Coexpression cluster:C1387

Full id: C1387_Neutrophils_Eosinophils_Whole_brain_parietal_optic_temporal

Phase1 CAGE Peaks

Hg19::chr14:102829269..102829295,+	p2@TECPR2
Hg19::chr14:102829302..102829332,+	p3@TECPR2
Hg19::chr19:17858547..17858582,+	p1@FCHO1
Hg19::chr19:18220958..18221027,+	p@chr19:18220958..18221027 +
Hg19::chr19:4969116..4969131,+	p1@KDM4B
Hg19::chr3:113557654..113557682,+	p3@GRAMD1C

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

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Cell Type

Ontology term	p-value	n
classical monocyte	1.01e-17	42
CD14-positive, CD16-negative classical monocyte	1.01e-17	42
defensive cell	7.00e-17	48
phagocyte	7.00e-17	48
myeloid leukocyte	6.18e-15	72
granulocyte monocyte progenitor cell	1.37e-12	67
macrophage dendritic cell progenitor	6.81e-12	61
monopoietic cell	1.03e-11	59
monocyte	1.03e-11	59
monoblast	1.03e-11	59
promonocyte	1.03e-11	59
myeloid lineage restricted progenitor cell	2.17e-11	66
leukocyte	5.28e-11	136
hematopoietic lineage restricted progenitor cell	7.04e-08	120
nongranular leukocyte	7.42e-08	115

Uber Anatomy

Ontology term	p-value	n
adult organism	4.33e-33	114
neural tube	2.20e-28	56
neural rod	2.20e-28	56
future spinal cord	2.20e-28	56
neural keel	2.20e-28	56
regional part of nervous system	1.83e-26	53
regional part of brain	1.83e-26	53
central nervous system	2.23e-26	81
nervous system	2.53e-23	89
brain	2.20e-22	68
future brain	2.20e-22	68
neural plate	9.84e-22	82
presumptive neural plate	9.84e-22	82
neurectoderm	1.36e-21	86
regional part of forebrain	1.93e-21	41
forebrain	1.93e-21	41
anterior neural tube	1.93e-21	41
future forebrain	1.93e-21	41
brain grey matter	1.49e-18	34
gray matter	1.49e-18	34
telencephalon	1.93e-18	34
cerebral hemisphere	2.48e-17	32
regional part of telencephalon	2.57e-17	32
pre-chordal neural plate	1.36e-16	61
hematopoietic system	1.69e-15	98
blood island	1.69e-15	98
ecto-epithelium	6.92e-15	104
hemolymphoid system	1.57e-14	108
regional part of cerebral cortex	1.86e-14	22
cerebral cortex	2.57e-13	25
pallium	2.57e-13	25
neocortex	2.91e-13	20
immune system	9.88e-11	93
bone element	5.02e-10	82
bone marrow	5.91e-10	76
structure with developmental contribution from neural crest	9.89e-10	132
lateral plate mesoderm	2.72e-09	203
ectoderm-derived structure	4.17e-09	171
ectoderm	4.17e-09	171
presumptive ectoderm	4.17e-09	171
posterior neural tube	4.34e-08	15
chordal neural plate	4.34e-08	15
tube	1.10e-07	192
skeletal element	4.10e-07	90
segmental subdivision of nervous system	6.33e-07	13
neural nucleus	9.28e-07	9
nucleus of brain	9.28e-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	6	6.33620157696263	1.54467812014647e-05	0.000362445828330661
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.0101324480779147
ELF1#1997	5	3.54841496567295	0.00344683777572169	0.017528572355193
IRF1#3659	4	5.09144250237593	0.00353524076589381	0.0179440615449642
IRF3#3661	2	15.6606507371632	0.00641762098993253	0.0279142858926144
MEF2A#4205	3	9.37161545482203	0.00268739994710391	0.0148008945354419
NFKB1#4790	4	3.65870894946256	0.0120792728901523	0.0438265479025401
PBX3#5090	3	10.9572563433721	0.00171175344181094	0.0106883784353278
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380133306855193
SP1#6667	4	3.7989209187606	0.0105224661679851	0.0389438266458128
SP2#6668	4	17.4356869958964	3.01067847232342e-05	0.000619570933932978
SREBF1#6720	3	23.5029247202441	0.000183371857143205	0.00222042590007874
TFAP2A#7020	3	8.25931718652248	0.00386073847705559	0.0190436719314792
TFAP2C#7022	4	7.20615240657348	0.000942141368921255	0.00681839806172594
ZNF143#7702	3	6.75043827611395	0.00685025920446858	0.0290390153450296

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.