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Coexpression cluster:C207: Difference between revisions

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|ontology_enrichment_disease=DOID:1749!8.67e-08!14
|ontology_enrichment_disease=DOID:1749!8.67e-08!14
|ontology_enrichment_uberon=UBERON:0001004!3.65e-14!72;UBERON:0004119!2.19e-13!169;UBERON:0000925!2.19e-13!169;UBERON:0006595!2.19e-13!169;UBERON:0000065!4.44e-10!53;UBERON:0000064!4.38e-09!219;UBERON:0001007!5.29e-09!155;UBERON:0001555!5.29e-09!155;UBERON:0007026!5.29e-09!155;UBERON:0000161!1.71e-08!35;UBERON:0003102!3.97e-08!95;UBERON:0000077!5.40e-08!130;UBERON:0000166!7.79e-08!21;UBERON:0000480!1.13e-07!626;UBERON:0000467!1.18e-07!625;UBERON:0000475!2.05e-07!365;UBERON:0005181!2.13e-07!35;UBERON:0000922!2.25e-07!612;UBERON:0000072!2.37e-07!46;UBERON:0000062!2.57e-07!511;UBERON:0000468!2.59e-07!659;UBERON:0002050!2.92e-07!605;UBERON:0005423!2.92e-07!605;UBERON:0004921!3.34e-07!129;UBERON:0004185!3.34e-07!129;UBERON:0005178!4.60e-07!34;UBERON:0002224!4.60e-07!34;UBERON:0000923!5.39e-07!604;UBERON:0005291!5.39e-07!604;UBERON:0006598!5.39e-07!604;UBERON:0002532!5.39e-07!604
|ontology_enrichment_uberon=UBERON:0001004!3.65e-14!72;UBERON:0004119!2.19e-13!169;UBERON:0000925!2.19e-13!169;UBERON:0006595!2.19e-13!169;UBERON:0000065!4.44e-10!53;UBERON:0000064!4.38e-09!219;UBERON:0001007!5.29e-09!155;UBERON:0001555!5.29e-09!155;UBERON:0007026!5.29e-09!155;UBERON:0000161!1.71e-08!35;UBERON:0003102!3.97e-08!95;UBERON:0000077!5.40e-08!130;UBERON:0000166!7.79e-08!21;UBERON:0000480!1.13e-07!626;UBERON:0000467!1.18e-07!625;UBERON:0000475!2.05e-07!365;UBERON:0005181!2.13e-07!35;UBERON:0000922!2.25e-07!612;UBERON:0000072!2.37e-07!46;UBERON:0000062!2.57e-07!511;UBERON:0000468!2.59e-07!659;UBERON:0002050!2.92e-07!605;UBERON:0005423!2.92e-07!605;UBERON:0004921!3.34e-07!129;UBERON:0004185!3.34e-07!129;UBERON:0005178!4.60e-07!34;UBERON:0002224!4.60e-07!34;UBERON:0000923!5.39e-07!604;UBERON:0005291!5.39e-07!604;UBERON:0006598!5.39e-07!604;UBERON:0002532!5.39e-07!604
|tf_chipseq_enrich=POLR2A#5430;53:1.51753357810104:2.06250747126477e-05:0.000456079224627189
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}}
}}

Revision as of 14:05, 5 September 2012


Full id: C207_Corneal_Keratinocyte_Esophageal_Mammary_Bronchial_Urothelial_Sebocyte



