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|full_id=C1965_Hepatocyte_liver_CD133_CD34_mesenchymal_placenta_kidney
|full_id=C1965_Hepatocyte_liver_CD133_CD34_mesenchymal_placenta_kidney
|id=C1965
|id=C1965
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.44e-54!115;UBERON:0003075!1.63e-40!86;UBERON:0007284!1.63e-40!86;UBERON:0001049!7.49e-39!57;UBERON:0005068!7.49e-39!57;UBERON:0006241!7.49e-39!57;UBERON:0007135!7.49e-39!57;UBERON:0005743!2.46e-38!86;UBERON:0001017!3.90e-38!82;UBERON:0002346!1.11e-37!90;UBERON:0001893!6.93e-36!34;UBERON:0002020!1.55e-35!34;UBERON:0003528!1.55e-35!34;UBERON:0002791!1.09e-34!33;UBERON:0002616!6.96e-34!59;UBERON:0001869!9.00e-34!32;UBERON:0002780!1.25e-33!41;UBERON:0001890!1.25e-33!41;UBERON:0006240!1.25e-33!41;UBERON:0000073!1.30e-32!94;UBERON:0001016!1.30e-32!94;UBERON:0003080!1.69e-32!42;UBERON:0000955!1.07e-31!69;UBERON:0006238!1.07e-31!69;UBERON:0003056!4.48e-30!61;UBERON:0000956!1.45e-27!25;UBERON:0000203!1.45e-27!25;UBERON:0000153!2.29e-25!129;UBERON:0007811!2.29e-25!129;UBERON:0002619!2.96e-24!22;UBERON:0000033!6.06e-24!123;UBERON:0001950!2.12e-22!20;UBERON:0004121!2.03e-20!169;UBERON:0000924!2.18e-19!173;UBERON:0006601!2.18e-19!173;UBERON:0000025!9.14e-19!194;UBERON:0000477!9.40e-16!286;UBERON:0004111!1.23e-15!241;UBERON:0000119!2.00e-11!312;UBERON:0000483!2.07e-11!309;UBERON:0000481!1.51e-10!347;UBERON:0002420!1.22e-09!9;UBERON:0007245!1.22e-09!9;UBERON:0010009!1.22e-09!9;UBERON:0010011!1.22e-09!9;UBERON:0000454!1.22e-09!9;UBERON:0001871!2.34e-09!7;UBERON:0002308!2.36e-09!9;UBERON:0000125!2.36e-09!9;UBERON:0000064!6.40e-09!219;UBERON:0007100!3.13e-08!27;UBERON:0000475!3.28e-08!365;UBERON:0000200!7.12e-08!6;UBERON:0003076!8.98e-08!15;UBERON:0003057!8.98e-08!15;UBERON:0003103!1.02e-07!69;UBERON:0000922!1.38e-07!612;UBERON:0009663!1.82e-07!7;UBERON:0000349!8.69e-07!5;UBERON:0002298!9.19e-07!8;UBERON:0000062!9.39e-07!511;UBERON:0001872!9.90e-07!5
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Revision as of 14:18, 21 May 2012


Full id: C1965_Hepatocyte_liver_CD133_CD34_mesenchymal_placenta_kidney



Phase1 CAGE Peaks

Hg19::chr5:76248681..76248690,+p5@CRHBP
Hg19::chr5:76248797..76248808,+p3@CRHBP
Hg19::chr5:76248833..76248836,+p9@CRHBP
Hg19::chr5:76248861..76248877,+p1@CRHBP
Hg19::chr5:76248878..76248889,+p4@CRHBP


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.44e-54115
neural plate1.63e-4086
presumptive neural plate1.63e-4086
neural tube7.49e-3957
neural rod7.49e-3957
future spinal cord7.49e-3957
neural keel7.49e-3957
central nervous system3.90e-3882
neurectoderm1.11e-3790
telencephalon6.93e-3634
gray matter1.55e-3534
brain grey matter1.55e-3534
regional part of telencephalon1.09e-3433
regional part of brain6.96e-3459
cerebral hemisphere9.00e-3432
regional part of forebrain1.25e-3341
forebrain1.25e-3341
future forebrain1.25e-3341
regional part of nervous system1.30e-3294
nervous system1.30e-3294
anterior neural tube1.69e-3242
brain1.07e-3169
future brain1.07e-3169
pre-chordal neural plate4.48e-3061
cerebral cortex1.45e-2725
pallium1.45e-2725
anterior region of body2.29e-25129
craniocervical region2.29e-25129
regional part of cerebral cortex2.96e-2422
head6.06e-24123
neocortex2.12e-2220
ectoderm-derived structure2.03e-20169
ectoderm2.18e-19173
presumptive ectoderm2.18e-19173
tube9.14e-19194
anatomical cluster9.40e-16286
anatomical conduit1.23e-15241
cell layer2.00e-11312
epithelium2.07e-11309
multi-tissue structure1.51e-10347
basal ganglion1.22e-099
nuclear complex of neuraxis1.22e-099
aggregate regional part of brain1.22e-099
collection of basal ganglia1.22e-099
cerebral subcortex1.22e-099
temporal lobe2.34e-097
nucleus of brain2.36e-099
neural nucleus2.36e-099
organ part6.40e-09219
primary circulatory organ3.13e-0827
organism subdivision3.28e-08365
gyrus7.12e-086
posterior neural tube8.98e-0815
chordal neural plate8.98e-0815
compound organ1.02e-0769
embryo1.38e-07612
telencephalic nucleus1.82e-077
limbic system8.69e-075
brainstem9.19e-078
organ9.39e-07511
parietal lobe9.90e-075


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.