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Coexpression cluster:C2613: Difference between revisions

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|full_id=C2613_tonsil_trachea_salivary_hepatocellular_throat_tongue_breast
|full_id=C2613_tonsil_trachea_salivary_hepatocellular_throat_tongue_breast
|id=C2613
|id=C2613
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000167!1.06e-09!1;CL:0000164!1.06e-09!1;CL:0000502!1.06e-09!1;CL:0000172!1.06e-09!1;CL:0000173!1.06e-09!1;CL:0002351!1.06e-09!1;CL:0000181!5.52e-07!12;CL:0000417!5.52e-07!12;CL:0000668!5.52e-07!12;CL:0000412!5.52e-07!12;CL:0000182!5.52e-07!12
|ontology_enrichment_disease=DOID:114!1.79e-08!2
|ontology_enrichment_disease=DOID:4430!1.06e-09!1;DOID:178!1.76e-09!1;DOID:326!1.76e-09!1;DOID:3978!1.76e-09!1;DOID:3394!1.76e-09!1;DOID:5844!1.76e-09!1
|ontology_enrichment_uberon=UBERON:0001041!5.74e-11!98;UBERON:0004921!4.51e-10!129;UBERON:0004185!4.51e-10!129;UBERON:0007023!1.34e-09!115;UBERON:0003127!2.36e-09!2;UBERON:0001829!4.11e-09!2;UBERON:0000341!5.42e-09!2;UBERON:0002365!7.68e-09!31;UBERON:0002330!7.68e-09!31;UBERON:0001007!2.28e-08!155;UBERON:0001555!2.28e-08!155;UBERON:0007026!2.28e-08!155;UBERON:0002530!3.40e-08!59;UBERON:0000077!4.67e-08!130;UBERON:0000078!1.33e-07!18;UBERON:0004119!3.10e-07!169;UBERON:0000925!3.10e-07!169;UBERON:0006595!3.10e-07!169
|ontology_enrichment_uberon=UBERON:0003127!3.76e-18!2;UBERON:0001829!6.82e-18!2;UBERON:0000341!2.85e-17!2;UBERON:0000166!1.69e-13!22;UBERON:0001044!1.95e-13!6;UBERON:0003293!1.95e-13!6;UBERON:0003294!1.95e-13!6;UBERON:0010047!1.95e-13!6;UBERON:0000167!1.95e-13!6;UBERON:0002365!8.24e-13!31;UBERON:0002330!8.24e-13!31;UBERON:0001723!3.77e-12!3;UBERON:0001033!3.77e-12!3;UBERON:0010056!3.77e-12!3;UBERON:0001041!5.32e-12!87;UBERON:0004921!2.13e-11!118;UBERON:0000161!9.67e-11!36;UBERON:0000165!3.99e-10!29;UBERON:0000930!3.99e-10!29;UBERON:0002372!4.09e-10!1;UBERON:0001961!4.09e-10!1;UBERON:0001744!4.09e-10!1;UBERON:0001735!4.09e-10!1;UBERON:0007023!4.55e-10!114;UBERON:0001831!6.88e-10!1;UBERON:0001567!6.88e-10!1;UBERON:0008801!6.88e-10!1;UBERON:0001736!9.70e-10!1;UBERON:0006298!9.70e-10!1;UBERON:0000989!1.62e-09!1;UBERON:0008811!1.62e-09!1;UBERON:0006258!1.62e-09!1;UBERON:0005876!1.62e-09!1;UBERON:0004874!1.62e-09!1;UBERON:0001007!7.84e-09!145;UBERON:0001555!7.84e-09!145;UBERON:0007026!7.84e-09!145;UBERON:0003408!2.92e-08!10;UBERON:0001042!3.30e-08!10;UBERON:0009145!3.30e-08!10;UBERON:0002530!3.54e-08!59;UBERON:0001004!5.93e-08!74;UBERON:0004119!8.86e-08!160;UBERON:0000925!8.86e-08!160;UBERON:0006595!8.86e-08!160;UBERON:0000153!1.21e-07!62;UBERON:0007811!1.21e-07!62;UBERON:0006562!1.67e-07!11
|tf_chipseq_enrich=BHLHE40#8553;2:22.4359067734887:0.00289146449685312:0.0156410452471561!FOSL2#2355;3:12.6976504534213:0.00078756857297571:0.00616726956534529!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353488494193027!HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390749605609343!HNF4G#3174;2:14.3767112632234:0.00692416998043918:0.0293083159839138!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123859882906981!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.0488828121969766
|tf_chipseq_enrich=BHLHE40#8553;2:22.4359067734887:0.00289146449685312:0.0156410452471561!FOSL2#2355;3:12.6976504534213:0.00078756857297571:0.00616726956534529!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353488494193027!HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390749605609343!HNF4G#3174;2:14.3767112632234:0.00692416998043918:0.0293083159839138!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123859882906981!RXRA#6256;2:10.0373085695666:0.0139170380592011:0.0488828121969766
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}}
}}

