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Coexpression cluster:C2566: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000477!4.54e-28!286;UBERON:0000119!1.03e-27!312;UBERON:0000483!2.09e-26!309;UBERON:0004111!8.92e-26!241;UBERON:0000481!1.01e-25!347;UBERON:0000033!5.12e-24!123;UBERON:0000475!1.92e-23!365;UBERON:0000153!4.55e-22!129;UBERON:0007811!4.55e-22!129;UBERON:0000025!1.02e-21!194;UBERON:0004121!4.04e-21!169;UBERON:0003075!7.02e-21!86;UBERON:0007284!7.02e-21!86;UBERON:0000924!1.13e-20!173;UBERON:0006601!1.13e-20!173;UBERON:0005743!1.39e-20!86;UBERON:0000468!3.01e-20!659;UBERON:0002346!5.50e-20!90;UBERON:0001017!9.67e-20!82;UBERON:0000955!1.13e-19!69;UBERON:0006238!1.13e-19!69;UBERON:0000073!3.58e-19!94;UBERON:0001016!3.58e-19!94;UBERON:0000467!3.22e-18!625;UBERON:0002616!5.11e-18!59;UBERON:0002050!5.56e-18!605;UBERON:0005423!5.56e-18!605;UBERON:0000480!6.31e-18!626;UBERON:0000922!7.25e-18!612;UBERON:0000923!9.18e-18!604;UBERON:0005291!9.18e-18!604;UBERON:0006598!9.18e-18!604;UBERON:0002532!9.18e-18!604;UBERON:0001049!1.12e-16!57;UBERON:0005068!1.12e-16!57;UBERON:0006241!1.12e-16!57;UBERON:0007135!1.12e-16!57;UBERON:0003056!2.70e-15!61;UBERON:0000062!5.68e-15!511;UBERON:0002780!1.69e-12!41;UBERON:0001890!1.69e-12!41;UBERON:0006240!1.69e-12!41;UBERON:0003080!3.13e-12!42;UBERON:0000064!8.35e-12!219;UBERON:0002020!9.17e-12!34;UBERON:0003528!9.17e-12!34;UBERON:0001893!1.61e-11!34;UBERON:0002791!2.25e-11!33;UBERON:0001869!5.28e-11!32;UBERON:0000956!3.20e-09!25;UBERON:0000203!3.20e-09!25;UBERON:0003914!8.49e-09!118;UBERON:0002049!8.56e-09!79;UBERON:0007798!8.56e-09!79;UBERON:0005256!1.14e-08!143;UBERON:0002619!1.09e-07!22;UBERON:0002100!1.91e-07!216;UBERON:0000058!2.71e-07!26;UBERON:0003104!2.94e-07!238;UBERON:0009142!2.94e-07!238;UBERON:0007023!3.37e-07!115;UBERON:0001950!6.23e-07!20
|ontology_enrichment_uberon=UBERON:0000477!4.54e-28!286;UBERON:0000119!1.03e-27!312;UBERON:0000483!2.09e-26!309;UBERON:0004111!8.92e-26!241;UBERON:0000481!1.01e-25!347;UBERON:0000033!5.12e-24!123;UBERON:0000475!1.92e-23!365;UBERON:0000153!4.55e-22!129;UBERON:0007811!4.55e-22!129;UBERON:0000025!1.02e-21!194;UBERON:0004121!4.04e-21!169;UBERON:0003075!7.02e-21!86;UBERON:0007284!7.02e-21!86;UBERON:0000924!1.13e-20!173;UBERON:0006601!1.13e-20!173;UBERON:0005743!1.39e-20!86;UBERON:0000468!3.01e-20!659;UBERON:0002346!5.50e-20!90;UBERON:0001017!9.67e-20!82;UBERON:0000955!1.13e-19!69;UBERON:0006238!1.13e-19!69;UBERON:0000073!3.58e-19!94;UBERON:0001016!3.58e-19!94;UBERON:0000467!3.22e-18!625;UBERON:0002616!5.11e-18!59;UBERON:0002050!5.56e-18!605;UBERON:0005423!5.56e-18!605;UBERON:0000480!6.31e-18!626;UBERON:0000922!7.25e-18!612;UBERON:0000923!9.18e-18!604;UBERON:0005291!9.18e-18!604;UBERON:0006598!9.18e-18!604;UBERON:0002532!9.18e-18!604;UBERON:0001049!1.12e-16!57;UBERON:0005068!1.12e-16!57;UBERON:0006241!1.12e-16!57;UBERON:0007135!1.12e-16!57;UBERON:0003056!2.70e-15!61;UBERON:0000062!5.68e-15!511;UBERON:0002780!1.69e-12!41;UBERON:0001890!1.69e-12!41;UBERON:0006240!1.69e-12!41;UBERON:0003080!3.13e-12!42;UBERON:0000064!8.35e-12!219;UBERON:0002020!9.17e-12!34;UBERON:0003528!9.17e-12!34;UBERON:0001893!1.61e-11!34;UBERON:0002791!2.25e-11!33;UBERON:0001869!5.28e-11!32;UBERON:0000956!3.20e-09!25;UBERON:0000203!3.20e-09!25;UBERON:0003914!8.49e-09!118;UBERON:0002049!8.56e-09!79;UBERON:0007798!8.56e-09!79;UBERON:0005256!1.14e-08!143;UBERON:0002619!1.09e-07!22;UBERON:0002100!1.91e-07!216;UBERON:0000058!2.71e-07!26;UBERON:0003104!2.94e-07!238;UBERON:0009142!2.94e-07!238;UBERON:0007023!3.37e-07!115;UBERON:0001950!6.23e-07!20
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897,0.0926658,0.222091,0.205977,0.34423,0.0936726,0.0671916,0.00917587,0.285122,0.0280766,0.203996,0.276721,0.00732664,0.264707,0.121257
}}
}}

