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{{Coexpression_clusters
{
|full_id=C2414_kidney_smallcell_seminal_somatostatinoma_ductus_small_Fibroblast
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Latest revision as of 12:05, 17 September 2013


Full id: C2414_kidney_smallcell_seminal_somatostatinoma_ductus_small_Fibroblast



Phase1 CAGE Peaks

Hg19::chr17:46667561..46667572,-p4@HOXB3
Hg19::chr17:46667594..46667619,-p1@HOXB3
Hg19::chr17:46667628..46667642,-p2@HOXB3
Hg19::chr17:46668194..46668198,+p1@ENST00000429755
p1@ENST00000487849
p1@ENST00000492897


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:0030878thyroid gland development0.008242081714353
GO:0035270endocrine system development0.0180540837552494
GO:0048732gland development0.0180540837552494



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
kidney tubule cell1.74e-1410
nephron tubule epithelial cell1.74e-1410
epithelial cell of nephron9.33e-1415
kidney cell1.10e-1117
kidney epithelial cell1.10e-1117
kidney cortical cell7.35e-1012
renal cortical epithelial cell7.35e-1012
preadipocyte2.49e-0712
Uber Anatomy
Ontology termp-valuen
cavitated compound organ1.41e-1831
kidney6.33e-1826
kidney mesenchyme6.33e-1826
upper urinary tract6.33e-1826
kidney rudiment6.33e-1826
kidney field6.33e-1826
abdominal segment of trunk2.93e-1760
abdomen2.93e-1760
subdivision of trunk3.05e-17112
excretory tube3.94e-1516
kidney epithelium3.94e-1516
trunk1.49e-14199
nephron tubule epithelium1.74e-1410
mesenchyme1.84e-14160
entire embryonic mesenchyme1.84e-14160
gastrointestinal system7.38e-1425
nephron epithelium9.33e-1415
renal tubule9.33e-1415
nephron tubule9.33e-1415
nephron9.33e-1415
uriniferous tubule9.33e-1415
nephrogenic mesenchyme9.33e-1415
intestine1.64e-1317
trunk region element5.94e-13101
abdomen element1.60e-1254
abdominal segment element1.60e-1254
renal system1.67e-1248
urinary system structure7.34e-1247
large intestine2.63e-1111
cortex of kidney7.35e-1012
renal parenchyma7.35e-1012
parenchyma6.96e-0915
colon8.37e-099
organism subdivision3.55e-08264
omentum5.54e-086
peritoneum5.54e-086
abdominal cavity5.54e-086
visceral peritoneum5.54e-086
cavity lining6.88e-0812
serous membrane6.88e-0812
intraembryonic coelom1.09e-0712
cortex2.15e-0715
anatomical space2.93e-0795
internal genitalia5.10e-0725
subdivision of digestive tract6.67e-07118
intervertebral cartilage7.65e-075
symphysis7.65e-075
nonsynovial joint7.65e-075
fibrous joint7.65e-075
cartilaginous joint7.65e-075
developing mesenchymal condensation7.65e-075
pre-cartilage condensation7.65e-075
cartilaginous condensation7.65e-075
cartilage element7.65e-075
post-cranial axial skeletal system7.65e-075
vertebral column7.65e-075
intervertebral disk7.65e-075
intervertebral joint7.65e-075
immaterial anatomical entity9.79e-07117


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)
MA0003.10.0938548
MA0004.12.8475
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.11.47358
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.13.35176
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.12.41215
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.657636
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
ESR1#2099323.07645247211590.0001339105244968570.0017578533519265
TRIM28#10155418.59052504526258.36730015875654e-060.00023002697059236
USF1#739134.771124457905970.01370465887188020.0482976503431852
ZNF263#1012736.166381227758010.006539814347975980.027970501277213



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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