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Coexpression cluster:C1122: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!2.12e-09!31;DOID:3095!2.83e-07!22;DOID:2994!2.83e-07!22
|ontology_enrichment_disease=DOID:8692!2.12e-09!31;DOID:3095!2.83e-07!22;DOID:2994!2.83e-07!22
|ontology_enrichment_uberon=UBERON:0000073!1.24e-21!94;UBERON:0001016!1.24e-21!94;UBERON:0005743!3.66e-21!86;UBERON:0001017!1.26e-20!82;UBERON:0000955!5.95e-16!69;UBERON:0006238!5.95e-16!69;UBERON:0002346!3.04e-15!90;UBERON:0001869!1.01e-14!32;UBERON:0002020!1.23e-14!34;UBERON:0003528!1.23e-14!34;UBERON:0001893!1.81e-14!34;UBERON:0002791!6.20e-14!33;UBERON:0002616!1.35e-13!59;UBERON:0003075!1.58e-13!86;UBERON:0007284!1.58e-13!86;UBERON:0002780!2.00e-13!41;UBERON:0001890!2.00e-13!41;UBERON:0006240!2.00e-13!41;UBERON:0001049!2.45e-13!57;UBERON:0005068!2.45e-13!57;UBERON:0006241!2.45e-13!57;UBERON:0007135!2.45e-13!57;UBERON:0003080!1.27e-12!42;UBERON:0003056!2.42e-12!61;UBERON:0002619!3.75e-12!22;UBERON:0000956!5.44e-12!25;UBERON:0000203!5.44e-12!25;UBERON:0001950!5.43e-11!20;UBERON:0000924!7.45e-09!173;UBERON:0006601!7.45e-09!173;UBERON:0004121!9.64e-08!169;UBERON:0000033!1.47e-07!123;UBERON:0000153!5.69e-07!129;UBERON:0007811!5.69e-07!129
|ontology_enrichment_uberon=UBERON:0000073!1.24e-21!94;UBERON:0001016!1.24e-21!94;UBERON:0005743!3.66e-21!86;UBERON:0001017!1.26e-20!82;UBERON:0000955!5.95e-16!69;UBERON:0006238!5.95e-16!69;UBERON:0002346!3.04e-15!90;UBERON:0001869!1.01e-14!32;UBERON:0002020!1.23e-14!34;UBERON:0003528!1.23e-14!34;UBERON:0001893!1.81e-14!34;UBERON:0002791!6.20e-14!33;UBERON:0002616!1.35e-13!59;UBERON:0003075!1.58e-13!86;UBERON:0007284!1.58e-13!86;UBERON:0002780!2.00e-13!41;UBERON:0001890!2.00e-13!41;UBERON:0006240!2.00e-13!41;UBERON:0001049!2.45e-13!57;UBERON:0005068!2.45e-13!57;UBERON:0006241!2.45e-13!57;UBERON:0007135!2.45e-13!57;UBERON:0003080!1.27e-12!42;UBERON:0003056!2.42e-12!61;UBERON:0002619!3.75e-12!22;UBERON:0000956!5.44e-12!25;UBERON:0000203!5.44e-12!25;UBERON:0001950!5.43e-11!20;UBERON:0000924!7.45e-09!173;UBERON:0006601!7.45e-09!173;UBERON:0004121!9.64e-08!169;UBERON:0000033!1.47e-07!123;UBERON:0000153!5.69e-07!129;UBERON:0007811!5.69e-07!129
|tf_chipseq_enrich=CCNT2#905;5:4.52585826925902:0.0015515733062647:0.0098549391554448!E2F6#1876;5:3.58368266549813:0.00459810189782724:0.0217216014161018!EGR1#1958;5:3.56298506772153:0.00472235121105893:0.02225621110703!ZBTB7A#51341;5:5.25136379133993:0.000768769248321446:0.00602955027977196
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}}
}}

Revision as of 12:14, 5 September 2012


Full id: C1122_granulocyte_brain_acute_biphenotypic_occipital_duodenum_myelodysplastic



Phase1 CAGE Peaks

Hg19::chr10:77191203..77191214,+p2@C10orf11
Hg19::chr19:822044..822085,-p2@MIR3187
Hg19::chr19:822219..822240,-p5@MIR3187
Hg19::chr19:822261..822271,-p10@MIR3187
Hg19::chr19:822276..822295,-p6@MIR3187
Hg19::chr19:822320..822332,-p7@MIR3187
Hg19::chr5:79366406..79366421,+p@chr5:79366406..79366421
+


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.24e-2194
nervous system1.24e-2194
central nervous system1.26e-2082
brain5.95e-1669
future brain5.95e-1669
neurectoderm3.04e-1590
cerebral hemisphere1.01e-1432
gray matter1.23e-1434
brain grey matter1.23e-1434
telencephalon1.81e-1434
regional part of telencephalon6.20e-1433
regional part of brain1.35e-1359
neural plate1.58e-1386
presumptive neural plate1.58e-1386
regional part of forebrain2.00e-1341
forebrain2.00e-1341
future forebrain2.00e-1341
neural tube2.45e-1357
neural rod2.45e-1357
future spinal cord2.45e-1357
neural keel2.45e-1357
anterior neural tube1.27e-1242
pre-chordal neural plate2.42e-1261
regional part of cerebral cortex3.75e-1222
cerebral cortex5.44e-1225
pallium5.44e-1225
neocortex5.43e-1120
ectoderm7.45e-09173
presumptive ectoderm7.45e-09173
ectoderm-derived structure9.64e-08169
head1.47e-07123
anterior region of body5.69e-07129
craniocervical region5.69e-07129
Disease
Ontology termp-valuen
myeloid leukemia2.12e-0931
germ cell and embryonal cancer2.83e-0722
germ cell cancer2.83e-0722


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#90554.525858269259020.00155157330626470.0098549391554448
E2F6#187653.583682665498130.004598101897827240.0217216014161018
EGR1#195853.562985067721530.004722351211058930.02225621110703
ZBTB7A#5134155.251363791339930.0007687692483214460.00602955027977196



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.