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Coexpression cluster:C1775

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Full id: C1775_neuroblastoma_iPS_testicular_H9_HES3GFP_skeletal_Melanocyte



Phase1 CAGE Peaks

Hg19::chr17:27370003..27370010,+p7@PIPOX
Hg19::chr17:27370022..27370051,+p2@PIPOX
Hg19::chr1:63788080..63788093,-p2@ENST00000418244
Hg19::chr1:63788098..63788150,-p1@ENST00000418244
p1@ENST00000449386
Hg19::chr1:63788229..63788250,+p1@FOXD3


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:0008115sarcosine oxidase activity0.00174651065699534
GO:0001829trophectodermal cell differentiation0.00174651065699534
GO:0050031L-pipecolate oxidase activity0.00174651065699534
GO:0046653tetrahydrofolate metabolic process0.00174651065699534
GO:0001825blastocyst formation0.00174651065699534
GO:0016647oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor0.00174651065699534
GO:0001892embryonic placenta development0.0029939301333032
GO:0001824blastocyst development0.00873088237650159
GO:0001890placenta development0.00873088237650159
GO:0006760folic acid and derivative metabolic process0.0226879294561886
GO:0001701in utero embryonic development0.0226879294561886
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0226879294561886
GO:0009792embryonic development ending in birth or egg hatching0.0326998395213866
GO:0043009chordate embryonic development0.0326998395213866
GO:0042579microbody0.0326998395213866
GO:0005777peroxisome0.0326998395213866
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0363413184827587
GO:0046483heterocycle metabolic process0.0363413184827587
GO:0006752group transfer coenzyme metabolic process0.0363413184827587
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0363413184827587
GO:0048646anatomical structure formation0.0380888911765254
GO:0006725aromatic compound metabolic process0.0434672701333003
GO:0045892negative regulation of transcription, DNA-dependent0.0461077525897228
GO:0045893positive regulation of transcription, DNA-dependent0.0485256242130203
GO:0009790embryonic development0.0490826948160948



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>

Cell Type
Ontology termp-valuen
melanocyte2.26e-1410
melanoblast2.26e-1410
embryonic stem cell2.05e-105
pigment cell1.31e-0914
neurectodermal cell3.30e-0959
migratory neural crest cell1.28e-0841
Uber Anatomy
Ontology termp-valuen
testis6.74e-088
male reproductive organ3.85e-0711
brainstem6.25e-076
uterine cervix9.88e-076
neck of organ9.88e-076
Disease
Ontology termp-valuen
cell type cancer1.53e-08143
germ cell and embryonal cancer8.94e-0822
germ cell cancer8.94e-0822
carcinoma1.60e-07106


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)
MA0003.11.80249
MA0004.12.5741
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.14.45064
MA0059.13.2914
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.14.40502
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.14.06535
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.12.26263
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.11.72991
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.13.21279
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.13391
MA0140.10.692258
MA0141.10.520334
MA0142.12.10746
MA0143.11.87149
MA0144.10.356507
MA0145.12.01656
MA0146.10.333008
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.83106
MA0137.21.20193
MA0104.21.54865
MA0047.20.767096
MA0112.23.37937
MA0065.22.03954
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.12.24205
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.77901
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.11.99104
MA0164.10.810347
MA0080.20.456437
MA0018.23.06493
MA0099.20.699641
MA0079.21.27276
MA0102.21.66336
MA0258.11.63655
MA0259.10.395396
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
ATF3#467313.47790471560530.0008241088551409360.00627371562956952
CTBP2#1488225.08680013573130.002461438599678380.0138492719487022
CTCFL#140690311.84788461538460.001201770348538230.00815010996305092
FOXA1#316936.648851849631270.006389025166568720.0278095940389793
FOXA2#3170314.77827825159910.0006289192851194480.00517398197862072
HNF4G#3174211.50136901057870.01127438304921050.0413806111852572
NANOG#79923317.54686708860760.0003794200090681830.0037606763146125
POU5F1#54602134.1756805807628.81868530743257e-050.00130160355401774
TAF1#687253.343046285745290.002394600090870310.0135329891174461
TBP#690853.706770687096390.001428755106721120.00918771963492687
USF2#739237.795318431041750.004048927661722050.0193761893357125



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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