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Coexpression cluster:C3874: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.12e-44!115;UBERON:0001017!6.41e-35!82;UBERON:0001049!2.85e-34!57;UBERON:0005068!2.85e-34!57;UBERON:0006241!2.85e-34!57;UBERON:0007135!2.85e-34!57;UBERON:0005743!2.88e-34!86;UBERON:0000073!1.06e-31!94;UBERON:0001016!1.06e-31!94;UBERON:0002616!9.41e-29!59;UBERON:0000955!6.24e-28!69;UBERON:0006238!6.24e-28!69;UBERON:0002780!6.72e-27!41;UBERON:0001890!6.72e-27!41;UBERON:0006240!6.72e-27!41;UBERON:0003080!6.87e-27!42;UBERON:0003075!3.36e-25!86;UBERON:0007284!3.36e-25!86;UBERON:0002346!4.68e-25!90;UBERON:0002020!6.54e-23!34;UBERON:0003528!6.54e-23!34;UBERON:0001893!1.41e-22!34;UBERON:0002791!4.23e-22!33;UBERON:0001869!3.72e-21!32;UBERON:0003056!1.36e-18!61;UBERON:0000956!3.51e-16!25;UBERON:0000203!3.51e-16!25;UBERON:0000924!1.21e-15!173;UBERON:0006601!1.21e-15!173;UBERON:0000153!1.39e-15!129;UBERON:0007811!1.39e-15!129;UBERON:0004111!1.63e-15!241;UBERON:0004121!2.00e-15!169;UBERON:0002619!3.51e-15!22;UBERON:0000033!6.04e-15!123;UBERON:0000025!2.39e-14!194;UBERON:0001950!6.65e-14!20;UBERON:0000477!1.14e-12!286;UBERON:0000483!5.56e-10!309;UBERON:0000119!6.16e-10!312;UBERON:0003076!1.70e-08!15;UBERON:0003057!1.70e-08!15;UBERON:0002308!2.90e-08!9;UBERON:0000125!2.90e-08!9;UBERON:0000922!3.34e-08!612;UBERON:0002420!3.56e-08!9;UBERON:0007245!3.56e-08!9;UBERON:0010009!3.56e-08!9;UBERON:0010011!3.56e-08!9;UBERON:0000454!3.56e-08!9;UBERON:0002050!4.64e-07!605;UBERON:0005423!4.64e-07!605;UBERON:0000480!4.79e-07!626;UBERON:0001871!6.65e-07!7;UBERON:0009663!7.99e-07!7;UBERON:0000468!8.90e-07!659;UBERON:0000467!8.92e-07!625;UBERON:0000923!8.93e-07!604;UBERON:0005291!8.93e-07!604;UBERON:0006598!8.93e-07!604;UBERON:0002532!8.93e-07!604
|ontology_enrichment_uberon=UBERON:0007023!1.12e-44!115;UBERON:0001017!6.41e-35!82;UBERON:0001049!2.85e-34!57;UBERON:0005068!2.85e-34!57;UBERON:0006241!2.85e-34!57;UBERON:0007135!2.85e-34!57;UBERON:0005743!2.88e-34!86;UBERON:0000073!1.06e-31!94;UBERON:0001016!1.06e-31!94;UBERON:0002616!9.41e-29!59;UBERON:0000955!6.24e-28!69;UBERON:0006238!6.24e-28!69;UBERON:0002780!6.72e-27!41;UBERON:0001890!6.72e-27!41;UBERON:0006240!6.72e-27!41;UBERON:0003080!6.87e-27!42;UBERON:0003075!3.36e-25!86;UBERON:0007284!3.36e-25!86;UBERON:0002346!4.68e-25!90;UBERON:0002020!6.54e-23!34;UBERON:0003528!6.54e-23!34;UBERON:0001893!1.41e-22!34;UBERON:0002791!4.23e-22!33;UBERON:0001869!3.72e-21!32;UBERON:0003056!1.36e-18!61;UBERON:0000956!3.51e-16!25;UBERON:0000203!3.51e-16!25;UBERON:0000924!1.21e-15!173;UBERON:0006601!1.21e-15!173;UBERON:0000153!1.39e-15!129;UBERON:0007811!1.39e-15!129;UBERON:0004111!1.63e-15!241;UBERON:0004121!2.00e-15!169;UBERON:0002619!3.51e-15!22;UBERON:0000033!6.04e-15!123;UBERON:0000025!2.39e-14!194;UBERON:0001950!6.65e-14!20;UBERON:0000477!1.14e-12!286;UBERON:0000483!5.56e-10!309;UBERON:0000119!6.16e-10!312;UBERON:0003076!1.70e-08!15;UBERON:0003057!1.70e-08!15;UBERON:0002308!2.90e-08!9;UBERON:0000125!2.90e-08!9;UBERON:0000922!3.34e-08!612;UBERON:0002420!3.56e-08!9;UBERON:0007245!3.56e-08!9;UBERON:0010009!3.56e-08!9;UBERON:0010011!3.56e-08!9;UBERON:0000454!3.56e-08!9;UBERON:0002050!4.64e-07!605;UBERON:0005423!4.64e-07!605;UBERON:0000480!4.79e-07!626;UBERON:0001871!6.65e-07!7;UBERON:0009663!7.99e-07!7;UBERON:0000468!8.90e-07!659;UBERON:0000467!8.92e-07!625;UBERON:0000923!8.93e-07!604;UBERON:0005291!8.93e-07!604;UBERON:0006598!8.93e-07!604;UBERON:0002532!8.93e-07!604
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}}
}}

