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Coexpression cluster:C4716: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!7.41e-28!241;UBERON:0000025!1.01e-25!194;UBERON:0000477!1.53e-25!286;UBERON:0007023!1.10e-24!115;UBERON:0000119!2.48e-23!312;UBERON:0000483!2.63e-23!309;UBERON:0001049!4.60e-19!57;UBERON:0005068!4.60e-19!57;UBERON:0006241!4.60e-19!57;UBERON:0007135!4.60e-19!57;UBERON:0001017!1.19e-18!82;UBERON:0000955!1.34e-18!69;UBERON:0006238!1.34e-18!69;UBERON:0002616!1.58e-18!59;UBERON:0005743!4.52e-18!86;UBERON:0004872!5.32e-18!84;UBERON:0000073!6.12e-18!94;UBERON:0001016!6.12e-18!94;UBERON:0000475!1.04e-16!365;UBERON:0003075!4.03e-16!86;UBERON:0007284!4.03e-16!86;UBERON:0000055!4.39e-16!69;UBERON:0002346!5.21e-16!90;UBERON:0002049!1.20e-15!79;UBERON:0007798!1.20e-15!79;UBERON:0001981!9.25e-15!60;UBERON:0007500!9.25e-15!60;UBERON:0004537!9.25e-15!60;UBERON:0006965!9.25e-15!60;UBERON:0001009!9.55e-15!113;UBERON:0003080!2.68e-14!42;UBERON:0000468!3.08e-14!659;UBERON:0002780!1.01e-13!41;UBERON:0001890!1.01e-13!41;UBERON:0006240!1.01e-13!41;UBERON:0004535!1.12e-13!110;UBERON:0002020!5.94e-13!34;UBERON:0003528!5.94e-13!34;UBERON:0000481!6.44e-13!347;UBERON:0001893!1.32e-12!34;UBERON:0001869!1.43e-12!32;UBERON:0000467!1.91e-12!625;UBERON:0002791!2.92e-12!33;UBERON:0000480!3.26e-12!626;UBERON:0002619!1.94e-11!22;UBERON:0000956!2.68e-11!25;UBERON:0000203!2.68e-11!25;UBERON:0000033!3.97e-11!123;UBERON:0000153!4.42e-11!129;UBERON:0007811!4.42e-11!129;UBERON:0002385!7.53e-11!63;UBERON:0001015!7.53e-11!63;UBERON:0000383!7.53e-11!63;UBERON:0003914!1.66e-10!118;UBERON:0001134!2.02e-10!61;UBERON:0002036!2.02e-10!61;UBERON:0003082!2.02e-10!61;UBERON:0001950!3.61e-10!20;UBERON:0000490!3.95e-10!138;UBERON:0000924!4.72e-10!173;UBERON:0006601!4.72e-10!173;UBERON:0004121!6.24e-10!169;UBERON:0001637!1.04e-09!42;UBERON:0003509!1.04e-09!42;UBERON:0004572!1.04e-09!42;UBERON:0003056!2.54e-09!61;UBERON:0007100!2.98e-09!27;UBERON:0004573!8.11e-09!33;UBERON:0004571!8.11e-09!33;UBERON:0002050!3.10e-08!605;UBERON:0005423!3.10e-08!605;UBERON:0004290!3.28e-08!70;UBERON:0000922!4.04e-08!612;UBERON:0000948!5.10e-08!24;UBERON:0005498!5.10e-08!24;UBERON:0004140!5.10e-08!24;UBERON:0009881!5.10e-08!24;UBERON:0004141!5.10e-08!24;UBERON:0003084!5.10e-08!24;UBERON:0007005!5.10e-08!24;UBERON:0004139!5.10e-08!24;UBERON:0004291!5.10e-08!24;UBERON:0000923!5.99e-08!604;UBERON:0005291!5.99e-08!604;UBERON:0006598!5.99e-08!604;UBERON:0002532!5.99e-08!604;UBERON:0000486!5.96e-07!82
