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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000025!1.50e-27!194;UBERON:0005743!2.77e-23!86;UBERON:0000073!1.76e-22!94;UBERON:0001016!1.76e-22!94;UBERON:0000119!4.38e-22!312;UBERON:0000955!8.63e-22!69;UBERON:0006238!8.63e-22!69;UBERON:0000483!2.90e-21!309;UBERON:0001017!4.79e-21!82;UBERON:0000481!1.13e-20!347;UBERON:0001049!2.39e-20!57;UBERON:0005068!2.39e-20!57;UBERON:0006241!2.39e-20!57;UBERON:0007135!2.39e-20!57;UBERON:0003075!4.57e-20!86;UBERON:0007284!4.57e-20!86;UBERON:0002616!1.22e-19!59;UBERON:0002346!6.30e-19!90;UBERON:0004111!1.16e-18!241;UBERON:0002020!3.95e-15!34;UBERON:0003528!3.95e-15!34;UBERON:0001893!4.71e-15!34;UBERON:0000477!8.12e-15!286;UBERON:0002780!8.47e-15!41;UBERON:0001890!8.47e-15!41;UBERON:0006240!8.47e-15!41;UBERON:0002791!1.64e-14!33;UBERON:0003080!7.81e-14!42;UBERON:0001869!9.81e-14!32;UBERON:0003056!1.18e-13!61;UBERON:0007023!2.35e-13!115;UBERON:0005177!4.86e-13!107;UBERON:0000475!5.03e-13!365;UBERON:0005172!2.11e-12!55;UBERON:0005173!2.11e-12!55;UBERON:0000466!2.54e-12!126;UBERON:0000033!2.69e-10!123;UBERON:0002619!2.78e-10!22;UBERON:0003914!5.90e-10!118;UBERON:0000956!7.60e-10!25;UBERON:0000203!7.60e-10!25;UBERON:0002417!7.95e-10!61;UBERON:0000916!7.95e-10!61;UBERON:0000922!1.17e-09!612;UBERON:0009497!1.22e-09!25;UBERON:0000015!1.22e-09!25;UBERON:0002423!1.22e-09!25;UBERON:0006235!1.22e-09!25;UBERON:0004161!1.22e-09!25;UBERON:0009856!1.47e-09!26;UBERON:0007499!1.85e-09!25;UBERON:0000153!2.50e-09!129;UBERON:0007811!2.50e-09!129;UBERON:0001950!2.95e-09!20;UBERON:0009854!5.36e-09!23;UBERON:0008835!6.64e-09!22;UBERON:0003894!6.64e-09!22;UBERON:0002050!6.72e-09!605;UBERON:0005423!6.72e-09!605;UBERON:0000923!9.52e-09!604;UBERON:0005291!9.52e-09!604;UBERON:0006598!9.52e-09!604;UBERON:0002532!9.52e-09!604;UBERON:0000064!1.23e-08!219;UBERON:0003076!6.34e-08!15;UBERON:0003057!6.34e-08!15;UBERON:0000062!6.55e-08!511;UBERON:0002107!1.02e-07!19;UBERON:0006925!1.02e-07!19;UBERON:0008836!1.02e-07!19;UBERON:0003104!1.30e-07!238;UBERON:0009142!1.30e-07!238;UBERON:0000489!1.33e-07!32;UBERON:0003886!1.39e-07!63;UBERON:0005256!2.12e-07!143;UBERON:0004121!2.83e-07!169;UBERON:0000058!3.94e-07!26;UBERON:0002308!4.28e-07!9;UBERON:0000125!4.28e-07!9;UBERON:0000924!5.42e-07!173;UBERON:0006601!5.42e-07!173;UBERON:0001048!6.99e-07!168
|ontology_enrichment_uberon=UBERON:0000025!1.50e-27!194;UBERON:0005743!2.77e-23!86;UBERON:0000073!1.76e-22!94;UBERON:0001016!1.76e-22!94;UBERON:0000119!4.38e-22!312;UBERON:0000955!8.63e-22!69;UBERON:0006238!8.63e-22!69;UBERON:0000483!2.90e-21!309;UBERON:0001017!4.79e-21!82;UBERON:0000481!1.13e-20!347;UBERON:0001049!2.39e-20!57;UBERON:0005068!2.39e-20!57;UBERON:0006241!2.39e-20!57;UBERON:0007135!2.39e-20!57;UBERON:0003075!4.57e-20!86;UBERON:0007284!4.57e-20!86;UBERON:0002616!1.22e-19!59;UBERON:0002346!6.30e-19!90;UBERON:0004111!1.16e-18!241;UBERON:0002020!3.95e-15!34;UBERON:0003528!3.95e-15!34;UBERON:0001893!4.71e-15!34;UBERON:0000477!8.12e-15!286;UBERON:0002780!8.47e-15!41;UBERON:0001890!8.47e-15!41;UBERON:0006240!8.47e-15!41;UBERON:0002791!1.64e-14!33;UBERON:0003080!7.81e-14!42;UBERON:0001869!9.81e-14!32;UBERON:0003056!1.18e-13!61;UBERON:0007023!2.35e-13!115;UBERON:0005177!4.86e-13!107;UBERON:0000475!5.03e-13!365;UBERON:0005172!2.11e-12!55;UBERON:0005173!2.11e-12!55;UBERON:0000466!2.54e-12!126;UBERON:0000033!2.69e-10!123;UBERON:0002619!2.78e-10!22;UBERON:0003914!5.90e-10!118;UBERON:0000956!7.60e-10!25;UBERON:0000203!7.60e-10!25;UBERON:0002417!7.95e-10!61;UBERON:0000916!7.95e-10!61;UBERON:0000922!1.17e-09!612;UBERON:0009497!1.22e-09!25;UBERON:0000015!1.22e-09!25;UBERON:0002423!1.22e-09!25;UBERON:0006235!1.22e-09!25;UBERON:0004161!1.22e-09!25;UBERON:0009856!1.47e-09!26;UBERON:0007499!1.85e-09!25;UBERON:0000153!2.50e-09!129;UBERON:0007811!2.50e-09!129;UBERON:0001950!2.95e-09!20;UBERON:0009854!5.36e-09!23;UBERON:0008835!6.64e-09!22;UBERON:0003894!6.64e-09!22;UBERON:0002050!6.72e-09!605;UBERON:0005423!6.72e-09!605;UBERON:0000923!9.52e-09!604;UBERON:0005291!9.52e-09!604;UBERON:0006598!9.52e-09!604;UBERON:0002532!9.52e-09!604;UBERON:0000064!1.23e-08!219;UBERON:0003076!6.34e-08!15;UBERON:0003057!6.34e-08!15;UBERON:0000062!6.55e-08!511;UBERON:0002107!1.02e-07!19;UBERON:0006925!1.02e-07!19;UBERON:0008836!1.02e-07!19;UBERON:0003104!1.30e-07!238;UBERON:0009142!1.30e-07!238;UBERON:0000489!1.33e-07!32;UBERON:0003886!1.39e-07!63;UBERON:0005256!2.12e-07!143;UBERON:0004121!2.83e-07!169;UBERON:0000058!3.94e-07!26;UBERON:0002308!4.28e-07!9;UBERON:0000125!4.28e-07!9;UBERON:0000924!5.42e-07!173;UBERON:0006601!5.42e-07!173;UBERON:0001048!6.99e-07!168
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2782,0.410951,0.289049,0.266974,0.125746,0.112897,0.0926658,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.0386145,0.450113
}}
}}

