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Coexpression cluster:C1994: Difference between revisions

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|full_id=C1994_thyroid_optic_Mast_corpus_substantia_thalamus_anaplastic
|full_id=C1994_thyroid_optic_Mast_corpus_substantia_thalamus_anaplastic
|id=C1994
|id=C1994
|ontology_enrichment_celltype=CL:0000037!6.43e-19!172;CL:0000566!6.43e-19!172;CL:0000988!4.53e-18!182;CL:0002032!1.74e-17!165;CL:0000837!1.74e-17!165;CL:0000738!3.20e-17!140;CL:0002031!4.87e-12!124;CL:0002087!1.91e-10!119;CL:0000763!2.87e-10!112;CL:0000049!2.87e-10!112;CL:0000791!4.44e-08!18;CL:0000789!4.44e-08!18;CL:0002420!4.44e-08!18;CL:0002419!4.44e-08!18;CL:0000790!4.44e-08!18;CL:0000838!4.78e-08!52;CL:0000084!7.51e-08!25;CL:0000827!7.51e-08!25;CL:0000542!1.27e-07!53;CL:0000051!1.27e-07!53;CL:0000766!2.72e-07!76
|ontology_enrichment_celltype=CL:0000738!2.96e-07!136;CL:0000084!3.89e-07!25;CL:0000827!3.89e-07!25;CL:0000791!9.49e-07!18;CL:0000789!9.49e-07!18;CL:0002420!9.49e-07!18;CL:0002419!9.49e-07!18;CL:0000790!9.49e-07!18
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.33e-48!115;UBERON:0001049!1.42e-29!57;UBERON:0005068!1.42e-29!57;UBERON:0006241!1.42e-29!57;UBERON:0007135!1.42e-29!57;UBERON:0003080!4.63e-24!42;UBERON:0001017!6.91e-24!82;UBERON:0002780!7.30e-24!41;UBERON:0001890!7.30e-24!41;UBERON:0006240!7.30e-24!41;UBERON:0002616!9.05e-23!59;UBERON:0005743!2.75e-22!86;UBERON:0002020!4.59e-21!34;UBERON:0003528!4.59e-21!34;UBERON:0001893!4.75e-21!34;UBERON:0000955!1.31e-20!69;UBERON:0006238!1.31e-20!69;UBERON:0002791!2.24e-20!33;UBERON:0000073!1.12e-19!94;UBERON:0001016!1.12e-19!94;UBERON:0001869!1.65e-19!32;UBERON:0003075!1.54e-18!86;UBERON:0007284!1.54e-18!86;UBERON:0002346!2.32e-16!90;UBERON:0000956!3.52e-15!25;UBERON:0000203!3.52e-15!25;UBERON:0002619!2.59e-14!22;UBERON:0003056!2.80e-13!61;UBERON:0001950!4.55e-13!20;UBERON:0002193!1.41e-09!112;UBERON:0002390!3.57e-09!102;UBERON:0003061!3.57e-09!102;UBERON:0000153!1.69e-07!129;UBERON:0007811!1.69e-07!129;UBERON:0002308!2.18e-07!9;UBERON:0000125!2.18e-07!9;UBERON:0002420!4.48e-07!9;UBERON:0007245!4.48e-07!9;UBERON:0010009!4.48e-07!9;UBERON:0010011!4.48e-07!9;UBERON:0000454!4.48e-07!9;UBERON:0000178!5.21e-07!15;UBERON:0000179!5.21e-07!15;UBERON:0000463!5.21e-07!15;UBERON:0003076!8.09e-07!15;UBERON:0003057!8.09e-07!15;UBERON:0002298!8.52e-07!8
|ontology_enrichment_uberon=UBERON:0007023!3.11e-49!114;UBERON:0001049!1.71e-34!56;UBERON:0005068!1.71e-34!56;UBERON:0006241!1.71e-34!56;UBERON:0007135!1.71e-34!56;UBERON:0000073!8.12e-32!53;UBERON:0002616!8.12e-32!53;UBERON:0002780!4.56e-27!41;UBERON:0001890!4.56e-27!41;UBERON:0003080!4.56e-27!41;UBERON:0006240!4.56e-27!41;UBERON:0001017!1.21e-25!81;UBERON:0000955!3.14e-25!68;UBERON:0006238!3.14e-25!68;UBERON:0003528!6.84e-24!34;UBERON:0002020!6.84e-24!34;UBERON:0001893!8.07e-24!34;UBERON:0003075!3.08e-23!82;UBERON:0007284!3.08e-23!82;UBERON:0001016!4.62e-22!89;UBERON:0002791!5.00e-22!32;UBERON:0001869!7.64e-22!32;UBERON:0002346!3.95e-21!86;UBERON:0000956!1.61e-16!25;UBERON:0000203!1.61e-16!25;UBERON:0003056!2.29e-16!61;UBERON:0002619!3.64e-15!22;UBERON:0010371!1.40e-14!104;UBERON:0001950!1.48e-13!20;UBERON:0010314!4.20e-11!132;UBERON:0000125!5.85e-09!9;UBERON:0002308!5.85e-09!9;UBERON:0002420!1.45e-08!9;UBERON:0007245!1.45e-08!9;UBERON:0010009!1.45e-08!9;UBERON:0010011!1.45e-08!9;UBERON:0000454!1.45e-08!9;UBERON:0003076!1.46e-08!15;UBERON:0003057!1.46e-08!15;UBERON:0011216!5.70e-08!223;UBERON:0002298!3.20e-07!6;UBERON:0009663!4.35e-07!7;UBERON:0004732!5.36e-07!13
|tf_chipseq_enrich=CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250298892932141!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00323285846389824!EBF1#1879;3:5.3438801079414:0.0118761556386811:0.043247343749938!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00331156326918407!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00573849436705403!GABPB1#2553;5:7.06768383618217:5.6685482528729e-05:0.000949659144982022!IRF4#3662;5:21.9145126867441:1.97628413609567e-07:1.07388729911392e-05!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130840659617282!MEF2A#4205;5:18.7432309096441:4.31877656850983e-07:2.07378715420045e-05!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117168082610577!POU2F2#5452;5:9.10612405774252:1.59639992500654e-05:0.00037017409362291!RAD21#5885;5:10.3550338954563:8.39503550283973e-06:0.000230002390577408!REST#5978;5:9.65002871612802:1.19441074361324e-05:0.000301676091057371!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.1734189879886e-05!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000575755014564612!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135564635131399!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00920415461330171!TCF12#6938;5:10.6344649021864:7.34844389925727e-06:0.000211539176514479!TRIM28#10155;5:18.5905250452625:4.49912775886781e-07:2.13778163789079e-05!ZNF263#10127;5:8.22184163701068:2.6606316672286e-05:0.000572699321297791
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}}
}}

