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{{Coexpression_clusters
{
|full_id=C683_esophagus_tongue_tonsil_Corneal_cervical_Esophageal_throat
 

Latest revision as of 11:28, 17 September 2013


Full id: C683_esophagus_tongue_tonsil_Corneal_cervical_Esophageal_throat



Phase1 CAGE Peaks

Hg19::chr11:119039032..119039058,+p5@NLRX1
Hg19::chr11:119039069..119039081,+p9@NLRX1
Hg19::chr14:24732368..24732391,-p1@TGM1
Hg19::chr14:24732403..24732410,-p4@TGM1
Hg19::chr14:24732738..24732753,-p3@TGM1
Hg19::chr1:153285441..153285450,-p@chr1:153285441..153285450
-
Hg19::chr1:24645832..24645853,+p1@GRHL3
Hg19::chr1:24645865..24645871,+p6@GRHL3
Hg19::chr1:24645921..24645973,+p2@GRHL3
Hg19::chr20:33880168..33880183,-p2@FAM83C
Hg19::chr6:53794788..53794806,+p12@MLIP
Hg19::chr7:44029862..44029900,-p1@ENST00000420754


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:0043163cell envelope organization and biogenesis0.0157183645563999
GO:0005913cell-cell adherens junction0.0336544548770559
GO:0003810protein-glutamine gamma-glutamyltransferase activity0.0336544548770559
GO:0001533cornified envelope0.0336544548770559
GO:0045229external encapsulating structure organization and biogenesis0.0336544548770559
GO:0018149peptide cross-linking0.0336544548770559
GO:0030216keratinocyte differentiation0.0336544548770559
GO:0031424keratinization0.0357618532746787
GO:0016755transferase activity, transferring amino-acyl groups0.0357618532746787
GO:0009913epidermal cell differentiation0.0359650815239245
GO:0005912adherens junction0.0359650815239245
GO:0048730epidermis morphogenesis0.0359650815239245
GO:0048729tissue morphogenesis0.0434381461036677



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><br>

Cell Type
Ontology termp-valuen
endo-epithelial cell1.60e-1942
respiratory epithelial cell1.66e-1713
acinar cell3.37e-165
general ecto-epithelial cell1.44e-1314
protein secreting cell1.94e-136
transitional epithelial cell4.87e-134
urothelial cell4.87e-134
endodermal cell6.96e-1358
bronchial epithelial cell2.24e-103
acinar cell of salivary gland3.08e-103
epithelial cell of alimentary canal6.41e-0920
glandular epithelial cell7.85e-099
epidermal cell1.01e-089
epithelial cell of tracheobronchial tree1.21e-089
epithelial cell of lower respiratory tract1.21e-089
stratified squamous epithelial cell1.54e-086
keratin accumulating cell1.54e-086
stratified epithelial cell1.54e-086
keratinizing barrier epithelial cell1.54e-086
epithelial fate stem cell1.54e-086
stratified epithelial stem cell1.54e-086
surface ectodermal cell1.54e-086
corneal epithelial cell4.19e-082
epithelial cell1.16e-07253
sebum secreting cell1.17e-072
epithelial cell of sweat gland1.17e-072
epithelial cell of skin gland1.17e-072
acinar cell of sebaceous gland1.17e-072
CD1a-positive Langerhans cell3.90e-072
immature CD1a-positive Langerhans cell3.90e-072
Uber Anatomy
Ontology termp-valuen
respiratory system2.99e-1674
endoderm-derived structure8.97e-16160
endoderm8.97e-16160
presumptive endoderm8.97e-16160
orifice7.23e-1436
surface structure1.48e-1399
oral opening9.17e-1322
mouth3.87e-1129
stomodeum3.87e-1129
respiratory tract7.90e-1154
anterior region of body1.24e-1062
craniocervical region1.24e-1062
urothelium1.95e-105
lower respiratory tract epithelium2.24e-103
epithelium of bronchus2.24e-103
gland of gut2.25e-1010
tracheobronchial tree1.86e-0915
lower respiratory tract1.86e-0915
digestive system9.99e-09145
digestive tract9.99e-09145
primitive gut9.99e-09145
transitional epithelium1.07e-086
saliva-secreting gland1.26e-086
gland of oral region1.26e-086
gland of foregut1.26e-086
oral gland1.26e-086
oral cavity1.26e-086
subdivision of head2.83e-0849
head5.00e-0856
chordate pharynx8.46e-0810
pharyngeal region of foregut8.46e-0810
skin gland1.17e-072
epidermis gland1.17e-072
gland of integumental system1.17e-072
sebaceous gland1.17e-072
skin sebaceous gland1.17e-072
sweat gland1.17e-072
sweat gland placode1.17e-072
sebaceous gland placode1.17e-072
foregut1.90e-0787
open tracheal system trachea2.36e-072
trachea2.39e-077
respiratory airway2.39e-077
subdivision of digestive tract2.94e-07118
skin epidermis3.80e-0715
outer epithelium3.80e-0715
enveloping layer of ectoderm3.80e-0715
segment of respiratory tract4.18e-0747
pharynx4.70e-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)
MA0003.10.514819
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.292292
MA0017.10.627635
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.11.06455
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.641892
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.11.22349
MA0056.10
MA0057.10.617373
MA0058.10.240796
MA0059.10.239727
MA0060.11.13897
MA0061.10.605357
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.14.60867
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.266215
MA0091.10.86696
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.564934
MA0103.10.535462
MA0105.10.563165
MA0106.10.452066
MA0107.10.843983
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.11.17934
MA0114.10.828144
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.10.64269
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.567946
MA0140.12.62247
MA0141.10.670251
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.12.38272
MA0146.10.391218
MA0147.10.143012
MA0148.10.344198
MA0149.10.963341
MA0062.20.0823902
MA0035.20.376007
MA0039.22.43186
MA0138.20.503176
MA0002.22.1904
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.21.00671
MA0065.21.07591
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.5526
MA0155.12.21597
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.0188054
MA0163.10.478611
MA0164.11.20414
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.21.48579
MA0102.21.28978
MA0258.10.375
MA0259.10.149181
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
MAFK#797536.775183284457480.008600060790385260.0327624201673188



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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