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{{Coexpression_clusters
{
|full_id=C190_colon_small_rectum_duodenum_appendix_temporal_oral
|

Latest revision as of 10:52, 17 September 2013


Full id: C190_colon_small_rectum_duodenum_appendix_temporal_oral



Phase1 CAGE Peaks

Hg19::chr10:112657988..112657991,+p35@PDCD4
Hg19::chr10:14574705..14574718,-p18@FAM107B
Hg19::chr11:114430588..114430608,-p1@FAM55A
Hg19::chr11:114466471..114466474,-p4@FAM55D
Hg19::chr11:114522262..114522267,-p@chr11:114522262..114522267
-
Hg19::chr11:118500762..118500765,+p11@PHLDB1
Hg19::chr11:130059981..130060005,+p5@ST14
Hg19::chr11:17036137..17036152,-p3@PLEKHA7
Hg19::chr11:46958029..46958041,+p4@C11orf49
Hg19::chr11:76746720..76746738,-p@chr11:76746720..76746738
-
Hg19::chr12:27849378..27849385,+p1@REP15
Hg19::chr14:47203595..47203635,-p@chr14:47203595..47203635
-
Hg19::chr15:40648362..40648364,+p@chr15:40648362..40648364
+
Hg19::chr15:41120932..41120960,-p2@PPP1R14D
Hg19::chr15:41224934..41224945,-p@chr15:41224934..41224945
-
Hg19::chr16:2034635..2034644,+p12@GFER
Hg19::chr16:25228264..25228273,+p1@AQP8
Hg19::chr16:29760335..29760341,+p@chr16:29760335..29760341
+
Hg19::chr16:29789573..29789606,+p1@ZG16
Hg19::chr16:67464830..67464845,-p@chr16:67464830..67464845
-
Hg19::chr16:67465190..67465197,+p4@HSD11B2
Hg19::chr16:67475274..67475285,-p7@ATP6V0D1
Hg19::chr16:79632234..79632245,-p@chr16:79632234..79632245
-
Hg19::chr16:79804394..79804433,-p@chr16:79804394..79804433
-
Hg19::chr17:26800296..26800314,+p4@SLC13A2
Hg19::chr17:42031300..42031313,-p1@PYY
Hg19::chr17:74639886..74639899,-p3@ST6GALNAC1
Hg19::chr19:3025659..3025672,-p6@TLE2
Hg19::chr19:39297150..39297157,-p@chr19:39297150..39297157
-
Hg19::chr19:39303110..39303129,-p@chr19:39303110..39303129
-
Hg19::chr19:42190911..42190925,-p@chr19:42190911..42190925
-
Hg19::chr19:42192156..42192171,-p2@CEACAM7
Hg19::chr19:42192189..42192207,-p1@CEACAM7
Hg19::chr19:56200410..56200417,+p@chr19:56200410..56200417
+
Hg19::chr19:7456079..7456083,-p@chr19:7456079..7456083
-
Hg19::chr1:149908217..149908248,-p4@MTMR11
Hg19::chr1:167059763..167059776,-p4@GPA33
Hg19::chr1:20141662..20141673,-p4@RNF186
Hg19::chr1:20141681..20141690,-p5@RNF186
Hg19::chr1:20141728..20141745,-p3@RNF186
Hg19::chr1:207241396..207241407,+p@chr1:207241396..207241407
+
Hg19::chr1:220100976..220100981,-p@chr1:220100976..220100981
-
Hg19::chr1:220101892..220101906,-p1@SLC30A10
Hg19::chr1:35150899..35150929,-p@chr1:35150899..35150929
-
Hg19::chr1:47905805..47905807,+p@chr1:47905805..47905807
+
Hg19::chr21:43733776..43733803,-p3@TFF3
Hg19::chr2:128375443..128375446,+p@chr2:128375443..128375446
+
Hg19::chr2:201242765..201242779,+p26@SPATS2L
Hg19::chr2:241625719..241625734,+p3@ENST00000407635
Hg19::chr2:241625749..241625758,+p6@ENST00000407635
Hg19::chr3:124355991..124356002,+p32@KALRN
Hg19::chr3:124646625..124646633,-p11@MUC13
Hg19::chr3:124646645..124646669,-p3@MUC13
Hg19::chr4:150822397..150822409,-p@chr4:150822397..150822409
-
Hg19::chr4:165675294..165675306,+p3@LOC100505989
Hg19::chr4:667307..667315,+p17@MYL5
Hg19::chr4:81974774..81974778,+p@chr4:81974774..81974778
+
Hg19::chr4:89708946..89708956,-p@chr4:89708946..89708956
-
Hg19::chr4:89730993..89730995,-p@chr4:89730993..89730995
-
Hg19::chr5:149340464..149340483,+p2@SLC26A2
Hg19::chr5:149363028..149363035,+p12@SLC26A2
Hg19::chr5:150829073..150829087,+p10@SLC36A1
Hg19::chr5:150829095..150829107,+p9@SLC36A1
Hg19::chr5:156496412..156496429,-p@chr5:156496412..156496429
-
Hg19::chr5:160112366..160112378,-p7@ATP10B
Hg19::chr5:160112386..160112405,-p3@ATP10B
Hg19::chr5:160112418..160112436,-p4@ATP10B
Hg19::chr5:160112447..160112454,-p9@ATP10B
Hg19::chr6:110887812..110887830,-p@chr6:110887812..110887830
-
Hg19::chr6:80340818..80340825,+p7@SH3BGRL2
Hg19::chr7:100612141..100612155,-p@chr7:100612141..100612155
-
Hg19::chr7:87856280..87856298,-p2@SRI
Hg19::chr7:87856303..87856312,-p3@SRI
Hg19::chr7:92848861..92848873,-p7@HEPACAM2
Hg19::chr7:92848878..92848889,-p2@HEPACAM2
Hg19::chr8:146253359..146253362,-p@chr8:146253359..146253362
-
Hg19::chr8:24262894..24262908,+p6@ADAMDEC1
Hg19::chr8:24262931..24262946,+p5@ADAMDEC1
Hg19::chr8:24262965..24262986,+p@chr8:24262965..24262986
+
Hg19::chr8:24262988..24262999,+p@chr8:24262988..24262999
+
Hg19::chr8:24263041..24263045,+p@chr8:24263041..24263045
+
Hg19::chr8:8559690..8559736,+p2@CLDN23
Hg19::chr9:139658967..139658975,-p1@LCN15
Hg19::chr9:139683392..139683395,-p@chr9:139683392..139683395
-
Hg19::chr9:139688064..139688089,+p@chr9:139688064..139688089
+
Hg19::chr9:26994531..26994535,-p@chr9:26994531..26994535
-
Hg19::chr9:27005657..27005675,-p1@LRRC19
Hg19::chrX:15620273..15620294,-p3@ACE2


