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Coexpression cluster:C2431: Difference between revisions

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|full_id=C2431_heart_thalamus_substantia_spinal_corpus_globus_ovary
|full_id=C2431_heart_thalamus_substantia_spinal_corpus_globus_ovary
|id=C2431
|id=C2431
|ontology_enrichment_celltype=CL:0000680!1.17e-09!57;CL:0000056!1.17e-09!57;CL:0000355!1.17e-09!57;CL:0000187!5.00e-09!54;CL:0000055!8.17e-08!180;CL:0000183!1.39e-07!59;CL:0000393!3.73e-07!60;CL:0000211!3.73e-07!60;CL:0000192!4.40e-07!42;CL:0000514!4.40e-07!42
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.14e-47!115;UBERON:0001049!6.84e-27!57;UBERON:0005068!6.84e-27!57;UBERON:0006241!6.84e-27!57;UBERON:0007135!6.84e-27!57;UBERON:0002616!8.61e-27!59;UBERON:0000477!1.51e-26!286;UBERON:0004111!1.57e-23!241;UBERON:0000025!2.49e-23!194;UBERON:0000481!7.77e-23!347;UBERON:0000955!2.65e-22!69;UBERON:0006238!2.65e-22!69;UBERON:0001017!6.43e-22!82;UBERON:0003075!2.00e-21!86;UBERON:0007284!2.00e-21!86;UBERON:0005743!4.13e-21!86;UBERON:0002346!9.32e-21!90;UBERON:0003080!1.91e-20!42;UBERON:0002780!6.91e-20!41;UBERON:0001890!6.91e-20!41;UBERON:0006240!6.91e-20!41;UBERON:0000119!1.97e-19!312;UBERON:0000475!5.27e-19!365;UBERON:0000483!5.98e-19!309;UBERON:0000073!1.18e-17!94;UBERON:0001016!1.18e-17!94;UBERON:0000153!4.15e-16!129;UBERON:0007811!4.15e-16!129;UBERON:0000033!9.59e-16!123;UBERON:0002020!1.79e-15!34;UBERON:0003528!1.79e-15!34;UBERON:0001893!2.08e-15!34;UBERON:0002791!7.30e-15!33;UBERON:0001869!5.30e-14!32;UBERON:0003056!2.48e-13!61;UBERON:0000468!1.88e-12!659;UBERON:0002385!7.07e-12!63;UBERON:0001015!7.07e-12!63;UBERON:0000383!7.07e-12!63;UBERON:0004872!7.33e-12!84;UBERON:0002619!1.26e-11!22;UBERON:0007100!2.62e-11!27;UBERON:0000479!3.03e-11!787;UBERON:0001134!4.96e-11!61;UBERON:0002036!4.96e-11!61;UBERON:0003082!4.96e-11!61;UBERON:0004121!9.56e-11!169;UBERON:0000924!1.21e-10!173;UBERON:0006601!1.21e-10!173;UBERON:0001950!1.43e-10!20;UBERON:0000922!3.65e-10!612;UBERON:0002050!3.66e-10!605;UBERON:0005423!3.66e-10!605;UBERON:0000956!5.27e-10!25;UBERON:0000203!5.27e-10!25;UBERON:0000923!6.61e-10!604;UBERON:0005291!6.61e-10!604;UBERON:0006598!6.61e-10!604;UBERON:0002532!6.61e-10!604;UBERON:0000948!9.67e-10!24;UBERON:0005498!9.67e-10!24;UBERON:0004140!9.67e-10!24;UBERON:0009881!9.67e-10!24;UBERON:0004141!9.67e-10!24;UBERON:0003084!9.67e-10!24;UBERON:0007005!9.67e-10!24;UBERON:0004139!9.67e-10!24;UBERON:0004291!9.67e-10!24;UBERON:0004290!1.31e-09!70;UBERON:0000467!3.59e-09!625;UBERON:0000480!5.31e-09!626;UBERON:0000914!5.74e-09!83;UBERON:0002329!5.74e-09!83;UBERON:0003077!5.74e-09!83;UBERON:0003059!5.74e-09!83;UBERON:0007282!5.74e-09!83;UBERON:0009618!5.74e-09!83;UBERON:0007285!5.74e-09!83;UBERON:0003076!1.30e-07!15;UBERON:0003057!1.30e-07!15;UBERON:0000062!2.47e-07!511;UBERON:0002308!2.62e-07!9;UBERON:0000125!2.62e-07!9;UBERON:0002298!5.18e-07!8;UBERON:0001981!5.98e-07!60;UBERON:0007500!5.98e-07!60;UBERON:0004537!5.98e-07!60;UBERON:0006965!5.98e-07!60;UBERON:0003914!7.23e-07!118;UBERON:0002420!7.25e-07!9;UBERON:0007245!7.25e-07!9;UBERON:0010009!7.25e-07!9;UBERON:0010011!7.25e-07!9;UBERON:0000454!7.25e-07!9;UBERON:0000486!8.67e-07!82
