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Coexpression cluster:C466: Difference between revisions

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|tf_chipseq_enrich=MYC#4609;10:2.48680089124257:0.00291429073905418:0.0157473929271564!NR2C2#7182;10:15.5307670977337:1.88496708895321e-10:1.96079758768112e-08
|tf_chipseq_enrich=MYC#4609;10:2.48680089124257:0.00291429073905418:0.0157473929271564!NR2C2#7182;10:15.5307670977337:1.88496708895321e-10:1.96079758768112e-08
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|tfbs_overrepresentation_for_novel_motifs=0.102469,6.17588e-05,0.0984893,0.18689,5.47325,0.185775,0.239567,0.0302452,0.121741,0.00531327,0.165709,0.272066,0.0182787,0.231159,0.264653,0.296747,0.416635,0.196076,0.0212388,0.0216083,0.0985208,0.008045,0.180548,0.0748199,0.124129,0.289541,0.0139215,0.179098,0.0787487,0.0545069,0.462061,0.448071,0.0406138,0.0187954,0.221271,0.00860299,0.0600845,0.547612,0.188523,0.25574,0.21951,0.141543,0.00160738,0.0758747,8.32893e-05,0.115453,0.240368,0.158699,0.0087826,0.27085,0.300624,1.28662,0.0057749,0.515129,0.653159,0.233295,0.08088,0.209799,0.0110646,0.209089,0.483605,0.242112,0.0296398,0.393294,0.71007,0.364726,0.73513,1.08739,0.43915,0.930562,0.133532,0.130122,0.0305792,0.651319,0.0785724,0.0146455,0.0588919,0.379205,0.436366,0.382881,0.0224356,0.392395,0.25519,0.127139,0.604277,1.80912,50.9148,0.0102959,0.321213,1.18432,0.823081,0.579812,0.462581,0.672886,0.0776122,0.0481302,0.0208754,0.499768,1.5628,0.00795051,0.0509974,0.45769,0.494867,7.34929,0.355282,0.16277,0.406348,0.228655,0.123981,0.0697646,0.104554,0.492438,4.2983,0.511934,0.777703,0.0594109,0.00245646,0.15094,0.362802,4.47285,0.64371,0.319278,0.183912,0.263675,0.882719,0.379837,0.234914,0.466912,0.683004,0.048498,0.580435,0.153507,0.696335,0.26116,0.835304,0.130453,0.147939,0.179476,0.795107,1.6331,1.23566,0.759951,30.0504,0.496668,0.938543,0.20386,0.343142,1.4753,0.139503,0.0420132,0.00447134,0.0328567,0.58078,0.113903,0.241755,0.959994,0.308372,73.6709,258.19,0.107739,0.758809,0.564094,0.435692,0.109525,0.36994,0.254599,0.148935,0.238589,0.000121294
}}
}}

Revision as of 14:14, 26 November 2012


Full id: C466_cerebellum_retinoblastoma_pineal_small_pituitary_parietal_pons



Phase1 CAGE Peaks

Hg19::chr11:17785684..17785695,+p@chr11:17785684..17785695
+
Hg19::chr18:35128158..35128201,-p@chr18:35128158..35128201
-
Hg19::chr18:35145981..35146017,-p3@CELF4
Hg19::chr20:24945160..24945169,-p@chr20:24945160..24945169
-
Hg19::chr7:149700383..149700403,-p@chr7:149700383..149700403
-
Hg19::chr7:149700477..149700562,-p@chr7:149700477..149700562
-
Hg19::chr7:149700569..149700636,-p@chr7:149700569..149700636
-
Hg19::chr7:149700639..149700651,-p@chr7:149700639..149700651
-
Hg19::chr7:149700652..149700676,-p@chr7:149700652..149700676
-
Hg19::chr7:149700678..149700703,-p@chr7:149700678..149700703
-
Hg19::chr7:149700712..149700747,-p@chr7:149700712..149700747
-
Hg19::chr7:149700748..149700770,-p@chr7:149700748..149700770
-
Hg19::chr7:149700790..149700823,-p@chr7:149700790..149700823
-
Hg19::chr7:149700827..149700889,-p@chr7:149700827..149700889
-
Hg19::chr7:149700989..149701027,-p@chr7:149700989..149701027
-
Hg19::chr7:149701365..149701397,-p@chr7:149701365..149701397
-
Hg19::chr7:149701457..149701484,-p@chr7:149701457..149701484
-
Hg19::chr7:149745353..149745375,-p@chr7:149745353..149745375
-
Hg19::chr7:153790013..153790040,+p@chr7:153790013..153790040
+
Hg19::chr7:153790151..153790200,+p@chr7:153790151..153790200
+
Hg19::chr7:153931630..153931643,+p@chr7:153931630..153931643
+