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

p.valueFDRnGenesnPathwayName
1.89711789408108e-050.01200875626953326401Transmembrane transport of small molecules (Reactome):REACT_15518



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:0016021integral to membrane0.0208338023654932
GO:0031224intrinsic to membrane0.0208338023654932
GO:0044425membrane part0.0285712177267866
GO:0022804active transmembrane transporter activity0.0338759110886178
GO:0005886plasma membrane0.0338759110886178
GO:0006937regulation of muscle contraction0.0338759110886178
GO:0022857transmembrane transporter activity0.0338759110886178
GO:0015361low affinity sodium:dicarboxylate symporter activity0.0338759110886178
GO:0001665alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity0.0338759110886178
GO:0001977renal regulation of blood volume0.0338759110886178
GO:0002017aldosterone mediated regulation of blood volume0.0338759110886178
GO:000384511-beta-hydroxysteroid dehydrogenase activity0.0338759110886178
GO:0022892substrate-specific transporter activity0.0338759110886178
GO:0015075ion transmembrane transporter activity0.0338759110886178
GO:0005774vacuolar membrane0.0338759110886178
GO:0044437vacuolar part0.0338759110886178
GO:0032328alanine transport0.0338759110886178
GO:0001618viral receptor activity0.0338759110886178
GO:0015808L-alanine transport0.0338759110886178
GO:0015193L-proline transmembrane transporter activity0.0338759110886178
GO:0016972thiol oxidase activity0.0338759110886178
GO:0015180L-alanine transmembrane transporter activity0.0338759110886178
GO:0006880intracellular sequestering of iron ion0.0338759110886178
GO:0015816glycine transport0.0338759110886178
GO:0043508negative regulation of JNK activity0.0338759110886178
GO:0022858alanine transmembrane transporter activity0.0338759110886178
GO:0016020membrane0.0338759110886178
GO:0015824proline transport0.046281544289703
GO:0003071renal regulation of systemic arterial blood pressure0.046281544289703
GO:0022891substrate-specific transmembrane transporter activity0.0479725523165227



