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Coexpression cluster:C2656: Difference between revisions

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|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186339153672817!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000827381189889423!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322707798971594!TAL1#6886;2:14.9343083387201:0.00642807757788807:0.0279516193753457!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.0002303908413605
|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186339153672817!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000827381189889423!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322707798971594!TAL1#6886;2:14.9343083387201:0.00642807757788807:0.0279516193753457!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.0002303908413605
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}}
}}

Revision as of 15:38, 26 November 2012


Full id: C2656_Renal_lung_Lymphatic_kidney_medulla_Endothelial_uterus



Phase1 CAGE Peaks

Hg19::chr2:108994403..108994461,+p1@SULT1C4
Hg19::chr2:108994466..108994485,+p3@SULT1C4
Hg19::chr2:108994565..108994623,+p2@SULT1C4
Hg19::chr2:108994633..108994650,+p4@SULT1C4


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>

Uber Anatomy
Ontology termp-valuen
adult organism1.59e-48114
anatomical cluster1.49e-42373
central nervous system1.27e-3881
neural tube3.64e-3856
neural rod3.64e-3856
future spinal cord3.64e-3856
neural keel3.64e-3856
nervous system1.76e-3789
regional part of nervous system1.89e-3553
regional part of brain1.89e-3553
brain5.54e-3368
future brain5.54e-3368
neural plate1.98e-3282
presumptive neural plate1.98e-3282
organ system subdivision5.35e-30223
neurectoderm8.84e-3086
anatomical conduit4.34e-29240
tube2.20e-28192
regional part of forebrain7.05e-2741
forebrain7.05e-2741
anterior neural tube7.05e-2741
future forebrain7.05e-2741
pre-chordal neural plate4.47e-2261
multi-tissue structure5.61e-22342
brain grey matter6.25e-2234
gray matter6.25e-2234
ecto-epithelium1.10e-21104
telencephalon1.72e-2134
structure with developmental contribution from neural crest1.25e-20132
cell layer1.46e-20309
regional part of telencephalon3.29e-2032
cerebral hemisphere4.05e-2032
epithelium2.01e-19306
ectoderm-derived structure1.55e-18171
ectoderm1.55e-18171
presumptive ectoderm1.55e-18171
regional part of cerebral cortex8.18e-1622
cerebral cortex2.63e-1525
pallium2.63e-1525
cavitated compound organ4.91e-1531
multi-cellular organism9.21e-15656
embryo1.12e-14592
neocortex2.45e-1420
anatomical system3.65e-13624
anatomical group4.80e-13625
kidney6.42e-1326
kidney mesenchyme6.42e-1326
upper urinary tract6.42e-1326
kidney rudiment6.42e-1326
kidney field6.42e-1326
excretory tube6.60e-1316
kidney epithelium6.60e-1316
developing anatomical structure9.95e-13581
nephron epithelium2.44e-1215
renal tubule2.44e-1215
nephron tubule2.44e-1215
nephron2.44e-1215
uriniferous tubule2.44e-1215
nephrogenic mesenchyme2.44e-1215
posterior neural tube2.83e-1215
chordal neural plate2.83e-1215
organ part5.33e-12218
abdomen element2.95e-1154
abdominal segment element2.95e-1154
nephron tubule epithelium6.44e-1110
compound organ8.83e-1168
segmental subdivision of nervous system4.09e-1013
segmental subdivision of hindbrain1.06e-0912
hindbrain1.06e-0912
presumptive hindbrain1.06e-0912
organ1.17e-09503
renal system1.45e-0948
parenchyma1.47e-0915
cortex of kidney2.05e-0912
renal parenchyma2.05e-0912
urinary system structure3.47e-0947
abdominal segment of trunk4.83e-0960
abdomen4.83e-0960
embryonic structure3.30e-08564
neural nucleus3.41e-089
nucleus of brain3.41e-089
germ layer3.92e-08560
germ layer / neural crest3.92e-08560
embryonic tissue3.92e-08560
presumptive structure3.92e-08560
germ layer / neural crest derived structure3.92e-08560
epiblast (generic)3.92e-08560
basal ganglion1.32e-079
nuclear complex of neuraxis1.32e-079
aggregate regional part of brain1.32e-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
HEY1#2346244.040111043105710.00375304636917980.0186339153672817
RFX5#5993412.04791082719514.74457429336527e-050.000827381189889423
TAF1#687243.343046285745290.008005664898701650.0322707798971594
TAL1#6886214.93430833872010.006428077577888070.0279516193753457
TRIM28#10155418.59052504526258.36730015875654e-060.0002303908413605



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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