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Coexpression cluster:C4126: Difference between revisions

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|full_id=C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala
|full_id=C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala
|id=C4126
|id=C4126
|ontology_enrichment_celltype=CL:0000066!5.22e-19!254;CL:0002076!9.35e-14!43;CL:0000223!2.07e-10!59;CL:0002368!3.88e-07!13;CL:0002251!6.84e-07!21
|ontology_enrichment_celltype=CL:0000066!5.19e-18!253;CL:0002076!5.10e-16!42;CL:0000223!1.28e-11!58;CL:0002368!1.33e-08!13;CL:0002251!6.19e-08!20
|ontology_enrichment_disease=DOID:305!2.32e-18!106;DOID:0050687!1.56e-15!143;DOID:162!2.86e-08!235;DOID:14566!4.15e-08!239;DOID:1749!2.80e-07!14
|ontology_enrichment_disease=DOID:305!8.27e-17!106;DOID:0050687!7.74e-13!143;DOID:1749!2.64e-08!14;DOID:162!1.23e-07!235;DOID:14566!1.46e-07!239
|ontology_enrichment_uberon=UBERON:0005743!2.00e-33!86;UBERON:0000073!2.62e-33!94;UBERON:0001016!2.62e-33!94;UBERON:0001017!4.39e-33!82;UBERON:0001049!6.75e-33!57;UBERON:0005068!6.75e-33!57;UBERON:0006241!6.75e-33!57;UBERON:0007135!6.75e-33!57;UBERON:0000924!2.80e-32!173;UBERON:0006601!2.80e-32!173;UBERON:0004121!1.61e-31!169;UBERON:0000033!6.13e-28!123;UBERON:0000955!9.51e-28!69;UBERON:0006238!9.51e-28!69;UBERON:0000153!9.82e-28!129;UBERON:0007811!9.82e-28!129;UBERON:0002616!1.44e-25!59;UBERON:0002780!7.58e-25!41;UBERON:0001890!7.58e-25!41;UBERON:0006240!7.58e-25!41;UBERON:0002346!1.11e-24!90;UBERON:0003075!4.12e-24!86;UBERON:0007284!4.12e-24!86;UBERON:0003080!9.15e-24!42;UBERON:0002020!1.49e-21!34;UBERON:0003528!1.49e-21!34;UBERON:0001893!1.85e-21!34;UBERON:0002791!7.32e-21!33;UBERON:0001869!6.28e-20!32;UBERON:0007023!5.72e-19!115;UBERON:0003056!5.40e-18!61;UBERON:0000064!2.73e-15!219;UBERON:0000956!3.22e-15!25;UBERON:0000203!3.22e-15!25;UBERON:0000922!5.60e-15!612;UBERON:0000062!5.71e-15!511;UBERON:0002619!5.95e-14!22;UBERON:0002050!1.27e-12!605;UBERON:0005423!1.27e-12!605;UBERON:0001950!1.87e-12!20;UBERON:0000923!2.65e-12!604;UBERON:0005291!2.65e-12!604;UBERON:0006598!2.65e-12!604;UBERON:0002532!2.65e-12!604;UBERON:0001004!2.79e-12!72;UBERON:0000475!3.16e-12!365;UBERON:0004119!7.20e-12!169;UBERON:0000925!7.20e-12!169;UBERON:0006595!7.20e-12!169;UBERON:0000481!1.39e-11!347;UBERON:0000468!2.01e-11!659;UBERON:0001007!8.35e-11!155;UBERON:0001555!8.35e-11!155;UBERON:0007026!8.35e-11!155;UBERON:0000477!1.45e-10!286;UBERON:0004111!2.75e-10!241;UBERON:0003076!3.46e-10!15;UBERON:0003057!3.46e-10!15;UBERON:0000467!3.66e-10!625;UBERON:0000480!5.16e-10!626;UBERON:0001041!8.30e-10!98;UBERON:0000464!2.31e-09!104;UBERON:0000065!2.32e-09!53;UBERON:0004921!3.21e-09!129;UBERON:0004185!3.21e-09!129;UBERON:0000072!5.15e-09!46;UBERON:0000077!1.65e-08!130;UBERON:0008947!3.23e-08!38;UBERON:0003258!3.23e-08!38;UBERON:0004732!3.79e-08!13;UBERON:0002308!7.07e-08!9;UBERON:0000125!7.07e-08!9;UBERON:0004733!8.30e-08!12;UBERON:0002028!8.30e-08!12;UBERON:0007277!8.30e-08!12;UBERON:0002420!1.01e-07!9;UBERON:0007245!1.01e-07!9;UBERON:0010009!1.01e-07!9;UBERON:0010011!1.01e-07!9;UBERON:0000454!1.01e-07!9;UBERON:0000063!1.26e-07!97;UBERON:0001048!1.83e-07!168;UBERON:0000466!3.62e-07!126;UBERON:0000025!7.30e-07!194
