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Coexpression cluster:C149: Difference between revisions

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|pathway_enrichment=0.00026644132796545;0.033731472120426;2;23;Proximal tubule bicarbonate reclamation (KEGG):04964!0.000111903295006833;0.0177086964348314;3;89;Salivary secretion (KEGG):04970!6.45586159951881e-05;0.0136218679749847;3;74;Gastric acid secretion (KEGG):04971!4.34530766860615e-07;0.000275057975422769;7;466;Hemostasis (Reactome):REACT_604!5.23845554546341e-05;0.0136218679749847;4;197;Synaptic Transmission (Reactome):REACT_13685
|pathway_enrichment=0.00026644132796545;0.033731472120426;2;23;Proximal tubule bicarbonate reclamation (KEGG):04964!0.000111903295006833;0.0177086964348314;3;89;Salivary secretion (KEGG):04970!6.45586159951881e-05;0.0136218679749847;3;74;Gastric acid secretion (KEGG):04971!4.34530766860615e-07;0.000275057975422769;7;466;Hemostasis (Reactome):REACT_604!5.23845554546341e-05;0.0136218679749847;4;197;Synaptic Transmission (Reactome):REACT_13685
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|tfbs_overrepresentation_for_novel_motifs=0.130562,1.1542,0.0304114,0.171781,0.115861,0.899158,0.303117,1.5815,0.290685,0.0889441,0.12788,0.225185,0.538405,0.150951,0.113622,0.15572,0.132554,0.686473,0.168282,0.523459,0.302426,0.398265,0.0781573,0.265164,0.201027,0.696776,0.718713,0.2705,0.0347947,0.277204,0.306347,0.161242,0.356893,0.989236,0.376673,2.30463,0.0155417,0.0344037,0.073259,1.0993,0.263306,0.265747,0.317804,1.09539,0.179876,0.0973377,0.0746735,0.33545,0.367011,0.560411,0.486891,0.527035,0.584615,0.49833,0.128145,0.689276,0.759416,0.2253,2.09436,0.223554,0.196661,0.0762593,1.55153,0.507574,0.029808,0.0910512,0.174926,0.430999,0.352053,0.307909,0.139081,0.114156,7.92944e-05,0.127167,0.0292511,0.175755,0.74664,1.51803,1.39396,0.188553,0.441541,0.112234,0.193035,0.107767,0.33763,3.47013e-05,0.507103,0.88664,1.55932,0.512335,1.21997,0.30672,0.700067,0.0860262,0.00138917,0.760796,0.773984,0.8103,0.170411,0.372786,0.274165,0.170526,0.795528,0.912258,0.673032,0.00579488,0.294667,0.064473,0.0253924,0.151258,0.481078,0.205932,0.285341,0.3925,0.583556,1.20594,0.00389352,0.0465953,0.0896609,2.24149,0.779401,0.325313,0.286264,0.586742,0.75029,0.0238486,0.290387,0.047557,0.144463,1.14882,0.0921133,0.313787,0.152022,0.204173,0.239747,0.158277,0.0438767,0.155774,0.610405,0.920776,0.556709,0.190255,0.159366,0.461227,0.678152,1.34267,0.0760738,0.772761,0.564372,0.795237,0.359835,3.85418e-06,1.57281,0.448083,1.33598,0.330069,0.512172,0.0254129,0.116623,0.00502966,0.554801,0.287447,0.0379902,0.0169711,0.0948751,0.801522,1.45709,0.48524,0.0447477
}}
}}