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
intestine6.33e-5417
gastrointestinal system3.24e-3725
large intestine4.21e-3511
small intestine3.34e-284
colon8.11e-289
vermiform appendix1.65e-161
caecum1.65e-161
midgut1.65e-161
lower digestive tract3.23e-135
digestive system1.00e-07145
digestive tract1.00e-07145
primitive gut1.00e-07145
subdivision of digestive tract1.20e-07118
endoderm-derived structure6.42e-07160
endoderm6.42e-07160
presumptive endoderm6.42e-07160


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)
MA0003.10.00204556
MA0004.10.0223218
MA0006.10.111164
MA0007.10.133652
MA0009.10.121077
MA0014.10.0297893
MA0017.15.05564
MA0019.10.0842226
MA0024.10.0755456
MA0025.11.6934
MA0027.11.49708
MA0028.10.000302971
MA0029.10.997876
MA0030.10.964471
MA0031.11.19471
MA0038.10.320429
MA0040.10.604257
MA0041.10.527235
MA0042.10.43061
MA0043.10.384656
MA0046.15.51006
MA0048.10.071107
MA0050.10.0192927
MA0051.10.0119106
MA0052.10.0870325
MA0055.11.00001
MA0056.10
MA0057.10.0911533
MA0058.10.0600471
MA0059.10.0223948
MA0060.10.590573
MA0061.10.217096
MA0063.10
MA0066.10.542362
MA0067.10.317663
MA0068.10.402206
MA0069.10.365832
MA0070.10.714591
MA0071.10.251796
MA0072.10.346623
MA0073.10.0907253
MA0074.10.0574926
MA0076.10.00110758
MA0077.10.337336
MA0078.10.116858
MA0081.10.222541
MA0083.10.7865
MA0084.10.46347
MA0087.11.69496
MA0088.10.0464209
MA0089.10
MA0090.10.0341279
MA0091.11.65
MA0092.10.369842
MA0093.10.0252
MA0095.10
MA0098.10
MA0100.10.346927
MA0101.10.20687
MA0103.12.49601
MA0105.10.0610018
MA0106.10.0181761
MA0107.10.315249
MA0108.21.18341
MA0109.10
MA0111.10.327039
MA0113.10.229376
MA0114.13.31777
MA0115.11.34065
MA0116.10.46061
MA0117.10.14006
MA0119.10.465499
MA0122.10.467533
MA0124.10.23582
MA0125.10.183459
MA0130.10
MA0131.10.130242
MA0132.10
MA0133.10
MA0135.10.136302
MA0136.10.560938
MA0139.10.344776
MA0140.12.54997
MA0141.11.24127
MA0142.10.394632
MA0143.10.711438
MA0144.10.353865
MA0145.10.329012
MA0146.10.00080301
MA0147.10.00740512
MA0148.10.799008
MA0149.10.00722685
MA0062.20.000107689
MA0035.22.54367
MA0039.20.189779
MA0138.20.0283091
MA0002.21.01799
MA0137.20.0768047
MA0104.20.00492913
MA0047.20.931423
MA0112.20.0230753
MA0065.20.911319
MA0150.10.279456
MA0151.10
MA0152.10.692149
MA0153.11.57691
MA0154.11.36453
MA0155.10.0282953
MA0156.10.251027
MA0157.12.4085
MA0158.10
MA0159.10.0451047
MA0160.10.379637
MA0161.10
MA0162.10.00104045
MA0163.10.0190423
MA0164.11.09771
MA0080.20.31363
MA0018.20.210085
MA0099.20.124927
MA0079.29.05962e-06
MA0102.20.494276
MA0258.10.215098
MA0259.10.0516452
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOXA1#3169202.518504488496699.2020631476479e-050.00134038252869902
FOXA2#3170164.478266136848234.79909341517431e-072.26281046134262e-05
HNF4A#3172112.891536295369210.001454666162509730.00932506011210125
HNF4G#3174103.267434378005320.0009791472464186920.00703599554621726



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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