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Coexpression cluster:C3007: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!1.50e-36!114;UBERON:0002346!4.64e-19!86;UBERON:0000073!1.06e-18!53;UBERON:0002616!1.06e-18!53;UBERON:0001049!3.49e-18!56;UBERON:0005068!3.49e-18!56;UBERON:0006241!3.49e-18!56;UBERON:0007135!3.49e-18!56;UBERON:0003075!4.15e-17!82;UBERON:0007284!4.15e-17!82;UBERON:0003528!9.17e-17!34;UBERON:0002020!9.17e-17!34;UBERON:0001893!1.12e-16!34;UBERON:0000955!5.25e-16!68;UBERON:0006238!5.25e-16!68;UBERON:0002791!1.07e-15!32;UBERON:0001869!1.73e-15!32;UBERON:0002780!7.85e-15!41;UBERON:0001890!7.85e-15!41;UBERON:0003080!7.85e-15!41;UBERON:0006240!7.85e-15!41;UBERON:0000477!1.90e-14!373;UBERON:0000956!4.97e-14!25;UBERON:0000203!4.97e-14!25;UBERON:0001017!6.24e-14!81;UBERON:0011216!1.67e-13!223;UBERON:0010371!7.65e-13!104;UBERON:0003056!1.56e-12!61;UBERON:0001016!3.80e-12!89;UBERON:0002619!2.08e-11!22;UBERON:0004121!2.26e-11!171;UBERON:0000924!2.26e-11!171;UBERON:0006601!2.26e-11!171;UBERON:0001950!2.49e-11!20;UBERON:0000481!4.19e-11!342;UBERON:0010314!4.37e-11!132;UBERON:0004111!4.40e-11!240;UBERON:0003135!1.70e-07!11
|ontology_enrichment_uberon=UBERON:0007023!1.50e-36!114;UBERON:0002346!4.64e-19!86;UBERON:0000073!1.06e-18!53;UBERON:0002616!1.06e-18!53;UBERON:0001049!3.49e-18!56;UBERON:0005068!3.49e-18!56;UBERON:0006241!3.49e-18!56;UBERON:0007135!3.49e-18!56;UBERON:0003075!4.15e-17!82;UBERON:0007284!4.15e-17!82;UBERON:0003528!9.17e-17!34;UBERON:0002020!9.17e-17!34;UBERON:0001893!1.12e-16!34;UBERON:0000955!5.25e-16!68;UBERON:0006238!5.25e-16!68;UBERON:0002791!1.07e-15!32;UBERON:0001869!1.73e-15!32;UBERON:0002780!7.85e-15!41;UBERON:0001890!7.85e-15!41;UBERON:0003080!7.85e-15!41;UBERON:0006240!7.85e-15!41;UBERON:0000477!1.90e-14!373;UBERON:0000956!4.97e-14!25;UBERON:0000203!4.97e-14!25;UBERON:0001017!6.24e-14!81;UBERON:0011216!1.67e-13!223;UBERON:0010371!7.65e-13!104;UBERON:0003056!1.56e-12!61;UBERON:0001016!3.80e-12!89;UBERON:0002619!2.08e-11!22;UBERON:0004121!2.26e-11!171;UBERON:0000924!2.26e-11!171;UBERON:0006601!2.26e-11!171;UBERON:0001950!2.49e-11!20;UBERON:0000481!4.19e-11!342;UBERON:0010314!4.37e-11!132;UBERON:0004111!4.40e-11!240;UBERON:0003135!1.70e-07!11
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 15:52, 26 November 2012


Full id: C3007_thyroid_skeletal_seminal_ductus_rectum_neuroectodermal_salivary



Phase1 CAGE Peaks

Hg19::chr10:24509705..24509709,+p@chr10:24509705..24509709
+
Hg19::chr10:24528439..24528445,+p@chr10:24528439..24528445
+
Hg19::chr10:24565554..24565558,+p@chr10:24565554..24565558
+


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.50e-36114
neurectoderm4.64e-1986
regional part of nervous system1.06e-1853
regional part of brain1.06e-1853
neural tube3.49e-1856
neural rod3.49e-1856
future spinal cord3.49e-1856
neural keel3.49e-1856
neural plate4.15e-1782
presumptive neural plate4.15e-1782
brain grey matter9.17e-1734
gray matter9.17e-1734
telencephalon1.12e-1634
brain5.25e-1668
future brain5.25e-1668
regional part of telencephalon1.07e-1532
cerebral hemisphere1.73e-1532
regional part of forebrain7.85e-1541
forebrain7.85e-1541
anterior neural tube7.85e-1541
future forebrain7.85e-1541
anatomical cluster1.90e-14373
cerebral cortex4.97e-1425
pallium4.97e-1425
central nervous system6.24e-1481
organ system subdivision1.67e-13223
ecto-epithelium7.65e-13104
pre-chordal neural plate1.56e-1261
nervous system3.80e-1289
regional part of cerebral cortex2.08e-1122
ectoderm-derived structure2.26e-11171
ectoderm2.26e-11171
presumptive ectoderm2.26e-11171
neocortex2.49e-1120
multi-tissue structure4.19e-11342
structure with developmental contribution from neural crest4.37e-11132
anatomical conduit4.40e-11240
male reproductive organ1.70e-0711


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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