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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:43, 17 September 2013


Full id: C4312_cervical_Small_malignant_Sebocyte_oral_epidermoid_squamous



Phase1 CAGE Peaks

Hg19::chr3:189507432..189507459,+p1@TP63
Hg19::chr3:189507460..189507471,+p3@TP63
Hg19::chr5:122758885..122758934,-p4@CEP120


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:0045747positive regulation of Notch signaling pathway0.00588720122453785
GO:0008593regulation of Notch signaling pathway0.00588720122453785
GO:0002347response to tumor cell0.00588720122453785
GO:0051289protein homotetramerization0.00662310137760509
GO:0051262protein tetramerization0.0100082420817143
GO:0051260protein homooligomerization0.0165912034509703
GO:0007219Notch signaling pathway0.0165912034509703
GO:0030308negative regulation of cell growth0.0165912034509703
GO:0045792negative regulation of cell size0.0165912034509703
GO:0045926negative regulation of growth0.0165912034509703
GO:0051259protein oligomerization0.0165912034509703
GO:0009967positive regulation of signal transduction0.0312582350731415
GO:0001558regulation of cell growth0.0312582350731415
GO:0016049cell growth0.0312582350731415
GO:0040008regulation of growth0.0312582350731415
GO:0045892negative regulation of transcription, DNA-dependent0.0312582350731415
GO:0008361regulation of cell size0.0312582350731415
GO:0006917induction of apoptosis0.0312582350731415
GO:0012502induction of programmed cell death0.0312582350731415
GO:0016564transcription repressor activity0.0312582350731415
GO:0045893positive regulation of transcription, DNA-dependent0.0312582350731415
GO:0043065positive regulation of apoptosis0.0317254732655651
GO:0043068positive regulation of programmed cell death0.0317254732655651
GO:0045941positive regulation of transcription0.0317254732655651
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0317254732655651
GO:0009607response to biotic stimulus0.0317254732655651
GO:0016481negative regulation of transcription0.0317254732655651
GO:0016563transcription activator activity0.0323796067349582
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0323796067349582
GO:0006461protein complex assembly0.0333608069390478
GO:0042802identical protein binding0.0335754444836924
GO:0031325positive regulation of cellular metabolic process0.0335754444836924
GO:0031324negative regulation of cellular metabolic process0.0338514070410927
GO:0009893positive regulation of metabolic process0.0338514070410927
GO:0009892negative regulation of metabolic process0.0366688533414072
GO:0000902cell morphogenesis0.0380281376395824
GO:0032989cellular structure morphogenesis0.0380281376395824
GO:0042981regulation of apoptosis0.0434747167350488
GO:0043067regulation of programmed cell death0.0434747167350488



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>

Uber Anatomy
Ontology termp-valuen
orifice3.31e-1836
respiratory system4.46e-1874
endoderm-derived structure1.84e-16160
endoderm1.84e-16160
presumptive endoderm1.84e-16160
oral opening2.38e-1522
anterior region of body3.70e-1362
craniocervical region3.70e-1362
surface structure2.08e-1299
mouth2.21e-1229
stomodeum2.21e-1229
digestive system3.94e-11145
digestive tract3.94e-11145
primitive gut3.94e-11145
respiratory tract1.02e-1054
head1.45e-1056
mucosa1.80e-1020
neck1.84e-1010
urothelium8.37e-105
subdivision of digestive tract9.21e-10118
mucosa of oral region2.31e-084
respiratory system mucosa2.31e-084
foregut2.32e-0887
subdivision of head2.69e-0849
mouth mucosa3.00e-0813
transitional epithelium4.66e-086
gland of gut5.69e-0810
tracheobronchial tree6.90e-0815
lower respiratory tract6.90e-0815
saliva-secreting gland1.20e-076
gland of oral region1.20e-076
gland of foregut1.20e-076
oral gland1.20e-076
oral cavity1.20e-076
thoracic cavity element1.27e-0734
thoracic cavity1.27e-0734
anatomical space1.40e-0795
thoracic segment organ2.67e-0735
organism subdivision5.38e-07264
pharynx7.62e-0711
Disease
Ontology termp-valuen
squamous cell carcinoma9.66e-1814


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0041.11.97353
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.22.07011
MA0039.20.432958
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
MA0154.10.838867
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
MA0079.20.181755
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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