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{{Coexpression_clusters
{
|full_id=C2166_pineal_cerebellum_pituitary_lung_Mast_spinal_occipital

Latest revision as of 12:00, 17 September 2013


Full id: C2166_pineal_cerebellum_pituitary_lung_Mast_spinal_occipital



Phase1 CAGE Peaks

Hg19::chr11:76156045..76156099,+p1@C11orf30
Hg19::chr2:233562028..233562056,+p1@GIGYF2
Hg19::chr2:71558882..71558936,+p1@ZNF638
Hg19::chr5:102455968..102456013,+p2@PPIP5K2


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
adult organism3.72e-37114
neural tube1.33e-2256
neural rod1.33e-2256
future spinal cord1.33e-2256
neural keel1.33e-2256
central nervous system1.17e-2181
regional part of nervous system2.99e-2153
regional part of brain2.99e-2153
nervous system1.62e-2089
regional part of forebrain4.12e-2041
forebrain4.12e-2041
anterior neural tube4.12e-2041
future forebrain4.12e-2041
brain1.05e-1868
future brain1.05e-1868
brain grey matter2.85e-1634
gray matter2.85e-1634
telencephalon3.69e-1634
regional part of telencephalon2.74e-1532
cerebral hemisphere3.26e-1532
neurectoderm2.58e-1286
regional part of cerebral cortex3.00e-1222
neural plate5.52e-1282
presumptive neural plate5.52e-1282
cerebral cortex1.50e-1125
pallium1.50e-1125
neocortex3.23e-1120
pre-chordal neural plate1.86e-0961
organ system subdivision1.30e-08223
hematopoietic system1.92e-0798
blood island1.92e-0798
ectoderm-derived structure6.58e-07171
ectoderm6.58e-07171
presumptive ectoderm6.58e-07171


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)
MA0003.10.233555
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.12.48281
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.11.51122
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
MA0093.11.32557
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
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
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
CCNT2#90534.752151182721970.01386206996689490.0487061204842058
ELF1#199744.258097958807540.003041525565781240.0160601591872505
HEY1#2346244.040111043105710.00375304636917980.0185606785562444
IRF1#365935.727872815172930.008097114790333330.0319911693874413
MXI1#460137.471178721569470.003741314738550960.0186243646320078
NRF1#4899412.21027944771094.49717228915276e-050.000792174357744688
PAX5#507935.002174148383370.01196533174786410.0434780906831527
RFX5#599339.035933120396320.002144561191324070.0123811954815199
RXRA#6256210.03730856956660.01391703805920110.0488729501635811
TAF1#687243.343046285745290.008005664898701650.0321331143872214
TBP#690843.706770687096390.005296377814784350.024354896204573
USF1#739134.771124457905970.01370465887188020.0482764728791248
YY1#752844.911170749853860.00171871838055440.0106642840391351
ZNF143#7702310.12565741417090.001534861610688180.00976185443996488
ZNF263#1012736.166381227758010.006539814347975980.0279590515652816



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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