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Coexpression cluster:C2108: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.77e-08!106;DOID:0050687!8.23e-07!143
|ontology_enrichment_disease=DOID:305!3.77e-08!106;DOID:0050687!8.23e-07!143
|ontology_enrichment_uberon=UBERON:0001049!3.46e-33!57;UBERON:0005068!3.46e-33!57;UBERON:0006241!3.46e-33!57;UBERON:0007135!3.46e-33!57;UBERON:0001017!1.62e-32!82;UBERON:0005743!2.45e-32!86;UBERON:0000073!1.13e-31!94;UBERON:0001016!1.13e-31!94;UBERON:0007023!2.60e-30!115;UBERON:0002616!4.41e-27!59;UBERON:0000955!1.14e-26!69;UBERON:0006238!1.14e-26!69;UBERON:0003075!3.72e-26!86;UBERON:0007284!3.72e-26!86;UBERON:0003080!3.70e-25!42;UBERON:0002780!1.04e-24!41;UBERON:0001890!1.04e-24!41;UBERON:0006240!1.04e-24!41;UBERON:0002346!6.63e-24!90;UBERON:0001893!1.05e-21!34;UBERON:0002020!1.19e-21!34;UBERON:0003528!1.19e-21!34;UBERON:0002791!4.40e-21!33;UBERON:0004121!5.99e-21!169;UBERON:0001869!1.86e-20!32;UBERON:0000924!9.96e-20!173;UBERON:0006601!9.96e-20!173;UBERON:0003056!1.08e-18!61;UBERON:0000033!4.88e-18!123;UBERON:0000153!2.98e-17!129;UBERON:0007811!2.98e-17!129;UBERON:0000481!1.13e-16!347;UBERON:0000956!4.93e-16!25;UBERON:0000203!4.93e-16!25;UBERON:0004111!8.40e-16!241;UBERON:0000477!1.09e-15!286;UBERON:0000025!2.94e-15!194;UBERON:0002619!3.55e-15!22;UBERON:0000064!5.88e-15!219;UBERON:0000062!5.00e-14!511;UBERON:0001950!8.37e-14!20;UBERON:0000475!1.50e-12!365;UBERON:0000119!2.38e-12!312;UBERON:0000483!4.51e-12!309;UBERON:0000922!3.63e-11!612;UBERON:0000468!7.73e-11!659;UBERON:0000480!7.35e-10!626;UBERON:0000467!1.06e-09!625;UBERON:0002050!1.91e-09!605;UBERON:0005423!1.91e-09!605;UBERON:0000923!3.19e-09!604;UBERON:0005291!3.19e-09!604;UBERON:0006598!3.19e-09!604;UBERON:0002532!3.19e-09!604;UBERON:0003076!4.39e-09!15;UBERON:0003057!4.39e-09!15;UBERON:0004732!1.11e-07!13;UBERON:0004733!3.00e-07!12;UBERON:0002028!3.00e-07!12;UBERON:0007277!3.00e-07!12;UBERON:0002420!3.78e-07!9;UBERON:0007245!3.78e-07!9;UBERON:0010009!3.78e-07!9;UBERON:0010011!3.78e-07!9;UBERON:0000454!3.78e-07!9;UBERON:0002308!4.44e-07!9;UBERON:0000125!4.44e-07!9;UBERON:0004921!5.57e-07!129;UBERON:0004185!5.57e-07!129;UBERON:0005172!7.73e-07!55;UBERON:0005173!7.73e-07!55
|ontology_enrichment_uberon=UBERON:0001049!3.46e-33!57;UBERON:0005068!3.46e-33!57;UBERON:0006241!3.46e-33!57;UBERON:0007135!3.46e-33!57;UBERON:0001017!1.62e-32!82;UBERON:0005743!2.45e-32!86;UBERON:0000073!1.13e-31!94;UBERON:0001016!1.13e-31!94;UBERON:0007023!2.60e-30!115;UBERON:0002616!4.41e-27!59;UBERON:0000955!1.14e-26!69;UBERON:0006238!1.14e-26!69;UBERON:0003075!3.72e-26!86;UBERON:0007284!3.72e-26!86;UBERON:0003080!3.70e-25!42;UBERON:0002780!1.04e-24!41;UBERON:0001890!1.04e-24!41;UBERON:0006240!1.04e-24!41;UBERON:0002346!6.63e-24!90;UBERON:0001893!1.05e-21!34;UBERON:0002020!1.19e-21!34;UBERON:0003528!1.19e-21!34;UBERON:0002791!4.40e-21!33;UBERON:0004121!5.99e-21!169;UBERON:0001869!1.86e-20!32;UBERON:0000924!9.96e-20!173;UBERON:0006601!9.96e-20!173;UBERON:0003056!1.08e-18!61;UBERON:0000033!4.88e-18!123;UBERON:0000153!2.98e-17!129;UBERON:0007811!2.98e-17!129;UBERON:0000481!1.13e-16!347;UBERON:0000956!4.93e-16!25;UBERON:0000203!4.93e-16!25;UBERON:0004111!8.40e-16!241;UBERON:0000477!1.09e-15!286;UBERON:0000025!2.94e-15!194;UBERON:0002619!3.55e-15!22;UBERON:0000064!5.88e-15!219;UBERON:0000062!5.00e-14!511;UBERON:0001950!8.37e-14!20;UBERON:0000475!1.50e-12!365;UBERON:0000119!2.38e-12!312;UBERON:0000483!4.51e-12!309;UBERON:0000922!3.63e-11!612;UBERON:0000468!7.73e-11!659;UBERON:0000480!7.35e-10!626;UBERON:0000467!1.06e-09!625;UBERON:0002050!1.91e-09!605;UBERON:0005423!1.91e-09!605;UBERON:0000923!3.19e-09!604;UBERON:0005291!3.19e-09!604;UBERON:0006598!3.19e-09!604;UBERON:0002532!3.19e-09!604;UBERON:0003076!4.39e-09!15;UBERON:0003057!4.39e-09!15;UBERON:0004732!1.11e-07!13;UBERON:0004733!3.00e-07!12;UBERON:0002028!3.00e-07!12;UBERON:0007277!3.00e-07!12;UBERON:0002420!3.78e-07!9;UBERON:0007245!3.78e-07!9;UBERON:0010009!3.78e-07!9;UBERON:0010011!3.78e-07!9;UBERON:0000454!3.78e-07!9;UBERON:0002308!4.44e-07!9;UBERON:0000125!4.44e-07!9;UBERON:0004921!5.57e-07!129;UBERON:0004185!5.57e-07!129;UBERON:0005172!7.73e-07!55;UBERON:0005173!7.73e-07!55
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}}
}}

