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Coexpression cluster:C3308: Difference between revisions

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|full_id=C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory
|full_id=C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory
|id=C3308
|id=C3308
|ontology_enrichment_celltype=CL:0000055!5.02e-13!180
|ontology_enrichment_celltype=CL:0000055!4.96e-09!106;CL:0000393!8.84e-07!61;CL:0000211!8.84e-07!61;CL:0000133!8.85e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.41e-32!94;UBERON:0001016!2.41e-32!94;UBERON:0001017!7.59e-31!82;UBERON:0005743!9.03e-30!86;UBERON:0000955!4.40e-27!69;UBERON:0006238!4.40e-27!69;UBERON:0001049!2.24e-26!57;UBERON:0005068!2.24e-26!57;UBERON:0006241!2.24e-26!57;UBERON:0007135!2.24e-26!57;UBERON:0002346!9.40e-26!90;UBERON:0000924!5.40e-25!173;UBERON:0006601!5.40e-25!173;UBERON:0002616!2.61e-24!59;UBERON:0003075!3.69e-24!86;UBERON:0007284!3.69e-24!86;UBERON:0004121!1.65e-23!169;UBERON:0000475!3.85e-21!365;UBERON:0003080!2.31e-20!42;UBERON:0007023!4.30e-20!115;UBERON:0002780!5.09e-20!41;UBERON:0001890!5.09e-20!41;UBERON:0006240!5.09e-20!41;UBERON:0000033!7.32e-20!123;UBERON:0002020!1.09e-18!34;UBERON:0003528!1.09e-18!34;UBERON:0001893!2.54e-18!34;UBERON:0001869!2.66e-18!32;UBERON:0000153!3.92e-18!129;UBERON:0007811!3.92e-18!129;UBERON:0002791!9.88e-18!33;UBERON:0003056!1.22e-17!61;UBERON:0002619!7.84e-16!22;UBERON:0000956!1.97e-15!25;UBERON:0000203!1.97e-15!25;UBERON:0000481!4.01e-15!347;UBERON:0001950!1.78e-14!20;UBERON:0000025!2.80e-13!194;UBERON:0000483!1.85e-12!309;UBERON:0000119!2.12e-12!312;UBERON:0004111!2.46e-12!241;UBERON:0000477!4.12e-10!286;UBERON:0000468!7.08e-10!659;UBERON:0000064!6.30e-09!219;UBERON:0000922!7.31e-09!612;UBERON:0002050!4.28e-08!605;UBERON:0005423!4.28e-08!605;UBERON:0000923!7.97e-08!604;UBERON:0005291!7.97e-08!604;UBERON:0006598!7.97e-08!604;UBERON:0002532!7.97e-08!604;UBERON:0003076!3.33e-07!15;UBERON:0003057!3.33e-07!15;UBERON:0000467!8.33e-07!625
|ontology_enrichment_uberon=UBERON:0001016!1.11e-32!89;UBERON:0001017!5.34e-30!81;UBERON:0000955!2.80e-26!68;UBERON:0006238!2.80e-26!68;UBERON:0001049!5.10e-26!56;UBERON:0005068!5.10e-26!56;UBERON:0006241!5.10e-26!56;UBERON:0007135!5.10e-26!56;UBERON:0002346!6.78e-26!86;UBERON:0004121!3.71e-25!171;UBERON:0000924!3.71e-25!171;UBERON:0006601!3.71e-25!171;UBERON:0000073!9.02e-25!53;UBERON:0002616!9.02e-25!53;UBERON:0003075!2.65e-24!82;UBERON:0007284!2.65e-24!82;UBERON:0010314!1.45e-20!132;UBERON:0002780!7.38e-20!41;UBERON:0001890!7.38e-20!41;UBERON:0003080!7.38e-20!41;UBERON:0006240!7.38e-20!41;UBERON:0007023!4.93e-19!114;UBERON:0003528!1.90e-18!34;UBERON:0002020!1.90e-18!34;UBERON:0000477!3.08e-18!373;UBERON:0001869!5.25e-18!32;UBERON:0001893!5.47e-18!34;UBERON:0011216!5.77e-18!223;UBERON:0010371!1.31e-17!104;UBERON:0003056!1.76e-17!61;UBERON:0002791!1.87e-17!32;UBERON:0002619!1.62e-15!22;UBERON:0000956!5.64e-15!25;UBERON:0000203!5.64e-15!25;UBERON:0000481!1.13e-14!342;UBERON:0001950!3.58e-14!20;UBERON:0000025!1.71e-13!192;UBERON:0004111!3.06e-12!240;UBERON:0000483!4.49e-12!306;UBERON:0000119!5.32e-12!309;UBERON:0000468!1.72e-10!656;UBERON:0000064!1.27e-08!218;UBERON:0000922!5.71e-08!592;UBERON:0000467!1.51e-07!624;UBERON:0000480!1.88e-07!625;UBERON:0003076!2.35e-07!15;UBERON:0003057!2.35e-07!15;UBERON:0000923!5.52e-07!560;UBERON:0010316!5.52e-07!560;UBERON:0005291!5.52e-07!560;UBERON:0006598!5.52e-07!560;UBERON:0010317!5.52e-07!560;UBERON:0002532!5.52e-07!560;UBERON:0002050!8.23e-07!564
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189478262247415!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320995484885685!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246707987598847!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010906103351647
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189478262247415!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320995484885685!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246707987598847!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010906103351647
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}}
}}

