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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:51, 17 September 2013


Full id: C1753_neuroblastoma_pineal_rectum_retina_merkel_carcinosarcoma_eye



Phase1 CAGE Peaks

Hg19::chr15:78913289..78913302,-p4@CHRNA3
Hg19::chr15:78913306..78913349,-p1@CHRNA3
Hg19::chr15:78913353..78913365,-p3@CHRNA3
Hg19::chr15:78933542..78933562,-p2@CHRNB4
Hg19::chr15:78933567..78933604,-p1@CHRNB4


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

p.valueFDRnGenesnPathwayName
9.04613128104753e-050.01908733700301032272Neuroactive ligand-receptor interaction (KEGG):04080
4.73856659734924e-050.01499756328061032197Synaptic Transmission (Reactome):REACT_13685
1.91447319275479e-070.000121186153101378213{CHRNA1,13} (Static Module):NA



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:0005892nicotinic acetylcholine-gated receptor-channel complex9.64592211467951e-06
GO:0015464acetylcholine receptor activity9.64592211467951e-06
GO:0042166acetylcholine binding9.64592211467951e-06
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity9.64592211467951e-06
GO:0043176amine binding2.88538887604326e-05
GO:0005231excitatory extracellular ligand-gated ion channel activity6.4967001120213e-05
GO:0043235receptor complex0.000130609380186344
GO:0005230extracellular ligand-gated ion channel activity0.000145598413308646
GO:0030594neurotransmitter receptor activity0.000145598413308646
GO:0042165neurotransmitter binding0.000145598413308646
GO:0045211postsynaptic membrane0.000145598413308646
GO:0044456synapse part0.000145598413308646
GO:0015276ligand-gated ion channel activity0.000145598413308646
GO:0022834ligand-gated channel activity0.000145598413308646
GO:0035095behavioral response to nicotine0.00030474923985843
GO:0060073micturition0.00030474923985843
GO:0060084synaptic transmission involved in micturition0.00030474923985843
GO:0005261cation channel activity0.000736886645026226
GO:0030054cell junction0.000736886645026226
GO:0046873metal ion transmembrane transporter activity0.000924178466639651
GO:0022836gated channel activity0.000924178466639651
GO:0035094response to nicotine0.00117737092459055
GO:0005216ion channel activity0.00142681635278938
GO:0022838substrate specific channel activity0.00142681635278938
GO:0022803passive transmembrane transporter activity0.00142681635278938
GO:0015267channel activity0.00142681635278938
GO:0043279response to alkaloid0.00153487505515621
GO:0003014renal system process0.00160762563893901
GO:0007274neuromuscular synaptic transmission0.00160762563893901
GO:0014070response to organic cyclic substance0.00186392717093987
GO:0008324cation transmembrane transporter activity0.00186392717093987
GO:0046928regulation of neurotransmitter secretion0.00188359938245719
GO:0007271synaptic transmission, cholinergic0.00188359938245719
GO:0006940regulation of smooth muscle contraction0.00304664016645142
GO:0015075ion transmembrane transporter activity0.00363495337446202
GO:0005887integral to plasma membrane0.00363495337446202
GO:0031226intrinsic to plasma membrane0.00363495337446202
GO:0030534adult behavior0.00363495337446202
GO:0006811ion transport0.00363495337446202
GO:0022891substrate-specific transmembrane transporter activity0.00440723325204938
GO:0006939smooth muscle contraction0.00470705748726614
GO:0006937regulation of muscle contraction0.00470705748726614
GO:0022857transmembrane transporter activity0.00470705748726614
GO:0007269neurotransmitter secretion0.00470705748726614
GO:0022892substrate-specific transporter activity0.00528172907724811
GO:0045055regulated secretory pathway0.0059645416008552
GO:0051046regulation of secretion0.00649792663916262
GO:0004888transmembrane receptor activity0.00649813937510364
GO:0010033response to organic substance0.00654933290669141
GO:0003001generation of a signal involved in cell-cell signaling0.00724566593174309
GO:0044459plasma membrane part0.00776229847011137
GO:0001505regulation of neurotransmitter levels0.00776229847011137
GO:0043234protein complex0.0119540749559224
GO:0004872receptor activity0.0134608779566729
GO:0003012muscle system process0.0152278255222535
GO:0006936muscle contraction0.0152278255222535
GO:0007626locomotory behavior0.01640752823724
GO:0060089molecular transducer activity0.0177936923627931
GO:0004871signal transducer activity0.0177936923627931
GO:0005886plasma membrane0.0185014123823964
GO:0032991macromolecular complex0.0188428378990201
GO:0045045secretory pathway0.0197011740994843
GO:0006810transport0.0197011740994843
GO:0051234establishment of localization0.0203666329991751
GO:0051239regulation of multicellular organismal process0.021988223475816
GO:0007268synaptic transmission0.0222025422545425
GO:0007610behavior0.0222025422545425
GO:0051179localization0.0222025422545425
GO:0032940secretion by cell0.0222025422545425
GO:0019226transmission of nerve impulse0.0243052074014842
GO:0046903secretion0.0278618091882116
GO:0007165signal transduction0.027996284948599
GO:0007154cell communication0.0322850773249661
GO:0042221response to chemical stimulus0.040878993381908
GO:0007267cell-cell signaling0.0437931675882937
GO:0016021integral to membrane0.0448731129004987
GO:0031224intrinsic to membrane0.0448731129004987



