Coexpression cluster:C149

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

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p.value	FDR	nGenes	nPathway	Name
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

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

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GO ID	GO name	FDR corrected p-value
GO:0006836	neurotransmitter transport	0.00897919041513745
GO:0031402	sodium ion binding	0.00897919041513745
GO:0005391	sodium:potassium-exchanging ATPase activity	0.00897919041513745
GO:0006887	exocytosis	0.00897919041513745
GO:0005871	kinesin complex	0.0173895998883744
GO:0044459	plasma membrane part	0.0184246069135385
GO:0006814	sodium ion transport	0.018569695369367
GO:0005875	microtubule associated complex	0.018569695369367
GO:0005886	plasma membrane	0.018569695369367
GO:0031420	alkali metal ion binding	0.0217426956653378
GO:0044425	membrane part	0.0217426956653378
GO:0016142	O-glycoside catabolic process	0.0217426956653378
GO:0033130	acetylcholine receptor binding	0.0217426956653378
GO:0016140	O-glycoside metabolic process	0.0217426956653378
GO:0045045	secretory pathway	0.0229413380745906
GO:0016020	membrane	0.0231312271272513
GO:0016192	vesicle-mediated transport	0.0266852479449219
GO:0007268	synaptic transmission	0.0266852479449219
GO:0051649	establishment of cellular localization	0.0266852479449219
GO:0016137	glycoside metabolic process	0.0266852479449219
GO:0016139	glycoside catabolic process	0.0266852479449219
GO:0035235	ionotropic glutamate receptor signaling pathway	0.0266852479449219
GO:0032940	secretion by cell	0.0266852479449219
GO:0005874	microtubule	0.0266852479449219
GO:0051641	cellular localization	0.026699697161869
GO:0005794	Golgi apparatus	0.0294353054527756
GO:0019226	transmission of nerve impulse	0.0294353054527756
GO:0005737	cytoplasm	0.0294353054527756
GO:0035253	ciliary rootlet	0.0294353054527756
GO:0016081	synaptic vesicle docking during exocytosis	0.0294353054527756
GO:0008422	beta-glucosidase activity	0.0294353054527756
GO:0006810	transport	0.0351884991944362
GO:0007243	protein kinase cascade	0.0374902103733455
GO:0046903	secretion	0.0380766997085923
GO:0051234	establishment of localization	0.0380766997085923
GO:0044464	cell part	0.0403543762700639
GO:0004348	glucosylceramidase activity	0.0410719101615185
GO:0030054	cell junction	0.0467409041374484
GO:0046920	alpha(1,3)-fucosyltransferase activity	0.0467409041374484
GO:0000287	magnesium ion binding	0.0476209460943883
GO:0044441	cilium part	0.0476209460943883
GO:0008542	visual learning	0.0476209460943883
GO:0003777	microtubule motor activity	0.0476209460943883
GO:0030955	potassium ion binding	0.0476209460943883
GO:0015662	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism	0.0476209460943883
GO:0051179	localization	0.0476209460943883
GO:0016079	synaptic vesicle exocytosis	0.0476209460943883
GO:0001504	neurotransmitter uptake	0.0476209460943883
GO:0050796	regulation of insulin secretion	0.0476209460943883
GO:0006878	cellular copper ion homeostasis	0.0476209460943883
GO:0005890	sodium:potassium-exchanging ATPase complex	0.0476209460943883

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>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.09e-38	115
central nervous system	4.38e-32	82
neural tube	5.63e-31	57
neural rod	5.63e-31	57
future spinal cord	5.63e-31	57
neural keel	5.63e-31	57
regional part of nervous system	7.85e-31	94
nervous system	7.85e-31	94
anterior neural tube	1.70e-25	42
regional part of forebrain	1.81e-25	41
forebrain	1.81e-25	41
future forebrain	1.81e-25	41
brain	3.38e-25	69
future brain	3.38e-25	69
regional part of brain	1.29e-24	59
neurectoderm	1.01e-21	90
gray matter	1.84e-21	34
brain grey matter	1.84e-21	34
telencephalon	2.06e-21	34
neural plate	2.92e-21	86
presumptive neural plate	2.92e-21	86
regional part of telencephalon	8.56e-21	33
cerebral hemisphere	2.27e-20	32
cerebral cortex	3.51e-16	25
pallium	3.51e-16	25
pre-chordal neural plate	1.17e-15	61
regional part of cerebral cortex	1.30e-15	22
ectoderm	5.24e-15	173
presumptive ectoderm	5.24e-15	173
ectoderm-derived structure	1.82e-14	169
neocortex	2.39e-14	20
anterior region of body	4.81e-12	129
craniocervical region	4.81e-12	129
head	8.72e-12	123
tube	3.44e-11	194
anatomical conduit	4.59e-11	241
multi-cellular organism	4.97e-10	659
epithelium	4.31e-09	309
anatomical cluster	6.54e-09	286
organism subdivision	8.44e-09	365
cell layer	1.35e-08	312
embryo	1.38e-08	612
embryonic structure	3.29e-07	605
developing anatomical structure	3.29e-07	605
germ layer	3.91e-07	604
embryonic tissue	3.91e-07	604
presumptive structure	3.91e-07	604
epiblast (generic)	3.91e-07	604
anatomical system	4.89e-07	625
anatomical group	6.71e-07	626
basal ganglion	6.93e-07	9
nuclear complex of neuraxis	6.93e-07	9
aggregate regional part of brain	6.93e-07	9
collection of basal ganglia	6.93e-07	9
cerebral subcortex	6.93e-07	9
posterior neural tube	7.88e-07	15
chordal neural plate	7.88e-07	15
nucleus of brain	9.78e-07	9
neural nucleus	9.78e-07	9

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

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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

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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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