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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:16, 17 September 2013


Full id: C2984_parotid_duodenum_small_temporal_trachea_colon_tongue



Phase1 CAGE Peaks

Hg19::chr10:124320267..124320273,+p1@DMBT1
Hg19::chr17:70030407..70030411,-p1@ENST00000543512
Hg19::chr7:141811505..141811536,+p1@LOC93432


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:0030670phagocytic vesicle membrane0.00206052042858825
GO:0043152induction of bacterial agglutination0.00206052042858825
GO:0019731antibacterial humoral response0.00247255172797302
GO:0019730antimicrobial humoral response0.00247255172797302
GO:0045335phagocytic vesicle0.00247255172797302
GO:0030666endocytic vesicle membrane0.00412073758078951
GO:0048306calcium-dependent protein binding0.00529785721923082
GO:0008329pattern recognition receptor activity0.00618056047368765
GO:0030139endocytic vesicle0.0100705417910804
GO:0030855epithelial cell differentiation0.0148281045208829
GO:0002009morphogenesis of an epithelium0.0235807867716901
GO:0005044scavenger receptor activity0.0237493405768202
GO:0006959humoral immune response0.0237493405768202
GO:0042742defense response to bacterium0.0246851208649812
GO:0030659cytoplasmic vesicle membrane0.0246851208649812
GO:0009617response to bacterium0.0246851208649812
GO:0044433cytoplasmic vesicle part0.0246851208649812
GO:0012506vesicle membrane0.0246851208649812
GO:0045087innate immune response0.0246851208649812
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0390409815926034
GO:0051707response to other organism0.0401816159514654
GO:0016798hydrolase activity, acting on glycosyl bonds0.0401816159514654
GO:0045786negative regulation of progression through cell cycle0.0401816159514654
GO:0009607response to biotic stimulus0.0494138478198072



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 organism1.09e-17114
subdivision of digestive tract6.01e-14118
digestive system1.21e-11145
digestive tract1.21e-11145
primitive gut1.21e-11145
major salivary gland5.03e-112
open tracheal system trachea1.74e-102
throat2.01e-102
endoderm-derived structure4.47e-10160
endoderm4.47e-10160
presumptive endoderm4.47e-10160
small intestine1.54e-094
intestine2.82e-0917
gastrointestinal system2.51e-0825
saliva-secreting gland5.05e-086
gland of oral region5.05e-086
gland of foregut5.05e-086
oral gland5.05e-086
oral cavity5.05e-086
organ system subdivision6.17e-08223
gland of gut8.12e-0810
chordate pharynx1.48e-0710
pharyngeal region of foregut1.48e-0710
foregut1.77e-0787
oral opening2.26e-0722
tongue2.37e-073
gustatory system2.37e-073
future tongue2.37e-073
orifice3.75e-0736
pharynx7.14e-0711


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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