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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:20, 17 September 2013


Full id: C327_Melanocyte_corpus_thalamus_substantia_melanoma_globus_optic



Phase1 CAGE Peaks

Hg19::chr10:128358928..128358933,-p15@C10orf90
Hg19::chr10:128358986..128359007,-p2@C10orf90
Hg19::chr10:128359008..128359022,-p4@C10orf90
Hg19::chr10:128359027..128359032,-p13@C10orf90
Hg19::chr10:128359039..128359050,-p5@C10orf90
Hg19::chr10:14066761..14066793,-p@chr10:14066761..14066793
-
Hg19::chr11:73363887..73363920,+p13@PLEKHB1
Hg19::chr12:40704263..40704279,+p@chr12:40704263..40704279
+
Hg19::chr12:53438222..53438234,+p@chr12:53438222..53438234
+
Hg19::chr12:53438236..53438270,+p@chr12:53438236..53438270
+
Hg19::chr15:42696929..42696951,+p5@CAPN3
Hg19::chr15:42696954..42696986,+p1@CAPN3
Hg19::chr15:42696992..42697017,+p3@CAPN3
Hg19::chr15:42697018..42697035,+p6@CAPN3
Hg19::chr15:42697040..42697052,+p4@CAPN3
Hg19::chr16:19777384..19777399,-p@chr16:19777384..19777399
-
Hg19::chr16:48307127..48307152,+p@chr16:48307127..48307152
+
Hg19::chr17:76870126..76870201,-p10@TIMP2
Hg19::chr17:76870222..76870242,-p15@TIMP2
Hg19::chr17:79358943..79358954,-p@chr17:79358943..79358954
-
Hg19::chr17:79358956..79358981,-p@chr17:79358956..79358981
-
Hg19::chr17:79359021..79359029,-p@chr17:79359021..79359029
-
Hg19::chr17:79359048..79359058,-p@chr17:79359048..79359058
-
Hg19::chr17:79359154..79359164,-p@chr17:79359154..79359164
-
Hg19::chr17:79359173..79359188,-p@chr17:79359173..79359188
-
Hg19::chr17:79359195..79359212,-p@chr17:79359195..79359212
-
Hg19::chr19:3544836..3544874,-p@chr19:3544836..3544874
-
Hg19::chr22:38368890..38368901,-p@chr22:38368890..38368901
-
Hg19::chr22:38369134..38369144,-p@chr22:38369134..38369144
-
Hg19::chr22:38369664..38369689,+p2@CU678225
Hg19::chr22:38369881..38369891,-p@chr22:38369881..38369891
-
Hg19::chr22:38370098..38370111,-p@chr22:38370098..38370111
-
Hg19::chr22:38370123..38370134,-p@chr22:38370123..38370134
-
Hg19::chr22:38374029..38374049,+p@chr22:38374029..38374049
+
Hg19::chr22:38380543..38380569,-p1@SOX10


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

No results for this coexpression

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:0032501multicellular organismal process0.0227175415179066
GO:0030814regulation of cAMP metabolic process0.029251639102125
GO:0048856anatomical structure development0.029251639102125
GO:0030799regulation of cyclic nucleotide metabolic process0.029251639102125
GO:0006140regulation of nucleotide metabolic process0.0333906082972598
GO:0043408regulation of MAPKKK cascade0.0333906082972598
GO:0008191metalloendopeptidase inhibitor activity0.0333906082972598
GO:0046058cAMP metabolic process0.0333906082972598
GO:0045664regulation of neuron differentiation0.0333906082972598
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0333906082972598
GO:0004198calcium-dependent cysteine-type endopeptidase activity0.0333906082972598
GO:0007602phototransduction0.0333906082972598
GO:0032502developmental process0.0333906082972598
GO:0050962detection of light stimulus during sensory perception0.0333906082972598
GO:0050908detection of light stimulus during visual perception0.0333906082972598
GO:0009584detection of visible light0.0333906082972598
GO:0009583detection of light stimulus0.0333906082972598
GO:0007600sensory perception0.034757314032091
GO:0005178integrin binding0.034757314032091
GO:0048469cell maturation0.034757314032091
GO:0009582detection of abiotic stimulus0.034757314032091
GO:0050906detection of stimulus during sensory perception0.034757314032091
GO:0009187cyclic nucleotide metabolic process0.034757314032091
GO:0009581detection of external stimulus0.034757314032091
GO:0021700developmental maturation0.0353643566264006
GO:0048468cell development0.0416643861860936
GO:0050877neurological system process0.0418400056854547
GO:0005604basement membrane0.0440454197736863
GO:0051606detection of stimulus0.0449838416222539
GO:0009416response to light stimulus0.0449838416222539



