Personal tools

Coexpression cluster:C162: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:46, 17 September 2013


Full id: C162_spinal_locus_medulla_substantia_thalamus_globus_diencephalon



Phase1 CAGE Peaks

Hg19::chr10:116524662..116524709,+p1@ENST00000436932
p1@uc001lca.1
Hg19::chr10:60936921..60936943,+p4@PHYHIPL
Hg19::chr10:76910697..76910731,+p7@SAMD8
Hg19::chr11:117166261..117166272,-p12@BACE1
Hg19::chr11:36273802..36273808,+p@chr11:36273802..36273808
+
Hg19::chr11:50143419..50143424,+p@chr11:50143419..50143424
+
Hg19::chr11:73372767..73372810,+p@chr11:73372767..73372810
+
Hg19::chr11:92042465..92042492,+p@chr11:92042465..92042492
+
Hg19::chr12:106976774..106976788,+p1@RFX4
Hg19::chr12:41136112..41136141,+p6@CNTN1
Hg19::chr12:41136144..41136158,+p14@CNTN1
Hg19::chr12:55049321..55049324,+p@chr12:55049321..55049324
+
Hg19::chr13:78303937..78303949,+p@chr13:78303937..78303949
+
Hg19::chr14:23846027..23846042,+p7@CMTM5
Hg19::chr14:65453564..65453653,+p1@FNTB
Hg19::chr14:65482313..65482330,+p4@CHURC1-FNTB
p7@FNTB
Hg19::chr15:99666457..99666462,+p@chr15:99666457..99666462
+
Hg19::chr16:19800150..19800179,+p@chr16:19800150..19800179
+
Hg19::chr16:290098..290109,+p13@ITFG3
Hg19::chr17:32906595..32906615,+p@chr17:32906595..32906615
+
Hg19::chr17:42983087..42983097,-p@chr17:42983087..42983097
-
Hg19::chr17:42983129..42983138,-p@chr17:42983129..42983138
-
Hg19::chr17:42983160..42983176,-p@chr17:42983160..42983176
-
Hg19::chr17:42983263..42983264,-p@chr17:42983263..42983264
-
Hg19::chr17:42983316..42983326,-p@chr17:42983316..42983326
-
Hg19::chr17:42983338..42983350,-p@chr17:42983338..42983350
-
Hg19::chr17:42983463..42983466,-p45@GFAP
Hg19::chr17:42983500..42983503,-p44@GFAP
Hg19::chr17:42983532..42983541,-p35@GFAP
Hg19::chr17:42983555..42983568,-p13@GFAP
Hg19::chr17:42983708..42983726,-p14@GFAP
Hg19::chr17:42983912..42983931,-p16@GFAP
Hg19::chr17:42983985..42983996,-p18@GFAP
Hg19::chr17:42984179..42984190,-p34@GFAP
Hg19::chr17:42984370..42984375,-p42@GFAP
Hg19::chr17:42984539..42984540,-p49@GFAP
Hg19::chr17:42984746..42984762,-p17@GFAP
Hg19::chr17:42989121..42989166,-p7@GFAP
Hg19::chr17:42993851..42993858,-p@chr17:42993851..42993858
-
Hg19::chr18:24436354..24436377,-p@chr18:24436354..24436377
-
Hg19::chr18:2847842..2847876,-p@chr18:2847842..2847876
-
Hg19::chr18:44840511..44840522,+p@chr18:44840511..44840522
+
Hg19::chr18:74690959..74690970,-p@chr18:74690959..74690970
-
Hg19::chr18:74691120..74691129,-p@chr18:74691120..74691129
-
Hg19::chr18:74691629..74691639,+p@chr18:74691629..74691639
+
Hg19::chr18:74754861..74754870,+p@chr18:74754861..74754870
+
Hg19::chr18:76739685..76739700,-p@chr18:76739685..76739700
-
Hg19::chr18:76739816..76739822,+p1@SALL3
Hg19::chr18:77014816..77014819,-p@chr18:77014816..77014819
-
Hg19::chr19:19005434..19005439,-p@chr19:19005434..19005439
-
