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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:44, 17 September 2013


Full id: C1393_thyroid_lung_throat_Alveolar_small_nonsmall_papillary



Phase1 CAGE Peaks

Hg19::chr14:36983118..36983142,-p3@SFTA3
Hg19::chr14:36986015..36986024,-p@chr14:36986015..36986024
-
Hg19::chr14:36988729..36988748,-p2@ENST00000521945
Hg19::chr14:36988882..36988895,-p13@NKX2-1
Hg19::chr14:36989573..36989577,-p18@NKX2-1
Hg19::chr9:138336075..138336099,-p@chr9:138336075..138336099
-


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:0021798forebrain dorsal/ventral pattern formation0.00523960908983869
GO:0021871forebrain regionalization0.00523960908983869
GO:0030878thyroid gland development0.00589456022606853
GO:0007492endoderm development0.00589456022606853
GO:0009953dorsal/ventral pattern formation0.0109555462787536
GO:0035270endocrine system development0.0109555462787536
GO:0001764neuron migration0.0109555462787536
GO:0030324lung development0.0109555462787536
GO:0030323respiratory tube development0.0109555462787536
GO:0030900forebrain development0.0109555462787536
GO:0048732gland development0.0109555462787536
GO:0003002regionalization0.0189935829506652
GO:0035295tube development0.0227595519839868
GO:0007389pattern specification process0.0227595519839868
GO:0007420brain development0.0227595519839868
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0227595519839868
GO:0005667transcription factor complex0.030190128565261
GO:0045893positive regulation of transcription, DNA-dependent0.030190128565261
GO:0016477cell migration0.030190128565261
GO:0007417central nervous system development0.030190128565261
GO:0048699generation of neurons0.030190128565261
GO:0022008neurogenesis0.0311353693992338
GO:0045941positive regulation of transcription0.0311353693992338
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0311353693992338
GO:0009888tissue development0.0311353693992338
GO:0016563transcription activator activity0.0311353693992338
GO:0009887organ morphogenesis0.0330433411955956
GO:0031325positive regulation of cellular metabolic process0.0330433411955956
GO:0051674localization of cell0.0330433411955956
GO:0006928cell motility0.0330433411955956
GO:0009893positive regulation of metabolic process0.0330433411955956
GO:0006357regulation of transcription from RNA polymerase II promoter0.0346305413281526
GO:0044451nucleoplasm part0.0358833834637438
GO:0005654nucleoplasm0.0399905458474453
GO:0006366transcription from RNA polymerase II promoter0.0479049973928109



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
thyroid gland2.64e-215
pharyngeal pouch2.64e-215
thyroid diverticulum2.64e-215
pharyngeal pouch 22.64e-215
thyroid primordium2.64e-215
lung1.04e-1722
respiratory tube1.04e-1722
respiration organ1.04e-1722
pair of lungs1.04e-1722
lung primordium1.04e-1722
lung bud1.04e-1722
thoracic cavity element6.71e-1434
thoracic cavity6.71e-1434
throat9.23e-142
thoracic segment organ1.85e-1335
epithelial bud1.10e-1237
respiratory primordium2.79e-1238
endoderm of foregut2.79e-1238
endo-epithelium8.76e-1182
respiratory tract4.40e-1054
entire pharyngeal arch endoderm9.28e-1011
early pharyngeal endoderm9.28e-1011
epithelial fold1.14e-0947
pulmonary alveolus epithelium2.14e-093
alveolus2.14e-093
pulmonary lobule2.14e-093
lobule2.14e-093
alveolus of lung2.14e-093
alveolar system2.14e-093
pulmonary acinus2.14e-093
alveolar sac2.14e-093
alveolar wall2.14e-093
thoracic segment of trunk1.41e-0852
respiratory tract epithelium2.94e-0819
lung epithelium2.94e-0819
lower lobe of right lung4.57e-081
right lung lobe4.57e-081
lower lobe of lung4.57e-081
lobe of lung4.57e-081
right lung4.57e-081
respiratory system6.78e-0774
Disease
Ontology termp-valuen
papillary adenocarcinoma1.01e-071
somatostatinoma1.91e-071
lung cancer4.62e-0715
lung carcinoma5.36e-079


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.12.02362
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.12.04333
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.14.08272
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.13.94689
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.12.3765
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.10.093337
MA0147.10.327615
MA0148.12.43826
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.22.28878
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.22.79453
MA0112.20.332548
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.318517
MA0156.10.417278
MA0157.11.89858
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.62636
MA0163.11.18186
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.210.1105
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CTBP2#1488331.35850016966417.81255347077474e-050.00120308946023923
SUZ12#23512216.70526030368760.005660234682079570.0255610001280628



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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