Coexpression cluster:C413

Full id: C413_CD14_Smooth_gall_mesothelioma_meningioma_Fibroblast_Neutrophils

Phase1 CAGE Peaks

Hg19::chr11:4414880..4414953,-	p1@TRIM21
Hg19::chr11:5711010..5711105,+	p1@TRIM22
Hg19::chr11:615570..615721,-	p2@IRF7
Hg19::chr12:113344755..113344805,+	p1@OAS1
Hg19::chr12:113376261..113376324,+	p1@OAS3
Hg19::chr12:113376330..113376350,+	p3@OAS3
Hg19::chr12:113416191..113416202,+	p6@OAS2
Hg19::chr12:113416240..113416251,+	p5@OAS2
Hg19::chr12:113416265..113416287,+	p3@OAS2
Hg19::chr12:113416311..113416336,+	p2@OAS2
Hg19::chr12:113416340..113416363,+	p4@OAS2
Hg19::chr12:113416367..113416393,+	p1@OAS2
Hg19::chr14:24630902..24630948,+	p2@IRF9
Hg19::chr17:4847640..4847689,+	p@chr17:4847640..4847689 +
Hg19::chr17:6659354..6659398,+	p1@XAF1
Hg19::chr19:17516624..17516640,+	p3@FAM125A
Hg19::chr20:62205570..62205609,-	p1@PRIC285
Hg19::chr21:42798158..42798174,+	p1@MX1
Hg19::chr2:37384085..37384134,-	p1@EIF2AK2
Hg19::chr2:7005785..7005864,-	p1@CMPK2
Hg19::chr3:122283100..122283153,-	p1@PARP9
Hg19::chr3:122399656..122399694,+	p1@PARP14
Hg19::chr3:146262365..146262412,-	p1@PLSCR1
Hg19::chr3:187086155..187086211,+	p1@RTP4
Hg19::chr9:32526172..32526181,-	p3@DDX58

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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p.value	FDR	nGenes	nPathway	Name
1.37766611460316e-12	2.90687550181267e-10	7	135	Hepatitis C (KEGG):05160
8.02404527164351e-15	5.07922065695034e-12	8	134	Measles (KEGG):05162
7.38492015576474e-14	2.33732722929954e-11	8	176	Influenza A (KEGG):05164
4.05004898661881e-06	0.000512736201705942	3	50	Type II interferon signaling (IFNG) (Wikipathways):WP619
3.73290025145396e-10	5.90731464792589e-08	8	511	Signaling in Immune system (Reactome):REACT_6900

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:0009615	response to virus	1.85714517836697e-14
GO:0051707	response to other organism	4.03157118129478e-12
GO:0009607	response to biotic stimulus	4.11531196650602e-11
GO:0051704	multi-organism process	9.61507303276969e-11
GO:0003723	RNA binding	1.04948661341494e-05
GO:0005792	microsome	0.0024331112221386
GO:0042598	vesicular fraction	0.0024331112221386
GO:0003950	NAD+ ADP-ribosyltransferase activity	0.00417910917080701
GO:0005634	nucleus	0.00417910917080701
GO:0016779	nucleotidyltransferase activity	0.00417910917080701
GO:0006955	immune response	0.00449250958849504
GO:0003676	nucleic acid binding	0.00519863380303236
GO:0002376	immune system process	0.00772038312651502
GO:0016763	transferase activity, transferring pentosyl groups	0.0113341044691317
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0121968044765909
GO:0032553	ribonucleotide binding	0.0121968044765909
GO:0032555	purine ribonucleotide binding	0.0121968044765909
GO:0005737	cytoplasm	0.0133518821572491
GO:0017076	purine nucleotide binding	0.0136007388506822
GO:0005524	ATP binding	0.017442046567622
GO:0032559	adenyl ribonucleotide binding	0.017442046567622
GO:0017128	phospholipid scramblase activity	0.017442046567622
GO:0004694	eukaryotic translation initiation factor 2alpha kinase activity	0.017442046567622
GO:0017121	phospholipid scrambling	0.017442046567622
GO:0006926	virus-infected cell apoptosis	0.017442046567622
GO:0030554	adenyl nucleotide binding	0.0185944180558335
GO:0001580	detection of chemical stimulus during sensory perception of bitter taste	0.020182800670166
GO:0044424	intracellular part	0.0207146498389662
GO:0050913	sensory perception of bitter taste	0.0218595978581463
GO:0000166	nucleotide binding	0.0218595978581463
GO:0005622	intracellular	0.0221159790034413
GO:0050912	detection of chemical stimulus during sensory perception of taste	0.0231075963630502
GO:0050907	detection of chemical stimulus during sensory perception	0.0231075963630502
GO:0016740	transferase activity	0.0241057480557124
GO:0032606	interferon type I production	0.0241057480557124
GO:0045351	interferon type I biosynthetic process	0.0241057480557124
GO:0043231	intracellular membrane-bound organelle	0.0241057480557124
GO:0043227	membrane-bound organelle	0.0241057480557124
GO:0006355	regulation of transcription, DNA-dependent	0.0242975136235004
GO:0005624	membrane fraction	0.0242975136235004
GO:0006351	transcription, DNA-dependent	0.0258731915644999
GO:0032774	RNA biosynthetic process	0.0258731915644999
GO:0007009	plasma membrane organization and biogenesis	0.0321401529072117
GO:0030968	unfolded protein response	0.0321401529072117
GO:0045449	regulation of transcription	0.0323666252050385
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0342513187993206
GO:0006350	transcription	0.0375499264667628
GO:0004386	helicase activity	0.0375499264667628
GO:0010468	regulation of gene expression	0.0375499264667628
GO:0009593	detection of chemical stimulus	0.0391154881512025
GO:0031323	regulation of cellular metabolic process	0.0402711693658135
GO:0000267	cell fraction	0.0402711693658135
GO:0003712	transcription cofactor activity	0.0403451482669919
GO:0065007	biological regulation	0.0414568524609404
GO:0006984	ER-nuclear signaling pathway	0.0414568524609404
GO:0019222	regulation of metabolic process	0.0467566200919185
GO:0016070	RNA metabolic process	0.0467566200919185
GO:0030168	platelet activation	0.0467566200919185
GO:0017111	nucleoside-triphosphatase activity	0.0470607886633734

