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Coexpression cluster:C2246: Difference between revisions

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|full_id=C2246_carcinoid_Fibroblast_neuroblastoma_salivary_anaplastic_epitheloid_melanoma
|full_id=C2246_carcinoid_Fibroblast_neuroblastoma_salivary_anaplastic_epitheloid_melanoma
|id=C2246
|id=C2246
|ontology_enrichment_celltype=CL:0000055!7.96e-11!180;CL:0000221!4.07e-10!71;CL:0002321!1.22e-09!248;CL:0000220!2.07e-09!246;CL:0000393!3.61e-09!60;CL:0000211!3.61e-09!60;CL:0000680!1.51e-08!57;CL:0000056!1.51e-08!57;CL:0000355!1.51e-08!57;CL:0000187!6.80e-08!54;CL:0000183!9.11e-08!59;CL:0000133!1.87e-07!59
|ontology_enrichment_celltype=CL:0000221!3.63e-10!72;CL:0002321!9.04e-10!250;CL:0000393!3.94e-09!61;CL:0000211!3.94e-09!61;CL:0000055!5.68e-09!106;CL:0000680!1.48e-08!58;CL:0000056!1.48e-08!58;CL:0000355!1.48e-08!58;CL:0000187!6.54e-08!55;CL:0000183!7.75e-08!59;CL:0000133!2.32e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000924!7.89e-37!173;UBERON:0006601!7.89e-37!173;UBERON:0004121!2.98e-35!169;UBERON:0000033!1.40e-29!123;UBERON:0000073!1.66e-29!94;UBERON:0001016!1.66e-29!94;UBERON:0000153!3.97e-27!129;UBERON:0007811!3.97e-27!129;UBERON:0000475!5.77e-26!365;UBERON:0005743!1.11e-25!86;UBERON:0002346!2.70e-25!90;UBERON:0001017!7.27e-24!82;UBERON:0003075!7.38e-24!86;UBERON:0007284!7.38e-24!86;UBERON:0002616!2.11e-23!59;UBERON:0003056!4.31e-23!61;UBERON:0001049!7.25e-23!57;UBERON:0005068!7.25e-23!57;UBERON:0006241!7.25e-23!57;UBERON:0007135!7.25e-23!57;UBERON:0000955!7.15e-22!69;UBERON:0006238!7.15e-22!69;UBERON:0000119!2.31e-21!312;UBERON:0000483!6.45e-21!309;UBERON:0000481!7.64e-19!347;UBERON:0002780!1.25e-18!41;UBERON:0001890!1.25e-18!41;UBERON:0006240!1.25e-18!41;UBERON:0003080!1.87e-18!42;UBERON:0000468!5.02e-16!659;UBERON:0000922!6.91e-16!612;UBERON:0002020!7.77e-16!34;UBERON:0003528!7.77e-16!34;UBERON:0001893!2.17e-15!34;UBERON:0000064!2.53e-15!219;UBERON:0002791!6.70e-15!33;UBERON:0001869!1.26e-14!32;UBERON:0002050!1.82e-14!605;UBERON:0005423!1.82e-14!605;UBERON:0000923!2.11e-14!604;UBERON:0005291!2.11e-14!604;UBERON:0006598!2.11e-14!604;UBERON:0002532!2.11e-14!604;UBERON:0000467!1.31e-13!625;UBERON:0000480!1.38e-13!626;UBERON:0000477!1.56e-13!286;UBERON:0004111!1.34e-12!241;UBERON:0002619!3.35e-12!22;UBERON:0000956!1.83e-11!25;UBERON:0000203!1.83e-11!25;UBERON:0001950!3.75e-11!20;UBERON:0000025!1.98e-09!194;UBERON:0000486!2.18e-09!82;UBERON:0000914!2.57e-09!83;UBERON:0002329!2.57e-09!83;UBERON:0003077!2.57e-09!83;UBERON:0003059!2.57e-09!83;UBERON:0007282!2.57e-09!83;UBERON:0009618!2.57e-09!83;UBERON:0007285!2.57e-09!83;UBERON:0004290!6.46e-09!70;UBERON:0001444!1.70e-07!48;UBERON:0001134!2.68e-07!61;UBERON:0002036!2.68e-07!61;UBERON:0003082!2.68e-07!61;UBERON:0000063!4.52e-07!97;UBERON:0001032!4.80e-07!24;UBERON:0004456!4.80e-07!24;UBERON:0005085!5.17e-07!29;UBERON:0002385!5.77e-07!63;UBERON:0001015!5.77e-07!63;UBERON:0000383!5.77e-07!63;UBERON:0003102!7.15e-07!95;UBERON:0000020!7.57e-07!23