Revision as of 13:35, 26 November 2012


Full id: C149_occipital_medial_brain_amygdala_parietal_cerebral_cerebellum



Phase1 CAGE Peaks

Hg19::chr11:109295305..109295312,+p13@C11orf87
Hg19::chr11:117708272..117708286,-p@chr11:117708272..117708286
-
Hg19::chr11:117711055..117711088,-p@chr11:117711055..117711088
-
Hg19::chr11:124616783..124616814,+p@chr11:124616783..124616814
+
Hg19::chr11:124616829..124616838,+p@chr11:124616829..124616838
+
Hg19::chr11:124616862..124616874,+p@chr11:124616862..124616874
+
Hg19::chr11:124616993..124617007,+p@chr11:124616993..124617007
+
Hg19::chr11:1579486..1579500,-p@chr11:1579486..1579500
-
Hg19::chr11:35276496..35276513,-p@chr11:35276496..35276513
-
Hg19::chr11:62475766..62475783,+p2@GNG3
Hg19::chr11:62476322..62476329,+p@chr11:62476322..62476329
+
Hg19::chr11:62476418..62476427,+p@chr11:62476418..62476427
+
Hg19::chr11:788371..788384,-p7@CEND1
Hg19::chr11:788579..788588,-p10@CEND1
Hg19::chr12:50264369..50264380,-p13@FAIM2
Hg19::chr12:50284493..50284508,-p@chr12:50284493..50284508
-
Hg19::chr12:50291815..50291826,-p@chr12:50291815..50291826
-
Hg19::chr12:57957251..57957258,+p@chr12:57957251..57957258
+
Hg19::chr12:57974899..57974914,+p12@KIF5A
Hg19::chr12:6804679..6804701,-p@chr12:6804679..6804701
-
Hg19::chr12:99145213..99145224,-p21@ANKS1B
Hg19::chr14:103986341..103986353,-p@chr14:103986341..103986353
-
Hg19::chr14:60063355..60063387,-p@chr14:60063355..60063387
-
Hg19::chr14:60063439..60063448,-p@chr14:60063439..60063448
-
Hg19::chr14:60063478..60063487,-p@chr14:60063478..60063487
-
Hg19::chr14:90873274..90873290,+p43@CALM1
Hg19::chr15:43813238..43813252,+p17@MAP1A
Hg19::chr15:43823079..43823119,+p@chr15:43823079..43823119
+
Hg19::chr15:90809459..90809470,+p16@NGRN
Hg19::chr16:19871596..19871607,-p@chr16:19871596..19871607
-
Hg19::chr16:56388775..56388786,+p@chr16:56388775..56388786
+
Hg19::chr16:743174..743190,-p@chr16:743174..743190
-
Hg19::chr16:743985..744004,-p@chr16:743985..744004
-
Hg19::chr16:747239..747260,-p13@FBXL16
Hg19::chr16:7568245..7568260,+p@chr16:7568245..7568260
+
Hg19::chr17:26369560..26369599,+p5@NLK
Hg19::chr17:7560287..7560299,+p13@ATP1B2
Hg19::chr17:77111716..77111739,-p1@AB528944
Hg19::chr18:3814105..3814117,-p@chr18:3814105..3814117
-
Hg19::chr19:18308079..18308090,-p@chr19:18308079..18308090
-
Hg19::chr19:18731255..18731287,+p@chr19:18731255..18731287
+
Hg19::chr19:36523273..36523285,-p13@CLIP3
Hg19::chr19:42474687..42474704,-p7@ATP1A3
Hg19::chr19:42485760..42485786,-p@chr19:42485760..42485786
-
Hg19::chr19:47112153..47112167,+p3@AK124456
Hg19::chr19:49933161..49933172,-p@chr19:49933161..49933172
-
Hg19::chr19:55684730..55684739,-p@chr19:55684730..55684739
-
Hg19::chr19:6494544..6494555,-p@chr19:6494544..6494555
-
Hg19::chr1:155851785..155851821,+p@chr1:155851785..155851821
+
Hg19::chr1:20810135..20810150,-p12@CAMK2N1
Hg19::chr1:240370881..240370888,+p@chr1:240370881..240370888
+
Hg19::chr1:26609014..26609025,-p@chr1:26609014..26609025
-
Hg19::chr1:41107481..41107490,-p5@RIMS3
Hg19::chr1:50661281..50661326,+p@chr1:50661281..50661326
+
Hg19::chr1:77987565..77987576,+p@chr1:77987565..77987576
+
Hg19::chr1:78024449..78024457,+p@chr1:78024449..78024457
+
Hg19::chr20:10256108..10256138,+p5@SNAP25