|ontology_enrichment_uberon=UBERON:0001017!6.31e-34!81;UBERON:0001049!1.04e-33!56;UBERON:0005068!1.04e-33!56;UBERON:0006241!1.04e-33!56;UBERON:0007135!1.04e-33!56;UBERON:0001016!1.42e-32!89;UBERON:0011216!1.89e-32!223;UBERON:0004121!4.69e-31!171;UBERON:0000924!4.69e-31!171;UBERON:0006601!4.69e-31!171;UBERON:0000073!6.34e-31!53;UBERON:0002616!6.34e-31!53;UBERON:0000955!4.73e-29!68;UBERON:0006238!4.73e-29!68;UBERON:0010371!6.96e-28!104;UBERON:0002346!6.14e-25!86;UBERON:0003075!9.05e-25!82;UBERON:0007284!9.05e-25!82;UBERON:0002780!1.16e-23!41;UBERON:0001890!1.16e-23!41;UBERON:0003080!1.16e-23!41;UBERON:0006240!1.16e-23!41;UBERON:0003528!4.07e-20!34;UBERON:0002020!4.07e-20!34;UBERON:0001893!6.24e-20!34;UBERON:0003056!1.17e-18!61;UBERON:0002791!1.54e-18!32;UBERON:0007023!1.84e-18!114;UBERON:0001869!2.57e-18!32;UBERON:0000477!1.32e-15!373;UBERON:0010314!5.01e-15!132;UBERON:0000064!4.64e-14!218;UBERON:0000062!9.72e-14!503;UBERON:0000956!2.54e-13!25;UBERON:0000203!2.54e-13!25;UBERON:0001004!1.82e-12!74;UBERON:0002619!4.68e-12!22;UBERON:0000922!7.29e-12!592;UBERON:0003076!3.92e-11!15;UBERON:0003057!3.92e-11!15;UBERON:0000481!1.35e-10!342;UBERON:0001950!1.73e-10!20;UBERON:0000065!2.39e-10!54;UBERON:0000468!5.40e-10!656;UBERON:0000072!1.13e-09!47;UBERON:0004111!4.25e-09!240;UBERON:0008947!4.60e-09!38;UBERON:0003258!4.60e-09!38;UBERON:0002050!5.32e-09!564;UBERON:0005423!6.07e-09!581;UBERON:0004732!7.88e-09!13;UBERON:0000125!1.50e-08!9;UBERON:0002308!1.50e-08!9;UBERON:0000467!1.56e-08!624;UBERON:0004733!1.88e-08!12;UBERON:0002028!1.88e-08!12;UBERON:0007277!1.88e-08!12;UBERON:0000480!2.03e-08!625;UBERON:0000464!2.86e-08!95;UBERON:0000063!3.22e-08!98;UBERON:0002420!3.34e-08!9;UBERON:0007245!3.34e-08!9;UBERON:0010009!3.34e-08!9;UBERON:0010011!3.34e-08!9;UBERON:0000454!3.34e-08!9;UBERON:0001041!3.39e-08!87;UBERON:0000923!4.31e-08!560;UBERON:0010316!4.31e-08!560;UBERON:0005291!4.31e-08!560;UBERON:0006598!4.31e-08!560;UBERON:0010317!4.31e-08!560;UBERON:0002532!4.31e-08!560;UBERON:0004119!6.62e-08!160;UBERON:0000925!6.62e-08!160;UBERON:0006595!6.62e-08!160;UBERON:0001007!1.62e-07!145;UBERON:0001555!1.62e-07!145;UBERON:0007026!1.62e-07!145;UBERON:0009663!5.96e-07!7;UBERON:0004921!7.15e-07!118
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284936947760592!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326084670534092!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032128434250265!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015442102598474!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614862624410349!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190703452302989
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000284936947760592!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326084670534092!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032128434250265!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015442102598474!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614862624410349!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190703452302989
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}}
}}

