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Latest revision as of 03:26, 17 September 2013


Full id: C3425_prostate_papillary_bronchioalveolar_small_lung_thyroid_nonsmall



Phase1 CAGE Peaks

  Short description
Hg19::chr14:36982432..36982437,- p10@SFTA3
Hg19::chr14:36982707..36982717,- p8@SFTA3
Hg19::chr14:36982724..36982767,- p1@SFTA3


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Uber Anatomy
Ontology termp-valuen
thyroid gland1.55e-255
pharyngeal pouch1.55e-255
thyroid diverticulum1.55e-255
pharyngeal pouch 21.55e-255
thyroid primordium1.55e-255
lung7.04e-2222
respiratory tube7.04e-2222
respiration organ7.04e-2222
pair of lungs7.04e-2222
lung primordium7.04e-2222
lung bud7.04e-2222
thoracic cavity element2.45e-2134
thoracic cavity2.45e-2134
thoracic segment organ1.11e-2035
respiratory primordium6.38e-1938
endoderm of foregut6.38e-1938
epithelial bud5.89e-1637
respiratory tract1.58e-1554
endo-epithelium6.55e-1482
thoracic segment of trunk2.16e-1352
epithelial fold2.87e-1247
entire pharyngeal arch endoderm1.00e-1111
early pharyngeal endoderm1.00e-1111
respiratory system7.97e-1174
respiratory tract epithelium3.13e-1019
lung epithelium3.13e-1019
endoderm-derived structure1.87e-09160
endoderm1.87e-09160
presumptive endoderm1.87e-09160
digestive system2.64e-09145
digestive tract2.64e-09145
primitive gut2.64e-09145
lower lobe of right lung3.05e-091
right lung lobe3.05e-091
lower lobe of lung3.05e-091
lobe of lung3.05e-091
right lung3.05e-091
nucleus accumbens1.16e-081
ventral striatum1.16e-081
corpus striatum2.13e-084
striatum2.13e-084
ventral part of telencephalon2.13e-084
future corpus striatum2.13e-084
tracheobronchial tree2.24e-0815
lower respiratory tract2.24e-0815
foregut2.37e-0787
segment of respiratory tract2.55e-0747
pharyngeal arch system3.28e-0718
primordium5.12e-07160
respiratory system epithelium7.16e-0728
Disease
Ontology termp-valuen
papillary adenocarcinoma1.89e-091
somatostatinoma4.19e-091
lung cancer1.12e-0815
lung carcinoma1.51e-089
respiratory system cancer3.85e-0816
non-small cell lung carcinoma2.70e-075


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0057.10.333427
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
MA0073.10.407479
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
MA0146.14.51393
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
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
MA0079.20.481578
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488362.71700033932814.049570681927e-060.000129297802644382
SUZ12#23512350.11578091106297.93834897779404e-060.000221736621795087



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.