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Coexpression cluster:C2681: Difference between revisions

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|ontology_enrichment_disease=DOID:162!3.74e-12!235;DOID:14566!3.75e-12!239;DOID:0050687!9.28e-12!143;DOID:3095!1.76e-07!22;DOID:2994!1.76e-07!22;DOID:305!9.86e-07!106
|ontology_enrichment_disease=DOID:162!3.74e-12!235;DOID:14566!3.75e-12!239;DOID:0050687!9.28e-12!143;DOID:3095!1.76e-07!22;DOID:2994!1.76e-07!22;DOID:305!9.86e-07!106
|ontology_enrichment_uberon=UBERON:0000073!2.13e-37!94;UBERON:0001016!2.13e-37!94;UBERON:0005743!5.96e-36!86;UBERON:0001017!2.47e-35!82;UBERON:0002346!1.17e-29!90;UBERON:0000955!2.83e-29!69;UBERON:0006238!2.83e-29!69;UBERON:0001049!9.00e-29!57;UBERON:0005068!9.00e-29!57;UBERON:0006241!9.00e-29!57;UBERON:0007135!9.00e-29!57;UBERON:0003075!3.79e-28!86;UBERON:0007284!3.79e-28!86;UBERON:0002616!2.10e-25!59;UBERON:0000924!4.15e-23!173;UBERON:0006601!4.15e-23!173;UBERON:0002780!9.78e-23!41;UBERON:0001890!9.78e-23!41;UBERON:0006240!9.78e-23!41;UBERON:0003056!3.31e-22!61;UBERON:0003080!8.60e-22!42;UBERON:0004121!9.33e-22!169;UBERON:0001893!3.32e-20!34;UBERON:0002020!4.50e-20!34;UBERON:0003528!4.50e-20!34;UBERON:0001869!1.50e-19!32;UBERON:0002791!1.51e-19!33;UBERON:0000033!1.70e-18!123;UBERON:0000153!7.40e-18!129;UBERON:0007811!7.40e-18!129;UBERON:0000119!1.99e-17!312;UBERON:0000483!1.11e-16!309;UBERON:0000956!8.44e-16!25;UBERON:0000203!8.44e-16!25;UBERON:0000025!1.46e-15!194;UBERON:0000477!1.56e-14!286;UBERON:0002619!3.13e-14!22;UBERON:0000475!1.47e-13!365;UBERON:0000481!1.83e-13!347;UBERON:0001950!5.04e-13!20;UBERON:0004111!1.56e-12!241;UBERON:0003076!4.13e-08!15;UBERON:0003057!4.13e-08!15;UBERON:0000064!6.64e-08!219;UBERON:0000922!3.32e-07!612;UBERON:0004733!8.89e-07!12;UBERON:0002028!8.89e-07!12;UBERON:0007277!8.89e-07!12
|ontology_enrichment_uberon=UBERON:0000073!2.13e-37!94;UBERON:0001016!2.13e-37!94;UBERON:0005743!5.96e-36!86;UBERON:0001017!2.47e-35!82;UBERON:0002346!1.17e-29!90;UBERON:0000955!2.83e-29!69;UBERON:0006238!2.83e-29!69;UBERON:0001049!9.00e-29!57;UBERON:0005068!9.00e-29!57;UBERON:0006241!9.00e-29!57;UBERON:0007135!9.00e-29!57;UBERON:0003075!3.79e-28!86;UBERON:0007284!3.79e-28!86;UBERON:0002616!2.10e-25!59;UBERON:0000924!4.15e-23!173;UBERON:0006601!4.15e-23!173;UBERON:0002780!9.78e-23!41;UBERON:0001890!9.78e-23!41;UBERON:0006240!9.78e-23!41;UBERON:0003056!3.31e-22!61;UBERON:0003080!8.60e-22!42;UBERON:0004121!9.33e-22!169;UBERON:0001893!3.32e-20!34;UBERON:0002020!4.50e-20!34;UBERON:0003528!4.50e-20!34;UBERON:0001869!1.50e-19!32;UBERON:0002791!1.51e-19!33;UBERON:0000033!1.70e-18!123;UBERON:0000153!7.40e-18!129;UBERON:0007811!7.40e-18!129;UBERON:0000119!1.99e-17!312;UBERON:0000483!1.11e-16!309;UBERON:0000956!8.44e-16!25;UBERON:0000203!8.44e-16!25;UBERON:0000025!1.46e-15!194;UBERON:0000477!1.56e-14!286;UBERON:0002619!3.13e-14!22;UBERON:0000475!1.47e-13!365;UBERON:0000481!1.83e-13!347;UBERON:0001950!5.04e-13!20;UBERON:0004111!1.56e-12!241;UBERON:0003076!4.13e-08!15;UBERON:0003057!4.13e-08!15;UBERON:0000064!6.64e-08!219;UBERON:0000922!3.32e-07!612;UBERON:0004733!8.89e-07!12;UBERON:0002028!8.89e-07!12;UBERON:0007277!8.89e-07!12
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}}
}}

