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

Latest revision as of 11:11, 17 September 2013


Full id: C275_pons_medulla_cerebellum_locus_thalamus_diencephalon_spinal



Phase1 CAGE Peaks

Hg19::chr10:17045960..17045970,-p@chr10:17045960..17045970
-
Hg19::chr10:61043434..61043446,-p13@FAM13C
Hg19::chr10:61043452..61043467,-p16@FAM13C
Hg19::chr11:22359520..22359556,+p3@SLC17A6
Hg19::chr11:22359562..22359575,+p6@SLC17A6
Hg19::chr11:22359879..22359909,+p2@SLC17A6
Hg19::chr11:3224761..3224787,-p@chr11:3224761..3224787
-
Hg19::chr11:3224982..3224985,-p@chr11:3224982..3224985
-
Hg19::chr11:3224990..3225000,-p@chr11:3224990..3225000
-
Hg19::chr11:3253592..3253608,-p2@MRGPRE
Hg19::chr11:3253635..3253658,-p1@MRGPRE
Hg19::chr11:3253663..3253670,-p4@MRGPRE
Hg19::chr11:3253872..3253882,-p3@MRGPRE
Hg19::chr12:33592574..33592584,-p6@SYT10
Hg19::chr13:93587956..93587973,+p@chr13:93587956..93587973
+
Hg19::chr16:47920709..47920716,-p4@uc002eex.1
Hg19::chr16:49669972..49669983,-p@chr16:49669972..49669983
-
Hg19::chr16:49670005..49670020,-p@chr16:49670005..49670020
-
Hg19::chr16:67237164..67237171,+p@chr16:67237164..67237171
+
Hg19::chr17:68101117..68101162,+p2@KCNJ16
Hg19::chr1:205313500..205313511,-p11@KLHDC8A
Hg19::chr1:216692584..216692595,-p@chr1:216692584..216692595
-
Hg19::chr1:216692717..216692725,-p@chr1:216692717..216692725
-
Hg19::chr1:216692728..216692741,-p@chr1:216692728..216692741
-
Hg19::chr1:218222373..218222381,-p@chr1:218222373..218222381
-
Hg19::chr1:218222386..218222394,-p@chr1:218222386..218222394
-
Hg19::chr21:31312092..31312103,-p7@GRIK1
Hg19::chr2:17381145..17381164,-p@chr2:17381145..17381164
-
Hg19::chr2:72381655..72381673,-p@chr2:72381655..72381673
-
Hg19::chr4:117675601..117675614,+p@chr4:117675601..117675614
+
Hg19::chr4:117675642..117675654,+p@chr4:117675642..117675654
+
Hg19::chr4:186661365..186661384,-p46@SORBS2
Hg19::chr4:82965824..82965835,-p6@ENST00000508294
p6@ENST00000510780
p6@ENST00000512343
p6@ENST00000512716
p6@ENST00000514050
Hg19::chr5:126959224..126959239,+p@chr5:126959224..126959239
+
Hg19::chr5:126959900..126959932,+p@chr5:126959900..126959932
+
Hg19::chr5:126959946..126959960,+p@chr5:126959946..126959960
+
Hg19::chr6:140415977..140415987,-p@chr6:140415977..140415987
-
Hg19::chr6:140415989..140415997,-p@chr6:140415989..140415997
-
Hg19::chr6:140416018..140416025,-p@chr6:140416018..140416025
-
Hg19::chr6:71665623..71665630,-p13@B3GAT2
Hg19::chr7:31569075..31569083,+p3@CCDC129
Hg19::chr7:31569365..31569379,+p1@CCDC129
Hg19::chr9:135457530..135457541,+p2@BARHL1
Hg19::chr9:135457972..135457978,+p8@BARHL1
Hg19::chr9:135458021..135458030,+p6@BARHL1
Hg19::chr9:135458288..135458301,+p3@BARHL1
Hg19::chr9:135458306..135458314,+p9@BARHL1


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:0051966regulation of synaptic transmission, glutamatergic0.0414160162571539
GO:0035249synaptic transmission, glutamatergic0.0414160162571539
GO:0016021integral to membrane0.0414160162571539
GO:0031224intrinsic to membrane0.0414160162571539
GO:0051179localization0.0414160162571539
GO:0015018galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity0.0414160162571539
GO:0015277kainate selective glutamate receptor activity0.0414160162571539
GO:0044425membrane part0.04833425076599



