Coexpression cluster:C596

Full id: C596_testis_medulla_pituitary_caudate_amygdala_hippocampus_putamen

Phase1 CAGE Peaks

Hg19::chr13:26042916..26042952,+	p4@ATP8A2
Hg19::chr14:24025106..24025172,-	p2@ZFHX2
Hg19::chr14:74111671..74111730,+	p1@DNAL1
Hg19::chr15:40074996..40075059,-	p1@FSIP1
Hg19::chr16:81110786..81110863,-	p1@C16orf46
Hg19::chr1:42921677..42921722,-	p1@ZMYND12
Hg19::chr1:45140360..45140399,+	p2@C1orf228
Hg19::chr2:120301997..120302038,+	p1@PCDP1
Hg19::chr2:120302041..120302052,+	p2@PCDP1
Hg19::chr2:207630033..207630061,-	p2@MDH1B
Hg19::chr2:27712537..27712579,-	p2@IFT172
Hg19::chr3:27410847..27410917,-	p1@NEK10
Hg19::chr5:114515949..114516006,-	p2@TRIM36
Hg19::chr5:137475071..137475122,-	p1@NME5
Hg19::chr6:163148973..163149044,+	p1@PACRG

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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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

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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>

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Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.75e-39	94
nervous system	1.75e-39	94
central nervous system	1.33e-36	82
neural tube	1.49e-33	57
neural rod	1.49e-33	57
future spinal cord	1.49e-33	57
neural keel	1.49e-33	57
neurectoderm	3.24e-32	90
neural plate	1.92e-31	86
presumptive neural plate	1.92e-31	86
brain	4.10e-31	69
future brain	4.10e-31	69
adult organism	4.34e-31	115
regional part of brain	2.84e-29	59
anterior neural tube	2.63e-26	42
regional part of forebrain	3.59e-26	41
forebrain	3.59e-26	41
future forebrain	3.59e-26	41
ectoderm	2.54e-25	173
presumptive ectoderm	2.54e-25	173
ectoderm-derived structure	2.05e-24	169
pre-chordal neural plate	4.05e-23	61
telencephalon	7.08e-22	34
gray matter	7.41e-22	34
brain grey matter	7.41e-22	34
regional part of telencephalon	3.06e-21	33
head	3.90e-21	123
cerebral hemisphere	7.05e-21	32
anterior region of body	7.95e-21	129
craniocervical region	7.95e-21	129
cerebral cortex	1.79e-16	25
pallium	1.79e-16	25
regional part of cerebral cortex	2.13e-15	22
neocortex	4.04e-14	20
organism subdivision	6.10e-14	365
multi-tissue structure	8.94e-12	347
tube	8.45e-10	194
anatomical conduit	2.53e-09	241
epithelium	1.29e-08	309
cell layer	2.24e-08	312
posterior neural tube	2.28e-08	15
chordal neural plate	2.28e-08	15
organ part	4.59e-08	219
anatomical cluster	8.53e-08	286
organ	1.23e-07	511
segmental subdivision of nervous system	2.64e-07	13
basal ganglion	5.58e-07	9
nuclear complex of neuraxis	5.58e-07	9
aggregate regional part of brain	5.58e-07	9
collection of basal ganglia	5.58e-07	9
cerebral subcortex	5.58e-07	9
multi-cellular organism	7.12e-07	659
nucleus of brain	7.80e-07	9
neural nucleus	7.80e-07	9
segmental subdivision of hindbrain	7.99e-07	12
hindbrain	7.99e-07	12
presumptive hindbrain	7.99e-07	12

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	4	5.99017987360233	0.0036072141030584	0.0182596856198777
BRCA1#672	4	5.38246150485967	0.00528967376800273	0.0244966405931375
CHD2#1106	7	4.8272106559212	0.000251184975593986	0.00270643842629323
E2F1#1869	9	2.94443352892759	0.000905836863374802	0.00659725914741987
ELF1#1997	10	2.83873197253836	0.000463891534821351	0.00427045993875778
ETS1#2113	6	3.89150436888093	0.00259133152122708	0.0143307425335152
FOSL2#2355	4	4.51472016121645	0.00980874115445147	0.0368693581943407
FOXA1#3169	5	3.69380658312848	0.00829376303603737	0.0326754052480556
GABPB1#2553	6	2.82707353447287	0.0127308892844565	0.0459227487990657
HEY1#23462	9	2.42406662586343	0.00389687922250708	0.0189949672883141
HMGN3#9324	7	3.81665560423028	0.00106981790182462	0.00755549850207337
HSF1#3297	4	43.8108444444444	1.76670144256977e-06	6.63714143742966e-05
IRF1#3659	6	3.05486550142556	0.00874677282747603	0.0332280011395595
JUND#3727	6	2.79786557674841	0.0133797680819004	0.0472771119770477
MAX#4149	7	3.01119257086999	0.00435468918351306	0.020648296723732
MXI1#4601	10	6.6410477525062	1.93197229432088e-07	1.05144999711609e-05
NFKB1#4790	10	3.65870894946256	4.91132197708818e-05	0.00085219065619723
NR2C2#7182	3	6.52292218104817	0.0099413319894719	0.0372952610240474
NRF1#4899	5	4.07009314923697	0.00549368798581636	0.0248755811641307
POLR2A#5430	12	1.71796254124646	0.00885747283887137	0.0336179672863643
PPARGC1A#10891	2	46.6734848484848	0.000834446447818319	0.00629642024157918
RFX5#5993	7	5.62235838602438	9.57153219667447e-05	0.00136899650929675
SIN3A#25942	12	4.32710778145211	4.13656523923942e-07	1.98995272695037e-05
SIX5#147912	9	10.2520292132754	2.9069232749672e-08	1.97782514602149e-06
SP1#6667	7	2.65924464313242	0.00882458909217691	0.03350898997229
SREBF1#6720	9	28.203509664293	3.94371509408989e-12	5.20047551403604e-10
TAF1#6872	12	2.67443702859623	8.87480614411867e-05	0.00129978387166682
TBP#6908	9	2.22406241225783	0.0072569513450201	0.030031649622481
THAP1#55145	3	6.27382892057027	0.0110509450160292	0.0406490912030809
USF1#7391	7	2.96869966269705	0.00472637757287551	0.0222731769395156
YY1#7528	10	3.2741138332359	0.000132683792813446	0.00174328376369902
ZBTB33#10009	4	8.44392667466164	0.00102543738491965	0.00726564823905175
ZEB1#6935	4	4.50358187134503	0.00989309630417724	0.0371196366054237

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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This analysis result is provided for C0 - C305 clusters.