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Coexpression cluster:C1635

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Full id: C1635_brain_smallcell_occipital_somatostatinoma_temporal_duodenum_small



Phase1 CAGE Peaks

  Short description
Hg19::chr11:45307817..45307898,- p1@SYT13
Hg19::chr7:158380402..158380413,- p7@PTPRN2
Hg19::chr7:158380420..158380433,- p4@PTPRN2
Hg19::chr7:158380440..158380454,- p6@PTPRN2
Hg19::chr7:158380468..158380523,- p2@PTPRN2


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


GO IDGO nameFDR corrected p-value
GO:0019198transmembrane receptor protein phosphatase activity0.0203930061304151
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0203930061304151
GO:0005887integral to plasma membrane0.0203930061304151
GO:0031226intrinsic to plasma membrane0.0203930061304151
GO:0030133transport vesicle0.0385377429525907
GO:0044459plasma membrane part0.0391926789972099



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
neural tube3.48e-5856
neural rod3.48e-5856
future spinal cord3.48e-5856
neural keel3.48e-5856
regional part of nervous system2.40e-5453
regional part of brain2.40e-5453
central nervous system5.49e-5481
nervous system1.39e-5289
brain4.47e-4968
future brain4.47e-4968
regional part of forebrain8.96e-4941
forebrain8.96e-4941
anterior neural tube8.96e-4941
future forebrain8.96e-4941
telencephalon1.00e-4434
adult organism1.06e-44114
brain grey matter1.92e-4434
gray matter1.92e-4434
cerebral hemisphere1.40e-4232
regional part of telencephalon7.50e-4232
organ system subdivision1.40e-41223
neural plate4.74e-3882
presumptive neural plate4.74e-3882
regional part of cerebral cortex1.16e-3722
neurectoderm1.58e-3586
neocortex1.33e-3420
cerebral cortex2.40e-3225
pallium2.40e-3225
pre-chordal neural plate2.98e-3261
ecto-epithelium1.08e-30104
ectoderm-derived structure3.17e-26171
ectoderm3.17e-26171
presumptive ectoderm3.17e-26171
structure with developmental contribution from neural crest1.52e-23132
anatomical cluster2.99e-18373
tube2.20e-15192
basal ganglion5.03e-149
nuclear complex of neuraxis5.03e-149
aggregate regional part of brain5.03e-149
collection of basal ganglia5.03e-149
cerebral subcortex5.03e-149
neural nucleus2.25e-139
nucleus of brain2.25e-139
temporal lobe1.92e-126
anatomical conduit2.25e-12240
multi-tissue structure1.12e-11342
gyrus5.42e-116
telencephalic nucleus6.83e-117
posterior neural tube7.69e-1115
chordal neural plate7.69e-1115
organ part6.77e-10218
organ8.64e-10503
gastrointestinal system1.13e-0925
intestine1.48e-0917
occipital lobe1.58e-095
limbic system2.01e-095
parietal lobe2.07e-095
germ layer4.64e-09560
germ layer / neural crest4.64e-09560
embryonic tissue4.64e-09560
presumptive structure4.64e-09560
germ layer / neural crest derived structure4.64e-09560
epiblast (generic)4.64e-09560
epithelium7.01e-09306
embryo8.06e-09592
embryonic structure8.44e-09564
cell layer1.26e-08309
developing anatomical structure9.63e-08581
corpus striatum1.02e-074
striatum1.02e-074
ventral part of telencephalon1.02e-074
future corpus striatum1.02e-074
small intestine1.05e-074
segmental subdivision of hindbrain1.37e-0712
hindbrain1.37e-0712
presumptive hindbrain1.37e-0712
multi-cellular organism6.95e-07656
segmental subdivision of nervous system7.05e-0713


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)
MA0003.116.6523
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
MA0009.11.11255
MA0014.110.8853
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
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
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.19.26754
MA0056.10
MA0057.10.189508
MA0058.11.29981
MA0059.10.522232
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.13.88786
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
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
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.110.459
MA0147.10.386018
MA0148.10.653474
MA0149.11.63245
MA0062.20.284987
MA0035.20.691506
MA0039.216.2749
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.20.839774
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.16.71259
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.111.9702
MA0163.13.78273
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.220.6828
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
CHD2#110648.275218267293490.0004028373567101730.00387616829716729
E2F1#186943.925911371903460.007214984547106360.0298662612411907
E2F6#187644.013724585357910.006632118233933880.0282876662678192
EGR1#195843.990543275848110.0067800983001440.0287556014769031
ETS1#211347.783008737761870.0005121035947688870.00443920877606804
HMGN3#932446.542838178680470.00100801277768350.00721809026318048
IRF1#365946.109731002851120.001315525264767990.00880662413480575
REST#597847.720022972902420.0005286363773650570.00457114212747386
SIN3A#2594244.327107781452110.004977052855762880.0232364069379982
TAF1#687253.343046285745290.002394600090870310.0135147062356338
YY1#752843.928936599883080.007193866269917620.0298308663290688
ZBTB7A#5134145.881527446300720.001524947561042230.0097129961778185



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.