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Coexpression cluster:C888: Difference between revisions

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|full_id=C888_uterus_dura_CD14_mature_epididymis_prostate_cervix
|full_id=C888_uterus_dura_CD14_mature_epididymis_prostate_cervix
|id=C888
|id=C888
|ontology_enrichment_celltype=CL:0000136!2.75e-09!15
|ontology_enrichment_celltype=CL:0000136!8.43e-15!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.14e-38!115;UBERON:0001049!4.84e-13!57;UBERON:0005068!4.84e-13!57;UBERON:0006241!4.84e-13!57;UBERON:0007135!4.84e-13!57;UBERON:0003080!9.74e-12!42;UBERON:0001893!2.77e-11!34;UBERON:0002780!3.53e-11!41;UBERON:0001890!3.53e-11!41;UBERON:0006240!3.53e-11!41;UBERON:0001017!3.53e-11!82;UBERON:0002020!4.21e-11!34;UBERON:0003528!4.21e-11!34;UBERON:0002791!6.51e-11!33;UBERON:0001869!8.77e-11!32;UBERON:0005743!1.89e-10!86;UBERON:0002616!2.17e-10!59;UBERON:0000956!7.44e-10!25;UBERON:0000203!7.44e-10!25;UBERON:0002346!1.14e-09!90;UBERON:0000073!1.66e-09!94;UBERON:0001016!1.66e-09!94;UBERON:0002619!1.88e-09!22;UBERON:0000955!4.94e-09!69;UBERON:0006238!4.94e-09!69;UBERON:0003075!7.48e-09!86;UBERON:0007284!7.48e-09!86;UBERON:0001950!9.30e-09!20
|ontology_enrichment_uberon=UBERON:0007023!7.82e-48!114;UBERON:0002619!2.44e-11!22;UBERON:0001869!9.13e-11!32;UBERON:0001893!9.69e-11!34;UBERON:0001049!1.04e-10!56;UBERON:0005068!1.04e-10!56;UBERON:0006241!1.04e-10!56;UBERON:0007135!1.04e-10!56;UBERON:0003528!1.33e-10!34;UBERON:0002020!1.33e-10!34;UBERON:0001950!3.55e-10!20;UBERON:0004457!8.80e-10!12;UBERON:0000042!8.80e-10!12;UBERON:0002791!9.48e-10!32;UBERON:0002780!1.79e-09!41;UBERON:0001890!1.79e-09!41;UBERON:0003080!1.79e-09!41;UBERON:0006240!1.79e-09!41;UBERON:0000956!2.03e-09!25;UBERON:0000203!2.03e-09!25;UBERON:0000073!3.08e-09!53;UBERON:0002616!3.08e-09!53;UBERON:0011216!4.33e-09!223;UBERON:0001017!4.06e-08!81;UBERON:0001016!5.64e-08!89;UBERON:0002346!8.57e-08!86;UBERON:0003075!2.77e-07!82;UBERON:0007284!2.77e-07!82;UBERON:0003688!3.03e-07!6;UBERON:0002358!3.03e-07!6;UBERON:0003684!3.03e-07!6;UBERON:0001178!3.03e-07!6;UBERON:0000955!3.55e-07!68;UBERON:0006238!3.55e-07!68;UBERON:0010314!7.26e-07!132
|tf_chipseq_enrich=CCNT2#905;7:4.92815678208205:6.52167806614696e-05:0.00105878677996319!CEBPB#1051;7:6.19978148675264:1.39459740509258e-05:0.000336452664334637!CTCF#10664;7:4.16908829016947:0.000198281216330048:0.0023810845064153!GATA2#2624;7:9.9127246816531:5.71014888882728e-07:2.6329458710827e-05!NRF1#4899;7:9.49688401488626:7.65865712776971e-07:3.36500837933168e-05!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425775098357299!RAD21#5885;7:8.05391525202159:2.36147727378579e-06:8.37738875668866e-05!SRF#6722;7:10.7311386483527:3.31352184322677e-07:1.65737982655537e-05!TAL1#6886;7:23.2311463046757:1.59434073890572e-09:1.40279151163078e-07
|tf_chipseq_enrich=CCNT2#905;7:4.92815678208205:6.52167806614696e-05:0.00105878677996319!CEBPB#1051;7:6.19978148675264:1.39459740509258e-05:0.000336452664334637!CTCF#10664;7:4.16908829016947:0.000198281216330048:0.0023810845064153!GATA2#2624;7:9.9127246816531:5.71014888882728e-07:2.6329458710827e-05!NRF1#4899;7:9.49688401488626:7.65865712776971e-07:3.36500837933168e-05!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425775098357299!RAD21#5885;7:8.05391525202159:2.36147727378579e-06:8.37738875668866e-05!SRF#6722;7:10.7311386483527:3.31352184322677e-07:1.65737982655537e-05!TAL1#6886;7:23.2311463046757:1.59434073890572e-09:1.40279151163078e-07
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}}
}}

