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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:55, 17 September 2013


Full id: C201_colon_small_adenocarcinoma_duodenum_temporal_signet_gall



Phase1 CAGE Peaks

Hg19::chr11:1074870..1074883,+p1@MUC2
Hg19::chr11:1088694..1088705,+p@chr11:1088694..1088705
+
Hg19::chr11:1088789..1088796,+p@chr11:1088789..1088796
+
Hg19::chr11:1092201..1092208,+p@chr11:1092201..1092208
+
Hg19::chr11:1092226..1092243,+p@chr11:1092226..1092243
+
Hg19::chr11:1092262..1092271,+p@chr11:1092262..1092271
+
Hg19::chr11:1092292..1092322,+p6@MUC2
Hg19::chr11:1092326..1092337,+p12@MUC2
Hg19::chr11:1092353..1092368,+p9@MUC2
Hg19::chr11:1092380..1092383,+p19@MUC2
Hg19::chr11:1092389..1092394,+p14@MUC2
Hg19::chr11:1092424..1092439,-p@chr11:1092424..1092439
-
Hg19::chr11:1092657..1092728,+p2@MUC2
Hg19::chr11:1092822..1092856,+p7@MUC2
Hg19::chr11:1093018..1093037,+p5@MUC2
Hg19::chr11:1093152..1093171,+p11@MUC2
Hg19::chr11:1093183..1093189,+p13@MUC2
Hg19::chr11:1093323..1093345,+p3@MUC2
Hg19::chr11:1093354..1093373,-p@chr11:1093354..1093373
-
Hg19::chr11:1093438..1093450,+p10@MUC2
Hg19::chr11:1093458..1093487,+p8@MUC2
Hg19::chr11:1093499..1093543,+p4@MUC2
Hg19::chr11:1093649..1093652,+p20@MUC2
Hg19::chr11:1093831..1093850,+p15@MUC2
Hg19::chr11:114430570..114430581,-p2@FAM55A
Hg19::chr11:114466397..114466426,-p2@FAM55D
Hg19::chr11:2448612..2448615,-p@chr11:2448612..2448615
-
Hg19::chr11:60260248..60260251,+p1@MS4A12
Hg19::chr11:6251405..6251412,-p@chr11:6251405..6251412
-
Hg19::chr11:64660916..64660922,-p1@ENST00000413053
p1@uc009ypx.2
Hg19::chr11:69294647..69294668,-p1@ENST00000542064
Hg19::chr12:12223888..12223897,+p6@BCL2L14
Hg19::chr12:3842242..3842262,-p9@EFCAB4B
Hg19::chr13:28552810..28552817,-p@chr13:28552810..28552817
-
Hg19::chr13:28552848..28552849,-p@chr13:28552848..28552849
-
Hg19::chr15:45734062..45734081,-p1@ENST00000559553
Hg19::chr15:78384901..78384904,+p3@SH2D7
Hg19::chr16:1275258..1275289,-p1@TPSG1
Hg19::chr16:2034649..2034664,+p11@GFER
Hg19::chr16:23765964..23765976,+p4@CHP2
Hg19::chr16:23766398..23766403,+p6@CHP2
Hg19::chr16:27344604..27344606,+p@chr16:27344604..27344606
+
Hg19::chr16:29748234..29748245,-p@chr16:29748234..29748245
-
Hg19::chr16:66878311..66878325,+p1@CA7
Hg19::chr16:67463701..67463709,+p@chr16:67463701..67463709
+
Hg19::chr16:67493110..67493128,-p6@ATP6V0D1
Hg19::chr17:1013514..1013520,-p@chr17:1013514..1013520
-
Hg19::chr17:74639830..74639844,-p2@ST6GALNAC1
Hg19::chr18:8974567..8974578,+p@chr18:8974567..8974578
+
Hg19::chr18:8974610..8974620,+p@chr18:8974610..8974620
+
Hg19::chr19:39303576..39303591,-p1@LGALS4
Hg19::chr1:160851193..160851215,-p3@ITLN1
Hg19::chr1:19614537..19614565,+p@chr1:19614537..19614565
+
Hg19::chr1:38201159..38201166,-p@chr1:38201159..38201166
-
Hg19::chr1:86934584..86934598,+p2@CLCA1
Hg19::chr22:43567750..43567759,-p6@TTLL12
Hg19::chr2:200329672..200329678,-p50@SATB2
Hg19::chr2:200333534..200333558,+p1@ENST00000446911
Hg19::chr2:242716231..242716254,+p1@GAL3ST2
Hg19::chr2:85108164..85108218,-p1@C2orf89
Hg19::chr3:108476254..108476257,-p1@RETNLB
Hg19::chr3:112123245..112123271,-p@chr3:112123245..112123271
-
Hg19::chr4:2038275..2038288,+p@chr4:2038275..2038288
+
Hg19::chr4:2038291..2038303,+p@chr4:2038291..2038303
+
Hg19::chr5:149546334..149546364,+p1@CDX1
Hg19::chr5:179394236..179394243,-p@chr5:179394236..179394243
-
Hg19::chr6:168479679..168479688,-p6@FRMD1
Hg19::chr6:168479694..168479708,-p3@FRMD1
Hg19::chr6:31836976..31837017,-p2@SLC44A4
Hg19::chr6:36178216..36178249,+p15@BRPF3
Hg19::chr7:100612647..100612650,+p8@MUC12
Hg19::chr7:100612686..100612700,+p3@MUC12
Hg19::chr7:107443661..107443675,-p1@SLC26A3
Hg19::chr7:129007938..129007947,+p14@AHCYL2
Hg19::chr7:129007975..129007990,+p4@AHCYL2
Hg19::chr7:75452673..75452691,-p3@CCL24
Hg19::chr8:86253920..86253944,-p2@CA1
Hg19::chr9:124926856..124926884,+p2@MORN5
Hg19::chr9:33240157..33240173,+p1@SPINK4
Hg19::chrX:100129320..100129329,-p3@NOX1
Hg19::chrX:100129340..100129353,-p2@NOX1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
intestine2.42e-5817
gastrointestinal system2.63e-4025
large intestine7.49e-3811
small intestine1.73e-304
colon4.37e-309
vermiform appendix6.23e-181
caecum6.23e-181
midgut6.23e-181
lower digestive tract3.60e-145
subdivision of digestive tract1.27e-10118
digestive system1.48e-10145
digestive tract1.48e-10145
primitive gut1.48e-10145
endoderm-derived structure1.72e-09160
endoderm1.72e-09160
presumptive endoderm1.72e-09160
open tracheal system trachea1.86e-092
duodenum8.62e-072


