Coexpression cluster:C214

Full id: C214_Neurons_Neural_duodenum_temporal_occipital_parietal_brain

Phase1 CAGE Peaks

Hg19::chr10:112836138..112836159,+	p@chr10:112836138..112836159 +
Hg19::chr11:57335750..57335798,-	p2@UBE2L6
Hg19::chr12:111471526..111471541,+	p1@CUX2
Hg19::chr12:124265636..124265639,+	p3@DNAH10
Hg19::chr13:112721131..112721138,+	p@chr13:112721131..112721138 +
Hg19::chr14:23956535..23956550,-	p@chr14:23956535..23956550 -
Hg19::chr14:29235961..29236008,+	p1@FOXG1
Hg19::chr14:29236269..29236285,+	p3@FOXG1
Hg19::chr14:29236301..29236317,+	p5@FOXG1
Hg19::chr17:37764128..37764258,-	p1@NEUROD2
Hg19::chr17:79008476..79008509,-	p2@FLJ90757
Hg19::chr18:53069389..53069416,-	p40@TCF4
Hg19::chr18:53069419..53069450,-	p34@TCF4
Hg19::chr1:11539204..11539219,+	p1@PTCHD2
Hg19::chr1:151032922..151032951,+	p2@MLLT11
Hg19::chr1:151032957..151032968,+	p7@MLLT11
Hg19::chr20:656437..656451,-	p4@SRXN1
Hg19::chr20:657349..657358,-	p@chr20:657349..657358 -
Hg19::chr22:28197594..28197605,-	p8@MN1
Hg19::chr22:42393540..42393558,+	p@chr22:42393540..42393558 +
Hg19::chr22:45404770..45404812,-	p2@PHF21B
Hg19::chr22:45404819..45404830,-	p5@PHF21B
Hg19::chr2:104496537..104496544,-	p3@ENST00000455716
Hg19::chr2:104496562..104496570,-	p2@ENST00000455716
Hg19::chr2:104496621..104496635,-	p1@ENST00000455716
Hg19::chr2:105050903..105050923,+	p1@ENST00000447380
Hg19::chr2:105122941..105122944,+	p@chr2:105122941..105122944 +
Hg19::chr2:105470536..105470556,+	p4@POU3F3
Hg19::chr2:105470614..105470625,+	p7@POU3F3
Hg19::chr2:5835715..5835720,+	p@chr2:5835715..5835720 +
Hg19::chr2:5839854..5839869,+	p@chr2:5839854..5839869 +
Hg19::chr2:85413434..85413436,+	p1@TCF7L1-IT1
Hg19::chr3:115342138..115342157,+	p4@GAP43
Hg19::chr3:115342159..115342173,+	p5@GAP43
Hg19::chr3:36805787..36805798,-	p@chr3:36805787..36805798 -
Hg19::chr3:77087811..77087819,+	p@chr3:77087811..77087819 +
Hg19::chr3:89156763..89156797,+	p1@EPHA3
Hg19::chr3:89156799..89156831,+	p3@EPHA3
Hg19::chr3:89156832..89156848,+	p2@EPHA3
Hg19::chr3:89156872..89156883,+	p4@EPHA3
Hg19::chr3:89156891..89156894,+	p5@EPHA3
Hg19::chr5:140613949..140613969,+	p3@PCDHB18
Hg19::chr5:146257992..146258003,-	p18@PPP2R2B
Hg19::chr5:150284420..150284443,-	p2@ZNF300
Hg19::chr5:58295564..58295588,-	p59@PDE4D
Hg19::chr5:71479302..71479315,+	p@chr5:71479302..71479315 +
Hg19::chr5:87967371..87967404,-	p@chr5:87967371..87967404 -
Hg19::chr6:13925142..13925163,+	p3@RNF182
Hg19::chr6:13925170..13925234,+	p1@RNF182
Hg19::chr6:155334892..155334903,+	p18@TIAM2
Hg19::chr6:21594206..21594221,+	p15@SOX4
Hg19::chr6:21594252..21594285,+	p11@SOX4
Hg19::chr6:88876117..88876157,+	p@chr6:88876117..88876157 +
Hg19::chr6:88877062..88877073,-	p3@BC037581
Hg19::chr7:133261209..133261224,+	p7@EXOC4
Hg19::chr7:133261274..133261284,+	p10@EXOC4
Hg19::chr7:24323800..24323815,+	p1@NPY
Hg19::chr7:24324837..24324863,+	p2@NPY
Hg19::chr7:31380440..31380451,-	p4@NEUROD6
Hg19::chr7:80548757..80548764,-	p14@SEMA3C
Hg19::chr7:80632805..80632821,-	p@chr7:80632805..80632821 -
Hg19::chr8:134114832..134114863,-	p9@SLA
Hg19::chr8:134114866..134114880,-	p11@SLA
Hg19::chr8:134114887..134114896,-	p15@SLA
Hg19::chr8:134115035..134115072,-	p12@SLA
Hg19::chr8:134115118..134115121,-	p13@SLA
Hg19::chr9:14308004..14308041,-	p14@NFIB
Hg19::chr9:34990264..34990312,+	p3@DNAJB5
Hg19::chr9:38424443..38424458,-	p1@IGFBPL1

