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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.027549189648299,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.152902115792725,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.165493755864807,0,0,0,0,0,0,0,0,0,0,0.275482132507796,0.0938392746630608,0,0.0455495587624001,0.112453380477913,0.0861409897892114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.382993339906618,0,0.421579434615254,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.075522285417572,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.342588584645784,0.422074905043734,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.254120022070344,0.188876091037881,0,0,0,0,0,0.0727088341078527,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.626553243622454,0.493558648976517,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.135475749945113,0.176312323189237,0.647427490269002,0.52238033434173,0.549732916211065,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.106026559445686,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0993065657552758,0,0.214455838206723,0.149290789502833,0,0.10606470902502,0.171558826597626,0.385193981212532,0,0,0,0,0,0,0,0,0,0,0,0,0,0.126354806191501,0.187941822070953,0.209531203640986,0.140034794334561,0,0,0,0,0,0,0,0,0,0,0,0,0.319629756202055,0.123480492992954,0,0,0,0.118671766513265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.00130913765711,0.712536029915221,0.355636766070246,0,0,0,0,0,0,0,0,0,0.434580878552298,0,0.104475489260261,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.424610342996058,0.388822402344993,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C162_spinal_locus_medulla_substantia_thalamus_globus_diencephalon
|full_id=C162_spinal_locus_medulla_substantia_thalamus_globus_diencephalon
|id=C162
|id=C162

Revision as of 14:13, 12 September 2012


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
adult organism6.66e-41115
central nervous system2.32e-3882
regional part of nervous system1.77e-3594
nervous system1.77e-3594
neural tube4.13e-3557
neural rod4.13e-3557
future spinal cord4.13e-3557
neural keel4.13e-3557
brain1.66e-3169
future brain1.66e-3169
regional part of brain7.07e-3159
neurectoderm1.25e-2990
neural plate3.12e-2986
presumptive neural plate3.12e-2986
anterior neural tube1.33e-2642
regional part of forebrain3.13e-2641
forebrain3.13e-2641
future forebrain3.13e-2641
ectoderm2.62e-22173
presumptive ectoderm2.62e-22173
gray matter4.29e-2234
brain grey matter4.29e-2234
telencephalon5.39e-2234
ectoderm-derived structure1.09e-21169
pre-chordal neural plate2.10e-2161
regional part of telencephalon2.17e-2133
cerebral hemisphere1.22e-2032
anterior region of body7.60e-18129
craniocervical region7.60e-18129
head1.76e-17123
cerebral cortex2.54e-1625
pallium2.54e-1625
regional part of cerebral cortex9.10e-1522
neocortex1.69e-1320
organ part8.64e-12219
organ4.63e-10511
posterior neural tube1.58e-0915
chordal neural plate1.58e-0915
segmental subdivision of nervous system3.48e-0813
segmental subdivision of hindbrain1.53e-0712
hindbrain1.53e-0712
presumptive hindbrain1.53e-0712
nucleus of brain3.10e-079
neural nucleus3.10e-079
basal ganglion4.57e-079
nuclear complex of neuraxis4.57e-079
aggregate regional part of brain4.57e-079
collection of basal ganglia4.57e-079
cerebral subcortex4.57e-079
embryo6.99e-07612


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)

{{{tfbs_overrepresentation_jaspar}}}



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

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