Hg19::chr19:19006746..19006757,-p6@GDF1
Hg19::chr1:110546510..110546515,+p28@AHCYL1
Hg19::chr1:204245928..204245938,+p3@ENST00000437919
Hg19::chr1:204245955..204245976,+p1@ENST00000437919
Hg19::chr1:205473720..205473732,+p5@CDK18
Hg19::chr1:226927108..226927159,-p2@ITPKB
Hg19::chr1:60460743..60460750,+p@chr1:60460743..60460750
+
Hg19::chr1:84647240..84647255,+p25@PRKACB
Hg19::chr20:4802979..4803013,+p@chr20:4802979..4803013
+
Hg19::chr21:18811167..18811180,+p2@C21orf37
Hg19::chr21:18811183..18811203,+p1@C21orf37
Hg19::chr21:18811205..18811216,+p3@C21orf37
Hg19::chr21:42519981..42519997,-p1@LINC00323
Hg19::chr21:48022255..48022268,-p3@S100B
Hg19::chr2:153209536..153209539,+p@chr2:153209536..153209539
+
Hg19::chr2:238472387..238472392,+p@chr2:238472387..238472392
+
Hg19::chr2:25720324..25720333,-p15@DTNB
Hg19::chr2:25720352..25720388,-p7@DTNB
Hg19::chr2:25720404..25720435,-p8@DTNB
Hg19::chr2:25720449..25720463,-p9@DTNB
Hg19::chr2:25720468..25720501,-p3@DTNB
Hg19::chr2:25720514..25720525,-p16@DTNB
Hg19::chr2:25720534..25720541,-p22@DTNB
Hg19::chr2:27073036..27073042,-p@chr2:27073036..27073042
-
Hg19::chr2:30163755..30163780,+p@chr2:30163755..30163780
+
Hg19::chr2:44994986..44994992,-p@chr2:44994986..44994992
-
Hg19::chr3:129118836..129118841,+p@chr3:129118836..129118841
+
Hg19::chr3:187010042..187010066,-p4@MASP1
Hg19::chr4:151171730..151171740,+p@chr4:151171730..151171740
+
Hg19::chr4:79892692..79892714,+p3@LOC100505875
Hg19::chr4:79892726..79892755,+p1@LOC100505875
Hg19::chr4:79892769..79892792,+p2@LOC100505875
Hg19::chr4:79892794..79892803,+p9@LOC100505875
Hg19::chr4:79892823..79892836,+p7@LOC100505875
Hg19::chr4:79892846..79892875,+p6@LOC100505875
Hg19::chr4:79892974..79892983,+p8@LOC100505875
Hg19::chr5:72570747..72570764,-p@chr5:72570747..72570764
-
Hg19::chr5:77302570..77302586,+p@chr5:77302570..77302586
+
Hg19::chr5:82778804..82778813,+p@chr5:82778804..82778813
+
Hg19::chr6:115144144..115144160,+p@chr6:115144144..115144160
+
Hg19::chr6:149387191..149387204,+p3@UST
Hg19::chr6:151054827..151054836,+p23@PLEKHG1
Hg19::chr6:151054854..151054865,+p17@PLEKHG1
Hg19::chr6:71738302..71738338,+p@chr6:71738302..71738338
+
Hg19::chr8:124741451..124741493,-p3@ANXA13
Hg19::chr8:131864839..131864841,+p@chr8:131864839..131864841
+
Hg19::chr8:82354790..82354800,-p@chr8:82354790..82354800
-
Hg19::chr8:82357146..82357161,-p@chr8:82357146..82357161
-
Hg19::chr8:82357185..82357202,-p@chr8:82357185..82357202
-
Hg19::chr8:82357209..82357223,-p@chr8:82357209..82357223
-
Hg19::chr8:82359662..82359681,-p1@PMP2
Hg19::chr9:128998376..128998387,-p@chr9:128998376..128998387
-
Hg19::chr9:75653570..75653582,-p10@ALDH1A1
Hg19::chr9:75653599..75653622,-p5@ALDH1A1
Hg19::chr9:75653627..75653649,-p4@ALDH1A1
Hg19::chrX:16753203..16753238,+p@chrX:16753203..16753238
+
Hg19::chrX:18718181..18718200,+p2@PPEF1