|ontology_enrichment_uberon=UBERON:0007023!5.55e-80!114;UBERON:0001049!2.95e-41!56;UBERON:0005068!2.95e-41!56;UBERON:0006241!2.95e-41!56;UBERON:0007135!2.95e-41!56;UBERON:0000073!5.34e-38!53;UBERON:0002616!5.34e-38!53;UBERON:0002780!1.91e-32!41;UBERON:0001890!1.91e-32!41;UBERON:0003080!1.91e-32!41;UBERON:0006240!1.91e-32!41;UBERON:0000955!4.08e-32!68;UBERON:0006238!4.08e-32!68;UBERON:0001017!2.62e-31!81;UBERON:0003075!7.15e-31!82;UBERON:0007284!7.15e-31!82;UBERON:0002346!1.61e-29!86;UBERON:0001016!1.35e-27!89;UBERON:0010314!1.79e-26!132;UBERON:0003528!2.23e-25!34;UBERON:0002020!2.23e-25!34;UBERON:0001893!2.71e-25!34;UBERON:0002791!3.29e-23!32;UBERON:0001869!5.58e-23!32;UBERON:0010371!3.63e-22!104;UBERON:0003056!3.50e-20!61;UBERON:0002619!1.63e-19!22;UBERON:0004111!6.17e-19!240;UBERON:0011216!1.51e-18!223;UBERON:0000025!1.58e-18!192;UBERON:0001950!7.35e-18!20;UBERON:0000481!4.03e-17!342;UBERON:0000956!2.40e-16!25;UBERON:0000203!2.40e-16!25;UBERON:0000477!4.32e-16!373;UBERON:0004121!5.35e-15!171;UBERON:0000924!5.35e-15!171;UBERON:0006601!5.35e-15!171;UBERON:0000483!8.70e-13!306;UBERON:0000119!2.21e-12!309;UBERON:0000062!1.23e-11!503;UBERON:0000125!6.26e-11!9;UBERON:0002308!6.26e-11!9;UBERON:0000468!1.22e-10!656;UBERON:0002420!2.94e-10!9;UBERON:0007245!2.94e-10!9;UBERON:0010009!2.94e-10!9;UBERON:0010011!2.94e-10!9;UBERON:0000454!2.94e-10!9;UBERON:0003076!7.32e-10!15;UBERON:0003057!7.32e-10!15;UBERON:0002050!9.48e-10!564;UBERON:0000923!1.14e-09!560;UBERON:0010316!1.14e-09!560;UBERON:0005291!1.14e-09!560;UBERON:0006598!1.14e-09!560;UBERON:0010317!1.14e-09!560;UBERON:0002532!1.14e-09!560;UBERON:0000922!5.36e-09!592;UBERON:0005423!5.46e-09!581;UBERON:0001894!1.01e-08!7;UBERON:0006222!1.01e-08!7;UBERON:0009663!1.05e-08!7;UBERON:0000479!1.77e-08!773;UBERON:0000064!2.38e-08!218;UBERON:0002298!2.57e-08!6;UBERON:0007100!2.83e-08!27;UBERON:0004732!6.15e-08!13;UBERON:0000467!8.50e-08!624;UBERON:0000480!1.02e-07!625;UBERON:0001871!1.71e-07!6;UBERON:0004797!2.34e-07!7;UBERON:0000200!3.69e-07!6;UBERON:0004733!5.73e-07!12;UBERON:0002028!5.73e-07!12;UBERON:0007277!5.73e-07!12
|tf_chipseq_enrich=HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185976660538418!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000584114649186863!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322086226879118!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244107856398174
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}}
}}