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><br>

Cell Type
Ontology termp-valuen
neuron3.83e-106
neuroblast3.83e-106
electrically signaling cell3.83e-106
embryonic stem cell3.31e-095
neurectodermal cell1.67e-0759
neuronal stem cell2.33e-078
Uber Anatomy
Ontology termp-valuen
neural plate8.73e-3182
presumptive neural plate8.73e-3182
neurectoderm1.10e-2886
nervous system4.02e-2889
central nervous system2.54e-2781
neural tube1.14e-2556
neural rod1.14e-2556
future spinal cord1.14e-2556
neural keel1.14e-2556
adult organism1.60e-24114
regional part of nervous system3.83e-2453
regional part of brain3.83e-2453
ecto-epithelium4.37e-24104
ectoderm-derived structure3.14e-21171
ectoderm3.14e-21171
presumptive ectoderm3.14e-21171
organ system subdivision1.12e-20223
pre-chordal neural plate2.69e-2061
brain9.72e-1968
future brain9.72e-1968
structure with developmental contribution from neural crest2.54e-17132
regional part of forebrain3.98e-1541
forebrain3.98e-1541
anterior neural tube3.98e-1541
future forebrain3.98e-1541
anatomical cluster5.96e-15373
posterior neural tube1.29e-1215
chordal neural plate1.29e-1215
diencephalon1.04e-117
future diencephalon1.04e-117
segmental subdivision of hindbrain2.75e-1112
hindbrain2.75e-1112
presumptive hindbrain2.75e-1112
gastrointestinal system5.69e-1125
organ part1.26e-10218
segmental subdivision of nervous system3.06e-1013
intestine1.38e-0917
organ segment3.84e-0998
multi-tissue structure4.73e-09342
embryo5.36e-09592
brainstem1.24e-086
pigment epithelium of eye1.67e-0811
brain grey matter2.30e-0834
gray matter2.30e-0834
telencephalon2.84e-0834
gland of diencephalon6.08e-084
neuroendocrine gland6.08e-084
cerebral hemisphere7.99e-0832
regional part of metencephalon8.46e-089
metencephalon8.46e-089
future metencephalon8.46e-089
basal ganglion9.81e-089
nuclear complex of neuraxis9.81e-089
aggregate regional part of brain9.81e-089
collection of basal ganglia9.81e-089
cerebral subcortex9.81e-089
regional part of diencephalon1.43e-074
multi-cellular organism1.51e-07656
eye1.60e-0721
visual system1.60e-0721
neural nucleus1.93e-079
nucleus of brain1.93e-079
retina2.96e-076
photoreceptor array2.96e-076
posterior segment of eyeball2.96e-076
organ5.92e-07503
regional part of telencephalon8.12e-0732


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)
MA0003.14.96701
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.13.07977
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
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
MA0048.12.41212
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.10.554727
MA0058.10.523638
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
MA0073.10.0140295
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.12656
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.11.76306
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.11.99092
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.11.65391
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.12.7505
MA0062.20.284987
MA0035.20.691506
MA0039.21.50246
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.21.35805
MA0065.22.73531
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.514087
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.12.27598
MA0163.11.05321
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.21.81596
MA0102.21.66336
MA0258.10.345771
MA0259.12.71109
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
NANOG#79923211.69791139240510.01091164951956080.0402217119321431



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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