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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GO ID	GO name	FDR corrected p-value
GO:0050789	regulation of biological process	0.0220708125053184
GO:0065007	biological regulation	0.0497479221438013

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>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
neuronal stem cell	1.04e-12	8
neural cell	2.51e-12	25
astrocyte of the cerebral cortex	1.15e-11	3
oligodendrocyte	2.19e-08	7
macroglial cell	2.19e-08	7
astrocyte	2.19e-08	7
oligodendrocyte precursor cell	2.19e-08	7

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.33e-80	53
regional part of brain	1.33e-80	53
central nervous system	3.02e-78	81
neural tube	6.76e-76	56
neural rod	6.76e-76	56
future spinal cord	6.76e-76	56
neural keel	6.76e-76	56
nervous system	1.29e-69	89
brain	6.35e-68	68
future brain	6.35e-68	68
telencephalon	6.51e-67	34
brain grey matter	1.04e-66	34
gray matter	1.04e-66	34
cerebral hemisphere	6.01e-66	32
regional part of forebrain	1.49e-63	41
forebrain	1.49e-63	41
anterior neural tube	1.49e-63	41
future forebrain	1.49e-63	41
regional part of telencephalon	1.40e-60	32
neurectoderm	1.72e-55	86
neural plate	2.29e-55	82
presumptive neural plate	2.29e-55	82
cerebral cortex	6.12e-54	25
pallium	6.12e-54	25
pre-chordal neural plate	5.75e-47	61
ecto-epithelium	1.86e-44	104
regional part of cerebral cortex	2.33e-44	22
neocortex	3.55e-43	20
ectoderm-derived structure	1.76e-39	171
ectoderm	1.76e-39	171
presumptive ectoderm	1.76e-39	171
structure with developmental contribution from neural crest	3.68e-33	132
adult organism	2.84e-25	114
organ system subdivision	3.98e-25	223
segmental subdivision of hindbrain	2.00e-17	12
hindbrain	2.00e-17	12
presumptive hindbrain	2.00e-17	12
tube	2.88e-16	192
segmental subdivision of nervous system	5.48e-16	13
gyrus	2.79e-15	6
brainstem	2.00e-14	6
neural nucleus	3.53e-14	9
nucleus of brain	3.53e-14	9
posterior neural tube	1.09e-13	15
chordal neural plate	1.09e-13	15
temporal lobe	1.11e-13	6
regional part of metencephalon	1.45e-13	9
metencephalon	1.45e-13	9
future metencephalon	1.45e-13	9
anatomical cluster	1.85e-13	373
occipital lobe	1.02e-12	5
parietal lobe	1.19e-12	5
organ part	2.59e-12	218
anatomical conduit	2.38e-11	240
pons	3.19e-11	3
basal ganglion	2.21e-10	9
nuclear complex of neuraxis	2.21e-10	9
aggregate regional part of brain	2.21e-10	9
collection of basal ganglia	2.21e-10	9
cerebral subcortex	2.21e-10	9
epithelium	3.20e-09	306
corpus striatum	3.31e-09	4
striatum	3.31e-09	4
ventral part of telencephalon	3.31e-09	4
future corpus striatum	3.31e-09	4
cell layer	4.77e-09	309
telencephalic nucleus	8.79e-09	7
multi-tissue structure	1.16e-08	342
middle temporal gyrus	2.17e-08	2
locus ceruleus	5.63e-08	2
brainstem nucleus	5.63e-08	2
hindbrain nucleus	5.63e-08	2
limbic system	1.11e-07	5
embryo	2.08e-07	592

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
CTBP2#1488	7	6.36259423732314	0.000118437880671144	0.0016085219531097
NANOG#79923	8	3.39069895432031	0.00243215604043235	0.0136985355501652
RAD21#5885	20	3.00145910013227	5.22739825425055e-06	0.000160100951987001
TRIM28#10155	9	2.42485109286033	0.0114680501306614	0.0419484340009858
ZNF263#10127	22	2.62145675382949	1.35558385273272e-05	0.000328482185604531

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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