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Coexpression cluster:C197: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:54, 17 September 2013


Full id: C197_tongue_esophagus_tonsil_salivary_cervix_nasal_Gingival



Phase1 CAGE Peaks

Hg19::chr11:93754560..93754567,+p@chr11:93754560..93754567
+
Hg19::chr12:101962128..101962133,+p19@MYBPC1
Hg19::chr12:52862701..52862727,-p@chr12:52862701..52862727
-
Hg19::chr12:52867581..52867598,-p1@KRT6C
Hg19::chr12:53189894..53189905,-p1@KRT3
Hg19::chr12:57328187..57328195,-p1@SDR9C7
Hg19::chr13:103532389..103532398,+p3@METTL21CP1
Hg19::chr13:103532465..103532483,+p1@METTL21CP1
Hg19::chr13:103532691..103532727,+p@chr13:103532691..103532727
+
Hg19::chr13:103555653..103555668,+p@chr13:103555653..103555668
+
Hg19::chr13:103555674..103555696,+p@chr13:103555674..103555696
+
Hg19::chr13:103555720..103555725,+p@chr13:103555720..103555725
+
Hg19::chr16:28890820..28890826,+p@chr16:28890820..28890826
+
Hg19::chr17:10453082..10453093,-p7@MYH2
Hg19::chr17:10515218..10515226,+p@chr17:10515218..10515226
+
Hg19::chr17:39646159..39646164,-p1@KRT36
Hg19::chr17:39766130..39766139,-p@chr17:39766130..39766139
-
Hg19::chr17:7991002..7991009,-p8@ALOX12B
Hg19::chr17:7991027..7991040,-p1@ALOX12B
Hg19::chr17:7991064..7991073,-p4@ALOX12B
Hg19::chr17:7991075..7991086,-p2@ALOX12B
Hg19::chr18:28682160..28682171,-p11@DSC2
Hg19::chr18:52258473..52258477,+p1@C18orf26
Hg19::chr19:36018336..36018343,-p@chr19:36018336..36018343
-
Hg19::chr19:36591495..36591511,+p@chr19:36591495..36591511
+
Hg19::chr19:42891296..42891305,-p@chr19:42891296..42891305
-
Hg19::chr19:51563807..51563817,-p@chr19:51563807..51563817
-
Hg19::chr1:109427881..109427897,+p5@GPSM2
Hg19::chr1:152130293..152130302,-p@chr1:152130293..152130302
-
Hg19::chr1:152131703..152131706,-p1@RPTN
Hg19::chr1:152957997..152958025,+p4@SPRR1A
Hg19::chr1:153004800..153004809,+p6@SPRR1B
Hg19::chr1:153004839..153004866,+p2@SPRR1B
Hg19::chr1:153004879..153004890,+p4@SPRR1B
Hg19::chr1:153005112..153005146,+p@chr1:153005112..153005146
+
Hg19::chr1:153005159..153005205,+p@chr1:153005159..153005205
+
Hg19::chr1:153013588..153013605,-p1@SPRR2D
Hg19::chr1:153029029..153029042,-p@chr1:153029029..153029042
-
Hg19::chr1:153029980..153029995,-p1@SPRR2A
Hg19::chr1:153044083..153044088,-p1@SPRR2B
Hg19::chr1:153066998..153067008,-p1@SPRR2E
Hg19::chr1:153085984..153085999,-p1@SPRR2F
p2@SPRR2A
Hg19::chr1:153113940..153113972,-p1@SPRR2C
p2@SPRR2D
p3@SPRR2A
Hg19::chr1:153113974..153113991,-p3@SPRR2C
p4@SPRR2D
p5@SPRR2A
Hg19::chr1:153114001..153114013,-p2@SPRR2C
p3@SPRR2D
p4@SPRR2A
Hg19::chr1:153114023..153114029,-p4@SPRR2C
p5@SPRR2D
p6@SPRR2A
Hg19::chr1:153123359..153123372,-p1@SPRR2G
Hg19::chr1:153388993..153389000,+p1@S100A7A
Hg19::chr1:153430341..153430348,-p6@S100A7
Hg19::chr1:153430422..153430443,-p3@S100A7
Hg19::chr1:153431372..153431378,-p4@S100A7
Hg19::chr1:153433120..153433129,-p1@S100A7
Hg19::chr1:159832438..159832449,-p1@VSIG8
Hg19::chr1:1846607..1846616,+p6@CALML6
Hg19::chr1:1846804..1846823,+p3@CALML6
Hg19::chr20:2290823..2290833,+p@chr20:2290823..2290833
+
Hg19::chr20:2312685..2312717,+p@chr20:2312685..2312717
+
Hg19::chr20:2321399..2321407,+p@chr20:2321399..2321407
+
Hg19::chr20:43803535..43803553,+p1@PI3
Hg19::chr20:43804494..43804505,+p@chr20:43804494..43804505
+
Hg19::chr20:43804621..43804628,+p@chr20:43804621..43804628
+
Hg19::chr20:43804675..43804691,+p@chr20:43804675..43804691
+
Hg19::chr21:31768348..31768356,+p1@KRTAP13-1
Hg19::chr21:45743612..45743625,+p@chr21:45743612..45743625
+
Hg19::chr2:106128079..106128106,+p@chr2:106128079..106128106
+
Hg19::chr2:113816771..113816777,+p1@IL36RN
Hg19::chr3:133348367..133348368,-p@chr3:133348367..133348368
-
Hg19::chr3:46027166..46027193,-p@chr3:46027166..46027193
-
Hg19::chr3:57286665..57286681,+p@chr3:57286665..57286681
+
Hg19::chr3:57326704..57326721,-p1@ASB14
Hg19::chr4:68749705..68749725,-p1@TMPRSS11D
Hg19::chr4:68749745..68749756,-p2@TMPRSS11D
Hg19::chr5:147715119..147715124,+p1@SPINK9
Hg19::chr5:150040771..150040781,+p7@MYOZ3
Hg19::chr6:2744269..2744281,-p@chr6:2744269..2744281
-
Hg19::chr6:2744361..2744382,-p@chr6:2744361..2744382
-
Hg19::chr6:2744431..2744440,-p@chr6:2744431..2744440
-
Hg19::chr6:2751146..2751162,-p1@MYLK4
Hg19::chr7:141066909..141066949,+p@chr7:141066909..141066949
+
Hg19::chr7:46064019..46064047,-p@chr7:46064019..46064047
-
Hg19::chr7:80412875..80412912,-p@chr7:80412875..80412912
-
Hg19::chr8:143866581..143866589,-p@chr8:143866581..143866589
-
Hg19::chr8:143866652..143866665,-p@chr8:143866652..143866665
-
Hg19::chr9:136184568..136184572,+p1@LCN1P2