Revision as of 11:55, 19 October 2012


Full id: C1994_thyroid_optic_Mast_corpus_substantia_thalamus_anaplastic



Phase1 CAGE Peaks

Hg19::chr7:37488524..37488535,-p15@ELMO1
Hg19::chr7:37488547..37488560,-p6@ELMO1
Hg19::chr7:37488575..37488588,-p9@ELMO1
Hg19::chr7:37488607..37488614,-p21@ELMO1
Hg19::chr7:37488635..37488658,-p16@ELMO1


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
leukocyte2.96e-07136
T cell3.89e-0725
pro-T cell3.89e-0725
mature alpha-beta T cell9.49e-0718
alpha-beta T cell9.49e-0718
immature T cell9.49e-0718
mature T cell9.49e-0718
immature alpha-beta T cell9.49e-0718
Uber Anatomy
Ontology termp-valuen
adult organism3.11e-49114
neural tube1.71e-3456
neural rod1.71e-3456
future spinal cord1.71e-3456
neural keel1.71e-3456
regional part of nervous system8.12e-3253
regional part of brain8.12e-3253
regional part of forebrain4.56e-2741
forebrain4.56e-2741
anterior neural tube4.56e-2741
future forebrain4.56e-2741
central nervous system1.21e-2581
brain3.14e-2568
future brain3.14e-2568
brain grey matter6.84e-2434
gray matter6.84e-2434
telencephalon8.07e-2434
neural plate3.08e-2382
presumptive neural plate3.08e-2382
nervous system4.62e-2289
regional part of telencephalon5.00e-2232
cerebral hemisphere7.64e-2232
neurectoderm3.95e-2186
cerebral cortex1.61e-1625
pallium1.61e-1625
pre-chordal neural plate2.29e-1661
regional part of cerebral cortex3.64e-1522
ecto-epithelium1.40e-14104
neocortex1.48e-1320
structure with developmental contribution from neural crest4.20e-11132
neural nucleus5.85e-099
nucleus of brain5.85e-099
basal ganglion1.45e-089
nuclear complex of neuraxis1.45e-089
aggregate regional part of brain1.45e-089
collection of basal ganglia1.45e-089
cerebral subcortex1.45e-089
posterior neural tube1.46e-0815
chordal neural plate1.46e-0815
organ system subdivision5.70e-08223
brainstem3.20e-076
telencephalic nucleus4.35e-077
segmental subdivision of nervous system5.36e-0713


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#1066455.360256373075030.0002259278299937090.00250298892932141
E2F6#187655.017155731697390.0003144978599297790.00323285846389824
EBF1#187935.34388010794140.01187615563868110.043247343749938
EGR1#195854.988179094810140.0003237398000590710.00331156326918407
ELF1#199754.258097958807540.0007142416939776840.00573849436705403
GABPB1#255357.067683836182175.6685482528729e-050.000949659144982022
IRF4#3662521.91451268674411.97628413609567e-071.07388729911392e-05
MAX#414956.452555509007128.93743970843928e-050.00130840659617282
MEF2A#4205518.74323090964414.31877656850983e-072.07378715420045e-05
PAX5#507956.669565531177837.57493746384605e-050.00117168082610577
POU2F2#545259.106124057742521.59639992500654e-050.00037017409362291
RAD21#5885510.35503389545638.39503550283973e-060.000230002390577408
REST#597859.650028716128021.19441074361324e-050.000301676091057371
SMC3#9126515.04493284493281.29633924985553e-065.1734189879886e-05
SPI1#668858.204323508522732.68916109982495e-050.000575755014564612
TAF1#687253.343046285745290.002394600090870310.0135564635131399
TBP#690853.706770687096390.001428755106721120.00920415461330171
TCF12#6938510.63446490218647.34844389925727e-060.000211539176514479
TRIM28#10155518.59052504526254.49912775886781e-072.13778163789079e-05
ZNF263#1012758.221841637010682.6606316672286e-050.000572699321297791



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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