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

No GOStat results

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
neural tube5.21e-11656
neural rod5.21e-11656
future spinal cord5.21e-11656
neural keel5.21e-11656
regional part of nervous system3.83e-10353
regional part of brain3.83e-10353
central nervous system7.03e-8681
brain1.49e-8268
future brain1.49e-8268
neural plate1.04e-8182
presumptive neural plate1.04e-8182
nervous system6.03e-8189
regional part of forebrain9.68e-7941
forebrain9.68e-7941
anterior neural tube9.68e-7941
future forebrain9.68e-7941
neurectoderm1.35e-7786
brain grey matter1.82e-7534
gray matter1.82e-7534
telencephalon5.55e-7534
regional part of telencephalon5.17e-6732
cerebral hemisphere1.07e-6632
ecto-epithelium5.90e-63104
adult organism2.12e-60114
pre-chordal neural plate2.04e-5561
structure with developmental contribution from neural crest8.17e-51132
regional part of cerebral cortex3.06e-4622
neural nucleus1.13e-409
nucleus of brain1.13e-409
cerebral cortex1.74e-4025
pallium1.74e-4025
ectoderm-derived structure4.70e-39171
ectoderm4.70e-39171
presumptive ectoderm4.70e-39171
neocortex1.52e-3820
posterior neural tube1.06e-3615
chordal neural plate1.06e-3615
basal ganglion1.54e-319
nuclear complex of neuraxis1.54e-319
aggregate regional part of brain1.54e-319
collection of basal ganglia1.54e-319
cerebral subcortex1.54e-319
telencephalic nucleus1.85e-317
organ system subdivision9.24e-30223
brainstem3.47e-296
tube9.42e-29192
segmental subdivision of nervous system3.09e-2813
segmental subdivision of hindbrain2.86e-2412
hindbrain2.86e-2412
presumptive hindbrain2.86e-2412
anatomical conduit1.95e-21240
gyrus1.67e-186
corpus striatum4.92e-184
striatum4.92e-184
ventral part of telencephalon4.92e-184
future corpus striatum4.92e-184
epithelium2.95e-16306
cell layer5.08e-16309
medulla oblongata1.25e-153
myelencephalon1.25e-153
future myelencephalon1.25e-153
organ part1.33e-15218
spinal cord1.52e-153
dorsal region element1.52e-153
dorsum1.52e-153
pons2.45e-153
parietal lobe7.99e-155
limbic system8.29e-155
anatomical cluster1.24e-14373
caudate-putamen4.40e-143
dorsal striatum4.40e-143
regional part of metencephalon8.78e-139
metencephalon8.78e-139
future metencephalon8.78e-139
multi-tissue structure1.50e-11342
locus ceruleus5.82e-112
brainstem nucleus5.82e-112
hindbrain nucleus5.82e-112
dorsal plus ventral thalamus9.41e-112
thalamic complex9.41e-112
globus pallidus1.19e-102
pallidum1.19e-102
multi cell component structure1.25e-102
neuron projection bundle1.25e-102
temporal lobe2.39e-106
Ammon's horn2.42e-102
lobe parts of cerebral cortex2.42e-102
hippocampal formation2.42e-102
limbic lobe2.42e-102
caudate nucleus5.09e-102
future caudate nucleus5.09e-102
middle temporal gyrus7.68e-102
occipital lobe1.00e-085
organ6.04e-08503
germ layer6.45e-07560
germ layer / neural crest6.45e-07560
embryonic tissue6.45e-07560
presumptive structure6.45e-07560
germ layer / neural crest derived structure6.45e-07560
epiblast (generic)6.45e-07560