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:0030216keratinocyte differentiation1.41377271188228e-22
GO:0001533cornified envelope2.09843797592739e-21
GO:0008544epidermis development3.54818497190057e-18
GO:0007398ectoderm development6.47311958840782e-18
GO:0007566embryo implantation9.0240676857688e-17
GO:0031424keratinization1.15717915921942e-16
GO:0009913epidermal cell differentiation9.09423997553288e-16
GO:0048730epidermis morphogenesis2.14163868075365e-15
GO:0009888tissue development9.8258948593668e-15
GO:0042698menstrual cycle9.8258948593668e-15
GO:0048729tissue morphogenesis1.51753803813706e-14
GO:0005856cytoskeleton7.05958323542508e-13
GO:0048609reproductive process in a multicellular organism7.05958323542508e-13
GO:0032504multicellular organism reproduction7.05958323542508e-13
GO:0007565female pregnancy5.19500409919953e-12
GO:0022414reproductive process1.30575350682352e-09
GO:0051704multi-organism process2.46426429272213e-09
GO:0048513organ development8.42293050941528e-09
GO:0043232intracellular non-membrane-bound organelle1.28987918594192e-08
GO:0043228non-membrane-bound organelle1.28987918594192e-08
GO:0009653anatomical structure morphogenesis5.70036548952603e-08
GO:0048856anatomical structure development2.00814308172839e-07
GO:0048731system development2.28875902185992e-07
GO:0048869cellular developmental process7.19033913179365e-07
GO:0030154cell differentiation7.19033913179365e-07
GO:0032501multicellular organismal process3.43078017666563e-06
GO:0007275multicellular organismal development7.34854023939061e-06
GO:0005882intermediate filament9.40971067965266e-06
GO:0045111intermediate filament cytoskeleton9.40971067965266e-06
GO:0032502developmental process3.74286315267922e-05
GO:0044430cytoskeletal part4.87757962062124e-05
GO:0030017sarcomere5.39273216063763e-05
GO:0030016myofibril7.06316225131419e-05
GO:0044449contractile fiber part9.97559417589415e-05
GO:0043292contractile fiber0.000116884456891877
GO:0005737cytoplasm0.000116884456891877
GO:0032982myosin filament0.00041900365286357
GO:0005863striated muscle thick filament0.00041900365286357
GO:0005859muscle myosin complex0.00101597587724844
GO:0016460myosin II complex0.00104641705511306
GO:0018149peptide cross-linking0.00104641705511306
GO:0006941striated muscle contraction0.00208158898038636
GO:0044424intracellular part0.00283298113520072
GO:0050829defense response to Gram-negative bacterium0.00746985107196519
GO:0004052arachidonate 12-lipoxygenase activity0.00746985107196519
GO:0043229intracellular organelle0.00845113269078566
GO:0043226organelle0.00845113269078566
GO:0030674protein binding, bridging0.0108954268859156
GO:0016459myosin complex0.0146609841768646
GO:0007620copulation0.0167871400047718
GO:0005622intracellular0.0239417025024281
GO:0005509calcium ion binding0.0244490687094494
GO:0003012muscle system process0.0304615149269455
GO:0006936muscle contraction0.0304615149269455
GO:0030280structural constituent of epidermis0.0304615149269455
GO:0004867serine-type endopeptidase inhibitor activity0.0307654972726924
GO:0007618mating0.0346355881358288
GO:0016165lipoxygenase activity0.0346355881358288
GO:0051238sequestering of metal ion0.0368712827874512
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0383904072748272
GO:0030018Z disc0.0383904072748272
GO:0045103intermediate filament-based process0.0398109792250047
GO:0000146microfilament motor activity0.0398109792250047
GO:0031674I band0.0443788883667347



