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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:28, 17 September 2013


Full id: C690_duodenum_small_temporal_gall_colon_Neurons_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr11:67418140..67418149,-p8@ACY3
Hg19::chr12:121417546..121417562,-p5@HNF1A-AS1
Hg19::chr1:1179741..1179746,-p@chr1:1179741..1179746
-
Hg19::chr22:32614389..32614392,-p@chr22:32614389..32614392
-
Hg19::chr22:39867407..39867414,-p@chr22:39867407..39867414
-
Hg19::chr7:100550785..100550819,+p1@uc003uxk.1
p1@uc003uxl.1
Hg19::chr7:100550980..100551001,+p4@uc003uxk.1
p4@uc003uxl.1
Hg19::chr7:100551127..100551197,+p9@MUC3A
p9@MUC3B
Hg19::chr7:100610742..100610760,+p@chr7:100610742..100610760
+
Hg19::chr7:100610789..100610813,+p@chr7:100610789..100610813
+
Hg19::chr7:141900897..141900901,+p@chr7:141900897..141900901
+
Hg19::chr8:48911425..48911428,-p@chr8:48911425..48911428
-


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:0005727extrachromosomal circular DNA0.000912516189803367
GO:0046821extrachromosomal DNA0.000912516189803367
GO:0019807aspartoacylase activity0.00121667034532259
GO:0030277maintenance of gastrointestinal epithelium0.00136873399227078
GO:0004046aminoacylase activity0.00145996143579055
GO:0030197extracellular matrix constituent, lubricant activity0.00334540023286012
GO:0022600digestive system process0.00495234693393053
GO:0016324apical plasma membrane0.0154974775324448
GO:0045177apical part of cell0.0157398365245999
GO:0016811hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides0.0157398365245999
GO:0007586digestion0.0157398365245999
GO:0005201extracellular matrix structural constituent0.0186729914315964
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0260409010895861
GO:0042802identical protein binding0.0471973218733263



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
germ line cell1.68e-077
germ cell1.68e-077
Uber Anatomy
Ontology termp-valuen
intestine1.06e-3117
small intestine3.10e-224
gastrointestinal system8.50e-2225
large intestine2.76e-1011
subdivision of digestive tract6.02e-07118
digestive system8.50e-07145
digestive tract8.50e-07145
primitive gut8.50e-07145
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma3.48e-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)
MA0003.10.050563
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.0339142
MA0017.10.627635
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.583404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.14.26214
MA0048.10.155795
MA0050.10.837296
MA0051.10.410316
MA0052.10.682867
MA0055.10.107116
MA0056.10
MA0057.10.0373953
MA0058.10.676094
MA0059.10.673606
MA0060.10.103131
MA0061.10.0856761
MA0063.10
MA0066.11.0654
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.987752
MA0072.10.726666
MA0073.10.678645
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.67392
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.0806254
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.558691
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.535462
MA0105.10.563165
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.761158
MA0113.10.467266
MA0114.11.34132
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.268952
MA0140.10.376643
MA0141.11.24597
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.0932202
MA0146.10.00710499
MA0147.10.440281
MA0148.10.344198
MA0149.10.367947
MA0062.20.589182
MA0035.20.376007
MA0039.20.0300713
MA0138.23.20599
MA0002.20.652621
MA0137.20.20663
MA0104.20.335786
MA0047.20.440861
MA0112.20.0859008
MA0065.21.47455
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.11.98449
MA0154.10.30107
MA0155.10.202876
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.441451
MA0160.10.357736
MA0161.10
MA0162.10.0188054
MA0163.11.22194
MA0164.11.20414
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.20.00539704
MA0102.21.28978
MA0258.10.117513
MA0259.10.891845
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

This analysis result is provided for C0 - C305 clusters.

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