Phase1 CAGE Peaks

Hg19::chr10:49674719..49674730,-p12@ARHGAP22
Hg19::chr11:128812744..128812786,-p1@TP53AIP1
Hg19::chr12:52844247..52844256,-p@chr12:52844247..52844256
-
Hg19::chr12:52908461..52908496,+p2@CU687195
Hg19::chr12:52908498..52908505,-p@chr12:52908498..52908505
-
Hg19::chr12:52908501..52908527,+p8@CU687195
Hg19::chr12:52908517..52908524,-p@chr12:52908517..52908524
-
Hg19::chr12:52908533..52908575,+p1@CU687195
Hg19::chr12:52908551..52908580,-p@chr12:52908551..52908580
-
Hg19::chr12:52908618..52908629,-p@chr12:52908618..52908629
-
Hg19::chr12:52908669..52908680,-p@chr12:52908669..52908680
-
Hg19::chr12:52908696..52908709,-p@chr12:52908696..52908709
-
Hg19::chr12:52908723..52908727,-p@chr12:52908723..52908727
-
Hg19::chr12:52908728..52908738,-p@chr12:52908728..52908738
-
Hg19::chr12:52908739..52908758,-p@chr12:52908739..52908758
-
Hg19::chr12:52908759..52908818,-p@chr12:52908759..52908818
-
Hg19::chr12:52908762..52908781,+p10@CU687195
Hg19::chr12:52908829..52908860,+p3@CU687195
Hg19::chr12:52908841..52908856,-p@chr12:52908841..52908856
-
Hg19::chr12:52908868..52908889,+p4@CU687195
Hg19::chr12:52908875..52908887,-p@chr12:52908875..52908887
-
Hg19::chr12:52908957..52908986,+p6@CU687195
Hg19::chr12:52910482..52910540,-p2@S90014
Hg19::chr12:52910564..52910603,-p3@S90014
Hg19::chr12:52910585..52910610,+p@chr12:52910585..52910610
+
Hg19::chr12:52910624..52910647,-p4@S90014
Hg19::chr12:52910911..52910946,+p@chr12:52910911..52910946
+
Hg19::chr12:52910917..52911028,-p1@S90014
Hg19::chr12:52910971..52910983,+p@chr12:52910971..52910983
+
Hg19::chr12:52911361..52911376,+p@chr12:52911361..52911376
+
Hg19::chr12:52911397..52911445,-p5@KRT5
Hg19::chr12:52911408..52911421,+p@chr12:52911408..52911421
+
Hg19::chr12:52911499..52911548,-p6@KRT5
Hg19::chr12:52911502..52911509,+p@chr12:52911502..52911509
+
Hg19::chr12:52911698..52911719,+p@chr12:52911698..52911719
+
Hg19::chr12:52911718..52911760,-p3@KRT5
Hg19::chr12:52911720..52911745,+p@chr12:52911720..52911745
+
Hg19::chr12:52911768..52911778,-p9@KRT5
Hg19::chr12:52911872..52911905,+p@chr12:52911872..52911905
+
Hg19::chr12:52911917..52911958,-p2@KRT5
Hg19::chr12:52912754..52912774,+p@chr12:52912754..52912774
+
Hg19::chr12:52912779..52912805,-p7@KRT5
Hg19::chr12:52913553..52913601,+p@chr12:52913553..52913601
+
Hg19::chr12:52913583..52913599,-p8@KRT5
Hg19::chr12:52913604..52913643,-p4@KRT5
Hg19::chr12:52913641..52913652,+p@chr12:52913641..52913652
+
Hg19::chr12:52913675..52913704,+p@chr12:52913675..52913704
+
Hg19::chr12:52913706..52913725,+p@chr12:52913706..52913725
+
Hg19::chr12:52913727..52913740,+p@chr12:52913727..52913740
+
Hg19::chr12:52913754..52913774,+p@chr12:52913754..52913774
+
Hg19::chr12:52913784..52913810,+p@chr12:52913784..52913810
+
Hg19::chr12:52913812..52913837,+p@chr12:52913812..52913837
+
Hg19::chr12:52913881..52913889,+p@chr12:52913881..52913889
+
Hg19::chr12:52914170..52914185,-p1@KRT5
Hg19::chr17:39738605..39738632,-p@chr17:39738605..39738632
-
Hg19::chr17:39738761..39738776,-p@chr17:39738761..39738776
-
Hg19::chr17:39738777..39738791,-p@chr17:39738777..39738791
-
Hg19::chr17:39739641..39739684,-p5@KRT14
Hg19::chr17:39740090..39740108,+p@chr17:39740090..39740108
+
Hg19::chr17:39740112..39740148,-p4@KRT14
Hg19::chr17:39740611..39740628,+p@chr17:39740611..39740628
+
Hg19::chr17:39740629..39740632,-p9@KRT14
Hg19::chr17:39740633..39740663,-p3@KRT14
Hg19::chr17:39741306..39741320,-p@chr17:39741306..39741320
-
Hg19::chr17:39742594..39742616,+p@chr17:39742594..39742616
+
Hg19::chr17:39742637..39742657,-p3@BC127260
Hg19::chr17:39742770..39742785,+p@chr17:39742770..39742785
+
Hg19::chr17:39742793..39742826,-p2@BC127260
Hg19::chr17:39742822..39742850,+p@chr17:39742822..39742850
+
Hg19::chr17:39742866..39742894,-p1@BC127260
Hg19::chr17:39742930..39742950,-p2@KRT14
Hg19::chr17:39743139..39743155,-p1@KRT14
Hg19::chr19:14638523..14638574,+p@chr19:14638523..14638574
+
Hg19::chr1:27190453..27190483,-p6@uc010ofi.1
Hg19::chr5:65542106..65542109,+p@chr5:65542106..65542109
+