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)
MA0003.12.05286e-06
MA0004.10.0827147
MA0006.10.00213619
MA0007.10.0261638
MA0009.10.0858216
MA0014.10.000243219
MA0017.10.146765
MA0019.10.131849
MA0024.10.728754
MA0025.10.148261
MA0027.11.41368
MA0028.10.00309365
MA0029.11.18931
MA0030.10.0516972
MA0031.10.323147
MA0038.10.0313519
MA0040.10.457335
MA0041.10.50943
MA0042.11.07994
MA0043.10.0859488
MA0046.10.278344
MA0048.10.126545
MA0050.10.00777338
MA0051.10.0895922
MA0052.10.212021
MA0055.11.34826
MA0056.10
MA0057.10.00291239
MA0058.10.112893
MA0059.10.303897
MA0060.10.0151077
MA0061.10.245226
MA0063.10
MA0066.10.00573092
MA0067.10.259834
MA0068.10.0147038
MA0069.10.0799999
MA0070.10.94316
MA0071.11.24285
MA0072.13.16975
MA0073.11.37477e-06
MA0074.10.348235
MA0076.10.00252423
MA0077.11.36471
MA0078.10.601509
MA0081.10.0240287
MA0083.11.03968
MA0084.10.3968
MA0087.10.923506
MA0088.10.0165127
MA0089.10
MA0090.10.15873
MA0091.10.293451
MA0092.10.509761
MA0093.10.0215192
MA0095.10
MA0098.10
MA0100.10.88524
MA0101.10.161725
MA0103.10.20935
MA0105.12.81599e-05
MA0106.10.128176
MA0107.10.0497568
MA0108.20.580278
MA0109.10
MA0111.10.098848
MA0113.10.499873
MA0114.10.286991
MA0115.11.7827
MA0116.10.149931
MA0117.10.333225
MA0119.10.00588022
MA0122.10.113397
MA0124.10.185252
MA0125.10.429914
MA0130.10
MA0131.10.0178134
MA0132.10
MA0133.10
MA0135.10.098506
MA0136.10.211022
MA0139.10.354118
MA0140.10.064021
MA0141.10.439107
MA0142.11.19075
MA0143.12.3013
MA0144.10.44087
MA0145.10.00666439
MA0146.16.31057e-07
MA0147.10.0296278
MA0148.10.2058
MA0149.10.0582231
MA0062.20.000226634
MA0035.20.145096
MA0039.21.68473e-12
MA0138.20.185498
MA0002.20.68222
MA0137.20.594146
MA0104.20.0527644
MA0047.20.117079
MA0112.20.0133323
MA0065.20.0338143
MA0150.10.750273
MA0151.10
MA0152.10.154001
MA0153.10.130364
MA0154.10.062938
MA0155.10.036862
MA0156.10.00374239
MA0157.10.73484
MA0158.10
MA0159.10.159917
MA0160.10.584692
MA0161.10
MA0162.11.66595e-08
MA0163.10.000115366
MA0164.10.0584306
MA0080.20.15515
MA0018.20.0465255
MA0099.20.285905
MA0079.21.83222e-15
MA0102.20.426198
MA0258.10.134386
MA0259.10.0164506
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
FOSL1#806182.969239604962470.005791318636574250.026037000735479
JUNB#372692.574726111573740.008566344927844790.0326399306063182
MAFK#7975123.039334557513640.0006070652303768060.0050684535610619
SMARCC1#6599114.488756565569593.70453526672292e-050.000715417823079281



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C162&oldid=3067280"