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
brainstem7.67e-1036
pons1.66e-743
segmental subdivision of hindbrain6.69e-7412
hindbrain6.69e-7412
presumptive hindbrain6.69e-7412
segmental subdivision of nervous system2.95e-6813
posterior neural tube3.20e-5915
chordal neural plate3.20e-5915
locus ceruleus5.15e-502
brainstem nucleus5.15e-502
hindbrain nucleus5.15e-502
regional part of metencephalon3.55e-449
metencephalon3.55e-449
future metencephalon3.55e-449
medulla oblongata3.94e-343
myelencephalon3.94e-343
future myelencephalon3.94e-343
regional part of nervous system3.04e-2953
regional part of brain3.04e-2953
neural tube1.03e-2756
neural rod1.03e-2756
future spinal cord1.03e-2756
neural keel1.03e-2756
paracentral gyrus5.93e-261
nucleus accumbens1.26e-251
ventral striatum1.26e-251
neural nucleus3.17e-259
nucleus of brain3.17e-259
brain1.35e-2268
future brain1.35e-2268
central nervous system4.48e-1981
neural plate4.48e-1982
presumptive neural plate4.48e-1982
neurectoderm3.34e-1886
nervous system3.23e-1789
ecto-epithelium4.31e-15104
adult organism6.68e-14114
structure with developmental contribution from neural crest6.49e-12132
organ segment3.13e-0998
ectoderm-derived structure4.33e-09171
ectoderm4.33e-09171
presumptive ectoderm4.33e-09171
tube3.49e-08192
corpus striatum2.04e-074
striatum2.04e-074
ventral part of telencephalon2.04e-074
future corpus striatum2.04e-074
organ part3.42e-07218
brain grey matter5.30e-0734
gray matter5.30e-0734
organ system subdivision6.23e-07223


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)
MA0003.10.12437
MA0004.10.143101
MA0006.10.111305
MA0007.10.301699
MA0009.10.275766
MA0014.10.00119152
MA0017.10.155235
MA0019.10.298267
MA0024.10.204363
MA0025.10.376628
MA0027.11.7662
MA0028.10.00904529
MA0029.10.216921
MA0030.10.209437
MA0031.10.169247
MA0038.10.898443
MA0040.10.22078
MA0041.10.159732
MA0042.10.0324618
MA0043.10.275993
MA0046.10.267991
MA0048.10.780223
MA0050.11.74588
MA0051.10.885612
MA0052.10.635267
MA0055.12.58216
MA0056.10
MA0057.10.0681362
MA0058.10.187307
MA0059.10.0153731
MA0060.10.00705091
MA0061.10.177509
MA0063.10
MA0066.10.0700626
MA0067.10.529198
MA0068.10.0506786
MA0069.12.07365
MA0070.10.257372
MA0071.10.0556134
MA0072.10.707234
MA0073.10.0721726
MA0074.10.51581
MA0076.10.209003
MA0077.10.248866
MA0078.10.360912
MA0081.11.26097
MA0083.10.281174
MA0084.10.695499
MA0087.10.252522
MA0088.10.030038
MA0089.10
MA0090.10.0920042
MA0091.10.956027
MA0092.10.816938
MA0093.10.0401794
MA0095.10
MA0098.10
MA0100.10.55433
MA0101.10.429843
MA0103.10.217682
MA0105.10.463525
MA0106.10.0870163
MA0107.10.125877
MA0108.20.167426
MA0109.10
MA0111.10.249833
MA0113.10.0943593
MA0114.10.227879
MA0115.11.17291
MA0116.10.0562776
MA0117.10.818959
MA0119.10.0620298
MA0122.10.322548
MA0124.11.09872
MA0125.10.362554
MA0130.10
MA0131.10.384838
MA0132.10
MA0133.10
MA0135.10.297838
MA0136.10.0726858
MA0139.10.0354674
MA0140.10.201276
MA0141.10.360029
MA0142.10.898493
MA0143.10.09444
MA0144.13.26179
MA0145.10.1252
MA0146.10.000530401
MA0147.10.0587539
MA0148.10.37675
MA0149.10.0514353
MA0062.20.0886255
MA0035.20.0544556
MA0039.20.000207583
MA0138.23.81826
MA0002.20.513919
MA0137.20.732697
MA0104.20.137501
MA0047.20.0817751
MA0112.20.0172474
MA0065.20.402665
MA0150.10.0879472
MA0151.10
MA0152.11.20952
MA0153.10.349438
MA0154.10.222107
MA0155.10.0912357
MA0156.10.138218
MA0157.10.135578
MA0158.10
MA0159.10.0592107
MA0160.10.180181
MA0161.10
MA0162.12.4021e-06
MA0163.10.0033373
MA0164.10.329079
MA0080.20.114527
MA0018.20.0876241
MA0099.20.0571009
MA0079.24.01281e-09
MA0102.20.729507
MA0258.10.474019
MA0259.10.14777
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
SUZ12#2351255.331466054368390.002412655065050490.0135989682302773



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

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