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Coexpression cluster:C207: Difference between revisions

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|tf_chipseq_enrich=POLR2A#5430;53:1.51753357810104:2.06250747126477e-05:0.000456079224627189
|tf_chipseq_enrich=POLR2A#5430;53:1.51753357810104:2.06250747126477e-05:0.000456079224627189
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|tfbs_overrepresentation_for_novel_motifs=0.0381511,21.0263,0.0864027,0.286742,2.16,0.283786,1.04307,2.98908,0.196868,0.121404,0.0383274,0.289142,0.0965059,0.410382,0.323657,1.67244,0.0851779,0.601157,1.80098,5.8063,3.53387,0.0721551,1.76294,1.14488,0.136146,0.0344875,3.33291,0.266265,0.3369,5.93958,0.0307573,0.100866,0.0655901,0.608352,0.233268,0.828591,0.225368,0.285864,0.568376,0.024236,1.17858,0.317705,0.0172546,3.33821,3.11342,0.118388,0.0920534,0.00637871,0.0207408,0.115432,0.974626,0.749105,0.669751,0.137942,0.227322,0.0192997,0.000774541,0.876733,2.34086,0.3473,0.381278,0.0213699,0.123539,0.0742882,0.105408,0.834794,0.287088,0.580634,0.0962983,0.444105,0.156355,5.63345,0.22567,0.226032,0.423739,0.0185305,0.656791,0.516227,0.649816,0.6075,2.80359,0.0738825,0.105167,0.443743,0.193886,1.05946e-10,0.000257276,0.563182,0.0450711,0.668278,0.355549,0.177849,0.108485,0.0043213,0.492092,0.382175,0.00695369,0.129039,0.0463939,0.172434,0.278213,0.105891,0.397609,0.610254,0.0580206,0.0366696,0.0802968,0.403094,0.135836,0.0150617,0.325788,0.124875,0.642035,0.958476,0.856158,2.0639,0.0178821,0.8138,0.0610903,5.62129,0.220722,0.0443837,2.23787,0.113004,0.404098,0.517663,0.0196712,0.110804,0.24858,0.385947,0.178252,0.00577507,0.258266,0.0262382,0.95766,0.207706,0.189098,0.00916752,0.886614,1.09329,0.715488,0.305992,0.222269,0.127272,1.22798,0.0132287,2.16847,0.941225,0.310327,0.0131538,0.540177,7.08068e-05,0.528013,0.679436,0.232286,0.469137,0.0406076,0.00388816,0.256279,0.00194157,0.305115,0.167809,0.314106,0.349613,0.495275,0.0245001,0.179527,0.704285,5.15181e-07
}}
}}

Revision as of 13:47, 26 November 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 cell1.74e-3442
endodermal cell5.34e-2358
epithelial cell2.16e-22253
epithelial cell of alimentary canal5.53e-2020
respiratory epithelial cell5.88e-2013
general ecto-epithelial cell3.26e-1914
acinar cell2.52e-145
squamous epithelial cell7.14e-1263
protein secreting cell7.25e-126
transitional epithelial cell2.02e-114
urothelial cell2.02e-114
epithelial cell of tracheobronchial tree2.16e-119
epithelial cell of lower respiratory tract2.16e-119
bronchial epithelial cell8.10e-103
ecto-epithelial cell1.65e-0934
duct epithelial cell2.06e-093
branched duct epithelial cell2.06e-093
tracheal epithelial cell2.06e-093
tracheoblast2.06e-093
acinar cell of salivary gland2.57e-093
epithelial cell of Malassez3.58e-093
gingival epithelial cell5.25e-093
stratified squamous epithelial cell2.26e-086
keratin accumulating cell2.26e-086
stratified epithelial cell2.26e-086
keratinizing barrier epithelial cell2.26e-086
epithelial fate stem cell2.26e-086
stratified epithelial stem cell2.26e-086
surface ectodermal cell2.26e-086
epidermal cell4.58e-089
glandular epithelial cell9.24e-089
mammary gland epithelial cell3.44e-074
corneal epithelial cell3.44e-072
Uber Anatomy
Ontology termp-valuen
respiratory system4.38e-1974
oral opening1.18e-1722
endoderm-derived structure3.29e-16160
endoderm3.29e-16160
presumptive endoderm3.29e-16160
surface structure1.12e-1599
anterior region of body3.20e-1562
craniocervical region3.20e-1562
orifice5.01e-1536
mouth5.82e-1529
stomodeum5.82e-1529
urothelium2.35e-135
head8.21e-1356
mouth mucosa6.56e-1213
respiratory tract2.38e-1154
neck4.10e-1110
mucosa4.30e-1120
transitional epithelium4.54e-116
tracheobronchial tree8.98e-1115
lower respiratory tract8.98e-1115
subdivision of head2.37e-1049
mucosa of oral region2.77e-104
respiratory system mucosa2.77e-104
pharynx4.23e-1011
lower respiratory tract epithelium8.10e-103
epithelium of bronchus8.10e-103
trachea1.63e-097
respiratory airway1.63e-097
gingival epithelium5.25e-093
digestive system1.19e-08145
digestive tract1.19e-08145
primitive gut1.19e-08145
tongue1.75e-083
gustatory system1.75e-083
future tongue1.75e-083
chordate pharynx2.07e-0810
pharyngeal region of foregut2.07e-0810
extraembryonic membrane2.78e-0814
membranous layer2.78e-0814
pharyngeal arch system5.09e-0818
segment of respiratory tract7.90e-0847
organ component layer2.97e-0766
mammary gland3.44e-074
mammary bud3.44e-074
mammary ridge3.44e-074
mammary placode3.44e-074
jaw skeleton5.85e-074
splanchnocranium5.85e-074
Disease
Ontology termp-valuen
squamous cell carcinoma2.56e-1914


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

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