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Coexpression cluster:C1095: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.91e-34!115;UBERON:0002616!1.14e-21!59;UBERON:0001049!2.62e-21!57;UBERON:0005068!2.62e-21!57;UBERON:0006241!2.62e-21!57;UBERON:0007135!2.62e-21!57;UBERON:0003080!8.85e-18!42;UBERON:0000073!9.06e-18!94;UBERON:0001016!9.06e-18!94;UBERON:0002346!1.04e-17!90;UBERON:0002780!3.84e-17!41;UBERON:0001890!3.84e-17!41;UBERON:0006240!3.84e-17!41;UBERON:0003075!8.93e-17!86;UBERON:0007284!8.93e-17!86;UBERON:0000955!2.02e-16!69;UBERON:0006238!2.02e-16!69;UBERON:0001017!1.17e-15!82;UBERON:0005743!2.08e-15!86;UBERON:0000475!3.92e-15!365;UBERON:0001893!6.50e-15!34;UBERON:0002020!6.68e-15!34;UBERON:0003528!6.68e-15!34;UBERON:0002791!2.34e-14!33;UBERON:0000477!2.36e-14!286;UBERON:0001869!4.66e-14!32;UBERON:0000153!1.97e-13!129;UBERON:0007811!1.97e-13!129;UBERON:0004111!2.05e-13!241;UBERON:0000924!2.51e-13!173;UBERON:0006601!2.51e-13!173;UBERON:0000033!4.46e-13!123;UBERON:0000119!4.57e-13!312;UBERON:0000468!8.25e-13!659;UBERON:0000025!1.25e-12!194;UBERON:0000481!1.36e-12!347;UBERON:0000483!1.46e-12!309;UBERON:0004121!1.60e-12!169;UBERON:0003056!3.03e-12!61;UBERON:0000914!1.23e-11!83;UBERON:0002329!1.23e-11!83;UBERON:0003077!1.23e-11!83;UBERON:0003059!1.23e-11!83;UBERON:0007282!1.23e-11!83;UBERON:0009618!1.23e-11!83;UBERON:0007285!1.23e-11!83;UBERON:0002619!2.54e-11!22;UBERON:0000956!3.89e-11!25;UBERON:0000203!3.89e-11!25;UBERON:0001950!7.73e-11!20;UBERON:0000479!1.71e-10!787;UBERON:0004290!2.80e-10!70;UBERON:0002385!1.05e-09!63;UBERON:0001015!1.05e-09!63;UBERON:0000383!1.05e-09!63;UBERON:0000480!1.29e-09!626;UBERON:0000467!1.31e-09!625;UBERON:0001134!5.40e-09!61;UBERON:0002036!5.40e-09!61;UBERON:0003082!5.40e-09!61;UBERON:0007100!4.87e-08!27;UBERON:0004872!1.50e-07!84;UBERON:0000922!2.78e-07!612;UBERON:0002050!2.96e-07!605;UBERON:0005423!2.96e-07!605;UBERON:0000486!2.97e-07!82;UBERON:0000923!5.83e-07!604;UBERON:0005291!5.83e-07!604;UBERON:0006598!5.83e-07!604;UBERON:0002532!5.83e-07!604;UBERON:0001009!8.41e-07!113
|ontology_enrichment_uberon=UBERON:0007023!1.91e-34!115;UBERON:0002616!1.14e-21!59;UBERON:0001049!2.62e-21!57;UBERON:0005068!2.62e-21!57;UBERON:0006241!2.62e-21!57;UBERON:0007135!2.62e-21!57;UBERON:0003080!8.85e-18!42;UBERON:0000073!9.06e-18!94;UBERON:0001016!9.06e-18!94;UBERON:0002346!1.04e-17!90;UBERON:0002780!3.84e-17!41;UBERON:0001890!3.84e-17!41;UBERON:0006240!3.84e-17!41;UBERON:0003075!8.93e-17!86;UBERON:0007284!8.93e-17!86;UBERON:0000955!2.02e-16!69;UBERON:0006238!2.02e-16!69;UBERON:0001017!1.17e-15!82;UBERON:0005743!2.08e-15!86;UBERON:0000475!3.92e-15!365;UBERON:0001893!6.50e-15!34;UBERON:0002020!6.68e-15!34;UBERON:0003528!6.68e-15!34;UBERON:0002791!2.34e-14!33;UBERON:0000477!2.36e-14!286;UBERON:0001869!4.66e-14!32;UBERON:0000153!1.97e-13!129;UBERON:0007811!1.97e-13!129;UBERON:0004111!2.05e-13!241;UBERON:0000924!2.51e-13!173;UBERON:0006601!2.51e-13!173;UBERON:0000033!4.46e-13!123;UBERON:0000119!4.57e-13!312;UBERON:0000468!8.25e-13!659;UBERON:0000025!1.25e-12!194;UBERON:0000481!1.36e-12!347;UBERON:0000483!1.46e-12!309;UBERON:0004121!1.60e-12!169;UBERON:0003056!3.03e-12!61;UBERON:0000914!1.23e-11!83;UBERON:0002329!1.23e-11!83;UBERON:0003077!1.23e-11!83;UBERON:0003059!1.23e-11!83;UBERON:0007282!1.23e-11!83;UBERON:0009618!1.23e-11!83;UBERON:0007285!1.23e-11!83;UBERON:0002619!2.54e-11!22;UBERON:0000956!3.89e-11!25;UBERON:0000203!3.89e-11!25;UBERON:0001950!7.73e-11!20;UBERON:0000479!1.71e-10!787;UBERON:0004290!2.80e-10!70;UBERON:0002385!1.05e-09!63;UBERON:0001015!1.05e-09!63;UBERON:0000383!1.05e-09!63;UBERON:0000480!1.29e-09!626;UBERON:0000467!1.31e-09!625;UBERON:0001134!5.40e-09!61;UBERON:0002036!5.40e-09!61;UBERON:0003082!5.40e-09!61;UBERON:0007100!4.87e-08!27;UBERON:0004872!1.50e-07!84;UBERON:0000922!2.78e-07!612;UBERON:0002050!2.96e-07!605;UBERON:0005423!2.96e-07!605;UBERON:0000486!2.97e-07!82;UBERON:0000923!5.83e-07!604;UBERON:0005291!5.83e-07!604;UBERON:0006598!5.83e-07!604;UBERON:0002532!5.83e-07!604;UBERON:0001009!8.41e-07!113
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}}
}}

