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Coexpression cluster:C1664

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Full id: C1664_uterus_epididymis_aorta_cervix_caudate_Adipocyte_ductus



Phase1 CAGE Peaks

  Short description
Hg19::chr12:15374234..15374247,- p3@RERG
Hg19::chr12:15374258..15374265,- p5@RERG
Hg19::chr12:15374283..15374294,- p4@RERG
Hg19::chr12:15374328..15374342,- p2@RERG
Hg19::chr12:15374343..15374416,- p1@RERG


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


uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism1.58e-66114
neural tube8.89e-3056
neural rod8.89e-3056
future spinal cord8.89e-3056
neural keel8.89e-3056
regional part of nervous system8.28e-2853
regional part of brain8.28e-2853
brain6.33e-2568
future brain6.33e-2568
central nervous system1.71e-2481
regional part of forebrain2.68e-2441
forebrain2.68e-2441
anterior neural tube2.68e-2441
future forebrain2.68e-2441
organ system subdivision1.15e-22223
nervous system4.42e-2289
cerebral hemisphere1.08e-2132
telencephalon3.12e-2134
brain grey matter3.89e-2134
gray matter3.89e-2134
neural plate4.56e-2182
presumptive neural plate4.56e-2182
neurectoderm3.76e-2086
regional part of telencephalon6.28e-2032
regional part of cerebral cortex6.13e-1922
neocortex1.79e-1720
ecto-epithelium2.94e-16104
structure with developmental contribution from neural crest4.60e-16132
cerebral cortex7.75e-1625
pallium7.75e-1625
multi-tissue structure1.61e-15342
pre-chordal neural plate1.49e-1461
anatomical cluster2.53e-14373
organ part4.40e-13218
ectoderm-derived structure1.63e-11171
ectoderm1.63e-11171
presumptive ectoderm1.63e-11171
organ4.47e-11503
multi-cellular organism1.16e-09656
embryo1.23e-08592
tube1.42e-08192
developing anatomical structure5.36e-08581
anatomical conduit1.35e-07240
gyrus4.24e-076
embryonic structure6.16e-07564
basal ganglion7.76e-079
nuclear complex of neuraxis7.76e-079
aggregate regional part of brain7.76e-079
collection of basal ganglia7.76e-079
cerebral subcortex7.76e-079
posterior neural tube8.00e-0715
chordal neural plate8.00e-0715
germ layer8.22e-07560
germ layer / neural crest8.22e-07560
embryonic tissue8.22e-07560
presumptive structure8.22e-07560
germ layer / neural crest derived structure8.22e-07560
epiblast (generic)8.22e-07560
neural nucleus9.31e-079
nucleus of brain9.31e-079


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)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
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
MA0058.10.523638
MA0059.10.522232
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
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.13.60303
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.12.96863
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.21.96224
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.475695
MA0102.21.66336
MA0258.12.47453
MA0259.10.395396
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
CTCF#1066455.360256373075030.0002259278299937090.00249531267308724
CTCFL#140690519.74647435897443.32745051287657e-071.65641374697005e-05
MAX#414956.452555509007128.93743970843928e-050.00130584396433924
MYC#460944.177825497287520.005691969036823440.0256710089492077
NFKB1#479055.488063424193840.0002008162847462320.00238818628588154
PAX5#507956.669565531177837.57493746384605e-050.00116942925910808
RAD21#5885510.35503389545638.39503550283973e-060.000229340599759633
SMC3#9126515.04493284493281.29633924985553e-065.15568830600387e-05
SPI1#668858.204323508522732.68916109982495e-050.000574107310107559
ZNF143#7702513.50087655222792.22790360787208e-067.97395561694831e-05
ZNF263#1012758.221841637010682.6606316672286e-050.000570699754967525



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.