|ontology_enrichment_uberon=UBERON:0004111!7.41e-28!241;UBERON:0000025!1.01e-25!194;UBERON:0000477!1.53e-25!286;UBERON:0007023!1.10e-24!115;UBERON:0000119!2.48e-23!312;UBERON:0000483!2.63e-23!309;UBERON:0001049!4.60e-19!57;UBERON:0005068!4.60e-19!57;UBERON:0006241!4.60e-19!57;UBERON:0007135!4.60e-19!57;UBERON:0001017!1.19e-18!82;UBERON:0000955!1.34e-18!69;UBERON:0006238!1.34e-18!69;UBERON:0002616!1.58e-18!59;UBERON:0005743!4.52e-18!86;UBERON:0004872!5.32e-18!84;UBERON:0000073!6.12e-18!94;UBERON:0001016!6.12e-18!94;UBERON:0000475!1.04e-16!365;UBERON:0003075!4.03e-16!86;UBERON:0007284!4.03e-16!86;UBERON:0000055!4.39e-16!69;UBERON:0002346!5.21e-16!90;UBERON:0002049!1.20e-15!79;UBERON:0007798!1.20e-15!79;UBERON:0001981!9.25e-15!60;UBERON:0007500!9.25e-15!60;UBERON:0004537!9.25e-15!60;UBERON:0006965!9.25e-15!60;UBERON:0001009!9.55e-15!113;UBERON:0003080!2.68e-14!42;UBERON:0000468!3.08e-14!659;UBERON:0002780!1.01e-13!41;UBERON:0001890!1.01e-13!41;UBERON:0006240!1.01e-13!41;UBERON:0004535!1.12e-13!110;UBERON:0002020!5.94e-13!34;UBERON:0003528!5.94e-13!34;UBERON:0000481!6.44e-13!347;UBERON:0001893!1.32e-12!34;UBERON:0001869!1.43e-12!32;UBERON:0000467!1.91e-12!625;UBERON:0002791!2.92e-12!33;UBERON:0000480!3.26e-12!626;UBERON:0002619!1.94e-11!22;UBERON:0000956!2.68e-11!25;UBERON:0000203!2.68e-11!25;UBERON:0000033!3.97e-11!123;UBERON:0000153!4.42e-11!129;UBERON:0007811!4.42e-11!129;UBERON:0002385!7.53e-11!63;UBERON:0001015!7.53e-11!63;UBERON:0000383!7.53e-11!63;UBERON:0003914!1.66e-10!118;UBERON:0001134!2.02e-10!61;UBERON:0002036!2.02e-10!61;UBERON:0003082!2.02e-10!61;UBERON:0001950!3.61e-10!20;UBERON:0000490!3.95e-10!138;UBERON:0000924!4.72e-10!173;UBERON:0006601!4.72e-10!173;UBERON:0004121!6.24e-10!169;UBERON:0001637!1.04e-09!42;UBERON:0003509!1.04e-09!42;UBERON:0004572!1.04e-09!42;UBERON:0003056!2.54e-09!61;UBERON:0007100!2.98e-09!27;UBERON:0004573!8.11e-09!33;UBERON:0004571!8.11e-09!33;UBERON:0002050!3.10e-08!605;UBERON:0005423!3.10e-08!605;UBERON:0004290!3.28e-08!70;UBERON:0000922!4.04e-08!612;UBERON:0000948!5.10e-08!24;UBERON:0005498!5.10e-08!24;UBERON:0004140!5.10e-08!24;UBERON:0009881!5.10e-08!24;UBERON:0004141!5.10e-08!24;UBERON:0003084!5.10e-08!24;UBERON:0007005!5.10e-08!24;UBERON:0004139!5.10e-08!24;UBERON:0004291!5.10e-08!24;UBERON:0000923!5.99e-08!604;UBERON:0005291!5.99e-08!604;UBERON:0006598!5.99e-08!604;UBERON:0002532!5.99e-08!604;UBERON:0000486!5.96e-07!82
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0191208012568817!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032442091436071!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00765519464219439!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109248641717329!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140969448445456!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110167310784036
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}}
}}

