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Coexpression cluster:C2575: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!1.15e-47!81;UBERON:0001016!1.64e-46!89;UBERON:0001049!2.43e-43!56;UBERON:0005068!2.43e-43!56;UBERON:0006241!2.43e-43!56;UBERON:0007135!2.43e-43!56;UBERON:0000073!1.95e-42!53;UBERON:0002616!1.95e-42!53;UBERON:0000955!1.23e-38!68;UBERON:0006238!1.23e-38!68;UBERON:0003075!5.51e-36!82;UBERON:0007284!5.51e-36!82;UBERON:0002346!1.78e-33!86;UBERON:0002780!3.73e-30!41;UBERON:0001890!3.73e-30!41;UBERON:0003080!3.73e-30!41;UBERON:0006240!3.73e-30!41;UBERON:0001893!6.68e-29!34;UBERON:0003528!1.22e-28!34;UBERON:0002020!1.22e-28!34;UBERON:0010371!2.73e-27!104;UBERON:0001869!5.77e-27!32;UBERON:0002791!1.53e-26!32;UBERON:0000956!1.82e-26!25;UBERON:0000203!1.82e-26!25;UBERON:0003056!3.30e-26!61;UBERON:0002619!7.49e-26!22;UBERON:0004121!4.93e-25!171;UBERON:0000924!4.93e-25!171;UBERON:0006601!4.93e-25!171;UBERON:0001950!2.64e-23!20;UBERON:0010314!1.28e-18!132;UBERON:0007023!1.66e-18!114;UBERON:0011216!2.23e-15!223;UBERON:0003076!4.27e-14!15;UBERON:0003057!4.27e-14!15;UBERON:0004733!1.58e-13!12;UBERON:0002028!1.58e-13!12;UBERON:0007277!1.58e-13!12;UBERON:0002680!1.31e-12!9;UBERON:0001895!1.31e-12!9;UBERON:0010092!1.31e-12!9;UBERON:0004732!3.08e-12!13;UBERON:0000200!2.20e-09!6;UBERON:0002037!2.77e-09!6;UBERON:0006215!2.77e-09!6;UBERON:0001872!4.14e-08!5;UBERON:0000349!5.37e-08!5;UBERON:0001871!5.72e-08!6
|ontology_enrichment_uberon=UBERON:0001017!1.15e-47!81;UBERON:0001016!1.64e-46!89;UBERON:0001049!2.43e-43!56;UBERON:0005068!2.43e-43!56;UBERON:0006241!2.43e-43!56;UBERON:0007135!2.43e-43!56;UBERON:0000073!1.95e-42!53;UBERON:0002616!1.95e-42!53;UBERON:0000955!1.23e-38!68;UBERON:0006238!1.23e-38!68;UBERON:0003075!5.51e-36!82;UBERON:0007284!5.51e-36!82;UBERON:0002346!1.78e-33!86;UBERON:0002780!3.73e-30!41;UBERON:0001890!3.73e-30!41;UBERON:0003080!3.73e-30!41;UBERON:0006240!3.73e-30!41;UBERON:0001893!6.68e-29!34;UBERON:0003528!1.22e-28!34;UBERON:0002020!1.22e-28!34;UBERON:0010371!2.73e-27!104;UBERON:0001869!5.77e-27!32;UBERON:0002791!1.53e-26!32;UBERON:0000956!1.82e-26!25;UBERON:0000203!1.82e-26!25;UBERON:0003056!3.30e-26!61;UBERON:0002619!7.49e-26!22;UBERON:0004121!4.93e-25!171;UBERON:0000924!4.93e-25!171;UBERON:0006601!4.93e-25!171;UBERON:0001950!2.64e-23!20;UBERON:0010314!1.28e-18!132;UBERON:0007023!1.66e-18!114;UBERON:0011216!2.23e-15!223;UBERON:0003076!4.27e-14!15;UBERON:0003057!4.27e-14!15;UBERON:0004733!1.58e-13!12;UBERON:0002028!1.58e-13!12;UBERON:0007277!1.58e-13!12;UBERON:0002680!1.31e-12!9;UBERON:0001895!1.31e-12!9;UBERON:0010092!1.31e-12!9;UBERON:0004732!3.08e-12!13;UBERON:0000200!2.20e-09!6;UBERON:0002037!2.77e-09!6;UBERON:0006215!2.77e-09!6;UBERON:0001872!4.14e-08!5;UBERON:0000349!5.37e-08!5;UBERON:0001871!5.72e-08!6
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,0.581696,0.741427,0.534346,1.75218,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,1.3102,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.6318,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,1.12407,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,4.9159,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,4.35748,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.156682
}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2575_cerebellum_Neurons_occipital_duodenum_temporal_parietal_brain



Phase1 CAGE Peaks

Hg19::chr1:244214577..244214593,+p1@ZNF238
Hg19::chr1:244214611..244214624,+p4@ZNF238
Hg19::chr1:244217279..244217295,+p1@AK310634
Hg19::chr8:9761693..9761730,-p2@ENST00000521863


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
neural cell8.90e-0925
neurectodermal cell6.57e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system1.15e-4781
nervous system1.64e-4689
neural tube2.43e-4356
neural rod2.43e-4356
future spinal cord2.43e-4356
neural keel2.43e-4356
regional part of nervous system1.95e-4253
regional part of brain1.95e-4253
brain1.23e-3868
future brain1.23e-3868
neural plate5.51e-3682
presumptive neural plate5.51e-3682
neurectoderm1.78e-3386
regional part of forebrain3.73e-3041
forebrain3.73e-3041
anterior neural tube3.73e-3041
future forebrain3.73e-3041
telencephalon6.68e-2934
brain grey matter1.22e-2834
gray matter1.22e-2834
ecto-epithelium2.73e-27104
cerebral hemisphere5.77e-2732
regional part of telencephalon1.53e-2632
cerebral cortex1.82e-2625
pallium1.82e-2625
pre-chordal neural plate3.30e-2661
regional part of cerebral cortex7.49e-2622
ectoderm-derived structure4.93e-25171
ectoderm4.93e-25171
presumptive ectoderm4.93e-25171
neocortex2.64e-2320
structure with developmental contribution from neural crest1.28e-18132
adult organism1.66e-18114
organ system subdivision2.23e-15223
posterior neural tube4.27e-1415
chordal neural plate4.27e-1415
segmental subdivision of hindbrain1.58e-1312
hindbrain1.58e-1312
presumptive hindbrain1.58e-1312
regional part of metencephalon1.31e-129
metencephalon1.31e-129
future metencephalon1.31e-129
segmental subdivision of nervous system3.08e-1213
gyrus2.20e-096
cerebellum2.77e-096
rhombic lip2.77e-096
parietal lobe4.14e-085
limbic system5.37e-085
temporal lobe5.72e-086


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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