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>disease_data<br>

Cell Type
Ontology termp-valuen
melanocyte2.45e-2210
melanoblast2.45e-2210
pigment cell1.57e-1514
light melanocyte4.78e-123
neurecto-epithelial cell1.98e-1020
columnar/cuboidal epithelial cell2.35e-0727
Uber Anatomy
Ontology termp-valuen
neural tube2.00e-8656
neural rod2.00e-8656
future spinal cord2.00e-8656
neural keel2.00e-8656
regional part of nervous system1.51e-7753
regional part of brain1.51e-7753
central nervous system4.25e-6981
brain1.02e-6468
future brain1.02e-6468
nervous system2.08e-6489
neural plate1.34e-6282
presumptive neural plate1.34e-6282
regional part of forebrain3.68e-6141
forebrain3.68e-6141
anterior neural tube3.68e-6141
future forebrain3.68e-6141
neurectoderm3.01e-5986
telencephalon5.33e-5934
brain grey matter5.60e-5934
gray matter5.60e-5934
regional part of telencephalon6.10e-5332
ecto-epithelium6.21e-53104
cerebral hemisphere1.39e-5232
adult organism4.46e-50114
pre-chordal neural plate4.99e-4561
structure with developmental contribution from neural crest3.11e-39132
regional part of cerebral cortex7.09e-3822
ectoderm-derived structure2.72e-34171
ectoderm2.72e-34171
presumptive ectoderm2.72e-34171
cerebral cortex5.25e-3325
pallium5.25e-3325
neocortex2.84e-3220
neural nucleus4.78e-309
nucleus of brain4.78e-309
basal ganglion9.47e-309
nuclear complex of neuraxis9.47e-309
aggregate regional part of brain9.47e-309
collection of basal ganglia9.47e-309
cerebral subcortex9.47e-309
posterior neural tube3.64e-2515
chordal neural plate3.64e-2515
telencephalic nucleus1.20e-237
organ system subdivision5.40e-21223
brainstem1.70e-206
segmental subdivision of nervous system2.01e-1913
tube1.46e-18192
limbic system6.40e-175
segmental subdivision of hindbrain8.12e-1712
hindbrain8.12e-1712
presumptive hindbrain8.12e-1712
gyrus7.55e-146
corpus striatum1.71e-134
striatum1.71e-134
ventral part of telencephalon1.71e-134
future corpus striatum1.71e-134
anatomical conduit5.84e-13240
temporal lobe5.83e-126
epithelium3.17e-11306
pons3.21e-113
parietal lobe5.09e-115
cell layer5.09e-11309
medulla oblongata5.20e-113
myelencephalon5.20e-113
future myelencephalon5.20e-113
spinal cord5.39e-113
dorsal region element5.39e-113
dorsum5.39e-113
caudate-putamen2.00e-103
dorsal striatum2.00e-103
organ part3.10e-10218
anatomical cluster4.12e-09373
regional part of metencephalon4.15e-099
metencephalon4.15e-099
future metencephalon4.15e-099
globus pallidus2.12e-082
pallidum2.12e-082
dorsal plus ventral thalamus2.20e-082
thalamic complex2.20e-082
locus ceruleus4.16e-082
brainstem nucleus4.16e-082
hindbrain nucleus4.16e-082
multi cell component structure4.79e-082
neuron projection bundle4.79e-082
middle temporal gyrus8.05e-082
amygdala8.33e-082
Ammon's horn9.88e-082
lobe parts of cerebral cortex9.88e-082
hippocampal formation9.88e-082
limbic lobe9.88e-082
caudate nucleus1.30e-072
future caudate nucleus1.30e-072
meninx4.27e-072
membrane organ4.27e-072

Disease
Ontology termp-valuen


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)
MA0003.10.383588
MA0004.10.250106
MA0006.10.0212634
MA0007.10.494381
MA0009.10.366503
MA0014.10.00647602
MA0017.10.2976
MA0019.10.145319
MA0024.10.285711
MA0025.10.47683
MA0027.11.89328
MA0028.10.0248137
MA0029.10.30014
MA0030.10.291553
MA0031.10.24472
MA0038.10.120244
MA0040.10.304553
MA0041.10.0793669
MA0042.10.065999
MA0043.10.366755
MA0046.10.357837
MA0048.10.0347795
MA0050.10.23549
MA0051.10.756429
MA0052.10.307481
MA0055.10.070867
MA0056.10
MA0057.11.17484
MA0058.10.618695
MA0059.10.962645
MA0060.10.519009
MA0061.10.132313
MA0063.10
MA0066.10.382686
MA0067.10.638784
MA0068.10.278942
MA0069.11.66814
MA0070.10.345954
MA0071.10.675927
MA0072.10.342425
MA0073.10.47771
MA0074.11.80033
MA0076.10.042375
MA0077.10.336397
MA0078.10.175262
MA0081.10.0371987
MA0083.10.372513
MA0084.10.811454
MA0087.10.340509
MA0088.10.0432759
MA0089.10
MA0090.10.178129
MA0091.10.253205
MA0092.12.24758
MA0093.10.0954868
MA0095.10
MA0098.10
MA0100.10.40142
MA0101.10.741131
MA0103.10.0863031
MA0105.10.107539
MA0106.10.865966
MA0107.11.04329
MA0108.20.242565
MA0109.10
MA0111.10.192269
MA0113.10.152632
MA0114.11.01377
MA0115.10.570409
MA0116.10.491211
MA0117.10.396851
MA0119.10.132155
MA0122.11.07313
MA0124.10.533912
MA0125.10.461632
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.10.390959
MA0136.10.124027
MA0139.10.113636
MA0140.10.0991227
MA0141.12.35739
MA0142.10.222682
MA0143.10.152737
MA0144.10.0075623
MA0145.11.42766
MA0146.10.0277626
MA0147.10.294751
MA0148.10.280213
MA0149.10.313847
MA0062.20.0161739
MA0035.20.325494
MA0039.20.037514
MA0138.20.522056
MA0002.20.472005
MA0137.20.268939
MA0104.20.757404
MA0047.20.136179
MA0112.20.67359
MA0065.20.291442
MA0150.10.0451191
MA0151.10
MA0152.11.13366
MA0153.11.1366
MA0154.10.420913
MA0155.10.461258
MA0156.10.112887
MA0157.10.590166
MA0158.10
MA0159.11.45359
MA0160.10.621983
MA0161.10
MA0162.12.83695e-05
MA0163.10.121946
MA0164.10.482782
MA0080.20.0219279
MA0018.20.143876
MA0099.20.102528
MA0079.20.31495
MA0102.20.846442
MA0258.11.95474
MA0259.10.531383
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

No analysis results for this cluster

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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