Hg19::chr20:10256139..10256151,+p6@SNAP25
Hg19::chr20:10258344..10258353,+p@chr20:10258344..10258353
+
Hg19::chr20:10277603..10277615,+p@chr20:10277603..10277615
+
Hg19::chr20:23356084..23356097,-p@chr20:23356084..23356097
-
Hg19::chr20:34820071..34820089,+p@chr20:34820071..34820089
+
Hg19::chr20:36572681..36572688,+p@chr20:36572681..36572688
+
Hg19::chr20:44038648..44038659,+p@chr20:44038648..44038659
+
Hg19::chr21:27394184..27394203,-p35@APP
Hg19::chr2:149679712..149679726,+p@chr2:149679712..149679726
+
Hg19::chr2:149679731..149679740,+p@chr2:149679731..149679740
+
Hg19::chr2:166246839..166246855,+p6@SCN2A
Hg19::chr2:17836942..17836979,+p@chr2:17836942..17836979
+
Hg19::chr2:210557572..210557587,+p@chr2:210557572..210557587
+
Hg19::chr2:241724426..241724440,-p@chr2:241724426..241724440
-
Hg19::chr2:26205144..26205178,-p8@KIF3C
Hg19::chr2:44546521..44546539,-p@chr2:44546521..44546539
-
Hg19::chr3:149684096..149684130,-p@chr3:149684096..149684130
-
Hg19::chr3:49662624..49662643,+p@chr3:49662624..49662643
+
Hg19::chr3:85008200..85008248,+p2@CADM2
Hg19::chr4:176556169..176556177,-p@chr4:176556169..176556177
-
Hg19::chr4:780193..780202,-p@chr4:780193..780202
-
Hg19::chr4:786348..786365,-p7@CPLX1
Hg19::chr5:149601723..149601751,-p@chr5:149601723..149601751
-
Hg19::chr5:149601763..149601781,-p@chr5:149601763..149601781
-
Hg19::chr5:149602244..149602265,-p@chr5:149602244..149602265
-
Hg19::chr5:149644556..149644576,-p@chr5:149644556..149644576
-
Hg19::chr5:175305938..175305959,+p@chr5:175305938..175305959
+
Hg19::chr5:175307176..175307188,+p@chr5:175307176..175307188
+
Hg19::chr5:176047349..176047358,-p@chr5:176047349..176047358
-
Hg19::chr5:176047426..176047433,-p@chr5:176047426..176047433
-
Hg19::chr5:176047734..176047748,-p@chr5:176047734..176047748
-
Hg19::chr6:17463258..17463269,+p@chr6:17463258..17463269
+
Hg19::chr6:31513145..31513194,-p@chr6:31513145..31513194
-
Hg19::chr6:31513206..31513220,-p@chr6:31513206..31513220
-
Hg19::chr6:31513929..31513944,-p@chr6:31513929..31513944
-
Hg19::chr6:46191004..46191017,-p@chr6:46191004..46191017
-
Hg19::chr6:5999372..5999383,-p@chr6:5999372..5999383
-
Hg19::chr6:96463946..96463957,+p4@FUT9
Hg19::chr7:104844144..104844161,-p7@SRPK2
Hg19::chr7:54617830..54617836,+p@chr7:54617830..54617836
+
Hg19::chr7:75959123..75959144,-p@chr7:75959123..75959144
-
Hg19::chr7:98445661..98445681,-p11@TMEM130
Hg19::chr7:98452904..98452938,-p@chr7:98452904..98452938
-
Hg19::chr7:98457898..98457907,-p@chr7:98457898..98457907
-
Hg19::chr7:98457936..98457953,-p@chr7:98457936..98457953
-
Hg19::chr8:107531209..107531222,+p@chr8:107531209..107531222
+
Hg19::chr8:24810399..24810424,-p@chr8:24810399..24810424
-
Hg19::chr8:24811752..24811777,-p@chr8:24811752..24811777
-
Hg19::chr9:130454420..130454442,+p@chr9:130454420..130454442
+
Hg19::chr9:137982097..137982113,+p@chr9:137982097..137982113
+
Hg19::chr9:138011822..138011833,+p17@OLFM1
Hg19::chr9:35748867..35748868,-p13@GBA2
Hg19::chr9:93375167..93375214,-p6@DIRAS2
Hg19::chr9:99220754..99220765,+p6@HABP4
Hg19::chrX:38525424..38525435,+p8@TSPAN7
Hg19::chrX:38547270..38547317,+p@chrX:38547270..38547317
+
Hg19::chrX:48689784..48689807,-p@chrX:48689784..48689807
-


