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Coexpression cluster:C1905: Difference between revisions

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|full_id=C1905_caudate_putamen_embryonic_pituitary_globus_cord_rhabdomyosarcoma
|full_id=C1905_caudate_putamen_embryonic_pituitary_globus_cord_rhabdomyosarcoma
|id=C1905
|id=C1905
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0002586!5.58e-08!3;CL:0000064!7.05e-08!3;CL:0000067!7.05e-08!3;CL:0005012!7.05e-08!3;CL:0002304!7.05e-08!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:171!3.52e-10!10;DOID:169!2.55e-09!6
|ontology_enrichment_uberon=UBERON:0002346!1.13e-24!90;UBERON:0003075!5.44e-23!86;UBERON:0007284!5.44e-23!86;UBERON:0003056!4.02e-22!61;UBERON:0000073!1.30e-19!94;UBERON:0001016!1.30e-19!94;UBERON:0005743!7.17e-16!86;UBERON:0002616!2.49e-15!59;UBERON:0001049!5.15e-15!57;UBERON:0005068!5.15e-15!57;UBERON:0006241!5.15e-15!57;UBERON:0007135!5.15e-15!57;UBERON:0002780!2.03e-14!41;UBERON:0001890!2.03e-14!41;UBERON:0006240!2.03e-14!41;UBERON:0000924!3.52e-14!173;UBERON:0006601!3.52e-14!173;UBERON:0003080!7.79e-14!42;UBERON:0000955!1.91e-13!69;UBERON:0006238!1.91e-13!69;UBERON:0000033!2.42e-13!123;UBERON:0001017!3.62e-13!82;UBERON:0004121!5.84e-13!169;UBERON:0000153!7.74e-13!129;UBERON:0007811!7.74e-13!129;UBERON:0007625!2.20e-12!11;UBERON:0002104!2.78e-11!21;UBERON:0000970!1.70e-10!20;UBERON:0000019!1.30e-09!19;UBERON:0000047!1.30e-09!19;UBERON:0004088!1.30e-09!19;UBERON:0003072!1.30e-09!19;UBERON:0003071!1.30e-09!19;UBERON:0004128!1.30e-09!19;UBERON:0001893!2.94e-09!34;UBERON:0001032!3.89e-09!24;UBERON:0004456!3.89e-09!24;UBERON:0001869!3.99e-09!32;UBERON:0002791!5.38e-09!33;UBERON:0000020!2.03e-08!23;UBERON:0002020!2.96e-08!34;UBERON:0003528!2.96e-08!34;UBERON:0001456!3.18e-08!21;UBERON:0001894!4.72e-08!7;UBERON:0006222!4.72e-08!7;UBERON:0000966!8.99e-07!5;UBERON:0005388!8.99e-07!5;UBERON:0001802!8.99e-07!5
|ontology_enrichment_uberon=UBERON:0003056!1.63e-26!61;UBERON:0002346!8.36e-22!86;UBERON:0007625!2.28e-20!11;UBERON:0003075!3.24e-20!82;UBERON:0007284!3.24e-20!82;UBERON:0001016!1.51e-17!89;UBERON:0004121!2.47e-17!171;UBERON:0000924!2.47e-17!171;UBERON:0006601!2.47e-17!171;UBERON:0000970!8.39e-17!21;UBERON:0002104!8.39e-17!21;UBERON:0010371!3.18e-15!104;UBERON:0000019!5.09e-15!20;UBERON:0000047!5.09e-15!20;UBERON:0010312!5.09e-15!20;UBERON:0004088!5.09e-15!20;UBERON:0010230!5.09e-15!20;UBERON:0003072!5.09e-15!20;UBERON:0004128!5.09e-15!20;UBERON:0003071!5.09e-15!20;UBERON:0000020!2.87e-14!24;UBERON:0001032!2.87e-14!24;UBERON:0004456!2.87e-14!24;UBERON:0002780!1.36e-13!41;UBERON:0001890!1.36e-13!41;UBERON:0003080!1.36e-13!41;UBERON:0006240!1.36e-13!41;UBERON:0001456!2.26e-13!22;UBERON:0009663!6.80e-13!7;UBERON:0010314!7.69e-13!132;UBERON:0001894!1.67e-12!7;UBERON:0006222!1.67e-12!7;UBERON:0001017!1.68e-12!81;UBERON:0000955!2.77e-12!68;UBERON:0006238!2.77e-12!68;UBERON:0000073!7.27e-12!53;UBERON:0002616!7.27e-12!53;UBERON:0000369!4.03e-11!4;UBERON:0002435!4.03e-11!4;UBERON:0000204!4.03e-11!4;UBERON:0010082!4.03e-11!4;UBERON:0001049!5.78e-11!56;UBERON:0005068!5.78e-11!56;UBERON:0006241!5.78e-11!56;UBERON:0007135!5.78e-11!56;UBERON:0000966!2.51e-10!6;UBERON:0005388!2.51e-10!6;UBERON:0001802!2.51e-10!6;UBERON:0000488!5.40e-10!4;UBERON:0002420!8.14e-10!9;UBERON:0000125!8.14e-10!9;UBERON:0007245!8.14e-10!9;UBERON:0002308!8.14e-10!9;UBERON:0010009!8.14e-10!9;UBERON:0010011!8.14e-10!9;UBERON:0000454!8.14e-10!9;UBERON:0005383!7.56e-09!3;UBERON:0005382!7.56e-09!3;UBERON:0005085!1.25e-08!31;UBERON:0000010!2.33e-08!8;UBERON:0001782!5.58e-08!3;UBERON:0005424!5.58e-08!3;UBERON:0001264!5.62e-08!10;UBERON:0001778!7.05e-08!3;UBERON:0001775!7.05e-08!3;UBERON:0000013!1.31e-07!5;UBERON:0002410!1.31e-07!5;UBERON:0001801!1.48e-07!14;UBERON:0006876!5.66e-07!11;UBERON:0001893!7.66e-07!34;UBERON:0002075!7.77e-07!18
|tf_chipseq_enrich=GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215762148528964!PBX3#5090;3:13.1487076120465:0.000886046932280843:0.00660560036836883!SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62747195171092e-07!ZNF263#10127;4:6.57747330960854:0.000987510323790016:0.00709365091865366
|tf_chipseq_enrich=GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215762148528964!PBX3#5090;3:13.1487076120465:0.000886046932280843:0.00660560036836883!SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62747195171092e-07!ZNF263#10127;4:6.57747330960854:0.000987510323790016:0.00709365091865366
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}}
}}

