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{{Coexpression_clusters
{
|full_id=C4701_Mast_optic_mature_small_substantia_adrenal_serous

Latest revision as of 14:18, 17 September 2013


Full id: C4701_Mast_optic_mature_small_substantia_adrenal_serous



Phase1 CAGE Peaks

Hg19::chr7:79764112..79764209,+p1@GNAI1
Hg19::chr7:79764242..79764256,+p3@GNAI1
Hg19::chr7:79764393..79764437,+p2@GNAI1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system3.87e-2381
nervous system1.99e-2289
neural tube1.05e-2156
neural rod1.05e-2156
future spinal cord1.05e-2156
neural keel1.05e-2156
regional part of nervous system5.64e-2053
regional part of brain5.64e-2053
organ system subdivision6.11e-20223
brain1.08e-1968
future brain1.08e-1968
ectoderm-derived structure3.60e-18171
ectoderm3.60e-18171
presumptive ectoderm3.60e-18171
neural plate2.12e-1782
presumptive neural plate2.12e-1782
ecto-epithelium2.61e-17104
telencephalon4.11e-1734
brain grey matter4.35e-1734
gray matter4.35e-1734
regional part of forebrain6.23e-1741
forebrain6.23e-1741
anterior neural tube6.23e-1741
future forebrain6.23e-1741
neurectoderm7.56e-1686
regional part of telencephalon8.27e-1632
cerebral hemisphere8.85e-1632
structure with developmental contribution from neural crest3.13e-15132
pre-chordal neural plate4.67e-1461
multi-cellular organism4.75e-14656
regional part of cerebral cortex1.64e-1322
organ2.24e-13503
anatomical system2.32e-13624
anatomical group4.50e-13625
neocortex2.00e-1220
cerebral cortex4.09e-1225
pallium4.09e-1225
anatomical cluster1.94e-11373
adult organism3.28e-11114
organ part3.56e-10218
multi-tissue structure4.56e-09342
embryonic structure1.56e-07564
developing anatomical structure7.39e-07581
germ layer8.83e-07560
germ layer / neural crest8.83e-07560
embryonic tissue8.83e-07560
presumptive structure8.83e-07560
germ layer / neural crest derived structure8.83e-07560
epiblast (generic)8.83e-07560


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)
MA0003.13.22681
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
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
MA0051.12.15619
MA0052.11.24796
MA0055.10.190716
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
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.13.923
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
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
MA0116.11.3784
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.14.51393
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.22.07067
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.776149
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285853597184222
CTBP2#1488241.81133355955210.0007543408259914850.00593644800887082
CTCF#1066435.360256373075030.0064925092527670.0281322314172399
E2F1#186934.907389214879320.008460985347239390.0327741580253814
NR3C1#290829.982015554115360.01278474365547170.0460819962945232
SMARCB1#6598212.16847718743830.008675002221921740.0330141951337421
SMC3#9126210.02995522995520.0126656379767470.0457822505331215
TFAP2A#7020211.01242291536330.01054990655215560.0390357007865295
USF1#739136.361499277207960.00388404057290560.0191197828711203



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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