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|full_id=C2913_extraskeletal_nonsmall_chronic_parietal_occipital_putamen_duodenum
|full_id=C2913_extraskeletal_nonsmall_chronic_parietal_occipital_putamen_duodenum
|id=C2913
|id=C2913
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!3.49e-72!57;UBERON:0005068!3.49e-72!57;UBERON:0006241!3.49e-72!57;UBERON:0007135!3.49e-72!57;UBERON:0001017!4.94e-68!82;UBERON:0005743!2.36e-66!86;UBERON:0002780!1.71e-61!41;UBERON:0001890!1.71e-61!41;UBERON:0006240!1.71e-61!41;UBERON:0000955!4.60e-61!69;UBERON:0006238!4.60e-61!69;UBERON:0000073!9.37e-61!94;UBERON:0001016!9.37e-61!94;UBERON:0002616!3.04e-60!59;UBERON:0003080!9.16e-60!42;UBERON:0002346!1.07e-56!90;UBERON:0003075!3.27e-55!86;UBERON:0007284!3.27e-55!86;UBERON:0002020!1.67e-49!34;UBERON:0003528!1.67e-49!34;UBERON:0001893!1.95e-49!34;UBERON:0002791!1.45e-47!33;UBERON:0001869!2.23e-46!32;UBERON:0003056!1.32e-41!61;UBERON:0002619!3.64e-39!22;UBERON:0007023!1.06e-36!115;UBERON:0001950!1.98e-35!20;UBERON:0000924!3.88e-35!173;UBERON:0006601!3.88e-35!173;UBERON:0000956!8.50e-34!25;UBERON:0000203!8.50e-34!25;UBERON:0000153!1.43e-33!129;UBERON:0007811!1.43e-33!129;UBERON:0004121!1.45e-33!169;UBERON:0000033!3.75e-33!123;UBERON:0002420!1.10e-17!9;UBERON:0007245!1.10e-17!9;UBERON:0010009!1.10e-17!9;UBERON:0010011!1.10e-17!9;UBERON:0000454!1.10e-17!9;UBERON:0002308!3.65e-17!9;UBERON:0000125!3.65e-17!9;UBERON:0000025!4.10e-14!194;UBERON:0009663!9.10e-14!7;UBERON:0003076!1.58e-13!15;UBERON:0003057!1.58e-13!15;UBERON:0001894!3.09e-13!7;UBERON:0006222!3.09e-13!7;UBERON:0001871!1.05e-12!7;UBERON:0000200!2.37e-12!6;UBERON:0000349!3.39e-11!5;UBERON:0002021!2.32e-10!5;UBERON:0001872!2.46e-10!5;UBERON:0000064!8.58e-10!219;UBERON:0004111!9.30e-10!241;UBERON:0000475!1.09e-09!365;UBERON:0000369!2.17e-09!4;UBERON:0002435!2.17e-09!4;UBERON:0000204!2.17e-09!4;UBERON:0010082!2.17e-09!4;UBERON:0004733!3.09e-09!12;UBERON:0002028!3.09e-09!12;UBERON:0007277!3.09e-09!12;UBERON:0000477!1.76e-08!286;UBERON:0004732!2.10e-08!13;UBERON:0002298!2.60e-08!8;UBERON:0003296!3.00e-08!4;UBERON:0010133!3.00e-08!4;UBERON:0000483!7.13e-08!309;UBERON:0000119!1.16e-07!312;UBERON:0005383!1.76e-07!3;UBERON:0005382!1.76e-07!3;UBERON:0002680!1.90e-07!9;UBERON:0001895!1.90e-07!9;UBERON:0010092!1.90e-07!9;UBERON:0002771!4.23e-07!3;UBERON:0000988!7.10e-07!3
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}}

Revision as of 14:30, 21 May 2012


Full id: C2913_extraskeletal_nonsmall_chronic_parietal_occipital_putamen_duodenum



Phase1 CAGE Peaks

Hg19::chr8:114449458..114449469,-p8@CSMD3
Hg19::chr8:114449484..114449517,-p2@CSMD3
Hg19::chr8:114449556..114449571,-p5@CSMD3
Hg19::chr8:114449595..114449607,-p6@CSMD3


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
neural tube3.49e-7257
neural rod3.49e-7257
future spinal cord3.49e-7257
neural keel3.49e-7257
central nervous system4.94e-6882
regional part of forebrain1.71e-6141
forebrain1.71e-6141
future forebrain1.71e-6141
brain4.60e-6169
future brain4.60e-6169
regional part of nervous system9.37e-6194
nervous system9.37e-6194
regional part of brain3.04e-6059
anterior neural tube9.16e-6042
neurectoderm1.07e-5690
neural plate3.27e-5586
presumptive neural plate3.27e-5586
gray matter1.67e-4934
brain grey matter1.67e-4934
telencephalon1.95e-4934
regional part of telencephalon1.45e-4733
cerebral hemisphere2.23e-4632
pre-chordal neural plate1.32e-4161
regional part of cerebral cortex3.64e-3922
adult organism1.06e-36115
neocortex1.98e-3520
ectoderm3.88e-35173
presumptive ectoderm3.88e-35173
cerebral cortex8.50e-3425
pallium8.50e-3425
anterior region of body1.43e-33129
craniocervical region1.43e-33129
ectoderm-derived structure1.45e-33169
head3.75e-33123
basal ganglion1.10e-179
nuclear complex of neuraxis1.10e-179
aggregate regional part of brain1.10e-179
collection of basal ganglia1.10e-179
cerebral subcortex1.10e-179
nucleus of brain3.65e-179
neural nucleus3.65e-179
tube4.10e-14194
telencephalic nucleus9.10e-147
posterior neural tube1.58e-1315
chordal neural plate1.58e-1315
diencephalon3.09e-137
future diencephalon3.09e-137
temporal lobe1.05e-127
gyrus2.37e-126
limbic system3.39e-115
occipital lobe2.32e-105
parietal lobe2.46e-105
organ part8.58e-10219
anatomical conduit9.30e-10241
organism subdivision1.09e-09365
corpus striatum2.17e-094
striatum2.17e-094
ventral part of telencephalon2.17e-094
future corpus striatum2.17e-094
segmental subdivision of hindbrain3.09e-0912
hindbrain3.09e-0912
presumptive hindbrain3.09e-0912
anatomical cluster1.76e-08286
segmental subdivision of nervous system2.10e-0813
brainstem2.60e-088
gland of diencephalon3.00e-084
neuroendocrine gland3.00e-084
epithelium7.13e-08309
cell layer1.16e-07312
caudate-putamen1.76e-073
dorsal striatum1.76e-073
regional part of metencephalon1.90e-079
metencephalon1.90e-079
future metencephalon1.90e-079
middle temporal gyrus4.23e-073
pons7.10e-073


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.