Revision as of 13:59, 5 September 2012


Full id: C4716_cerebellum_Myoblast_tridermal_osteosarcoma_skeletal_myxofibrosarcoma_synovial



Phase1 CAGE Peaks

Hg19::chr8:106330543..106330554,+p4@ZFPM2
Hg19::chr8:106330656..106330684,+p1@ZFPM2
Hg19::chr8:106330696..106330719,+p2@ZFPM2


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>

Uber Anatomy
Ontology termp-valuen
anatomical conduit7.41e-28241
tube1.01e-25194
anatomical cluster1.53e-25286
adult organism1.10e-24115
cell layer2.48e-23312
epithelium2.63e-23309
neural tube4.60e-1957
neural rod4.60e-1957
future spinal cord4.60e-1957
neural keel4.60e-1957
central nervous system1.19e-1882
brain1.34e-1869
future brain1.34e-1869
regional part of brain1.58e-1859
splanchnic layer of lateral plate mesoderm5.32e-1884
regional part of nervous system6.12e-1894
nervous system6.12e-1894
organism subdivision1.04e-16365
neural plate4.03e-1686
presumptive neural plate4.03e-1686
vessel4.39e-1669
neurectoderm5.21e-1690
vasculature1.20e-1579
vascular system1.20e-1579
blood vessel9.25e-1560
epithelial tube open at both ends9.25e-1560
blood vasculature9.25e-1560
vascular cord9.25e-1560
circulatory system9.55e-15113
anterior neural tube2.68e-1442
multi-cellular organism3.08e-14659
regional part of forebrain1.01e-1341
forebrain1.01e-1341
future forebrain1.01e-1341
cardiovascular system1.12e-13110
gray matter5.94e-1334
brain grey matter5.94e-1334
multi-tissue structure6.44e-13347
telencephalon1.32e-1234
cerebral hemisphere1.43e-1232
anatomical system1.91e-12625
regional part of telencephalon2.92e-1233
anatomical group3.26e-12626
regional part of cerebral cortex1.94e-1122
cerebral cortex2.68e-1125
pallium2.68e-1125
head3.97e-11123
anterior region of body4.42e-11129
craniocervical region4.42e-11129
muscle tissue7.53e-1163
musculature7.53e-1163
musculature of body7.53e-1163
epithelial tube1.66e-10118
skeletal muscle tissue2.02e-1061
striated muscle tissue2.02e-1061
myotome2.02e-1061
neocortex3.61e-1020
unilaminar epithelium3.95e-10138
ectoderm4.72e-10173
presumptive ectoderm4.72e-10173
ectoderm-derived structure6.24e-10169
artery1.04e-0942
arterial blood vessel1.04e-0942
arterial system1.04e-0942
pre-chordal neural plate2.54e-0961
primary circulatory organ2.98e-0927
systemic artery8.11e-0933
systemic arterial system8.11e-0933
embryonic structure3.10e-08605
developing anatomical structure3.10e-08605
dermomyotome3.28e-0870
embryo4.04e-08612
heart5.10e-0824
primitive heart tube5.10e-0824
primary heart field5.10e-0824
anterior lateral plate mesoderm5.10e-0824
heart tube5.10e-0824
heart primordium5.10e-0824
cardiac mesoderm5.10e-0824
cardiogenic plate5.10e-0824
heart rudiment5.10e-0824
germ layer5.99e-08604
embryonic tissue5.99e-08604
presumptive structure5.99e-08604


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
CCNT2#90536.336201576962630.003930750035764890.0191208012568817
E2F6#187635.017155731697390.00791769806886330.032442091436071
ETS1#211339.728760922202340.001085840092584840.00765519464219439
HMGN3#932438.178547723350590.001827766942164210.0109248641717329
ZBTB7A#5134137.35190930787590.002516255860282270.0140969448445456
ZNF263#1012738.221841637010680.001799043925565870.0110167310784036



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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