Revision as of 12:01, 5 September 2012


Full id: C2566_Lens_gall_papillotubular_anaplastic_Ciliary_osteoclastoma_alveolar



Phase1 CAGE Peaks

Hg19::chr1:218518669..218518689,+p1@TGFB2
Hg19::chr1:218518858..218518869,+p21@TGFB2
Hg19::chr1:218518942..218518953,+p28@TGFB2
Hg19::chr1:218519057..218519070,+p11@TGFB2


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
vascular associated smooth muscle cell8.39e-0832
Uber Anatomy
Ontology termp-valuen
anatomical cluster4.54e-28286
cell layer1.03e-27312
epithelium2.09e-26309
anatomical conduit8.92e-26241
multi-tissue structure1.01e-25347
head5.12e-24123
organism subdivision1.92e-23365
anterior region of body4.55e-22129
craniocervical region4.55e-22129
tube1.02e-21194
ectoderm-derived structure4.04e-21169
neural plate7.02e-2186
presumptive neural plate7.02e-2186
ectoderm1.13e-20173
presumptive ectoderm1.13e-20173
multi-cellular organism3.01e-20659
neurectoderm5.50e-2090
central nervous system9.67e-2082
brain1.13e-1969
future brain1.13e-1969
regional part of nervous system3.58e-1994
nervous system3.58e-1994
anatomical system3.22e-18625
regional part of brain5.11e-1859
embryonic structure5.56e-18605
developing anatomical structure5.56e-18605
anatomical group6.31e-18626
embryo7.25e-18612
germ layer9.18e-18604
embryonic tissue9.18e-18604
presumptive structure9.18e-18604
epiblast (generic)9.18e-18604
neural tube1.12e-1657
neural rod1.12e-1657
future spinal cord1.12e-1657
neural keel1.12e-1657
pre-chordal neural plate2.70e-1561
organ5.68e-15511
regional part of forebrain1.69e-1241
forebrain1.69e-1241
future forebrain1.69e-1241
anterior neural tube3.13e-1242
organ part8.35e-12219
gray matter9.17e-1234
brain grey matter9.17e-1234
telencephalon1.61e-1134
regional part of telencephalon2.25e-1133
cerebral hemisphere5.28e-1132
cerebral cortex3.20e-0925
pallium3.20e-0925
epithelial tube8.49e-09118
vasculature8.56e-0979
vascular system8.56e-0979
trunk mesenchyme1.14e-08143
regional part of cerebral cortex1.09e-0722
trunk1.91e-07216
duct2.71e-0726
mesenchyme2.94e-07238
entire embryonic mesenchyme2.94e-07238
adult organism3.37e-07115
neocortex6.23e-0720


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
CEBPB#105135.978360719368610.007153832484726970.0297309634250856
CTBP2#1488462.71700033932816.45042639894877e-083.96047079764733e-06
CTCF#1066445.360256373075030.001211145381643620.0081770516848845
E2F6#187645.017155731697390.00157802193473060.00997379767860863
GATA2#2624412.7449317335543.78864877853583e-050.000722312321616473
GATA3#2625427.2365163572061.81561517799785e-066.77702049946094e-05
MAX#414934.839416631755340.01315737137836840.0466269454509658
TAL1#6886429.86861667744021.25525650806991e-065.04222055562743e-05
TBP#690843.706770687096390.005296377814784350.0244431463808335
USF1#739134.771124457905970.01370465887188020.0483090612906808
USF2#739239.74414803880220.001718341848410070.0107218248480165
ZNF263#1012748.221841637010680.0002187871180958320.00249072463776004



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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