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
0.000266441327965450.033731472120426223Proximal tubule bicarbonate reclamation (KEGG):04964
0.0001119032950068330.0177086964348314389Salivary secretion (KEGG):04970
6.45586159951881e-050.0136218679749847374Gastric acid secretion (KEGG):04971
4.34530766860615e-070.0002750579754227697466Hemostasis (Reactome):REACT_604
5.23845554546341e-050.01362186797498474197Synaptic Transmission (Reactome):REACT_13685



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:0006836neurotransmitter transport0.00897919041513745
GO:0031402sodium ion binding0.00897919041513745
GO:0005391sodium:potassium-exchanging ATPase activity0.00897919041513745
GO:0006887exocytosis0.00897919041513745
GO:0005871kinesin complex0.0173895998883744
GO:0044459plasma membrane part0.0184246069135385
GO:0006814sodium ion transport0.018569695369367
GO:0005875microtubule associated complex0.018569695369367
GO:0005886plasma membrane0.018569695369367
GO:0031420alkali metal ion binding0.0217426956653378
GO:0044425membrane part0.0217426956653378
GO:0016142O-glycoside catabolic process0.0217426956653378
GO:0033130acetylcholine receptor binding0.0217426956653378
GO:0016140O-glycoside metabolic process0.0217426956653378
GO:0045045secretory pathway0.0229413380745906
GO:0016020membrane0.0231312271272513
GO:0016192vesicle-mediated transport0.0266852479449219
GO:0007268synaptic transmission0.0266852479449219
GO:0051649establishment of cellular localization0.0266852479449219
GO:0016137glycoside metabolic process0.0266852479449219
GO:0016139glycoside catabolic process0.0266852479449219
GO:0035235ionotropic glutamate receptor signaling pathway0.0266852479449219
GO:0032940secretion by cell0.0266852479449219
GO:0005874microtubule0.0266852479449219
GO:0051641cellular localization0.026699697161869
GO:0005794Golgi apparatus0.0294353054527756
GO:0019226transmission of nerve impulse0.0294353054527756
GO:0005737cytoplasm0.0294353054527756
GO:0035253ciliary rootlet0.0294353054527756
GO:0016081synaptic vesicle docking during exocytosis0.0294353054527756
GO:0008422beta-glucosidase activity0.0294353054527756
GO:0006810transport0.0351884991944362
GO:0007243protein kinase cascade0.0374902103733455
GO:0046903secretion0.0380766997085923
GO:0051234establishment of localization0.0380766997085923
GO:0044464cell part0.0403543762700639
GO:0004348glucosylceramidase activity0.0410719101615185
GO:0030054cell junction0.0467409041374484
GO:0046920alpha(1,3)-fucosyltransferase activity0.0467409041374484
GO:0000287magnesium ion binding0.0476209460943883
GO:0044441cilium part0.0476209460943883
GO:0008542visual learning0.0476209460943883
GO:0003777microtubule motor activity0.0476209460943883
GO:0030955potassium ion binding0.0476209460943883
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0476209460943883
GO:0051179localization0.0476209460943883
GO:0016079synaptic vesicle exocytosis0.0476209460943883
GO:0001504neurotransmitter uptake0.0476209460943883
GO:0050796regulation of insulin secretion0.0476209460943883
GO:0006878cellular copper ion homeostasis0.0476209460943883
GO:0005890sodium:potassium-exchanging ATPase complex0.0476209460943883



