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Coexpression cluster:C3927

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Full id: C3927_stomach_brain_temporal_occipital_insula_kidney_frontal



Phase1 CAGE Peaks

  Short description
Hg19::chr1:205538132..205538150,+ p1@MFSD4
Hg19::chr1:205538165..205538193,+ p2@MFSD4
Hg19::chr1:205538351..205538398,- p@chr1:205538351..205538398
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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 organism1.29e-87114
neural tube1.16e-5256
neural rod1.16e-5256
future spinal cord1.16e-5256
neural keel1.16e-5256
regional part of nervous system6.37e-4953
regional part of brain6.37e-4953
brain2.08e-4468
future brain2.08e-4468
central nervous system1.17e-4381
regional part of forebrain1.93e-4041
forebrain1.93e-4041
anterior neural tube1.93e-4041
future forebrain1.93e-4041
neural plate2.56e-3982
presumptive neural plate2.56e-3982
nervous system3.04e-3989
neurectoderm1.11e-3686
organ system subdivision3.80e-32223
telencephalon5.78e-3234
brain grey matter1.19e-3134
gray matter1.19e-3134
ecto-epithelium7.43e-30104
cerebral hemisphere8.95e-3032
regional part of telencephalon2.80e-2932
regional part of cerebral cortex1.33e-2822
pre-chordal neural plate2.33e-2861
neocortex8.79e-2620
structure with developmental contribution from neural crest5.04e-25132
cerebral cortex1.98e-2425
pallium1.98e-2425
ectoderm-derived structure1.65e-22171
ectoderm1.65e-22171
presumptive ectoderm1.65e-22171
anatomical cluster5.20e-20373
multi-tissue structure8.68e-16342
anatomical conduit1.20e-15240
organ1.65e-15503
tube3.83e-14192
posterior neural tube5.55e-1315
chordal neural plate5.55e-1315
developing anatomical structure4.04e-12581
germ layer5.57e-12560
germ layer / neural crest5.57e-12560
embryonic tissue5.57e-12560
presumptive structure5.57e-12560
germ layer / neural crest derived structure5.57e-12560
epiblast (generic)5.57e-12560
embryo6.55e-12592
organ part9.36e-12218
embryonic structure1.14e-11564
temporal lobe2.46e-116
segmental subdivision of nervous system1.01e-1013
gyrus1.29e-106
anatomical system1.30e-10624
anatomical group1.53e-10625
multi-cellular organism4.79e-10656
diencephalon6.38e-107
future diencephalon6.38e-107
segmental subdivision of hindbrain1.35e-0912
hindbrain1.35e-0912
presumptive hindbrain1.35e-0912
basal ganglion3.55e-099
nuclear complex of neuraxis3.55e-099
aggregate regional part of brain3.55e-099
collection of basal ganglia3.55e-099
cerebral subcortex3.55e-099
brainstem5.18e-096
limbic system5.71e-095
neural nucleus1.28e-089
nucleus of brain1.28e-089
epithelium2.61e-08306
cell layer4.68e-08309


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)
MA0003.14.57391
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.13.21605
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
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
MA0145.10.752137
MA0146.13.00132
MA0147.11.38767
MA0148.10.854239
MA0149.13.38595
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.15.63764
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.213.0679
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#1066435.360256373075030.0064925092527670.0279605448785507
MYC#460935.22228187160940.007020843755740150.0294714590436393
SUZ12#23512350.11578091106297.93834897779404e-060.000222569994333378



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.