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Coexpression cluster:C3239: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002780!3.81e-29!41;UBERON:0001890!3.81e-29!41;UBERON:0003080!3.81e-29!41;UBERON:0006240!3.81e-29!41;UBERON:0001016!9.79e-29!89;UBERON:0000073!1.72e-27!53;UBERON:0002616!1.72e-27!53;UBERON:0001017!9.48e-27!81;UBERON:0001869!4.33e-26!32;UBERON:0001049!1.20e-25!56;UBERON:0005068!1.20e-25!56;UBERON:0006241!1.20e-25!56;UBERON:0007135!1.20e-25!56;UBERON:0002619!2.48e-25!22;UBERON:0000955!2.76e-25!68;UBERON:0006238!2.76e-25!68;UBERON:0001950!9.91e-25!20;UBERON:0001893!2.77e-24!34;UBERON:0003528!3.18e-24!34;UBERON:0002020!3.18e-24!34;UBERON:0002791!2.20e-23!32;UBERON:0003056!5.54e-23!61;UBERON:0000956!6.49e-22!25;UBERON:0000203!6.49e-22!25;UBERON:0002346!1.07e-21!86;UBERON:0003075!1.15e-19!82;UBERON:0007284!1.15e-19!82;UBERON:0004121!1.88e-17!171;UBERON:0000924!1.88e-17!171;UBERON:0006601!1.88e-17!171;UBERON:0011216!3.97e-15!223;UBERON:0010371!4.59e-15!104;UBERON:0010314!3.78e-14!132;UBERON:0007023!5.67e-13!114;UBERON:0000200!2.21e-10!6;UBERON:0000477!7.07e-10!373;UBERON:0002021!4.09e-09!5;UBERON:0001872!1.25e-08!5;UBERON:0003135!4.22e-08!11;UBERON:0003101!5.92e-08!22;UBERON:0000079!5.92e-08!22;UBERON:0000473!6.00e-08!8;UBERON:0003296!7.61e-07!4;UBERON:0010133!7.61e-07!4;UBERON:0001905!8.12e-07!2;UBERON:0002757!8.12e-07!2;UBERON:0010134!8.12e-07!2;UBERON:0005408!8.12e-07!2;UBERON:0001899!8.12e-07!2
|ontology_enrichment_uberon=UBERON:0002780!3.81e-29!41;UBERON:0001890!3.81e-29!41;UBERON:0003080!3.81e-29!41;UBERON:0006240!3.81e-29!41;UBERON:0001016!9.79e-29!89;UBERON:0000073!1.72e-27!53;UBERON:0002616!1.72e-27!53;UBERON:0001017!9.48e-27!81;UBERON:0001869!4.33e-26!32;UBERON:0001049!1.20e-25!56;UBERON:0005068!1.20e-25!56;UBERON:0006241!1.20e-25!56;UBERON:0007135!1.20e-25!56;UBERON:0002619!2.48e-25!22;UBERON:0000955!2.76e-25!68;UBERON:0006238!2.76e-25!68;UBERON:0001950!9.91e-25!20;UBERON:0001893!2.77e-24!34;UBERON:0003528!3.18e-24!34;UBERON:0002020!3.18e-24!34;UBERON:0002791!2.20e-23!32;UBERON:0003056!5.54e-23!61;UBERON:0000956!6.49e-22!25;UBERON:0000203!6.49e-22!25;UBERON:0002346!1.07e-21!86;UBERON:0003075!1.15e-19!82;UBERON:0007284!1.15e-19!82;UBERON:0004121!1.88e-17!171;UBERON:0000924!1.88e-17!171;UBERON:0006601!1.88e-17!171;UBERON:0011216!3.97e-15!223;UBERON:0010371!4.59e-15!104;UBERON:0010314!3.78e-14!132;UBERON:0007023!5.67e-13!114;UBERON:0000200!2.21e-10!6;UBERON:0000477!7.07e-10!373;UBERON:0002021!4.09e-09!5;UBERON:0001872!1.25e-08!5;UBERON:0003135!4.22e-08!11;UBERON:0003101!5.92e-08!22;UBERON:0000079!5.92e-08!22;UBERON:0000473!6.00e-08!8;UBERON:0003296!7.61e-07!4;UBERON:0010133!7.61e-07!4;UBERON:0001905!8.12e-07!2;UBERON:0002757!8.12e-07!2;UBERON:0010134!8.12e-07!2;UBERON:0005408!8.12e-07!2;UBERON:0001899!8.12e-07!2
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705,0.252796,0.205954,0.361435
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:00, 26 November 2012


Full id: C3239_parietal_Small_brain_salivary_temporal_occipital_duodenum



Phase1 CAGE Peaks

Hg19::chr12:111480615..111480619,+p@chr12:111480615..111480619
+
Hg19::chr12:111486730..111486746,+p@chr12:111486730..111486746
+
Hg19::chr12:111613164..111613168,+p@chr12:111613164..111613168
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
regional part of forebrain3.81e-2941
forebrain3.81e-2941
anterior neural tube3.81e-2941
future forebrain3.81e-2941
nervous system9.79e-2989
regional part of nervous system1.72e-2753
regional part of brain1.72e-2753
central nervous system9.48e-2781
cerebral hemisphere4.33e-2632
neural tube1.20e-2556
neural rod1.20e-2556
future spinal cord1.20e-2556
neural keel1.20e-2556
regional part of cerebral cortex2.48e-2522
brain2.76e-2568
future brain2.76e-2568
neocortex9.91e-2520
telencephalon2.77e-2434
brain grey matter3.18e-2434
gray matter3.18e-2434
regional part of telencephalon2.20e-2332
pre-chordal neural plate5.54e-2361
cerebral cortex6.49e-2225
pallium6.49e-2225
neurectoderm1.07e-2186
neural plate1.15e-1982
presumptive neural plate1.15e-1982
ectoderm-derived structure1.88e-17171
ectoderm1.88e-17171
presumptive ectoderm1.88e-17171
organ system subdivision3.97e-15223
ecto-epithelium4.59e-15104
structure with developmental contribution from neural crest3.78e-14132
adult organism5.67e-13114
gyrus2.21e-106
anatomical cluster7.07e-10373
occipital lobe4.09e-095
parietal lobe1.25e-085
male reproductive organ4.22e-0811
male organism5.92e-0822
male reproductive system5.92e-0822
testis6.00e-088
gland of diencephalon7.61e-074
neuroendocrine gland7.61e-074
pineal body8.12e-072
regional part of epithalamus8.12e-072
secretory circumventricular organ8.12e-072
circumventricular organ8.12e-072
epithalamus8.12e-072
Disease
Ontology termp-valuen
germ cell and embryonal cancer3.91e-0822
germ cell cancer3.91e-0822
neuroectodermal tumor7.25e-0710


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.

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