Revision as of 12:37, 5 September 2012


Full id: C1095_heart_skin_lung_neuroblastoma_skeletal_adipose_rectum



Phase1 CAGE Peaks

Hg19::chr8:13154787..13154792,-p@chr8:13154787..13154792
-
Hg19::chr8:13372153..13372182,-p12@DLC1
Hg19::chr8:13372233..13372251,-p15@DLC1
Hg19::chr8:13372253..13372282,-p7@DLC1
Hg19::chr8:13372298..13372312,-p24@DLC1
Hg19::chr8:13372331..13372375,-p4@DLC1
Hg19::chr8:13372410..13372429,-p9@DLC1
Hg19::chr8:13372434..13372466,-p8@DLC1


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
non-terminally differentiated cell1.47e-15180
fibroblast5.56e-1375
muscle precursor cell1.90e-0757
myoblast1.90e-0757
multi-potent skeletal muscle stem cell1.90e-0757
muscle cell2.14e-0754
contractile cell4.63e-0759
Uber Anatomy
Ontology termp-valuen
adult organism1.91e-34115
regional part of brain1.14e-2159
neural tube2.62e-2157
neural rod2.62e-2157
future spinal cord2.62e-2157
neural keel2.62e-2157
anterior neural tube8.85e-1842
regional part of nervous system9.06e-1894
nervous system9.06e-1894
neurectoderm1.04e-1790
regional part of forebrain3.84e-1741
forebrain3.84e-1741
future forebrain3.84e-1741
neural plate8.93e-1786
presumptive neural plate8.93e-1786
brain2.02e-1669
future brain2.02e-1669
central nervous system1.17e-1582
organism subdivision3.92e-15365
telencephalon6.50e-1534
gray matter6.68e-1534
brain grey matter6.68e-1534
regional part of telencephalon2.34e-1433
anatomical cluster2.36e-14286
cerebral hemisphere4.66e-1432
anterior region of body1.97e-13129
craniocervical region1.97e-13129
anatomical conduit2.05e-13241
ectoderm2.51e-13173
presumptive ectoderm2.51e-13173
head4.46e-13123
cell layer4.57e-13312
multi-cellular organism8.25e-13659
tube1.25e-12194
multi-tissue structure1.36e-12347
epithelium1.46e-12309
ectoderm-derived structure1.60e-12169
pre-chordal neural plate3.03e-1261
somite1.23e-1183
paraxial mesoderm1.23e-1183
presomitic mesoderm1.23e-1183
presumptive segmental plate1.23e-1183
trunk paraxial mesoderm1.23e-1183
presumptive paraxial mesoderm1.23e-1183
regional part of cerebral cortex2.54e-1122
cerebral cortex3.89e-1125
pallium3.89e-1125
neocortex7.73e-1120
tissue1.71e-10787
dermomyotome2.80e-1070
muscle tissue1.05e-0963
musculature1.05e-0963
musculature of body1.05e-0963
anatomical group1.29e-09626
anatomical system1.31e-09625
skeletal muscle tissue5.40e-0961
striated muscle tissue5.40e-0961
myotome5.40e-0961
primary circulatory organ4.87e-0827
splanchnic layer of lateral plate mesoderm1.50e-0784
embryo2.78e-07612
embryonic structure2.96e-07605
developing anatomical structure2.96e-07605
multilaminar epithelium2.97e-0782
germ layer5.83e-07604
embryonic tissue5.83e-07604
presumptive structure5.83e-07604
epiblast (generic)5.83e-07604
circulatory system8.41e-07113


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#1066474.690224326440655.26249365325459e-050.000894255734871879
EP300#203375.92719901044531.06380393527283e-050.00027623724315256
RAD21#588579.060654658524295.73112922357867e-072.64028850896045e-05
YY1#752874.297274406122129.53674534900876e-050.00136476863182396



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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