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Coexpression cluster:C4823: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000025!1.62e-24!194;UBERON:0000477!2.20e-23!286;UBERON:0004111!2.35e-23!241;UBERON:0000483!5.67e-19!309;UBERON:0000119!1.94e-18!312;UBERON:0000475!6.58e-18!365;UBERON:0000481!2.34e-17!347;UBERON:0001637!4.45e-16!42;UBERON:0003509!4.45e-16!42;UBERON:0004572!4.45e-16!42;UBERON:0003914!4.87e-15!118;UBERON:0004573!6.45e-14!33;UBERON:0004571!6.45e-14!33;UBERON:0001981!3.13e-13!60;UBERON:0007500!3.13e-13!60;UBERON:0004537!3.13e-13!60;UBERON:0006965!3.13e-13!60;UBERON:0002049!6.44e-13!79;UBERON:0007798!6.44e-13!79;UBERON:0000055!8.38e-13!69;UBERON:0000490!1.27e-12!138;UBERON:0004872!1.36e-12!84;UBERON:0001017!1.01e-11!82;UBERON:0001049!1.29e-11!57;UBERON:0005068!1.29e-11!57;UBERON:0006241!1.29e-11!57;UBERON:0007135!1.29e-11!57;UBERON:0002616!1.83e-11!59;UBERON:0002780!2.25e-11!41;UBERON:0001890!2.25e-11!41;UBERON:0006240!2.25e-11!41;UBERON:0000468!3.82e-11!659;UBERON:0005743!4.24e-11!86;UBERON:0003080!4.29e-11!42;UBERON:0002619!7.78e-11!22;UBERON:0001869!8.19e-11!32;UBERON:0000073!8.77e-11!94;UBERON:0001016!8.77e-11!94;UBERON:0001893!9.22e-11!34;UBERON:0002100!1.10e-10!216;UBERON:0002020!1.25e-10!34;UBERON:0003528!1.25e-10!34;UBERON:0000955!1.69e-10!69;UBERON:0006238!1.69e-10!69;UBERON:0002791!2.59e-10!33;UBERON:0005256!3.77e-10!143;UBERON:0001950!5.40e-10!20;UBERON:0000480!1.45e-09!626;UBERON:0000467!1.60e-09!625;UBERON:0002346!1.92e-09!90;UBERON:0003075!2.27e-09!86;UBERON:0007284!2.27e-09!86;UBERON:0002385!1.97e-08!63;UBERON:0001015!1.97e-08!63;UBERON:0000383!1.97e-08!63;UBERON:0000956!2.42e-08!25;UBERON:0000203!2.42e-08!25;UBERON:0003056!3.71e-08!61;UBERON:0004535!4.11e-08!110;UBERON:0001009!4.97e-08!113;UBERON:0007023!5.53e-08!115;UBERON:0001134!9.59e-08!61;UBERON:0002036!9.59e-08!61;UBERON:0003082!9.59e-08!61;UBERON:0000922!9.68e-08!612;UBERON:0000947!1.19e-07!21;UBERON:0010191!1.19e-07!21;UBERON:0002050!1.36e-07!605;UBERON:0005423!1.36e-07!605;UBERON:0000923!1.75e-07!604;UBERON:0005291!1.75e-07!604;UBERON:0006598!1.75e-07!604;UBERON:0002532!1.75e-07!604;UBERON:0000914!1.89e-07!83;UBERON:0002329!1.89e-07!83;UBERON:0003077!1.89e-07!83;UBERON:0003059!1.89e-07!83;UBERON:0007282!1.89e-07!83;UBERON:0009618!1.89e-07!83;UBERON:0007285!1.89e-07!83;UBERON:0000033!4.33e-07!123
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}}
}}

Revision as of 20:21, 8 August 2012


Full id: C4823_signet_tubular_Smooth_small_Hepatocyte_Fibroblast_Sertoli



Phase1 CAGE Peaks

Hg19::chr9:4490394..4490446,+p2@SLC1A1
Hg19::chr9:4490449..4490481,+p1@SLC1A1
Hg19::chr9:4490482..4490518,+p3@SLC1A1


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
tube1.62e-24194
anatomical cluster2.20e-23286
anatomical conduit2.35e-23241
epithelium5.67e-19309
cell layer1.94e-18312
organism subdivision6.58e-18365
multi-tissue structure2.34e-17347
artery4.45e-1642
arterial blood vessel4.45e-1642
arterial system4.45e-1642
epithelial tube4.87e-15118
systemic artery6.45e-1433
systemic arterial system6.45e-1433
blood vessel3.13e-1360
epithelial tube open at both ends3.13e-1360
blood vasculature3.13e-1360
vascular cord3.13e-1360
vasculature6.44e-1379
vascular system6.44e-1379
vessel8.38e-1369
unilaminar epithelium1.27e-12138
splanchnic layer of lateral plate mesoderm1.36e-1284
central nervous system1.01e-1182
neural tube1.29e-1157
neural rod1.29e-1157
future spinal cord1.29e-1157
neural keel1.29e-1157
regional part of brain1.83e-1159
regional part of forebrain2.25e-1141
forebrain2.25e-1141
future forebrain2.25e-1141
multi-cellular organism3.82e-11659
anterior neural tube4.29e-1142
regional part of cerebral cortex7.78e-1122
cerebral hemisphere8.19e-1132
regional part of nervous system8.77e-1194
nervous system8.77e-1194
telencephalon9.22e-1134
trunk1.10e-10216
gray matter1.25e-1034
brain grey matter1.25e-1034
brain1.69e-1069
future brain1.69e-1069
regional part of telencephalon2.59e-1033
trunk mesenchyme3.77e-10143
neocortex5.40e-1020
anatomical group1.45e-09626
anatomical system1.60e-09625
neurectoderm1.92e-0990
neural plate2.27e-0986
presumptive neural plate2.27e-0986
muscle tissue1.97e-0863
musculature1.97e-0863
musculature of body1.97e-0863
cerebral cortex2.42e-0825
pallium2.42e-0825
pre-chordal neural plate3.71e-0861
cardiovascular system4.11e-08110
circulatory system4.97e-08113
adult organism5.53e-08115
skeletal muscle tissue9.59e-0861
striated muscle tissue9.59e-0861
myotome9.59e-0861
embryo9.68e-08612
aorta1.19e-0721
aortic system1.19e-0721
embryonic structure1.36e-07605
developing anatomical structure1.36e-07605
germ layer1.75e-07604
embryonic tissue1.75e-07604
presumptive structure1.75e-07604
epiblast (generic)1.75e-07604
somite1.89e-0783
paraxial mesoderm1.89e-0783
presomitic mesoderm1.89e-0783
presumptive segmental plate1.89e-0783
trunk paraxial mesoderm1.89e-0783
presumptive paraxial mesoderm1.89e-0783
head4.33e-07123


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

No analysis results for this cluster

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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