Coexpression cluster:C3354

Full id: C3354_gall_bronchogenic_Eosinophils_Neutrophils_lung_CD14_granulocyte

Phase1 CAGE Peaks

Hg19::chr13:113344345..113344359,+	p4@ATP11A
Hg19::chr13:113344371..113344404,+	p6@ATP11A
Hg19::chr13:113344409..113344440,+	p5@ATP11A

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
myeloid leukocyte	6.82e-20	76
CD14-positive, CD16-negative classical monocyte	3.40e-16	42
myeloid cell	2.78e-15	112
common myeloid progenitor	2.78e-15	112
monopoietic cell	2.97e-15	63
monocyte	2.97e-15	63
monoblast	2.97e-15	63
promonocyte	2.97e-15	63
granulocyte monocyte progenitor cell	4.25e-15	71
macrophage dendritic cell progenitor	2.81e-14	65
classical monocyte	3.11e-14	45
myeloid lineage restricted progenitor cell	5.37e-14	70
leukocyte	1.71e-07	140
hematopoietic stem cell	6.35e-07	172
angioblastic mesenchymal cell	6.35e-07	172

Uber Anatomy

Ontology term	p-value	n
adult organism	3.26e-15	115
hemolymphoid system	1.95e-14	112
immune system	6.31e-14	115
hematopoietic system	1.25e-13	102
blood island	1.25e-13	102
bone marrow	5.28e-11	80
bone element	1.04e-10	86
organ	3.08e-09	511
neural tube	5.42e-08	57
neural rod	5.42e-08	57
future spinal cord	5.42e-08	57
neural keel	5.42e-08	57
lateral plate mesoderm	1.28e-07	216
anatomical group	2.04e-07	626
anatomical system	3.82e-07	625
abdomen element	6.04e-07	55
abdominal segment element	6.04e-07	55
skeletal element	7.73e-07	101
skeletal system	7.73e-07	101

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	3	6.33620157696263	0.00393075003576489	0.0189513250385583
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659124430256938
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321082732241211
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319588105659446
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460766736965045
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167106581721134
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153778775811682
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039030413342932
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108466476318364
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00122609877401901
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.00075543669596285
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268984752829205
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000604069163226143
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470084406974372
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.0016495199624222
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000645740451092363
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139799577504
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109086361206557

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.