Revision as of 14:14, 19 October 2012


Full id: C2613_tonsil_trachea_salivary_hepatocellular_throat_tongue_breast



Phase1 CAGE Peaks

Hg19::chr20:31595419..31595426,+p2@BPIFB2
Hg19::chr20:31595501..31595519,+p1@BPIFB2
Hg19::chr20:31608346..31608355,+p@chr20:31608346..31608355
+
Hg19::chr20:31612754..31612763,+p@chr20:31612754..31612763
+


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>


Uber Anatomy
Ontology termp-valuen
open tracheal system trachea3.76e-182
major salivary gland6.82e-182
throat2.85e-172
oral opening1.69e-1322
saliva-secreting gland1.95e-136
gland of oral region1.95e-136
gland of foregut1.95e-136
oral gland1.95e-136
oral cavity1.95e-136
exocrine gland8.24e-1331
exocrine system8.24e-1331
tongue3.77e-123
gustatory system3.77e-123
future tongue3.77e-123
foregut5.32e-1287
subdivision of digestive tract2.13e-11118
orifice9.67e-1136
mouth3.99e-1029
stomodeum3.99e-1029
tonsil4.09e-101
mucosa-associated lymphoid tissue4.09e-101
lymphoid tissue4.09e-101
tonsillar ring4.09e-101
adult organism4.55e-10114
parotid gland6.88e-101
cheek6.88e-101
parotid gland primordium6.88e-101
submandibular gland9.70e-101
submandibular gland primordium9.70e-101
penis1.62e-091
intromittent organ1.62e-091
lateral plate mesenchyme1.62e-091
undifferentiated genital tubercle1.62e-091
somatopleure1.62e-091
digestive system7.84e-09145
digestive tract7.84e-09145
primitive gut7.84e-09145
gland of gut2.92e-0810
chordate pharynx3.30e-0810
pharyngeal region of foregut3.30e-0810
gland3.54e-0859
respiratory system5.93e-0874
endoderm-derived structure8.86e-08160
endoderm8.86e-08160
presumptive endoderm8.86e-08160
anterior region of body1.21e-0762
craniocervical region1.21e-0762
pharynx1.67e-0711
Disease
Ontology termp-valuen
somatostatinoma1.06e-091
vascular disease1.76e-091
ischemia1.76e-091
extrinsic cardiomyopathy1.76e-091
myocardial ischemia1.76e-091
myocardial infarction1.76e-091


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#8553222.43590677348870.002891464496853120.0156410452471561
FOSL2#2355312.69765045342130.000787568572975710.00616726956534529
FOXA2#3170212.31523187633260.009361916285467240.0353488494193027
HNF4A#3172211.56614518147680.01057585681762490.0390749605609343
HNF4G#3174214.37671126322340.006924169980439180.0293083159839138
RFX5#599339.035933120396320.002144561191324070.0123859882906981
RXRA#6256210.03730856956660.01391703805920110.0488828121969766



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.