|ontology_enrichment_uberon=UBERON:0004121!1.11e-37!171;UBERON:0000924!1.11e-37!171;UBERON:0006601!1.11e-37!171;UBERON:0010371!1.09e-28!104;UBERON:0001016!3.83e-27!89;UBERON:0002346!3.05e-26!86;UBERON:0003075!8.53e-25!82;UBERON:0007284!8.53e-25!82;UBERON:0010314!2.02e-24!132;UBERON:0001017!2.18e-23!81;UBERON:0003056!2.64e-23!61;UBERON:0001049!2.36e-22!56;UBERON:0005068!2.36e-22!56;UBERON:0006241!2.36e-22!56;UBERON:0007135!2.36e-22!56;UBERON:0000073!7.97e-22!53;UBERON:0002616!7.97e-22!53;UBERON:0000119!2.34e-21!309;UBERON:0000955!2.48e-21!68;UBERON:0006238!2.48e-21!68;UBERON:0000483!7.06e-21!306;UBERON:0000477!2.43e-20!373;UBERON:0000481!1.18e-19!342;UBERON:0002780!3.66e-18!41;UBERON:0001890!3.66e-18!41;UBERON:0003080!3.66e-18!41;UBERON:0006240!3.66e-18!41;UBERON:0003528!1.96e-15!34;UBERON:0002020!1.96e-15!34;UBERON:0000064!2.39e-15!218;UBERON:0001893!6.08e-15!34;UBERON:0000468!1.12e-14!656;UBERON:0011216!1.61e-14!223;UBERON:0002791!2.90e-14!32;UBERON:0001869!3.35e-14!32;UBERON:0000922!5.73e-14!592;UBERON:0000467!5.20e-13!624;UBERON:0000480!5.66e-13!625;UBERON:0002050!1.70e-12!564;UBERON:0004111!5.17e-12!240;UBERON:0002619!6.02e-12!22;UBERON:0000923!6.34e-12!560;UBERON:0010316!6.34e-12!560;UBERON:0005291!6.34e-12!560;UBERON:0006598!6.34e-12!560;UBERON:0010317!6.34e-12!560;UBERON:0002532!6.34e-12!560;UBERON:0005423!1.16e-11!581;UBERON:0000956!3.01e-11!25;UBERON:0000203!3.01e-11!25;UBERON:0001950!7.52e-11!20;UBERON:0000486!2.91e-09!83;UBERON:0003077!2.93e-09!72;UBERON:0007285!2.93e-09!72;UBERON:0000025!4.48e-09!192;UBERON:0002329!7.43e-09!71;UBERON:0003059!7.43e-09!71;UBERON:0007282!7.43e-09!71;UBERON:0004290!7.43e-09!71;UBERON:0009618!7.43e-09!71;UBERON:0007524!8.27e-09!73;UBERON:0000033!9.65e-09!56;UBERON:0007503!1.85e-08!78;UBERON:0001444!5.19e-08!49;UBERON:0003102!1.61e-07!99;UBERON:0005085!1.76e-07!31;UBERON:0000063!2.36e-07!98;UBERON:0001134!2.65e-07!62;UBERON:0002036!2.65e-07!62;UBERON:0003082!2.65e-07!62;UBERON:0000020!2.69e-07!24;UBERON:0001032!2.69e-07!24;UBERON:0004456!2.69e-07!24;UBERON:0000153!3.72e-07!62;UBERON:0007811!3.72e-07!62;UBERON:0002385!5.28e-07!64;UBERON:0001015!5.28e-07!64;UBERON:0000383!5.28e-07!64;UBERON:0000970!6.50e-07!21;UBERON:0002104!6.50e-07!21;UBERON:0000475!9.33e-07!264
|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346334351722038!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466048061517861!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195731203430085!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482862447851121!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107167027532605
|tf_chipseq_enrich=ATF3#467;3:16.8473808945066:0.000340998682365564:0.00346334351722038!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466048061517861!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195731203430085!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482862447851121!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107167027532605
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}}
}}