Revision as of 14:01, 19 October 2012


Full id: C2431_heart_thalamus_substantia_spinal_corpus_globus_ovary



Phase1 CAGE Peaks

Hg19::chr17:66951400..66951411,-p4@ABCA8
Hg19::chr17:66951415..66951429,-p2@ABCA8
Hg19::chr17:66951430..66951441,-p3@ABCA8
Hg19::chr17:66951474..66951550,-p1@ABCA8


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.55e-80114
neural tube2.95e-4156
neural rod2.95e-4156
future spinal cord2.95e-4156
neural keel2.95e-4156
regional part of nervous system5.34e-3853
regional part of brain5.34e-3853
regional part of forebrain1.91e-3241
forebrain1.91e-3241
anterior neural tube1.91e-3241
future forebrain1.91e-3241
brain4.08e-3268
future brain4.08e-3268
central nervous system2.62e-3181
neural plate7.15e-3182
presumptive neural plate7.15e-3182
neurectoderm1.61e-2986
nervous system1.35e-2789
structure with developmental contribution from neural crest1.79e-26132
brain grey matter2.23e-2534
gray matter2.23e-2534
telencephalon2.71e-2534
regional part of telencephalon3.29e-2332
cerebral hemisphere5.58e-2332
ecto-epithelium3.63e-22104
pre-chordal neural plate3.50e-2061
regional part of cerebral cortex1.63e-1922
anatomical conduit6.17e-19240
organ system subdivision1.51e-18223
tube1.58e-18192
neocortex7.35e-1820
multi-tissue structure4.03e-17342
cerebral cortex2.40e-1625
pallium2.40e-1625
anatomical cluster4.32e-16373
ectoderm-derived structure5.35e-15171
ectoderm5.35e-15171
presumptive ectoderm5.35e-15171
epithelium8.70e-13306
cell layer2.21e-12309
organ1.23e-11503
neural nucleus6.26e-119
nucleus of brain6.26e-119
multi-cellular organism1.22e-10656
basal ganglion2.94e-109
nuclear complex of neuraxis2.94e-109
aggregate regional part of brain2.94e-109
collection of basal ganglia2.94e-109
cerebral subcortex2.94e-109
posterior neural tube7.32e-1015
chordal neural plate7.32e-1015
embryonic structure9.48e-10564
germ layer1.14e-09560
germ layer / neural crest1.14e-09560
embryonic tissue1.14e-09560
presumptive structure1.14e-09560
germ layer / neural crest derived structure1.14e-09560
epiblast (generic)1.14e-09560
embryo5.36e-09592
developing anatomical structure5.46e-09581
diencephalon1.01e-087
future diencephalon1.01e-087
telencephalic nucleus1.05e-087
tissue1.77e-08773
organ part2.38e-08218
brainstem2.57e-086
primary circulatory organ2.83e-0827
segmental subdivision of nervous system6.15e-0813
anatomical system8.50e-08624
anatomical group1.02e-07625
temporal lobe1.71e-076
blood vessel layer2.34e-077
gyrus3.69e-076
segmental subdivision of hindbrain5.73e-0712
hindbrain5.73e-0712
presumptive hindbrain5.73e-0712


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#2346244.040111043105710.00375304636917980.0185976660538418
SRF#6722413.79717826216782.75840773062708e-050.000584114649186863
TAF1#687243.343046285745290.008005664898701650.0322086226879118
TBP#690843.706770687096390.005296377814784350.0244107856398174



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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