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Coexpression cluster:C2240: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!2.75e-53!53;UBERON:0002616!2.75e-53!53;UBERON:0001049!3.66e-52!56;UBERON:0005068!3.66e-52!56;UBERON:0006241!3.66e-52!56;UBERON:0007135!3.66e-52!56;UBERON:0002780!9.96e-47!41;UBERON:0001890!9.96e-47!41;UBERON:0003080!9.96e-47!41;UBERON:0006240!9.96e-47!41;UBERON:0000955!6.23e-46!68;UBERON:0006238!6.23e-46!68;UBERON:0001893!1.03e-45!34;UBERON:0003528!2.64e-45!34;UBERON:0002020!2.64e-45!34;UBERON:0001016!8.63e-45!89;UBERON:0001869!2.49e-43!32;UBERON:0002791!1.24e-42!32;UBERON:0002346!4.95e-42!86;UBERON:0001017!7.48e-42!81;UBERON:0003075!4.84e-39!82;UBERON:0007284!4.84e-39!82;UBERON:0003056!1.90e-34!61;UBERON:0007023!3.37e-33!114;UBERON:0000956!8.08e-33!25;UBERON:0000203!8.08e-33!25;UBERON:0002619!3.09e-32!22;UBERON:0001950!4.09e-29!20;UBERON:0010371!1.93e-27!104;UBERON:0004121!1.01e-22!171;UBERON:0000924!1.01e-22!171;UBERON:0006601!1.01e-22!171;UBERON:0010314!1.87e-21!132;UBERON:0011216!2.29e-20!223;UBERON:0002420!2.65e-14!9;UBERON:0007245!2.65e-14!9;UBERON:0010009!2.65e-14!9;UBERON:0010011!2.65e-14!9;UBERON:0000454!2.65e-14!9;UBERON:0000125!9.25e-14!9;UBERON:0002308!9.25e-14!9;UBERON:0000025!4.92e-12!192;UBERON:0000200!1.00e-11!6;UBERON:0009663!3.33e-11!7;UBERON:0000477!6.32e-11!373;UBERON:0000064!8.80e-10!218;UBERON:0004111!1.08e-09!240;UBERON:0002021!1.21e-09!5;UBERON:0001871!1.43e-09!6;UBERON:0000349!1.70e-09!5;UBERON:0000481!2.03e-08!342;UBERON:0004733!3.16e-08!12;UBERON:0002028!3.16e-08!12;UBERON:0007277!3.16e-08!12;UBERON:0003076!7.55e-08!15;UBERON:0003057!7.55e-08!15;UBERON:0004732!1.84e-07!13;UBERON:0000369!1.93e-07!4;UBERON:0002435!1.93e-07!4;UBERON:0000204!1.93e-07!4;UBERON:0010082!1.93e-07!4;UBERON:0000483!9.88e-07!306
|ontology_enrichment_uberon=UBERON:0000073!2.75e-53!53;UBERON:0002616!2.75e-53!53;UBERON:0001049!3.66e-52!56;UBERON:0005068!3.66e-52!56;UBERON:0006241!3.66e-52!56;UBERON:0007135!3.66e-52!56;UBERON:0002780!9.96e-47!41;UBERON:0001890!9.96e-47!41;UBERON:0003080!9.96e-47!41;UBERON:0006240!9.96e-47!41;UBERON:0000955!6.23e-46!68;UBERON:0006238!6.23e-46!68;UBERON:0001893!1.03e-45!34;UBERON:0003528!2.64e-45!34;UBERON:0002020!2.64e-45!34;UBERON:0001016!8.63e-45!89;UBERON:0001869!2.49e-43!32;UBERON:0002791!1.24e-42!32;UBERON:0002346!4.95e-42!86;UBERON:0001017!7.48e-42!81;UBERON:0003075!4.84e-39!82;UBERON:0007284!4.84e-39!82;UBERON:0003056!1.90e-34!61;UBERON:0007023!3.37e-33!114;UBERON:0000956!8.08e-33!25;UBERON:0000203!8.08e-33!25;UBERON:0002619!3.09e-32!22;UBERON:0001950!4.09e-29!20;UBERON:0010371!1.93e-27!104;UBERON:0004121!1.01e-22!171;UBERON:0000924!1.01e-22!171;UBERON:0006601!1.01e-22!171;UBERON:0010314!1.87e-21!132;UBERON:0011216!2.29e-20!223;UBERON:0002420!2.65e-14!9;UBERON:0007245!2.65e-14!9;UBERON:0010009!2.65e-14!9;UBERON:0010011!2.65e-14!9;UBERON:0000454!2.65e-14!9;UBERON:0000125!9.25e-14!9;UBERON:0002308!9.25e-14!9;UBERON:0000025!4.92e-12!192;UBERON:0000200!1.00e-11!6;UBERON:0009663!3.33e-11!7;UBERON:0000477!6.32e-11!373;UBERON:0000064!8.80e-10!218;UBERON:0004111!1.08e-09!240;UBERON:0002021!1.21e-09!5;UBERON:0001871!1.43e-09!6;UBERON:0000349!1.70e-09!5;UBERON:0000481!2.03e-08!342;UBERON:0004733!3.16e-08!12;UBERON:0002028!3.16e-08!12;UBERON:0007277!3.16e-08!12;UBERON:0003076!7.55e-08!15;UBERON:0003057!7.55e-08!15;UBERON:0004732!1.84e-07!13;UBERON:0000369!1.93e-07!4;UBERON:0002435!1.93e-07!4;UBERON:0000204!1.93e-07!4;UBERON:0010082!1.93e-07!4;UBERON:0000483!9.88e-07!306
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912,0.171704,0.208256,0.265058,0.256405,0.00120337,0.302133,0.40806,0.151361,0.000371318,0.286696,0.150674,0.000231487,0.246177,0.0103202,0.0737175,0.318525,0.213257,0.00502917,0.122782,0.410951,0.0465068,0.266974,0.125746,0.112897,0.00185587,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.00445319,0.321965,0.0386145,0.00331953
|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,2.42852,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,1.18986,0.581762,0.169357,0.731221,0.528529,0.632849,2.06579,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.911389,0.49475,0.598278,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.314427,0.61613,0.822818,0.694903,0.99221,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,1.28263,1.32819,0.336329,0.321165,1.49254,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,4.31432,1.44378,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,2.27689,0.456994,0.354969,2.60183,0.939507,1.37313,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,2.14757,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,1.41398,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.521611,1.24902,0.383416,1.92786,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:23, 26 November 2012