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

GO IDGO nameFDR corrected p-value
GO:0005200structural constituent of cytoskeleton0.000878018334852565
GO:0048513organ development0.000878018334852565
GO:0008544epidermis development0.000878018334852565
GO:0007398ectoderm development0.000878018334852565
GO:0048731system development0.00131206275837639
GO:0045111intermediate filament cytoskeleton0.00131206275837639
GO:0005882intermediate filament0.00131206275837639
GO:0048856anatomical structure development0.00164232096474494
GO:0009888tissue development0.00170377596638035
GO:0007275multicellular organismal development0.00198109349149403
GO:0032502developmental process0.00555955545177272
GO:0032501multicellular organismal process0.00758935412211755
GO:0044430cytoskeletal part0.0105794298352566
GO:0009653anatomical structure morphogenesis0.0127474370629858
GO:0030855epithelial cell differentiation0.0135501413078613
GO:0005856cytoskeleton0.0202840232292874
GO:0002009morphogenesis of an epithelium0.020906381332408
GO:0045095keratin filament0.0262705481782099
GO:0048869cellular developmental process0.0262705481782099
GO:0030154cell differentiation0.0262705481782099
GO:0001525angiogenesis0.0345870162891932
GO:0048514blood vessel morphogenesis0.037345395197481
GO:0048646anatomical structure formation0.037345395197481
GO:0001568blood vessel development0.037345395197481
GO:0001944vasculature development0.037345395197481
GO:0043232intracellular non-membrane-bound organelle0.0495124065123042
GO:0043228non-membrane-bound organelle0.0495124065123042



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
endo-epithelial cell1.14e-1343
epithelial cell9.36e-10254
respiratory epithelial cell4.90e-0813
endodermal cell1.70e-0759
general ecto-epithelial cell6.08e-0713
Uber Anatomy
Ontology termp-valuen
respiratory system3.65e-1472
endoderm-derived structure2.19e-13169
endoderm2.19e-13169
presumptive endoderm2.19e-13169
respiratory tract4.44e-1053
organ part4.38e-09219
digestive system5.29e-09155
digestive tract5.29e-09155
primitive gut5.29e-09155
orifice1.71e-0835
surface structure3.97e-0895
mixed endoderm/mesoderm-derived structure5.40e-08130
oral opening7.79e-0821
anatomical group1.13e-07626
anatomical system1.18e-07625
organism subdivision2.05e-07365
thoracic segment organ2.13e-0735
embryo2.25e-07612
segment of respiratory tract2.37e-0746
organ2.57e-07511
multi-cellular organism2.59e-07659
embryonic structure2.92e-07605
developing anatomical structure2.92e-07605
subdivision of digestive tract3.34e-07129
endodermal part of digestive tract3.34e-07129
thoracic cavity element4.60e-0734
thoracic cavity4.60e-0734
germ layer5.39e-07604
embryonic tissue5.39e-07604
presumptive structure5.39e-07604
epiblast (generic)5.39e-07604
Disease
Ontology termp-valuen
squamous cell carcinoma8.67e-0814


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
POLR2A#5430531.517533578101042.06250747126477e-050.000456079224627189



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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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