Revision as of 11:52, 5 September 2012


Full id: C3874_caudate_hippocampus_amygdala_putamen_uterus_thalamus_cervix



Phase1 CAGE Peaks

Hg19::chr1:154842741..154842772,-p1@KCNN3
Hg19::chr1:154842778..154842790,-p8@KCNN3
Hg19::chr1:154842792..154842816,-p7@KCNN3


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 organism1.12e-44115
central nervous system6.41e-3582
neural tube2.85e-3457
neural rod2.85e-3457
future spinal cord2.85e-3457
neural keel2.85e-3457
regional part of nervous system1.06e-3194
nervous system1.06e-3194
regional part of brain9.41e-2959
brain6.24e-2869
future brain6.24e-2869
regional part of forebrain6.72e-2741
forebrain6.72e-2741
future forebrain6.72e-2741
anterior neural tube6.87e-2742
neural plate3.36e-2586
presumptive neural plate3.36e-2586
neurectoderm4.68e-2590
gray matter6.54e-2334
brain grey matter6.54e-2334
telencephalon1.41e-2234
regional part of telencephalon4.23e-2233
cerebral hemisphere3.72e-2132
pre-chordal neural plate1.36e-1861
cerebral cortex3.51e-1625
pallium3.51e-1625
ectoderm1.21e-15173
presumptive ectoderm1.21e-15173
anterior region of body1.39e-15129
craniocervical region1.39e-15129
anatomical conduit1.63e-15241
ectoderm-derived structure2.00e-15169
regional part of cerebral cortex3.51e-1522
head6.04e-15123
tube2.39e-14194
neocortex6.65e-1420
anatomical cluster1.14e-12286
epithelium5.56e-10309
cell layer6.16e-10312
posterior neural tube1.70e-0815
chordal neural plate1.70e-0815
nucleus of brain2.90e-089
neural nucleus2.90e-089
embryo3.34e-08612
basal ganglion3.56e-089
nuclear complex of neuraxis3.56e-089
aggregate regional part of brain3.56e-089
collection of basal ganglia3.56e-089
cerebral subcortex3.56e-089
embryonic structure4.64e-07605
developing anatomical structure4.64e-07605
anatomical group4.79e-07626
temporal lobe6.65e-077
telencephalic nucleus7.99e-077
multi-cellular organism8.90e-07659
anatomical system8.92e-07625
germ layer8.93e-07604
embryonic tissue8.93e-07604
presumptive structure8.93e-07604
epiblast (generic)8.93e-07604


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
EGR1#195834.988179094810140.008056488137383440.0320733233429972
ELF1#199734.258097958807540.01295179875054610.04624364670296
ETS1#211339.728760922202340.001085840092584840.00762482709806144
FOXA1#3169311.08141974938550.000734755275698670.00581473867081104
HMGN3#932438.178547723350590.001827766942164210.0108732143809916
IRF1#365937.63716375356390.002244692747297240.0128126723416394
NFKB1#479035.488063424193840.006049381815655430.0269673633022553
POU2F2#545239.106124057742520.001324165192682130.00882430376202967
SIX5#147912317.0867153554590.0002004060546325010.00239805315533499
YY1#752834.911170749853860.008441455341808260.0329527231233876
ZEB1#6935316.88843201754390.0002075486917327580.00242815927141005
ZNF143#7702313.50087655222790.0004062804962997170.00389172968476989
ZNF263#1012738.221841637010680.001799043925565870.0109454939148418



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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