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Coexpression cluster:C3993: Difference between revisions

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|full_id=C3993_dura_heart_Lymphatic_lung_acute_Fibroblast_pituitary
|full_id=C3993_dura_heart_Lymphatic_lung_acute_Fibroblast_pituitary
|id=C3993
|id=C3993
|ontology_enrichment_celltype=CL:0005020!6.90e-07!6;CL:0002138!6.90e-07!6;CL:0005022!6.90e-07!6
|ontology_enrichment_celltype=CL:0002552!4.50e-07!5
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.15e-58!115;UBERON:0001049!2.74e-23!57;UBERON:0005068!2.74e-23!57;UBERON:0006241!2.74e-23!57;UBERON:0007135!2.74e-23!57;UBERON:0002616!8.44e-19!59;UBERON:0003075!1.93e-18!86;UBERON:0007284!1.93e-18!86;UBERON:0003080!2.20e-18!42;UBERON:0002780!1.78e-17!41;UBERON:0001890!1.78e-17!41;UBERON:0006240!1.78e-17!41;UBERON:0002346!8.08e-17!90;UBERON:0000477!4.98e-16!286;UBERON:0001017!7.47e-15!82;UBERON:0004111!1.07e-14!241;UBERON:0000955!1.16e-14!69;UBERON:0006238!1.16e-14!69;UBERON:0005743!1.91e-14!86;UBERON:0002020!2.87e-14!34;UBERON:0003528!2.87e-14!34;UBERON:0001893!3.99e-14!34;UBERON:0000153!5.28e-14!129;UBERON:0007811!5.28e-14!129;UBERON:0002791!1.43e-13!33;UBERON:0000073!5.00e-13!94;UBERON:0001016!5.00e-13!94;UBERON:0001869!6.05e-13!32;UBERON:0000033!7.99e-13!123;UBERON:0003056!3.54e-12!61;UBERON:0002619!5.63e-11!22;UBERON:0000025!1.46e-10!194;UBERON:0004121!7.97e-10!169;UBERON:0001950!1.13e-09!20;UBERON:0000924!3.69e-09!173;UBERON:0006601!3.69e-09!173;UBERON:0000956!5.29e-09!25;UBERON:0000203!5.29e-09!25;UBERON:0000481!4.66e-08!347;UBERON:0000468!5.58e-08!659;UBERON:0002298!1.31e-07!8;UBERON:0002308!3.41e-07!9;UBERON:0000125!3.41e-07!9;UBERON:0002420!3.81e-07!9;UBERON:0007245!3.81e-07!9;UBERON:0010009!3.81e-07!9;UBERON:0010011!3.81e-07!9;UBERON:0000454!3.81e-07!9
|ontology_enrichment_uberon=UBERON:0007023!3.05e-55!114;UBERON:0001049!9.83e-22!56;UBERON:0005068!9.83e-22!56;UBERON:0006241!9.83e-22!56;UBERON:0007135!9.83e-22!56;UBERON:0000073!8.88e-19!53;UBERON:0002616!8.88e-19!53;UBERON:0003075!4.58e-17!82;UBERON:0007284!4.58e-17!82;UBERON:0002346!1.05e-15!86;UBERON:0010314!2.54e-15!132;UBERON:0002780!2.64e-15!41;UBERON:0001890!2.64e-15!41;UBERON:0003080!2.64e-15!41;UBERON:0006240!2.64e-15!41;UBERON:0001017!1.11e-14!81;UBERON:0004111!2.01e-13!240;UBERON:0003528!2.17e-13!34;UBERON:0002020!2.17e-13!34;UBERON:0000955!2.76e-13!68;UBERON:0006238!2.76e-13!68;UBERON:0011216!3.45e-13!223;UBERON:0001893!3.52e-13!34;UBERON:0001016!4.21e-13!89;UBERON:0000477!7.18e-13!373;UBERON:0002791!9.87e-12!32;UBERON:0001869!1.20e-11!32;UBERON:0010371!5.65e-11!104;UBERON:0004121!7.19e-11!171;UBERON:0000924!7.19e-11!171;UBERON:0006601!7.19e-11!171;UBERON:0002420!5.91e-10!9;UBERON:0007245!5.91e-10!9;UBERON:0010009!5.91e-10!9;UBERON:0010011!5.91e-10!9;UBERON:0000454!5.91e-10!9;UBERON:0003056!6.38e-10!61;UBERON:0000125!8.12e-10!9;UBERON:0002308!8.12e-10!9;UBERON:0000481!1.86e-09!342;UBERON:0000025!2.01e-08!192;UBERON:0002298!3.22e-08!6;UBERON:0002619!4.14e-08!22;UBERON:0009663!8.04e-08!7;UBERON:0003076!1.00e-07!15;UBERON:0003057!1.00e-07!15;UBERON:0000956!8.88e-07!25;UBERON:0000203!8.88e-07!25
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032264874502088!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321002428116965!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388244281143607!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444672960192172
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032264874502088!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0321002428116965!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388244281143607!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00444672960192172
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}}
}}

Revision as of 15:34, 19 October 2012


Full id: C3993_dura_heart_Lymphatic_lung_acute_Fibroblast_pituitary



Phase1 CAGE Peaks

Hg19::chr1:65990881..65990916,+p5@LEPR
Hg19::chr1:65990922..65990927,+p12@LEPR
Hg19::chr1:65990933..65990946,+p8@LEPR


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
fibroblast of gingiva4.50e-075
Uber Anatomy
Ontology termp-valuen
adult organism3.05e-55114
neural tube9.83e-2256
neural rod9.83e-2256
future spinal cord9.83e-2256
neural keel9.83e-2256
regional part of nervous system8.88e-1953
regional part of brain8.88e-1953
neural plate4.58e-1782
presumptive neural plate4.58e-1782
neurectoderm1.05e-1586
structure with developmental contribution from neural crest2.54e-15132
regional part of forebrain2.64e-1541
forebrain2.64e-1541
anterior neural tube2.64e-1541
future forebrain2.64e-1541
central nervous system1.11e-1481
anatomical conduit2.01e-13240
brain grey matter2.17e-1334
gray matter2.17e-1334
brain2.76e-1368
future brain2.76e-1368
organ system subdivision3.45e-13223
telencephalon3.52e-1334
nervous system4.21e-1389
anatomical cluster7.18e-13373
regional part of telencephalon9.87e-1232
cerebral hemisphere1.20e-1132
ecto-epithelium5.65e-11104
ectoderm-derived structure7.19e-11171
ectoderm7.19e-11171
presumptive ectoderm7.19e-11171
basal ganglion5.91e-109
nuclear complex of neuraxis5.91e-109
aggregate regional part of brain5.91e-109
collection of basal ganglia5.91e-109
cerebral subcortex5.91e-109
pre-chordal neural plate6.38e-1061
neural nucleus8.12e-109
nucleus of brain8.12e-109
multi-tissue structure1.86e-09342
tube2.01e-08192
brainstem3.22e-086
regional part of cerebral cortex4.14e-0822
telencephalic nucleus8.04e-087
posterior neural tube1.00e-0715
chordal neural plate1.00e-0715
cerebral cortex8.88e-0725
pallium8.88e-0725


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
E2F6#187635.017155731697390.00791769806886330.032264874502088
EGR1#195834.988179094810140.008056488137383440.0321002428116965
GATA1#2623313.56030814380040.0004009615963782630.00388244281143607
JUN#3725312.51282919233630.0005103313992726250.00444672960192172



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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