Revision as of 16:49, 19 October 2012


Full id: C888_uterus_dura_CD14_mature_epididymis_prostate_cervix



Phase1 CAGE Peaks

Hg19::chr12:102791856..102791865,-p@chr12:102791856..102791865
-
Hg19::chr12:102872317..102872350,-p2@IGF1
Hg19::chr12:102874242..102874255,-p6@IGF1
Hg19::chr12:102874261..102874275,-p4@IGF1
Hg19::chr12:102874293..102874309,-p5@IGF1
Hg19::chr12:102874314..102874327,-p3@IGF1
Hg19::chr12:102874330..102874350,-p1@IGF1
Hg19::chr12:102874382..102874394,-p7@IGF1
Hg19::chr12:102874416..102874425,-p8@IGF1


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
fat cell8.43e-1515
Uber Anatomy
Ontology termp-valuen
adult organism7.82e-48114
regional part of cerebral cortex2.44e-1122
cerebral hemisphere9.13e-1132
telencephalon9.69e-1134
neural tube1.04e-1056
neural rod1.04e-1056
future spinal cord1.04e-1056
neural keel1.04e-1056
brain grey matter1.33e-1034
gray matter1.33e-1034
neocortex3.55e-1020
cavity lining8.80e-1012
serous membrane8.80e-1012
regional part of telencephalon9.48e-1032
regional part of forebrain1.79e-0941
forebrain1.79e-0941
anterior neural tube1.79e-0941
future forebrain1.79e-0941
cerebral cortex2.03e-0925
pallium2.03e-0925
regional part of nervous system3.08e-0953
regional part of brain3.08e-0953
organ system subdivision4.33e-09223
central nervous system4.06e-0881
nervous system5.64e-0889
neurectoderm8.57e-0886
neural plate2.77e-0782
presumptive neural plate2.77e-0782
omentum3.03e-076
peritoneum3.03e-076
abdominal cavity3.03e-076
visceral peritoneum3.03e-076
brain3.55e-0768
future brain3.55e-0768
structure with developmental contribution from neural crest7.26e-07132


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
CCNT2#90574.928156782082056.52167806614696e-050.00105878677996319
CEBPB#105176.199781486752641.39459740509258e-050.000336452664334637
CTCF#1066474.169088290169470.0001982812163300480.0023810845064153
GATA2#262479.91272468165315.71014888882728e-072.6329458710827e-05
NRF1#489979.496884014886267.65865712776971e-073.36500837933168e-05
POLR2A#543081.908847268051620.0116612289598830.0425775098357299
RAD21#588578.053915252021592.36147727378579e-068.37738875668866e-05
SRF#6722710.73113864835273.31352184322677e-071.65737982655537e-05
TAL1#6886723.23114630467571.59434073890572e-091.40279151163078e-07



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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