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Coexpression cluster:C1122: Difference between revisions

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|id=C1122
|id=C1122
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|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!2.53e-16!31;DOID:1240!4.80e-12!39;DOID:2531!3.28e-08!51;DOID:0060083!3.28e-08!51
|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:0001016!1.32e-28!89;UBERON:0001017!1.69e-27!81;UBERON:0001049!3.87e-26!56;UBERON:0005068!3.87e-26!56;UBERON:0006241!3.87e-26!56;UBERON:0007135!3.87e-26!56;UBERON:0000073!7.75e-24!53;UBERON:0002616!7.75e-24!53;UBERON:0000955!7.15e-23!68;UBERON:0006238!7.15e-23!68;UBERON:0003528!2.75e-22!34;UBERON:0002020!2.75e-22!34;UBERON:0001893!3.86e-22!34;UBERON:0001869!1.53e-21!32;UBERON:0002346!6.46e-21!86;UBERON:0002780!1.99e-19!41;UBERON:0001890!1.99e-19!41;UBERON:0003080!1.99e-19!41;UBERON:0006240!1.99e-19!41;UBERON:0002791!2.36e-19!32;UBERON:0003075!2.37e-19!82;UBERON:0007284!2.37e-19!82;UBERON:0002619!3.33e-18!22;UBERON:0000956!1.23e-15!25;UBERON:0000203!1.23e-15!25;UBERON:0003056!3.20e-15!61;UBERON:0001950!8.04e-15!20;UBERON:0010371!2.07e-13!104;UBERON:0004121!4.08e-13!171;UBERON:0000924!4.08e-13!171;UBERON:0006601!4.08e-13!171;UBERON:0010314!3.64e-11!132;UBERON:0011216!1.65e-10!223;UBERON:0007023!1.64e-09!114;UBERON:0000125!3.35e-08!9;UBERON:0002308!3.35e-08!9;UBERON:0003076!6.93e-08!15;UBERON:0003057!6.93e-08!15;UBERON:0000349!8.00e-08!5;UBERON:0001872!3.02e-07!5;UBERON:0000988!7.34e-07!3
|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
|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 10:52, 19 October 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
nervous system1.32e-2889
central nervous system1.69e-2781
neural tube3.87e-2656
neural rod3.87e-2656
future spinal cord3.87e-2656
neural keel3.87e-2656
regional part of nervous system7.75e-2453
regional part of brain7.75e-2453
brain7.15e-2368
future brain7.15e-2368
brain grey matter2.75e-2234
gray matter2.75e-2234
telencephalon3.86e-2234
cerebral hemisphere1.53e-2132
neurectoderm6.46e-2186
regional part of forebrain1.99e-1941
forebrain1.99e-1941
anterior neural tube1.99e-1941
future forebrain1.99e-1941
regional part of telencephalon2.36e-1932
neural plate2.37e-1982
presumptive neural plate2.37e-1982
regional part of cerebral cortex3.33e-1822
cerebral cortex1.23e-1525
pallium1.23e-1525
pre-chordal neural plate3.20e-1561
neocortex8.04e-1520
ecto-epithelium2.07e-13104
ectoderm-derived structure4.08e-13171
ectoderm4.08e-13171
presumptive ectoderm4.08e-13171
structure with developmental contribution from neural crest3.64e-11132
organ system subdivision1.65e-10223
adult organism1.64e-09114
neural nucleus3.35e-089
nucleus of brain3.35e-089
posterior neural tube6.93e-0815
chordal neural plate6.93e-0815
limbic system8.00e-085
parietal lobe3.02e-075
pons7.34e-073
Disease
Ontology termp-valuen
myeloid leukemia2.53e-1631
leukemia4.80e-1239
hematologic cancer3.28e-0851
immune system cancer3.28e-0851


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.