Revision as of 14:59, 19 October 2012


Full id: C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory



Phase1 CAGE Peaks

Hg19::chr12:58005170..58005192,+p2@ARHGEF25
Hg19::chr12:58005204..58005235,+p1@ARHGEF25
Hg19::chr12:58005243..58005248,+p3@ARHGEF25


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
non-terminally differentiated cell4.96e-09106
electrically responsive cell8.84e-0761
electrically active cell8.84e-0761
neurectodermal cell8.85e-0759
Uber Anatomy
Ontology termp-valuen
nervous system1.11e-3289
central nervous system5.34e-3081
brain2.80e-2668
future brain2.80e-2668
neural tube5.10e-2656
neural rod5.10e-2656
future spinal cord5.10e-2656
neural keel5.10e-2656
neurectoderm6.78e-2686
ectoderm-derived structure3.71e-25171
ectoderm3.71e-25171
presumptive ectoderm3.71e-25171
regional part of nervous system9.02e-2553
regional part of brain9.02e-2553
neural plate2.65e-2482
presumptive neural plate2.65e-2482
structure with developmental contribution from neural crest1.45e-20132
regional part of forebrain7.38e-2041
forebrain7.38e-2041
anterior neural tube7.38e-2041
future forebrain7.38e-2041
adult organism4.93e-19114
brain grey matter1.90e-1834
gray matter1.90e-1834
anatomical cluster3.08e-18373
cerebral hemisphere5.25e-1832
telencephalon5.47e-1834
organ system subdivision5.77e-18223
ecto-epithelium1.31e-17104
pre-chordal neural plate1.76e-1761
regional part of telencephalon1.87e-1732
regional part of cerebral cortex1.62e-1522
cerebral cortex5.64e-1525
pallium5.64e-1525
multi-tissue structure1.13e-14342
neocortex3.58e-1420
tube1.71e-13192
anatomical conduit3.06e-12240
epithelium4.49e-12306
cell layer5.32e-12309
multi-cellular organism1.72e-10656
organ part1.27e-08218
embryo5.71e-08592
anatomical system1.51e-07624
anatomical group1.88e-07625
posterior neural tube2.35e-0715
chordal neural plate2.35e-0715
germ layer5.52e-07560
germ layer / neural crest5.52e-07560
embryonic tissue5.52e-07560
presumptive structure5.52e-07560
germ layer / neural crest derived structure5.52e-07560
epiblast (generic)5.52e-07560
embryonic structure8.23e-07564


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189478262247415
E2F6#187635.017155731697390.00791769806886330.0320995484885685
HNF4A#3172215.42152690863580.005444210486686610.0246707987598847
ZNF263#1012738.221841637010680.001799043925565870.010906103351647



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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