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Coexpression cluster:C2291: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0019198!transmembrane receptor protein phosphatase activity!0.041376059867355!5803$GO:0005001!transmembrane receptor protein tyrosine phosphatase activity!0.041376059867355!5803
|gostat_on_coexpression_clusters=GO:0019198!transmembrane receptor protein phosphatase activity!0.041376059867355!5803$GO:0005001!transmembrane receptor protein tyrosine phosphatase activity!0.041376059867355!5803
|id=C2291
|id=C2291
|ontology_enrichment_celltype=CL:0000047!5.02e-08!8;CL:0002319!5.64e-08!25
|ontology_enrichment_celltype=CL:0000047!6.53e-09!8;CL:0002319!1.14e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!6.91e-48!94;UBERON:0001016!6.91e-48!94;UBERON:0005743!1.19e-47!86;UBERON:0001017!5.34e-47!82;UBERON:0001049!1.13e-45!57;UBERON:0005068!1.13e-45!57;UBERON:0006241!1.13e-45!57;UBERON:0007135!1.13e-45!57;UBERON:0003075!2.06e-42!86;UBERON:0007284!2.06e-42!86;UBERON:0002346!1.73e-41!90;UBERON:0007023!6.82e-39!115;UBERON:0002616!3.59e-38!59;UBERON:0000955!5.68e-36!69;UBERON:0006238!5.68e-36!69;UBERON:0003080!7.73e-35!42;UBERON:0004121!3.75e-34!169;UBERON:0002780!4.61e-34!41;UBERON:0001890!4.61e-34!41;UBERON:0006240!4.61e-34!41;UBERON:0000924!4.75e-34!173;UBERON:0006601!4.75e-34!173;UBERON:0003056!8.44e-32!61;UBERON:0000033!1.22e-29!123;UBERON:0002020!3.51e-29!34;UBERON:0003528!3.51e-29!34;UBERON:0001893!6.75e-29!34;UBERON:0000153!7.05e-29!129;UBERON:0007811!7.05e-29!129;UBERON:0002791!4.44e-28!33;UBERON:0001869!2.66e-27!32;UBERON:0000956!1.78e-21!25;UBERON:0000203!1.78e-21!25;UBERON:0002619!5.96e-20!22;UBERON:0001950!3.86e-18!20;UBERON:0000481!1.89e-14!347;UBERON:0000475!2.68e-14!365;UBERON:0000483!1.02e-13!309;UBERON:0000119!1.44e-13!312;UBERON:0000922!1.90e-13!612;UBERON:0000025!7.67e-12!194;UBERON:0003076!1.13e-11!15;UBERON:0003057!1.13e-11!15;UBERON:0004111!1.27e-11!241;UBERON:0002050!5.89e-11!605;UBERON:0005423!5.89e-11!605;UBERON:0000923!1.30e-10!604;UBERON:0005291!1.30e-10!604;UBERON:0006598!1.30e-10!604;UBERON:0002532!1.30e-10!604;UBERON:0000468!2.03e-10!659;UBERON:0000477!2.06e-10!286;UBERON:0004732!1.17e-09!13;UBERON:0002308!4.04e-09!9;UBERON:0000125!4.04e-09!9;UBERON:0002420!4.56e-09!9;UBERON:0007245!4.56e-09!9;UBERON:0010009!4.56e-09!9;UBERON:0010011!4.56e-09!9;UBERON:0000454!4.56e-09!9;UBERON:0004733!6.33e-09!12;UBERON:0002028!6.33e-09!12;UBERON:0007277!6.33e-09!12;UBERON:0002298!3.02e-08!8;UBERON:0000467!1.57e-07!625;UBERON:0000480!1.97e-07!626;UBERON:0009663!2.90e-07!7;UBERON:0000064!4.65e-07!219;UBERON:0000200!5.41e-07!6;UBERON:0000062!5.75e-07!511
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}}
}}

Revision as of 13:50, 19 October 2012


Full id: C2291_parietal_Neural_occipital_medial_spinal_locus_temporal



Phase1 CAGE Peaks

Hg19::chr14:27066880..27066891,-p12@NOVA1
Hg19::chr14:27066907..27066914,-p18@NOVA1
Hg19::chr14:27066917..27066929,-p15@NOVA1
Hg19::chr7:121651047..121651081,+p7@PTPRZ1


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


GO IDGO nameFDR corrected p-value
GO:0019198transmembrane receptor protein phosphatase activity0.041376059867355
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.041376059867355



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
neuronal stem cell6.53e-098
neural cell1.14e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system8.36e-6181
nervous system7.03e-6089
neural tube9.01e-6056
neural rod9.01e-6056
future spinal cord9.01e-6056
neural keel9.01e-6056
regional part of nervous system2.64e-5553
regional part of brain2.64e-5553
neural plate4.52e-5282
presumptive neural plate4.52e-5282
neurectoderm2.15e-5086
regional part of forebrain4.66e-4741
forebrain4.66e-4741
anterior neural tube4.66e-4741
future forebrain4.66e-4741
brain1.88e-4668
future brain1.88e-4668
brain grey matter1.91e-4434
gray matter1.91e-4434
telencephalon5.12e-4434
adult organism5.72e-42114
cerebral hemisphere1.34e-4132
regional part of telencephalon1.54e-4132
ecto-epithelium4.02e-41104
ectoderm-derived structure5.92e-39171
ectoderm5.92e-39171
presumptive ectoderm5.92e-39171
pre-chordal neural plate6.31e-3761
structure with developmental contribution from neural crest7.69e-34132
cerebral cortex1.15e-3225
pallium1.15e-3225
organ system subdivision1.06e-31223
regional part of cerebral cortex5.06e-3022
neocortex2.28e-2720
anatomical cluster3.33e-20373
multi-tissue structure4.15e-15342
tube1.48e-13192
posterior neural tube1.70e-1315
chordal neural plate1.70e-1315
neural nucleus4.82e-139
nucleus of brain4.82e-139
basal ganglion5.64e-139
nuclear complex of neuraxis5.64e-139
aggregate regional part of brain5.64e-139
collection of basal ganglia5.64e-139
cerebral subcortex5.64e-139
anatomical conduit2.79e-12240
embryo3.64e-11592
epithelium4.36e-11306
cell layer9.14e-11309
segmental subdivision of nervous system1.22e-1013
telencephalic nucleus3.04e-107
organ part3.77e-10218
gyrus7.15e-106
segmental subdivision of hindbrain1.50e-0912
hindbrain1.50e-0912
presumptive hindbrain1.50e-0912
brainstem2.47e-096
developing anatomical structure4.44e-09581
multi-cellular organism6.25e-09656
embryonic structure1.35e-08564
parietal lobe1.48e-085
germ layer1.92e-08560
germ layer / neural crest1.92e-08560
embryonic tissue1.92e-08560
presumptive structure1.92e-08560
germ layer / neural crest derived structure1.92e-08560
epiblast (generic)1.92e-08560
occipital lobe2.02e-085
temporal lobe2.22e-086
limbic system3.05e-085


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)

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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.