERON:0002308!3.43e-07!9;UBERON:0000125!3.43e-07!9;UBERON:0002420!3.64e-07!9;UBERON:0007245!3.64e-07!9;UBERON:0010009!3.64e-07!9;UBERON:0010011!3.64e-07!9;UBERON:0000454!3.64e-07!9;UBERON:0004732!9.43e-07!13
|ontology_enrichment_uberon=UBERON:0007023!2.91e-48!115;UBERON:0001049!1.17e-30!57;UBERON:0005068!1.17e-30!57;UBERON:0006241!1.17e-30!57;UBERON:0007135!1.17e-30!57;UBERON:0001017!2.84e-26!82;UBERON:0002616!5.20e-26!59;UBERON:0000955!1.60e-25!69;UBERON:0006238!1.60e-25!69;UBERON:0000073!3.40e-25!94;UBERON:0001016!3.40e-25!94;UBERON:0005743!5.49e-25!86;UBERON:0003080!5.78e-24!42;UBERON:0002780!6.51e-24!41;UBERON:0001890!6.51e-24!41;UBERON:0006240!6.51e-24!41;UBERON:0002346!2.37e-20!90;UBERON:0001893!1.93e-19!34;UBERON:0002020!2.44e-19!34;UBERON:0003528!2.44e-19!34;UBERON:0003075!2.51e-19!86;UBERON:0007284!2.51e-19!86;UBERON:0002791!8.00e-19!33;UBERON:0001869!4.51e-18!32;UBERON:0003056!5.18e-15!61;UBERON:0000153!7.35e-15!129;UBERON:0007811!7.35e-15!129;UBERON:0002619!2.68e-14!22;UBERON:0000956!1.08e-13!25;UBERON:0000203!1.08e-13!25;UBERON:0000924!4.57e-13!173;UBERON:0006601!4.57e-13!173;UBERON:0001950!4.59e-13!20;UBERON:0000033!7.41e-13!123;UBERON:0004121!3.16e-12!169;UBERON:0003076!7.58e-08!15;UBERON:0003057!7.58e-08!15;UBERON:0002308!3.43e-07!9;UBERON:0000125!3.43e-07!9;UBERON:0002420!3.64e-07!9;UBERON:0007245!3.64e-07!9;UBERON:0010009!3.64e-07!9;UBERON:0010011!3.64e-07!9;UBERON:0000454!3.64e-07!9;UBERON:0004732!9.43e-07!13
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}}
}}

Revision as of 13:17, 5 September 2012


Full id: C1381_corpus_thyroid_cerebellum_pineal_thalamus_pituitary_substantia



Phase1 CAGE Peaks

Hg19::chr13:41495851..41495883,-p1@SUGT1P3
Hg19::chr19:40502938..40502987,+p1@ZNF546
Hg19::chr22:38577782..38577858,-p1@PLA2G6
Hg19::chr2:203776982..203777014,+p1@ALS2CR8
Hg19::chr2:232646379..232646423,+p3@COPS7B
Hg19::chr4:74124877..74124918,+p1@ENST00000502790


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell4.57e-1252
lymphocyte5.02e-1253
common lymphoid progenitor5.02e-1253
mature alpha-beta T cell3.34e-0818
alpha-beta T cell3.34e-0818
immature T cell3.34e-0818
mature T cell3.34e-0818
immature alpha-beta T cell3.34e-0818
T cell1.48e-0725
pro-T cell1.48e-0725
Uber Anatomy
Ontology termp-valuen
adult organism2.91e-48115
neural tube1.17e-3057
neural rod1.17e-3057
future spinal cord1.17e-3057
neural keel1.17e-3057
central nervous system2.84e-2682
regional part of brain5.20e-2659
brain1.60e-2569
future brain1.60e-2569
regional part of nervous system3.40e-2594
nervous system3.40e-2594
anterior neural tube5.78e-2442
regional part of forebrain6.51e-2441
forebrain6.51e-2441
future forebrain6.51e-2441
neurectoderm2.37e-2090
telencephalon1.93e-1934
gray matter2.44e-1934
brain grey matter2.44e-1934
neural plate2.51e-1986
presumptive neural plate2.51e-1986
regional part of telencephalon8.00e-1933
cerebral hemisphere4.51e-1832
pre-chordal neural plate5.18e-1561
anterior region of body7.35e-15129
craniocervical region7.35e-15129
regional part of cerebral cortex2.68e-1422
cerebral cortex1.08e-1325
pallium1.08e-1325
ectoderm4.57e-13173
presumptive ectoderm4.57e-13173
neocortex4.59e-1320
head7.41e-13123
ectoderm-derived structure3.16e-12169
posterior neural tube7.58e-0815
chordal neural plate7.58e-0815
nucleus of brain3.43e-079
neural nucleus3.43e-079
basal ganglion3.64e-079
nuclear complex of neuraxis3.64e-079
aggregate regional part of brain3.64e-079
collection of basal ganglia3.64e-079
cerebral subcortex3.64e-079
segmental subdivision of nervous system9.43e-0713


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
ATF3#467311.23158726300440.001593459971184230.0100403840682057
E2F1#186964.907389214879327.15746523583771e-050.00112679908315595
ELF1#199764.258097958807540.0001677224776288830.00205210494858047
ELK4#200538.117840829234010.004056113134185760.0194079076199765
FOXA1#316935.540709874692730.01192178777860280.0433787267466641
GABPB1#255355.889736530151810.0003000175973670210.00309834251472504
HEY1#2346264.040111043105710.0002298968555807510.00253085250342553
MAX#414944.301703672671410.006644923910676370.028296061661385
NFKB1#479054.57338618682820.00102196259371130.00724397660680155
NRF1#489948.140186298473940.0005892175548383380.00493482696148846
PAX5#507944.446377020785220.005874733519240790.0263609578524592
POLR2A#543062.147453176558070.01019570676818780.0380106168045537
POU2F2#545246.070749371828350.001815326209524520.0108935218338618
SIX5#147912514.23892946288253.91539088341565e-060.000127508421725303
SREBF2#6721172.82387706855790.01365361575289130.0481697792661626
SRF#672249.19811884144520.0003672404582485860.00365766032987069
TAF1#687263.343046285745290.0007162474284635620.0057290468852957
TBP#690863.706770687096390.000385416472907960.00377674151004264
TCF7L2#693435.385088281568670.01290488779931040.046404544032233
YY1#752854.092642291544880.001743365462849530.0107248245022408
ZBTB33#10009210.55490834332710.01374250737140590.0483853193325779
ZNF143#7702511.25073046018991.25426047727876e-050.000309239164274119
ZNF263#1012745.481227758007120.002675609380607230.0147445107693773



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.

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