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 tube4.56e-11256
neural rod4.56e-11256
future spinal cord4.56e-11256
neural keel4.56e-11256
regional part of nervous system2.46e-10653
regional part of brain2.46e-10653
telencephalon8.20e-9634
brain grey matter1.14e-9534
gray matter1.14e-9534
cerebral hemisphere5.57e-9532
regional part of cerebral cortex2.09e-9222
regional part of forebrain8.95e-9141
forebrain8.95e-9141
anterior neural tube8.95e-9141
future forebrain8.95e-9141
brain2.73e-9068
future brain2.73e-9068
central nervous system5.12e-8881
regional part of telencephalon7.14e-8832
neocortex1.41e-8320
cerebral cortex3.94e-8125
pallium3.94e-8125
nervous system1.28e-7889
neural plate1.69e-7482
presumptive neural plate1.69e-7482
neurectoderm1.04e-7086
pre-chordal neural plate2.81e-5961
ecto-epithelium3.14e-57104
adult organism2.13e-49114
structure with developmental contribution from neural crest3.30e-46132
ectoderm-derived structure1.01e-37171
ectoderm1.01e-37171
presumptive ectoderm1.01e-37171
organ system subdivision1.89e-30223
gyrus1.38e-276
tube1.80e-27192
temporal lobe1.35e-236
occipital lobe2.70e-235
parietal lobe3.72e-235
limbic system4.68e-235
posterior neural tube1.05e-2115
chordal neural plate1.05e-2115
anatomical conduit2.21e-20240
brainstem2.02e-176
basal ganglion2.48e-179
nuclear complex of neuraxis2.48e-179
aggregate regional part of brain2.48e-179
collection of basal ganglia2.48e-179
cerebral subcortex2.48e-179
neural nucleus1.18e-169
nucleus of brain1.18e-169
segmental subdivision of hindbrain1.36e-1612
hindbrain1.36e-1612
presumptive hindbrain1.36e-1612
organ part2.22e-16218
segmental subdivision of nervous system2.99e-1513
anatomical cluster5.91e-15373
frontal cortex1.72e-143
epithelium3.05e-14306
cell layer5.03e-14309
pons2.30e-133
multi-tissue structure6.85e-12342
regional part of metencephalon7.51e-129
metencephalon7.51e-129
future metencephalon7.51e-129
middle temporal gyrus1.60e-102
amygdala1.68e-102
middle frontal gyrus2.12e-102
corpus striatum2.16e-104
striatum2.16e-104
ventral part of telencephalon2.16e-104
future corpus striatum2.16e-104
Ammon's horn2.32e-102
lobe parts of cerebral cortex2.32e-102
hippocampal formation2.32e-102
limbic lobe2.32e-102
telencephalic nucleus4.36e-107
locus ceruleus1.94e-092
brainstem nucleus1.94e-092
hindbrain nucleus1.94e-092
organ4.30e-08503
germ layer4.71e-07560
germ layer / neural crest4.71e-07560
embryonic tissue4.71e-07560
presumptive structure4.71e-07560
germ layer / neural crest derived structure4.71e-07560
epiblast (generic)4.71e-07560
embryonic structure6.11e-07564
spinal cord7.60e-073
dorsal region element7.60e-073
dorsum7.60e-073
caudate-putamen9.35e-073
dorsal striatum9.35e-073


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

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

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