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Coexpression cluster:C1392

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Full id: C1392_lung_thyroid_chorionic_epididymis_throat_seminal_tonsil



Phase1 CAGE Peaks

  Short description
Hg19::chr14:36983036..36983064,- p2@SFTA3
Hg19::chr14:36986924..36986931,- p@chr14:36986924..36986931
-
Hg19::chr1:8311992..8312003,+ p@chr1:8311992..8312003
+
Hg19::chr21:46982878..46982901,- p@chr21:46982878..46982901
-
Hg19::chr3:193272639..193272672,- p3@ATP13A4
Hg19::chr3:193272673..193272701,- p1@ATP13A4


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:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0458697078266135
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0458697078266135
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0458697078266135
GO:0043492ATPase activity, coupled to movement of substances0.0458697078266135
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0458697078266135
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0458697078266135
GO:0015399primary active transmembrane transporter activity0.0458697078266135



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 tube1.41e-7756
neural rod1.41e-7756
future spinal cord1.41e-7756
neural keel1.41e-7756
regional part of nervous system1.12e-6953
regional part of brain1.12e-6953
adult organism7.62e-62114
central nervous system7.81e-6281
brain4.35e-5868
future brain4.35e-5868
regional part of forebrain6.31e-5541
forebrain6.31e-5541
anterior neural tube6.31e-5541
future forebrain6.31e-5541
nervous system1.10e-5489
neural plate9.34e-5382
presumptive neural plate9.34e-5382
neurectoderm7.69e-5086
telencephalon1.66e-4534
brain grey matter6.46e-4534
gray matter6.46e-4534
cerebral hemisphere2.53e-4032
regional part of telencephalon3.43e-4032
ecto-epithelium1.79e-39104
pre-chordal neural plate2.85e-3761
structure with developmental contribution from neural crest1.04e-34132
regional part of cerebral cortex3.27e-3122
neocortex2.79e-3020
cerebral cortex3.97e-2725
pallium3.97e-2725
ectoderm-derived structure4.71e-25171
ectoderm4.71e-25171
presumptive ectoderm4.71e-25171
organ system subdivision6.62e-24223
tube4.84e-23192
posterior neural tube9.31e-2315
chordal neural plate9.31e-2315
basal ganglion1.72e-209
nuclear complex of neuraxis1.72e-209
aggregate regional part of brain1.72e-209
collection of basal ganglia1.72e-209
cerebral subcortex1.72e-209
neural nucleus2.30e-209
nucleus of brain2.30e-209
brainstem1.02e-186
anatomical conduit3.26e-16240
telencephalic nucleus2.43e-157
segmental subdivision of hindbrain2.58e-1512
hindbrain2.58e-1512
presumptive hindbrain2.58e-1512
anatomical cluster3.71e-14373
segmental subdivision of nervous system4.98e-1413
gyrus2.09e-136
epithelium7.84e-13306
cell layer1.35e-12309
temporal lobe6.83e-116
medulla oblongata1.01e-103
myelencephalon1.01e-103
future myelencephalon1.01e-103
diencephalon1.35e-107
future diencephalon1.35e-107
parietal lobe2.89e-105
multi-tissue structure3.43e-10342
limbic system3.51e-105
organ part4.58e-10218
spinal cord5.92e-103
dorsal region element5.92e-103
dorsum5.92e-103
pons9.98e-103
regional part of metencephalon4.85e-089
metencephalon4.85e-089
future metencephalon4.85e-089
throat6.46e-082
organ9.76e-08503
corpus striatum1.42e-074
striatum1.42e-074
ventral part of telencephalon1.42e-074
future corpus striatum1.42e-074
regional part of diencephalon1.91e-074
middle temporal gyrus2.68e-072
dorsal plus ventral thalamus3.34e-072
thalamic complex3.34e-072
globus pallidus4.70e-072
pallidum4.70e-072
amygdala6.59e-072
open tracheal system trachea7.67e-072
locus ceruleus9.19e-072
brainstem nucleus9.19e-072
hindbrain nucleus9.19e-072


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.464411
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.10.147053
MA0058.11.16137
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.11.51422
MA0072.11.00572
MA0073.10.00563817
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.12.99081
MA0142.10.838805
MA0143.10.725558
MA0144.10.811435
MA0145.11.16614
MA0146.10.093337
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0313803
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.101413
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.875329
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.10.508943
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.10486
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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
SUZ12#23512216.70526030368760.005660234682079570.0255598949308936



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.