Revision as of 13:54, 5 September 2012


Full id: C2681_amygdala_duodenum_insula_rhabdomyosarcoma_medial_frontal_brain



Phase1 CAGE Peaks

Hg19::chr2:204193085..204193096,+p3@ABI2
Hg19::chr2:204193101..204193128,+p2@ABI2
Hg19::chr2:204193129..204193139,+p4@ABI2
Hg19::chr2:204193149..204193156,+p5@ABI2


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>

Cell Type
Ontology termp-valuen
neural cell7.74e-1025
neurectodermal cell1.25e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.13e-3794
nervous system2.13e-3794
central nervous system2.47e-3582
neurectoderm1.17e-2990
brain2.83e-2969
future brain2.83e-2969
neural tube9.00e-2957
neural rod9.00e-2957
future spinal cord9.00e-2957
neural keel9.00e-2957
neural plate3.79e-2886
presumptive neural plate3.79e-2886
regional part of brain2.10e-2559
ectoderm4.15e-23173
presumptive ectoderm4.15e-23173
regional part of forebrain9.78e-2341
forebrain9.78e-2341
future forebrain9.78e-2341
pre-chordal neural plate3.31e-2261
anterior neural tube8.60e-2242
ectoderm-derived structure9.33e-22169
telencephalon3.32e-2034
gray matter4.50e-2034
brain grey matter4.50e-2034
cerebral hemisphere1.50e-1932
regional part of telencephalon1.51e-1933
head1.70e-18123
anterior region of body7.40e-18129
craniocervical region7.40e-18129
cell layer1.99e-17312
epithelium1.11e-16309
cerebral cortex8.44e-1625
pallium8.44e-1625
tube1.46e-15194
anatomical cluster1.56e-14286
regional part of cerebral cortex3.13e-1422
organism subdivision1.47e-13365
multi-tissue structure1.83e-13347
neocortex5.04e-1320
anatomical conduit1.56e-12241
posterior neural tube4.13e-0815
chordal neural plate4.13e-0815
organ part6.64e-08219
embryo3.32e-07612
segmental subdivision of hindbrain8.89e-0712
hindbrain8.89e-0712
presumptive hindbrain8.89e-0712
Disease
Ontology termp-valuen
cancer3.74e-12235
disease of cellular proliferation3.75e-12239
cell type cancer9.28e-12143
germ cell and embryonal cancer1.76e-0722
germ cell cancer1.76e-0722
carcinoma9.86e-07106


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#90546.336201576962630.0006203100587215640.00512901292239897
CHD2#1106410.34402283411698.73193255208051e-050.00129190296615206
E2F1#186944.907389214879320.001724022357361790.0106629853713436
EGR1#195844.988179094810140.001615011500076050.010155348669784
ELF1#199744.258097958807540.003041525565781240.0161122946266613
ELK4#2005416.2356816584681.43847748454449e-050.000343547107268104
EP300#203346.77394172622320.0004748459821442640.00434602046526727
FOXA1#3169411.08141974938556.62943068949433e-050.00107211383056689
GABPB1#255347.067683836182170.0004006876864423170.00390622806724065
HDAC2#3066413.41562023662633.0859005065161e-050.000627508494937763
HEY1#2346244.040111043105710.00375304636917980.0186374594527493
HMGN3#932448.178547723350590.0002234570284440470.00248378337523072
HNF4A#3172423.13229036295373.48990320893214e-060.000115745316366359
HNF4G#3174428.75342252644681.46167379934821e-065.67493494164044e-05
JUND#372746.994663941871030.000417684217818580.003920773146212
NANOG#79923429.24477848101271.36586687657858e-065.34468979853843e-05
NRF1#4899412.21027944771094.49717228915276e-050.000794586663351083
REST#597849.650028716128020.0001152825614219170.00157282762016246
RXRA#6256420.07461713913336.1537798808435e-060.000182480016177006
SIN3A#2594245.408884726815140.001168172384885160.00797299409913873
SP1#666745.69838137814090.0009482606065333980.00684986785763878
SREBF1#6720447.00584944048832.04523668136926e-071.1038887533102e-05
TAF1#687243.343046285745290.008005664898701650.0322757628394326
TBP#690843.706770687096390.005296377814784350.0244626040420247
YY1#752844.911170749853860.00171871838055440.0106966944131292
ZBTB33#10009431.66472502998129.93721537730495e-074.20175237566944e-05
ZBTB7A#5134147.35190930787590.000342223540015990.00347038394948344
ZNF143#7702413.50087655222793.00867915035614e-050.000621363341475272
ZNF263#1012748.221841637010680.0002187871180958320.00249398688352004



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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