Coexpression cluster:C1808

Full id: C1808_thalamus_substantia_Eosinophils_globus_CD14_optic_Neutrophils

Phase1 CAGE Peaks

Hg19::chr19:11457233..11457257,+	p2@CCDC159
Hg19::chr4:15004067..15004113,+	p1@CPEB2
Hg19::chr5:65221552..65221616,+	p@chr5:65221552..65221616 +
Hg19::chr6:163835167..163835226,+	p7@QKI
Hg19::chr6:163835734..163835758,+	p1@QKI

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:0006417	regulation of translation	0.000758142443290168
GO:0031326	regulation of cellular biosynthetic process	0.000758142443290168
GO:0009889	regulation of biosynthetic process	0.000758142443290168
GO:0051246	regulation of protein metabolic process	0.00215522757872212
GO:0003723	RNA binding	0.0092540737721995
GO:0006412	translation	0.0117723159075332
GO:0009059	macromolecule biosynthetic process	0.016945573322919
GO:0044249	cellular biosynthetic process	0.0216358830215907
GO:0051028	mRNA transport	0.0216358830215907
GO:0009058	biosynthetic process	0.0216358830215907
GO:0050658	RNA transport	0.0216358830215907
GO:0051236	establishment of RNA localization	0.0216358830215907
GO:0050657	nucleic acid transport	0.0216358830215907
GO:0006403	RNA localization	0.0216358830215907
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0228233871901247
GO:0010468	regulation of gene expression	0.0416891970694574
GO:0008380	RNA splicing	0.0416891970694574
GO:0031323	regulation of cellular metabolic process	0.0416891970694574
GO:0019222	regulation of metabolic process	0.0439740545531343
GO:0006397	mRNA processing	0.0448216054292201

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
myeloid leukocyte	7.93e-33	72
granulocyte monocyte progenitor cell	2.33e-29	67
macrophage dendritic cell progenitor	1.09e-28	61
monopoietic cell	1.11e-27	59
monocyte	1.11e-27	59
monoblast	1.11e-27	59
promonocyte	1.11e-27	59
leukocyte	4.46e-27	136
myeloid lineage restricted progenitor cell	2.18e-26	66
defensive cell	4.27e-26	48
phagocyte	4.27e-26	48
classical monocyte	3.52e-25	42
CD14-positive, CD16-negative classical monocyte	3.52e-25	42
hematopoietic lineage restricted progenitor cell	1.43e-20	120
nongranular leukocyte	1.79e-20	115
myeloid cell	2.12e-19	108
common myeloid progenitor	2.12e-19	108
hematopoietic stem cell	1.34e-18	168
angioblastic mesenchymal cell	1.34e-18	168
hematopoietic oligopotent progenitor cell	1.02e-16	161
hematopoietic multipotent progenitor cell	1.02e-16	161
hematopoietic cell	6.29e-16	177
stuff accumulating cell	3.16e-11	87

Uber Anatomy

Ontology term	p-value	n
adult organism	1.70e-29	114
hematopoietic system	1.87e-25	98
blood island	1.87e-25	98
hemolymphoid system	4.04e-25	108
bone marrow	4.81e-24	76
neural tube	2.47e-23	56
neural rod	2.47e-23	56
future spinal cord	2.47e-23	56
neural keel	2.47e-23	56
immune system	4.43e-23	93
bone element	9.84e-23	82
regional part of nervous system	1.03e-21	53
regional part of brain	1.03e-21	53
skeletal system	5.16e-20	100
skeletal element	5.58e-20	90
central nervous system	2.46e-18	81
regional part of forebrain	9.99e-18	41
forebrain	9.99e-18	41
anterior neural tube	9.99e-18	41
future forebrain	9.99e-18	41
brain	1.36e-17	68
future brain	1.36e-17	68
brain grey matter	3.09e-17	34
gray matter	3.09e-17	34
telencephalon	4.42e-17	34
regional part of telencephalon	4.89e-16	32
nervous system	7.90e-16	89
cerebral hemisphere	8.33e-16	32
neural plate	3.11e-15	82
presumptive neural plate	3.11e-15	82
neurectoderm	2.68e-14	86
cerebral cortex	5.29e-12	25
pallium	5.29e-12	25
regional part of cerebral cortex	8.33e-11	22
pre-chordal neural plate	4.48e-10	61
neocortex	9.86e-10	20
structure with developmental contribution from neural crest	4.91e-09	132
ecto-epithelium	1.59e-08	104
posterior neural tube	7.76e-07	15
chordal neural plate	7.76e-07	15
neural nucleus	7.92e-07	9
nucleus of brain	7.92e-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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CCNT2#905	4	5.06896126157011	0.00270999809128077	0.0148970730383321
CTBP2#1488	2	25.0868001357313	0.00246143859967838	0.0138500180977216
E2F1#1869	5	4.90738921487932	0.000351281809925646	0.00352866412877027
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0282980674197745
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287672836225366
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00573143974470498
ETS1#2113	3	5.8372565533214	0.00925327904563143	0.0349753251871702
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00674302102909977
MYC#4609	4	4.17782549728752	0.00569196903682344	0.0256798805234266
NRF1#4899	3	7.32616766862654	0.00483968981711754	0.0226894269789441
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135373843721124
TBP#6908	5	3.70677068709639	0.00142875510672112	0.00918885119717023
ZBTB7A#51341	5	7.3519093078759	4.65425347594289e-05	0.000815990563662916

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.