Revision as of 15:42, 19 October 2012


Full id: C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala



Phase1 CAGE Peaks

Hg19::chr2:131594446..131594472,+p3@ARHGEF4
Hg19::chr2:131594478..131594502,+p2@ARHGEF4
Hg19::chr2:131594505..131594522,+p5@ARHGEF4


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell5.19e-18253
endo-epithelial cell5.10e-1642
endodermal cell1.28e-1158
respiratory epithelial cell1.33e-0813
epithelial cell of alimentary canal6.19e-0820
Uber Anatomy
Ontology termp-valuen
central nervous system6.31e-3481
neural tube1.04e-3356
neural rod1.04e-3356
future spinal cord1.04e-3356
neural keel1.04e-3356
nervous system1.42e-3289
organ system subdivision1.89e-32223
ectoderm-derived structure4.69e-31171
ectoderm4.69e-31171
presumptive ectoderm4.69e-31171
regional part of nervous system6.34e-3153
regional part of brain6.34e-3153
brain4.73e-2968
future brain4.73e-2968
ecto-epithelium6.96e-28104
neurectoderm6.14e-2586
neural plate9.05e-2582
presumptive neural plate9.05e-2582
regional part of forebrain1.16e-2341
forebrain1.16e-2341
anterior neural tube1.16e-2341
future forebrain1.16e-2341
brain grey matter4.07e-2034
gray matter4.07e-2034
telencephalon6.24e-2034
pre-chordal neural plate1.17e-1861
regional part of telencephalon1.54e-1832
adult organism1.84e-18114
cerebral hemisphere2.57e-1832
anatomical cluster1.32e-15373
structure with developmental contribution from neural crest5.01e-15132
organ part4.64e-14218
organ9.72e-14503
cerebral cortex2.54e-1325
pallium2.54e-1325
respiratory system1.82e-1274
regional part of cerebral cortex4.68e-1222
embryo7.29e-12592
posterior neural tube3.92e-1115
chordal neural plate3.92e-1115
multi-tissue structure1.35e-10342
neocortex1.73e-1020
respiratory tract2.39e-1054
multi-cellular organism5.40e-10656
segment of respiratory tract1.13e-0947
anatomical conduit4.25e-09240
respiratory primordium4.60e-0938
endoderm of foregut4.60e-0938
embryonic structure5.32e-09564
developing anatomical structure6.07e-09581
segmental subdivision of nervous system7.88e-0913
neural nucleus1.50e-089
nucleus of brain1.50e-089
anatomical system1.56e-08624
segmental subdivision of hindbrain1.88e-0812
hindbrain1.88e-0812
presumptive hindbrain1.88e-0812
anatomical group2.03e-08625
anatomical space2.86e-0895
organ segment3.22e-0898
basal ganglion3.34e-089
nuclear complex of neuraxis3.34e-089
aggregate regional part of brain3.34e-089
collection of basal ganglia3.34e-089
cerebral subcortex3.34e-089
foregut3.39e-0887
germ layer4.31e-08560
germ layer / neural crest4.31e-08560
embryonic tissue4.31e-08560
presumptive structure4.31e-08560
germ layer / neural crest derived structure4.31e-08560
epiblast (generic)4.31e-08560
endoderm-derived structure6.62e-08160
endoderm6.62e-08160
presumptive endoderm6.62e-08160
digestive system1.62e-07145
digestive tract1.62e-07145
primitive gut1.62e-07145
telencephalic nucleus5.96e-077
subdivision of digestive tract7.15e-07118
Disease
Ontology termp-valuen
carcinoma8.27e-17106
cell type cancer7.74e-13143
squamous cell carcinoma2.64e-0814
cancer1.23e-07235
disease of cellular proliferation1.46e-07239


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000284936947760592
E2F1#186934.907389214879320.008460985347239390.0326084670534092
EGR1#195834.988179094810140.008056488137383440.032128434250265
GABPB1#255337.067683836182170.002832212825417420.015442102598474
TCF7L2#6934310.77017656313730.0008003181298398380.00614862624410349
USF1#739136.361499277207960.00388404057290560.0190703452302989



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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