Revision as of 11:49, 19 October 2012


Full id: C1905_caudate_putamen_embryonic_pituitary_globus_cord_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr2:45168959..45168990,+p6@SIX3
Hg19::chr2:45168997..45169020,+p4@SIX3
Hg19::chr2:45169024..45169033,+p12@SIX3
Hg19::chr2:45169317..45169326,+p13@SIX3
Hg19::chr2:45169684..45169715,+p9@SIX3


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
pre-chordal neural plate1.63e-2661
neurectoderm8.36e-2286
pigment epithelium of eye2.28e-2011
neural plate3.24e-2082
presumptive neural plate3.24e-2082
nervous system1.51e-1789
ectoderm-derived structure2.47e-17171
ectoderm2.47e-17171
presumptive ectoderm2.47e-17171
eye8.39e-1721
visual system8.39e-1721
ecto-epithelium3.18e-15104
camera-type eye5.09e-1520
simple eye5.09e-1520
immature eye5.09e-1520
ocular region5.09e-1520
eyeball of camera-type eye5.09e-1520
optic cup5.09e-1520
optic vesicle5.09e-1520
eye primordium5.09e-1520
sense organ2.87e-1424
sensory system2.87e-1424
entire sense organ system2.87e-1424
regional part of forebrain1.36e-1341
forebrain1.36e-1341
anterior neural tube1.36e-1341
future forebrain1.36e-1341
face2.26e-1322
telencephalic nucleus6.80e-137
structure with developmental contribution from neural crest7.69e-13132
diencephalon1.67e-127
future diencephalon1.67e-127
central nervous system1.68e-1281
brain2.77e-1268
future brain2.77e-1268
regional part of nervous system7.27e-1253
regional part of brain7.27e-1253
corpus striatum4.03e-114
striatum4.03e-114
ventral part of telencephalon4.03e-114
future corpus striatum4.03e-114
neural tube5.78e-1156
neural rod5.78e-1156
future spinal cord5.78e-1156
neural keel5.78e-1156
retina2.51e-106
photoreceptor array2.51e-106
posterior segment of eyeball2.51e-106
atypical epithelium5.40e-104
basal ganglion8.14e-109
neural nucleus8.14e-109
nuclear complex of neuraxis8.14e-109
nucleus of brain8.14e-109
aggregate regional part of brain8.14e-109
collection of basal ganglia8.14e-109
cerebral subcortex8.14e-109
caudate-putamen7.56e-093
dorsal striatum7.56e-093
ectodermal placode1.25e-0831
peripheral nervous system2.33e-088
pigmented layer of retina5.58e-083
presumptive retinal pigmented epithelium5.58e-083
pancreas5.62e-0810
ciliary epithelium7.05e-083
ciliary body7.05e-083
sympathetic nervous system1.31e-075
autonomic nervous system1.31e-075
anterior segment of eyeball1.48e-0714
vasculature of organ5.66e-0711
telencephalon7.66e-0734
viscus7.77e-0718
Disease
Ontology termp-valuen
neuroectodermal tumor3.52e-1010
neuroendocrine tumor2.55e-096


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
GATA2#2624410.19594538684320.0001775447777609820.00215762148528964
PBX3#5090313.14870761204650.0008860469322808430.00660560036836883
SUZ12#23512550.11578091106293.15480790456198e-092.62747195171092e-07
ZNF263#1012746.577473309608540.0009875103237900160.00709365091865366



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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