Revision as of 13:42, 5 September 2012


Full id: C2108_hepatocellular_hippocampus_amygdala_medulla_medial_middle_thalamus



Phase1 CAGE Peaks

Hg19::chr11:124806196..124806206,-p7@HEPACAM
Hg19::chr11:124806212..124806292,-p3@HEPACAM
Hg19::chr11:124806297..124806320,-p6@HEPACAM
Hg19::chr22:29279602..29279621,+p2@ZNRF3


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
neural tube3.46e-3357
neural rod3.46e-3357
future spinal cord3.46e-3357
neural keel3.46e-3357
central nervous system1.62e-3282
regional part of nervous system1.13e-3194
nervous system1.13e-3194
adult organism2.60e-30115
regional part of brain4.41e-2759
brain1.14e-2669
future brain1.14e-2669
neural plate3.72e-2686
presumptive neural plate3.72e-2686
anterior neural tube3.70e-2542
regional part of forebrain1.04e-2441
forebrain1.04e-2441
future forebrain1.04e-2441
neurectoderm6.63e-2490
telencephalon1.05e-2134
gray matter1.19e-2134
brain grey matter1.19e-2134
regional part of telencephalon4.40e-2133
ectoderm-derived structure5.99e-21169
cerebral hemisphere1.86e-2032
ectoderm9.96e-20173
presumptive ectoderm9.96e-20173
pre-chordal neural plate1.08e-1861
head4.88e-18123
anterior region of body2.98e-17129
craniocervical region2.98e-17129
multi-tissue structure1.13e-16347
cerebral cortex4.93e-1625
pallium4.93e-1625
anatomical conduit8.40e-16241
anatomical cluster1.09e-15286
tube2.94e-15194
regional part of cerebral cortex3.55e-1522
organ part5.88e-15219
organ5.00e-14511
neocortex8.37e-1420
organism subdivision1.50e-12365
cell layer2.38e-12312
epithelium4.51e-12309
embryo3.63e-11612
multi-cellular organism7.73e-11659
anatomical group7.35e-10626
anatomical system1.06e-09625
embryonic structure1.91e-09605
developing anatomical structure1.91e-09605
germ layer3.19e-09604
embryonic tissue3.19e-09604
presumptive structure3.19e-09604
epiblast (generic)3.19e-09604
posterior neural tube4.39e-0915
chordal neural plate4.39e-0915
segmental subdivision of nervous system1.11e-0713
segmental subdivision of hindbrain3.00e-0712
hindbrain3.00e-0712
presumptive hindbrain3.00e-0712
basal ganglion3.78e-079
nuclear complex of neuraxis3.78e-079
aggregate regional part of brain3.78e-079
collection of basal ganglia3.78e-079
cerebral subcortex3.78e-079
nucleus of brain4.44e-079
neural nucleus4.44e-079
subdivision of digestive tract5.57e-07129
endodermal part of digestive tract5.57e-07129
abdomen element7.73e-0755
abdominal segment element7.73e-0755
Disease
Ontology termp-valuen
carcinoma3.77e-08106
cell type cancer8.23e-07143


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#2346244.040111043105710.00375304636917980.0185510156538771
TAF1#687243.343046285745290.008005664898701650.0321207697408952



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.