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Coexpression cluster:C1296: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.02e-48!90;UBERON:0001049!3.97e-48!57;UBERON:0005068!3.97e-48!57;UBERON:0006241!3.97e-48!57;UBERON:0007135!3.97e-48!57;UBERON:0005743!6.40e-47!86;UBERON:0003075!4.28e-45!86;UBERON:0007284!4.28e-45!86;UBERON:0000073!5.51e-45!94;UBERON:0001016!5.51e-45!94;UBERON:0007023!8.17e-42!115;UBERON:0002616!4.31e-41!59;UBERON:0001017!7.10e-41!82;UBERON:0000955!3.32e-39!69;UBERON:0006238!3.32e-39!69;UBERON:0003080!5.09e-34!42;UBERON:0002780!1.99e-32!41;UBERON:0001890!1.99e-32!41;UBERON:0006240!1.99e-32!41;UBERON:0003056!4.46e-32!61;UBERON:0001893!1.65e-28!34;UBERON:0001950!2.01e-28!20;UBERON:0002020!3.59e-28!34;UBERON:0003528!3.59e-28!34;UBERON:0000153!5.28e-28!129;UBERON:0007811!5.28e-28!129;UBERON:0002791!9.79e-27!33;UBERON:0000033!1.09e-25!123;UBERON:0002619!1.77e-25!22;UBERON:0001869!2.53e-25!32;UBERON:0000924!2.17e-24!173;UBERON:0006601!2.17e-24!173;UBERON:0004121!6.21e-22!169;UBERON:0000956!6.42e-22!25;UBERON:0000203!6.42e-22!25;UBERON:0002298!1.45e-15!8;UBERON:0003076!7.02e-15!15;UBERON:0003057!7.02e-15!15;UBERON:0004733!6.43e-13!12;UBERON:0002028!6.43e-13!12;UBERON:0007277!6.43e-13!12;UBERON:0000483!7.82e-12!309;UBERON:0004732!9.06e-12!13;UBERON:0000025!1.38e-11!194;UBERON:0000119!1.46e-11!312;UBERON:0001872!5.70e-11!5;UBERON:0002021!8.43e-11!5;UBERON:0000966!2.42e-10!5;UBERON:0005388!2.42e-10!5;UBERON:0001802!2.42e-10!5;UBERON:0000062!5.09e-09!511;UBERON:0000200!9.06e-09!6;UBERON:0004111!9.83e-09!241;UBERON:0000064!1.16e-08!219;UBERON:0001871!1.44e-08!7;UBERON:0000475!1.90e-08!365;UBERON:0002680!3.85e-08!9;UBERON:0001895!3.85e-08!9;UBERON:0010092!3.85e-08!9;UBERON:0000477!5.45e-08!286;UBERON:0002308!1.10e-07!9;UBERON:0000125!1.10e-07!9;UBERON:0000481!1.76e-07!347;UBERON:0002420!2.10e-07!9;UBERON:0007245!2.10e-07!9;UBERON:0010009!2.10e-07!9;UBERON:0010011!2.10e-07!9;UBERON:0000454!2.10e-07!9;UBERON:0000988!3.86e-07!3;UBERON:0000922!4.73e-07!612;UBERON:0000468!4.75e-07!659;UBERON:0001896!6.47e-07!3;UBERON:0005290!6.47e-07!3;UBERON:0010096!6.47e-07!3;UBERON:0001781!8.08e-07!3;UBERON:0001782!8.08e-07!3;UBERON:0005424!8.08e-07!3;UBERON:0006331!9.69e-07!3
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}}
}}

Revision as of 17:07, 8 August 2012


Full id: C1296_thalamus_diencephalon_NK_corpus_heart_testis_left



Phase1 CAGE Peaks

Hg19::chr10:114886533..114886542,+p48@TCF7L2
Hg19::chr10:134901694..134901706,+p@chr10:134901694..134901706
+
Hg19::chr8:27336675..27336693,-p3@CHRNA2
Hg19::chr9:112191134..112191155,-p5@PTPN3
Hg19::chr9:112191163..112191174,-p10@PTPN3
Hg19::chr9:112191244..112191257,-p4@PTPN3


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
retinal pigment epithelial cell8.08e-073
Uber Anatomy
Ontology termp-valuen
neurectoderm1.02e-4890
neural tube3.97e-4857
neural rod3.97e-4857
future spinal cord3.97e-4857
neural keel3.97e-4857
neural plate4.28e-4586
presumptive neural plate4.28e-4586
regional part of nervous system5.51e-4594
nervous system5.51e-4594
adult organism8.17e-42115
regional part of brain4.31e-4159
central nervous system7.10e-4182
brain3.32e-3969
future brain3.32e-3969
anterior neural tube5.09e-3442
regional part of forebrain1.99e-3241
forebrain1.99e-3241
future forebrain1.99e-3241
pre-chordal neural plate4.46e-3261
telencephalon1.65e-2834
neocortex2.01e-2820
gray matter3.59e-2834
brain grey matter3.59e-2834
anterior region of body5.28e-28129
craniocervical region5.28e-28129
regional part of telencephalon9.79e-2733
head1.09e-25123
regional part of cerebral cortex1.77e-2522
cerebral hemisphere2.53e-2532
ectoderm2.17e-24173
presumptive ectoderm2.17e-24173
ectoderm-derived structure6.21e-22169
cerebral cortex6.42e-2225
pallium6.42e-2225
brainstem1.45e-158
posterior neural tube7.02e-1515
chordal neural plate7.02e-1515
segmental subdivision of hindbrain6.43e-1312
hindbrain6.43e-1312
presumptive hindbrain6.43e-1312
epithelium7.82e-12309
segmental subdivision of nervous system9.06e-1213
tube1.38e-11194
cell layer1.46e-11312
parietal lobe5.70e-115
occipital lobe8.43e-115
retina2.42e-105
photoreceptor array2.42e-105
posterior segment of eyeball2.42e-105
organ5.09e-09511
gyrus9.06e-096
anatomical conduit9.83e-09241
organ part1.16e-08219
temporal lobe1.44e-087
organism subdivision1.90e-08365
regional part of metencephalon3.85e-089
metencephalon3.85e-089
future metencephalon3.85e-089
anatomical cluster5.45e-08286
nucleus of brain1.10e-079
neural nucleus1.10e-079
multi-tissue structure1.76e-07347
basal ganglion2.10e-079
nuclear complex of neuraxis2.10e-079
aggregate regional part of brain2.10e-079
collection of basal ganglia2.10e-079
cerebral subcortex2.10e-079
pons3.86e-073
embryo4.73e-07612
multi-cellular organism4.75e-07659
medulla oblongata6.47e-073
myelencephalon6.47e-073
future myelencephalon6.47e-073
layer of retina8.08e-073
pigmented layer of retina8.08e-073
presumptive retinal pigmented epithelium8.08e-073
brainstem nucleus9.69e-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.