Revision as of 13:48, 5 September 2012


Full id: C2142_corpus_optic_Retinal_substantia_thalamus_globus_medulla



Phase1 CAGE Peaks

Hg19::chr11:61520075..61520136,+p1@C11orf9
Hg19::chr11:61533546..61533565,+p@chr11:61533546..61533565
+
Hg19::chr11:61537749..61537776,-p@chr11:61537749..61537776
-
Hg19::chr11:61539002..61539027,-p@chr11:61539002..61539027
-


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
mesothelial cell2.58e-0719
Uber Anatomy
Ontology termp-valuen
tube1.50e-27194
regional part of nervous system1.76e-2294
nervous system1.76e-2294
cell layer4.38e-22312
brain8.63e-2269
future brain8.63e-2269
epithelium2.90e-21309
central nervous system4.79e-2182
multi-tissue structure1.13e-20347
neural tube2.39e-2057
neural rod2.39e-2057
future spinal cord2.39e-2057
neural keel2.39e-2057
neural plate4.57e-2086
presumptive neural plate4.57e-2086
regional part of brain1.22e-1959
neurectoderm6.30e-1990
anatomical conduit1.16e-18241
gray matter3.95e-1534
brain grey matter3.95e-1534
telencephalon4.71e-1534
anatomical cluster8.12e-15286
regional part of forebrain8.47e-1541
forebrain8.47e-1541
future forebrain8.47e-1541
regional part of telencephalon1.64e-1433
anterior neural tube7.81e-1442
cerebral hemisphere9.81e-1432
pre-chordal neural plate1.18e-1361
adult organism2.35e-13115
trunk region element4.86e-13107
organism subdivision5.03e-13365
abdomen element2.11e-1255
abdominal segment element2.11e-1255
immaterial anatomical entity2.54e-12126
head2.69e-10123
regional part of cerebral cortex2.78e-1022
epithelial tube5.90e-10118
cerebral cortex7.60e-1025
pallium7.60e-1025
abdominal segment of trunk7.95e-1061
abdomen7.95e-1061
embryo1.17e-09612
epithelium of foregut-midgut junction1.22e-0925
anatomical boundary1.22e-0925
hepatobiliary system1.22e-0925
foregut-midgut junction1.22e-0925
septum transversum1.22e-0925
sac1.47e-0926
epithelial sac1.85e-0925
anterior region of body2.50e-09129
craniocervical region2.50e-09129
neocortex2.95e-0920
digestive tract diverticulum5.36e-0923
hepatic diverticulum6.64e-0922
liver primordium6.64e-0922
embryonic structure6.72e-09605
developing anatomical structure6.72e-09605
germ layer9.52e-09604
embryonic tissue9.52e-09604
presumptive structure9.52e-09604
epiblast (generic)9.52e-09604
organ part1.23e-08219
posterior neural tube6.34e-0815
chordal neural plate6.34e-0815
organ6.55e-08511
liver1.02e-0719
digestive gland1.02e-0719
liver bud1.02e-0719
mesenchyme1.30e-07238
entire embryonic mesenchyme1.30e-07238
cavitated compound organ1.33e-0732
body cavity precursor1.39e-0763
trunk mesenchyme2.12e-07143
ectoderm-derived structure2.83e-07169
duct3.94e-0726
nucleus of brain4.28e-079
neural nucleus4.28e-079
ectoderm5.42e-07173
presumptive ectoderm5.42e-07173
primordium6.99e-07168


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
CTCF#1066445.360256373075030.001211145381643620.00815806594733817



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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