Coexpression cluster:C898

Full id: C898_CD14_Mast_Basophils_Natural_CD19_immature_CD8

Phase1 CAGE Peaks

Hg19::chr12:7052974..7052985,+	p1@RNU7-1 p4@C12orf57
Hg19::chr14:35343199..35343210,-	p@chr14:35343199..35343210 -
Hg19::chr17:56736656..56736674,-	p1@ENST00000365207
Hg19::chr19:49382363..49382367,+	p@chr19:49382363..49382367 +
Hg19::chr19:49383883..49383887,+	p@chr19:49383883..49383887 +
Hg19::chr2:157189617..157189667,-	p4@NR4A2
Hg19::chr2:224702739..224702758,+	p@chr2:224702739..224702758 +
Hg19::chr8:81397820..81397836,+	p2@ZBTB10
Hg19::chrX:139014487..139014499,+	p@chrX:139014487..139014499 +

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:0042053	regulation of dopamine metabolic process	0.0100078001646933
GO:0042069	regulation of catecholamine metabolic process	0.0100078001646933
GO:0042417	dopamine metabolic process	0.0183457432124587
GO:0006584	catecholamine metabolic process	0.0266764682822135
GO:0018958	phenol metabolic process	0.0266764682822135
GO:0042133	neurotransmitter metabolic process	0.0266764682822135
GO:0006576	biogenic amine metabolic process	0.0450359718763971
GO:0001505	regulation of neurotransmitter levels	0.0450359718763971
GO:0006575	amino acid derivative metabolic process	0.0450359718763971
GO:0003707	steroid hormone receptor activity	0.0450359718763971
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0450359718763971
GO:0004879	ligand-dependent nuclear receptor activity	0.0450359718763971
GO:0006355	regulation of transcription, DNA-dependent	0.0450359718763971
GO:0006351	transcription, DNA-dependent	0.0450359718763971
GO:0032774	RNA biosynthetic process	0.0450359718763971
GO:0003677	DNA binding	0.0450359718763971
GO:0006725	aromatic compound metabolic process	0.0450359718763971
GO:0045449	regulation of transcription	0.0450359718763971
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0450359718763971
GO:0030182	neuron differentiation	0.0450359718763971
GO:0006350	transcription	0.0450359718763971
GO:0010468	regulation of gene expression	0.0450359718763971
GO:0045893	positive regulation of transcription, DNA-dependent	0.0450359718763971
GO:0031323	regulation of cellular metabolic process	0.0450359718763971
GO:0048699	generation of neurons	0.0450359718763971
GO:0019222	regulation of metabolic process	0.0450359718763971
GO:0016070	RNA metabolic process	0.0450359718763971
GO:0008270	zinc ion binding	0.0450359718763971
GO:0022008	neurogenesis	0.0450359718763971
GO:0045941	positive regulation of transcription	0.0451569455497714
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0451569455497714
GO:0007268	synaptic transmission	0.0451569455497714
GO:0019226	transmission of nerve impulse	0.049798892575355

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	3.93e-50	42
CD14-positive, CD16-negative classical monocyte	3.93e-50	42
leukocyte	2.24e-49	136
defensive cell	9.01e-42	48
phagocyte	9.01e-42	48
hematopoietic lineage restricted progenitor cell	9.53e-39	120
hematopoietic stem cell	1.00e-38	168
angioblastic mesenchymal cell	1.00e-38	168
myeloid leukocyte	1.85e-38	72
nongranular leukocyte	4.06e-38	115
hematopoietic cell	2.65e-37	177
granulocyte monocyte progenitor cell	3.43e-35	67
macrophage dendritic cell progenitor	5.10e-34	61
hematopoietic oligopotent progenitor cell	5.19e-34	161
hematopoietic multipotent progenitor cell	5.19e-34	161
myeloid lineage restricted progenitor cell	2.51e-32	66
monopoietic cell	6.83e-32	59
monocyte	6.83e-32	59
monoblast	6.83e-32	59
promonocyte	6.83e-32	59
myeloid cell	6.83e-27	108
common myeloid progenitor	6.83e-27	108
stuff accumulating cell	2.46e-20	87
intermediate monocyte	1.36e-11	9
CD14-positive, CD16-positive monocyte	1.36e-11	9
mesenchymal cell	1.12e-10	354
connective tissue cell	5.77e-10	361
motile cell	2.81e-08	386
lymphoid lineage restricted progenitor cell	2.09e-07	52
lymphocyte	3.80e-07	53
common lymphoid progenitor	3.80e-07	53

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.69e-30	76
hematopoietic system	3.98e-30	98
blood island	3.98e-30	98
bone element	5.39e-27	82
immune system	4.55e-26	93
hemolymphoid system	1.68e-25	108
skeletal element	4.42e-23	90
skeletal system	4.06e-19	100
connective tissue	3.09e-10	371
lateral plate mesoderm	2.31e-08	203

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
BCL3#602	3	11.5157009345794	0.00178591501782776	0.0109562487398328
BCLAF1#9774	3	7.21754920337395	0.0067040496194776	0.028501353016715
BRF2#55290	1	119.397286821705	0.00834447063348787	0.0328565890699306
FOXA2#3170	3	8.21015458422175	0.0046728123675689	0.0220535880905838
GATA1#2623	5	7.53350452433358	0.000213260104352918	0.00245835232213184
HDAC2#3066	4	5.962497882945	0.00286427198078623	0.0155228945774134
HEY1#23462	7	3.14230858908222	0.00125876346284377	0.0084586280591906
MAFK#7975	3	9.03357771260997	0.00356785471281375	0.0180832368412868
MEF2A#4205	3	6.24774363654802	0.0100000500846256	0.037498033562696
NFKB1#4790	6	3.65870894946256	0.00185064964860272	0.0109346005120174
PAX5#5079	5	3.70531418398768	0.00561655707771942	0.0253912044255882
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728640142941982
POU2F2#5452	4	4.04716624788557	0.0116142615615323	0.042435693507727
REST#5978	4	4.28890165161245	0.00945702594596283	0.0356654148257831
SIN3A#25942	5	3.00493595934174	0.0140161881734652	0.0491963258829957
SIRT6#51548	3	51.2128013300083	2.24384938017015e-05	0.000490775676263016
STAT1#6772	3	6.90219583239973	0.00759156108216665	0.0312874412162268
STAT2#6773	2	14.5030602636535	0.00786568313225965	0.0322973886632619
TCF7L2#6934	4	4.78674513917215	0.00638205399123472	0.0277827242211897
TRIM28#10155	3	6.19684168175417	0.010227806502978	0.0380840660070064
ZBTB33#10009	3	10.5549083433271	0.00229172162882116	0.0130043529036921
ZEB1#6935	3	5.62947733918129	0.0133048823634195	0.0470363756398743

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.