Revision as of 13:47, 19 October 2012


Full id: C2246_carcinoid_Fibroblast_neuroblastoma_salivary_anaplastic_epitheloid_melanoma



Phase1 CAGE Peaks

Hg19::chr12:85285909..85285928,-p3@SLC6A15
Hg19::chr12:85306494..85306558,-p1@SLC6A15
Hg19::chr12:85306562..85306591,-p2@SLC6A15
Hg19::chr12:85306594..85306622,-p4@SLC6A15


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>

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.11e-37171
ectoderm1.11e-37171
presumptive ectoderm1.11e-37171
ecto-epithelium1.09e-28104
nervous system3.83e-2789
neurectoderm3.05e-2686
neural plate8.53e-2582
presumptive neural plate8.53e-2582
structure with developmental contribution from neural crest2.02e-24132
central nervous system2.18e-2381
pre-chordal neural plate2.64e-2361
neural tube2.36e-2256
neural rod2.36e-2256
future spinal cord2.36e-2256
neural keel2.36e-2256
regional part of nervous system7.97e-2253
regional part of brain7.97e-2253
cell layer2.34e-21309
brain2.48e-2168
future brain2.48e-2168
epithelium7.06e-21306
anatomical cluster2.43e-20373
multi-tissue structure1.18e-19342
regional part of forebrain3.66e-1841
forebrain3.66e-1841
anterior neural tube3.66e-1841
future forebrain3.66e-1841
brain grey matter1.96e-1534
gray matter1.96e-1534
organ part2.39e-15218
telencephalon6.08e-1534
multi-cellular organism1.12e-14656
organ system subdivision1.61e-14223
regional part of telencephalon2.90e-1432
cerebral hemisphere3.35e-1432
embryo5.73e-14592
anatomical system5.20e-13624
anatomical group5.66e-13625
embryonic structure1.70e-12564
anatomical conduit5.17e-12240
regional part of cerebral cortex6.02e-1222
germ layer6.34e-12560
germ layer / neural crest6.34e-12560
embryonic tissue6.34e-12560
presumptive structure6.34e-12560
germ layer / neural crest derived structure6.34e-12560
epiblast (generic)6.34e-12560
developing anatomical structure1.16e-11581
cerebral cortex3.01e-1125
pallium3.01e-1125
neocortex7.52e-1120
multilaminar epithelium2.91e-0983
paraxial mesoderm2.93e-0972
presumptive paraxial mesoderm2.93e-0972
tube4.48e-09192
somite7.43e-0971
presomitic mesoderm7.43e-0971
presumptive segmental plate7.43e-0971
dermomyotome7.43e-0971
trunk paraxial mesoderm7.43e-0971
dense mesenchyme tissue8.27e-0973
head9.65e-0956
epithelial vesicle1.85e-0878
subdivision of head5.19e-0849
surface structure1.61e-0799
ectodermal placode1.76e-0731
organ segment2.36e-0798
skeletal muscle tissue2.65e-0762
striated muscle tissue2.65e-0762
myotome2.65e-0762
sense organ2.69e-0724
sensory system2.69e-0724
entire sense organ system2.69e-0724
anterior region of body3.72e-0762
craniocervical region3.72e-0762
muscle tissue5.28e-0764
musculature5.28e-0764
musculature of body5.28e-0764
eye6.50e-0721
visual system6.50e-0721
organism subdivision9.33e-07264


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
ATF3#467316.84738089450660.0003409986823655640.00346334351722038
MAX#414934.839416631755340.01315737137836840.0466048061517861
REST#597837.237521537096020.004104697304192610.0195731203430085
USF1#739134.771124457905970.01370465887188020.0482862447851121
USF2#739239.74414803880220.001718341848410070.0107167027532605



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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