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
neural tube2.25e-6756
neural rod2.25e-6756
future spinal cord2.25e-6756
neural keel2.25e-6756
regional part of nervous system3.26e-6253
regional part of brain3.26e-6253
central nervous system2.21e-5881
nervous system9.50e-5889
brain1.16e-5168
future brain1.16e-5168
regional part of forebrain1.23e-5041
forebrain1.23e-5041
anterior neural tube1.23e-5041
future forebrain1.23e-5041
neurectoderm5.97e-4786
adult organism1.09e-46114
neural plate1.73e-4582
presumptive neural plate1.73e-4582
brain grey matter6.19e-3934
gray matter6.19e-3934
telencephalon1.50e-3834
ecto-epithelium2.73e-37104
regional part of telencephalon1.70e-3532
cerebral hemisphere2.00e-3532
pre-chordal neural plate1.47e-3461
ectoderm-derived structure1.06e-28171
ectoderm1.06e-28171
presumptive ectoderm1.06e-28171
regional part of cerebral cortex1.29e-2822
structure with developmental contribution from neural crest1.69e-27132
organ system subdivision7.96e-26223
neocortex3.18e-2520
cerebral cortex1.40e-2425
pallium1.40e-2425
posterior neural tube4.00e-1715
chordal neural plate4.00e-1715
neural nucleus1.98e-169
nucleus of brain1.98e-169
basal ganglion3.83e-169
nuclear complex of neuraxis3.83e-169
aggregate regional part of brain3.83e-169
collection of basal ganglia3.83e-169
cerebral subcortex3.83e-169
tube1.49e-15192
diencephalon9.30e-147
future diencephalon9.30e-147
anatomical cluster2.46e-13373
telencephalic nucleus6.43e-137
segmental subdivision of hindbrain1.99e-1212
hindbrain1.99e-1212
presumptive hindbrain1.99e-1212
brainstem9.27e-126
segmental subdivision of nervous system2.67e-1113
anatomical conduit9.44e-11240
parietal lobe5.58e-105
limbic system5.90e-105
temporal lobe2.16e-096
gland of diencephalon3.52e-094
neuroendocrine gland3.52e-094
epithelium4.38e-09306
cell layer7.63e-09309
regional part of diencephalon8.18e-094
small intestine1.92e-084
corpus striatum3.40e-084
striatum3.40e-084
ventral part of telencephalon3.40e-084
future corpus striatum3.40e-084
multi-tissue structure3.92e-08342
regional part of metencephalon4.54e-089
metencephalon4.54e-089
future metencephalon4.54e-089
embryo5.91e-08592
gyrus9.45e-086
developing anatomical structure1.28e-07581
germ layer2.21e-07560
germ layer / neural crest2.21e-07560
embryonic tissue2.21e-07560
presumptive structure2.21e-07560
germ layer / neural crest derived structure2.21e-07560
epiblast (generic)2.21e-07560
embryonic structure3.60e-07564
pons4.69e-073
male reproductive organ6.63e-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)

{{{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
MYC#4609102.486800891242570.002914290739054180.0157473929271564
NR2C2#71821015.53076709773371.88496708895321e-101.96079758768112e-08



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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