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)
MA0003.10.00367505
MA0004.10.197709
MA0006.10.0126906
MA0007.12.10717
MA0009.10.13802
MA0014.10.00060874
MA0017.11.93282
MA0019.10.254644
MA0024.10.0887084
MA0025.10.215357
MA0027.11.53252
MA0028.10.0986456
MA0029.10.320629
MA0030.10.63611
MA0031.11.82996
MA0038.10.195484
MA0040.10.327552
MA0041.10.0370302
MA0042.10.080816
MA0043.10.138185
MA0046.11.92476
MA0048.10.120186
MA0050.10.179479
MA0051.10.190349
MA0052.10.679881
MA0055.10.0218415
MA0056.10
MA0057.10.15104
MA0058.10.287314
MA0059.10.44398
MA0060.10.0225816
MA0061.10.00434521
MA0063.10
MA0066.10.0166366
MA0067.10.343508
MA0068.11.45918
MA0069.10.130432
MA0070.10.124807
MA0071.10.0114223
MA0072.10.122581
MA0073.1349.148
MA0074.13.1641
MA0076.10.0979747
MA0077.10.118809
MA0078.10.328556
MA0081.10.164165
MA0083.10.141964
MA0084.10.492676
MA0087.10.385036
MA0088.10.820969
MA0089.10
MA0090.10.113239
MA0091.10.0315475
MA0092.10.276885
MA0093.10.157701
MA0095.10
MA0098.10
MA0100.10.0840352
MA0101.10.0034773
MA0103.10.70849
MA0105.10.0263627
MA0106.10.101403
MA0107.10.000650792
MA0108.21.30552
MA0109.10
MA0111.11.46697
MA0113.10.0268335
MA0114.12.30276
MA0115.10.287686
MA0116.10.299559
MA0117.10.158276
MA0119.12.39233
MA0122.10.514553
MA0124.10.717922
MA0125.10.204137
MA0130.10
MA0131.10.0398892
MA0132.10
MA0133.10
MA0135.10.154278
MA0136.10.395148
MA0139.10.0371923
MA0140.10.299927
MA0141.10.438126
MA0142.10.450844
MA0143.10.507149
MA0144.10.466419
MA0145.10.130093
MA0146.10.00900826
MA0147.10.123713
MA0148.10.646533
MA0149.10.138172
MA0062.20.0439502
MA0035.20.147478
MA0039.21.09955
MA0138.20.599132
MA0002.20.381793
MA0137.21.15482
MA0104.20.0460633
MA0047.20.718845
MA0112.20.763064
MA0065.21.59911
MA0150.10.0131861
MA0151.10
MA0152.10.528856
MA0153.11.69141
MA0154.10.563564
MA0155.13.80048
MA0156.10.483236
MA0157.11.09639
MA0158.10
MA0159.10.613807
MA0160.10.126816
MA0161.10
MA0162.10.000132684
MA0163.10.00160381
MA0164.10.0294806
MA0080.20.573786
MA0018.20.102331
MA0099.20.0579118
MA0079.20.000220294
MA0102.20.524013
MA0258.10.739158
MA0259.10.138914
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
SUZ12#23512127.424560134972287.74623847680728e-084.65482969090492e-06



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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