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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:53, 17 September 2013


Full id: C1843_signet_lung_cord_bile_colon_retina_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr1:205905161..205905166,-p5@SLC26A9
Hg19::chr7:129008057..129008070,+p10@AHCYL2
Hg19::chr7:129008104..129008114,+p15@AHCYL2
Hg19::chr7:129008147..129008158,+p7@AHCYL2
Hg19::chr7:129008160..129008180,+p5@AHCYL2


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:0015116sulfate transmembrane transporter activity0.00582832921229247
GO:0008271secondary active sulfate transmembrane transporter activity0.00582832921229247
GO:0008272sulfate transport0.00582832921229247
GO:0015103inorganic anion transmembrane transporter activity0.0114947603909102
GO:0008509anion transmembrane transporter activity0.027069351230425
GO:0015698inorganic anion transport0.0280623258369638
GO:0006820anion transport0.0291416460614624
GO:0015291secondary active transmembrane transporter activity0.0291416460614624
GO:0022804active transmembrane transporter activity0.0481376820126379



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
adult organism4.53e-15114
neural tube1.58e-1256
neural rod1.58e-1256
future spinal cord1.58e-1256
neural keel1.58e-1256
regional part of nervous system6.24e-1253
regional part of brain6.24e-1253
central nervous system5.40e-1081
nervous system2.33e-0989
neurectoderm2.53e-0986
brain3.94e-0968
future brain3.94e-0968
neural plate5.60e-0982
presumptive neural plate5.60e-0982
regional part of forebrain1.39e-0841
forebrain1.39e-0841
anterior neural tube1.39e-0841
future forebrain1.39e-0841
medulla oblongata1.49e-083
myelencephalon1.49e-083
future myelencephalon1.49e-083
telencephalon9.05e-0834
organ system subdivision1.16e-07223
brainstem5.15e-076


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.11.48719
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.11.29981
MA0059.11.29682
MA0060.10.321781
MA0061.11.44118
MA0063.10
MA0066.11.74614
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.12.96921
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.22.01584
MA0018.21.83842
MA0099.20.699641
MA0079.20.00207114
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
BATF#10538419.48624143384291.37275300118359e-050.000332257127904086
CEBPB#105146.376918100659850.001113944176677320.00765540671632573
EBF1#187947.12517347725520.0007230531046774210.00577198984937745
EP300#203345.419153380978560.00209386927943890.0121186818329354
FOXA1#316948.865135799508360.0003075468591372710.00316764165891888
GATA3#2625421.78921308576488.81158303710445e-060.000237612424686845
HDAC2#3066410.7324961893010.0001450965797478750.00188620135577399
NFKB1#479044.390450739355070.004707732692524960.022206354486004
SMARCC2#6601475.32429954151816.28893529700036e-083.88415206081266e-06
SPI1#668846.563458806818180.0009957429636454020.00714296307302439
STAT1#6772416.56526999775942.61308619905866e-050.000564092826671118



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

This analysis result is provided for C0 - C305 clusters.

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