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
leukocyte	4.22e-38	140
nongranular leukocyte	7.38e-36	119
hematopoietic lineage restricted progenitor cell	3.68e-33	124
hematopoietic stem cell	2.68e-28	172
angioblastic mesenchymal cell	2.68e-28	172
hematopoietic oligopotent progenitor cell	1.04e-26	165
hematopoietic multipotent progenitor cell	1.04e-26	165
myeloid leukocyte	3.96e-26	76
hematopoietic cell	5.71e-25	182
CD14-positive, CD16-negative classical monocyte	5.93e-24	42
monopoietic cell	1.36e-22	63
monocyte	1.36e-22	63
monoblast	1.36e-22	63
promonocyte	1.36e-22	63
macrophage dendritic cell progenitor	1.17e-21	65
myeloid lineage restricted progenitor cell	1.52e-21	70
granulocyte monocyte progenitor cell	1.58e-21	71
classical monocyte	5.13e-21	45
myeloid cell	1.65e-14	112
common myeloid progenitor	1.65e-14	112
lymphoid lineage restricted progenitor cell	3.65e-12	52
lymphocyte	4.28e-12	53
common lymphoid progenitor	4.28e-12	53
lymphocyte of B lineage	4.65e-07	24
pro-B cell	4.65e-07	24

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	7.53e-27	112
hematopoietic system	1.46e-26	102
blood island	1.46e-26	102
bone marrow	4.08e-19	80
immune system	2.36e-16	115
bone element	7.72e-15	86
skeletal element	2.46e-13	101
skeletal system	2.46e-13	101
lateral plate mesoderm	4.35e-08	216
adult organism	8.45e-07	115

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
EBF1#1879	13	4.63136276021588	6.26618592042133e-07	2.86279173815785e-05
EGR1#1958	13	2.59385312930127	0.00037778572640151	0.00374696709208427
ELF1#1997	13	2.21421093857992	0.00184770589513798	0.0109277170837712
HEY1#23462	14	2.2624621841392	0.000822070103237153	0.00625910764102829
IRF1#3659	9	2.749378951283	0.00318119929865019	0.0166980586797873
IRF4#3662	6	5.25948304481859	0.000752920458439941	0.0059266098702901
NFKB1#4790	22	4.82949581329057	6.96316904821618e-14	1.10688951632671e-11
POLR2A#5430	25	2.14745317655807	5.02456472262233e-09	4.04283909912137e-07
POU2F2#5452	14	5.09942947233581	5.03322093134357e-08	3.21901139527613e-06
SPI1#6688	9	2.95355646306818	0.00192675715308122	0.0113246997754882
STAT1#6772	23	19.0500604974233	1.42509837352088e-28	5.29664943174902e-26
STAT2#6773	23	60.0426694915254	4.88212981441461e-40	2.8326930871536e-37
STAT3#6774	10	4.2077859988617	5.1112914742446e-05	0.000870544961315446
SUZ12#23512	3	6.01389370932755	0.0131545520330818	0.0466391098816253
TAF1#6872	21	2.80815888002605	3.24290519342898e-08	2.18084852219272e-06
TBP#6908	20	2.96541654967711	5.02099441389296e-08	3.2131595318172e-06
YY1#7528	16	3.14314927990647	2.64335913146096e-06	9.267196519995e-05
ZBTB33#10009	4	5.06635600479698	0.00739199014156867	0.0305469100777624

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.