Full id: C2240_anaplastic_cerebellum_occipital_insula_medial_frontal_postcentral



Phase1 CAGE Peaks

Hg19::chr12:72665340..72665355,+p@chr12:72665340..72665355
+
Hg19::chr12:72665366..72665378,+p@chr12:72665366..72665378
+
Hg19::chr12:72665423..72665456,+p@chr12:72665423..72665456
+
Hg19::chr3:56809721..56809764,-p8@ARHGEF3


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
regional part of nervous system2.75e-5353
regional part of brain2.75e-5353
neural tube3.66e-5256
neural rod3.66e-5256
future spinal cord3.66e-5256
neural keel3.66e-5256
regional part of forebrain9.96e-4741
forebrain9.96e-4741
anterior neural tube9.96e-4741
future forebrain9.96e-4741
brain6.23e-4668
future brain6.23e-4668
telencephalon1.03e-4534
brain grey matter2.64e-4534
gray matter2.64e-4534
nervous system8.63e-4589
cerebral hemisphere2.49e-4332
regional part of telencephalon1.24e-4232
neurectoderm4.95e-4286
central nervous system7.48e-4281
neural plate4.84e-3982
presumptive neural plate4.84e-3982
pre-chordal neural plate1.90e-3461
adult organism3.37e-33114
cerebral cortex8.08e-3325
pallium8.08e-3325
regional part of cerebral cortex3.09e-3222
neocortex4.09e-2920
ecto-epithelium1.93e-27104
ectoderm-derived structure1.01e-22171
ectoderm1.01e-22171
presumptive ectoderm1.01e-22171
structure with developmental contribution from neural crest1.87e-21132
organ system subdivision2.29e-20223
basal ganglion2.65e-149
nuclear complex of neuraxis2.65e-149
aggregate regional part of brain2.65e-149
collection of basal ganglia2.65e-149
cerebral subcortex2.65e-149
neural nucleus9.25e-149
nucleus of brain9.25e-149
tube4.92e-12192
gyrus1.00e-116
telencephalic nucleus3.33e-117
anatomical cluster6.32e-11373
organ part8.80e-10218
anatomical conduit1.08e-09240
occipital lobe1.21e-095
temporal lobe1.43e-096
limbic system1.70e-095
multi-tissue structure2.03e-08342
segmental subdivision of hindbrain3.16e-0812
hindbrain3.16e-0812
presumptive hindbrain3.16e-0812
posterior neural tube7.55e-0815
chordal neural plate7.55e-0815
segmental subdivision of nervous system1.84e-0713
corpus striatum1.93e-074
striatum1.93e-074
ventral part of telencephalon1.93e-074
future corpus striatum1.93e-074
epithelium9.88e-07306


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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