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Coexpression cluster:C2450: Difference between revisions

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|full_id=C2450_Retinal_pineal_retina_Melanocyte_occipital_eye_Pericytes
|full_id=C2450_Retinal_pineal_retina_Melanocyte_occipital_eye_Pericytes
|id=C2450
|id=C2450
|ontology_enrichment_celltype=CL:0000147!5.25e-12!14;CL:0000148!1.55e-08!10;CL:0000541!1.55e-08!10
|ontology_enrichment_celltype=CL:0002586!1.71e-09!3;CL:0000147!1.45e-08!14;CL:0000064!3.74e-08!3;CL:0000067!3.74e-08!3;CL:0005012!3.74e-08!3;CL:0002304!3.74e-08!3;CL:0002274!3.93e-08!5;CL:0000457!3.93e-08!5;CL:0002191!3.93e-08!5;CL:0000097!3.93e-08!5;CL:0000831!3.93e-08!5;CL:0002028!3.93e-08!5;CL:0000149!3.51e-07!4
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.32e-52!115;UBERON:0003075!3.90e-34!86;UBERON:0007284!3.90e-34!86;UBERON:0002346!3.44e-33!90;UBERON:0001049!1.70e-32!57;UBERON:0005068!1.70e-32!57;UBERON:0006241!1.70e-32!57;UBERON:0007135!1.70e-32!57;UBERON:0003056!4.94e-31!61;UBERON:0005743!5.68e-29!86;UBERON:0000073!8.12e-29!94;UBERON:0001016!8.12e-29!94;UBERON:0002616!8.41e-29!59;UBERON:0003080!2.19e-28!42;UBERON:0002780!6.99e-28!41;UBERON:0001890!6.99e-28!41;UBERON:0006240!6.99e-28!41;UBERON:0000955!6.00e-26!69;UBERON:0006238!6.00e-26!69;UBERON:0001017!1.30e-25!82;UBERON:0000153!4.19e-23!129;UBERON:0007811!4.19e-23!129;UBERON:0000033!5.05e-23!123;UBERON:0001893!1.33e-22!34;UBERON:0002020!6.99e-22!34;UBERON:0003528!6.99e-22!34;UBERON:0002791!9.49e-22!33;UBERON:0001869!2.61e-21!32;UBERON:0004121!8.59e-19!169;UBERON:0002619!8.79e-19!22;UBERON:0000924!1.12e-18!173;UBERON:0006601!1.12e-18!173;UBERON:0001950!1.71e-17!20;UBERON:0000956!1.22e-16!25;UBERON:0000203!1.22e-16!25;UBERON:0000922!2.29e-11!612;UBERON:0000062!4.62e-11!511;UBERON:0000481!1.52e-10!347;UBERON:0000468!5.80e-10!659;UBERON:0000064!1.40e-09!219;UBERON:0002050!3.20e-09!605;UBERON:0005423!3.20e-09!605;UBERON:0000923!6.25e-09!604;UBERON:0005291!6.25e-09!604;UBERON:0006598!6.25e-09!604;UBERON:0002532!6.25e-09!604;UBERON:0000475!1.01e-07!365;UBERON:0002420!1.91e-07!9;UBERON:0007245!1.91e-07!9;UBERON:0010009!1.91e-07!9;UBERON:0010011!1.91e-07!9;UBERON:0000454!1.91e-07!9;UBERON:0000467!2.23e-07!625;UBERON:0000480!2.81e-07!626;UBERON:0001871!3.07e-07!7;UBERON:0001032!6.62e-07!24;UBERON:0004456!6.62e-07!24;UBERON:0000483!7.18e-07!309
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}}
}}

Revision as of 14:02, 19 October 2012


Full id: C2450_Retinal_pineal_retina_Melanocyte_occipital_eye_Pericytes



Phase1 CAGE Peaks

Hg19::chr17:935036..935083,-p4@ABR
Hg19::chr3:69928371..69928385,+p@chr3:69928371..69928385
+
Hg19::chr3:69928404..69928418,+p@chr3:69928404..69928418
+
Hg19::chr3:69928426..69928436,+p@chr3:69928426..69928436
+


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
pre-chordal neural plate4.02e-3861
cerebral hemisphere3.31e-3332
regional part of cerebral cortex3.43e-3322
neocortex9.68e-3320
neural plate1.91e-3182
presumptive neural plate1.91e-3182
telencephalon6.22e-3134
brain grey matter9.73e-3134
gray matter9.73e-3134
regional part of forebrain2.87e-3041
forebrain2.87e-3041
anterior neural tube2.87e-3041
future forebrain2.87e-3041
regional part of telencephalon4.36e-3032
neurectoderm1.62e-2986
adult organism3.49e-29114
cerebral cortex9.45e-2925
pallium9.45e-2925
regional part of nervous system6.17e-2653
regional part of brain6.17e-2653
ecto-epithelium2.92e-24104
neural tube3.60e-2456
neural rod3.60e-2456
future spinal cord3.60e-2456
neural keel3.60e-2456
structure with developmental contribution from neural crest7.64e-22132
brain6.05e-2068
future brain6.05e-2068
central nervous system5.30e-1781
ectoderm-derived structure4.49e-15171
ectoderm4.49e-15171
presumptive ectoderm4.49e-15171
nervous system1.39e-1489
pigment epithelium of eye2.30e-1411
occipital lobe1.48e-135
sense organ2.74e-1324
sensory system2.74e-1324
entire sense organ system2.74e-1324
organ part5.65e-11218
gyrus6.43e-116
eye6.86e-1121
visual system6.86e-1121
atypical epithelium1.48e-104
pigmented layer of retina1.71e-093
presumptive retinal pigmented epithelium1.71e-093
camera-type eye3.14e-0920
simple eye3.14e-0920
immature eye3.14e-0920
ocular region3.14e-0920
eyeball of camera-type eye3.14e-0920
optic cup3.14e-0920
optic vesicle3.14e-0920
eye primordium3.14e-0920
temporal lobe4.05e-096
parietal lobe5.33e-095
organ1.22e-08503
limbic system1.67e-085
face3.20e-0822
ciliary epithelium3.74e-083
ciliary body3.74e-083
retina5.44e-086
photoreceptor array5.44e-086
posterior segment of eyeball5.44e-086
multi-tissue structure1.91e-07342
layer of retina3.51e-074
vasculature of eye5.09e-076
uvea5.09e-076
vasculature of head5.09e-076
basal ganglion5.25e-079
nuclear complex of neuraxis5.25e-079
aggregate regional part of brain5.25e-079
collection of basal ganglia5.25e-079
cerebral subcortex5.25e-079
pineal body6.79e-072
regional part of epithalamus6.79e-072
secretory circumventricular organ6.79e-072
circumventricular organ6.79e-072
epithalamus6.79e-072
embryo7.08e-07592


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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