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
tongue2.81e-343
gustatory system2.81e-343
future tongue2.81e-343
tonsil4.61e-261
mucosa-associated lymphoid tissue4.61e-261
lymphoid tissue4.61e-261
tonsillar ring4.61e-261
penis5.93e-261
intromittent organ5.93e-261
lateral plate mesenchyme5.93e-261
undifferentiated genital tubercle5.93e-261
somatopleure5.93e-261
chordate pharynx3.80e-2310
pharyngeal region of foregut3.80e-2310
pharynx4.06e-2111
throat8.28e-142
open tracheal system trachea1.55e-132
upper respiratory tract1.51e-1219
oral opening6.26e-1122
adult organism1.19e-10114
esophagus1.54e-093
esophageal region1.54e-093
segment of respiratory tract6.62e-0947
mouth1.90e-0829
stomodeum1.90e-0829
respiratory tract8.46e-0854
foregut2.32e-0787
orifice6.39e-0736
anterior region of body7.17e-0762
craniocervical region7.17e-0762


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)
MA0003.11.26109e-08
MA0004.10.0812785
MA0006.10.00029387
MA0007.10.153821
MA0009.10.408371
MA0014.18.38974e-08
MA0017.10.493659
MA0019.10.095014
MA0024.10.0827819
MA0025.10.594059
MA0027.11.51696
MA0028.10.0137016
MA0029.10.0907289
MA0030.10.0859679
MA0031.10.0617301
MA0038.10.0685866
MA0040.10.0932118
MA0041.10.206235
MA0042.10.0716627
MA0043.10.130603
MA0046.10.124984
MA0048.10.0623092
MA0050.10.0722745
MA0051.10.0140693
MA0052.12.18329
MA0055.11.87324
MA0056.10
MA0057.10.0312659
MA0058.10.00773719
MA0059.10.00758284
MA0060.10.00717649
MA0061.10.265119
MA0063.10
MA0066.10.0147002
MA0067.10.332077
MA0068.10.193849
MA0069.10.389435
MA0070.10.117626
MA0071.10.738843
MA0072.10.115469
MA0073.10.127374
MA0074.10.575613
MA0076.10.0346576
MA0077.10.111817
MA0078.10.129979
MA0081.10.256248
MA0083.10.418149
MA0084.10.479797
MA0087.10.114304
MA0088.10.137191
MA0089.10
MA0090.10.100195
MA0091.12.62479
MA0092.10.133278
MA0093.10.0317968
MA0095.10
MA0098.10
MA0100.10.195981
MA0101.10.241912
MA0103.10.856051
MA0105.10.508085
MA0106.10.0925401
MA0107.10.0952427
MA0108.21.2514
MA0109.10
MA0111.10.560533
MA0113.11.98935
MA0114.10.3485
MA0115.10.277011
MA0116.12.27272
MA0117.10.150146
MA0119.10.973243
MA0122.10.95551
MA0124.10.694307
MA0125.10.567789
MA0130.10
MA0131.10.0363037
MA0132.10
MA0133.10
MA0135.10.879455
MA0136.11.67515
MA0139.10.00212572
MA0140.10.0487431
MA0141.12.83003
MA0142.10.191434
MA0143.10.0241357
MA0144.10.292917
MA0145.11.19278
MA0146.18.64466e-05
MA0147.10.000588652
MA0148.10.00643614
MA0149.10.0446969
MA0062.20.0172599
MA0035.20.00961179
MA0039.20.0179792
MA0138.20.130916
MA0002.20.029197
MA0137.20.430217
MA0104.29.46049e-05
MA0047.20.0850518
MA0112.21.39957
MA0065.20.929673
MA0150.10.703874
MA0151.10
MA0152.10.28785
MA0153.10.184818
MA0154.11.57411
MA0155.10.383126
MA0156.10.838133
MA0157.10.0434201
MA0158.10
MA0159.10.732229
MA0160.10.938254
MA0161.10
MA0162.11.95594e-10
MA0163.11.35388e-06
MA0164.10.270516
MA0080.20.937846
MA0018.20.0213307
MA0099.20.493541
MA0079.29.64327e-17
MA0102.20.510906
MA0258.11.28882
MA0259.10.00073602
MA0442.10



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

No analysis results for this cluster

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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