Coexpression cluster:C2958

Full id: C2958_migratory_Reticulocytes_Dendritic_CD14_vagina_thyroid_splenic

Phase1 CAGE Peaks

Hg19::chrX:154563855..154563876,-	p2@CLIC2
Hg19::chrX:154563879..154563884,-	p4@CLIC2
Hg19::chrX:154563889..154563966,-	p1@CLIC2
Hg19::chrX:154563975..154563992,-	p3@CLIC2

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 lineage restricted progenitor cell	2.39e-27	66
granulocyte monocyte progenitor cell	5.93e-26	67
myeloid cell	1.05e-24	108
common myeloid progenitor	1.05e-24	108
macrophage dendritic cell progenitor	2.47e-24	61
monopoietic cell	2.29e-23	59
monocyte	2.29e-23	59
monoblast	2.29e-23	59
promonocyte	2.29e-23	59
defensive cell	3.27e-23	48
phagocyte	3.27e-23	48
myeloid leukocyte	2.22e-22	72
classical monocyte	1.63e-20	42
CD14-positive, CD16-negative classical monocyte	1.63e-20	42
hematopoietic stem cell	6.02e-14	168
angioblastic mesenchymal cell	6.02e-14	168
hematopoietic oligopotent progenitor cell	4.81e-13	161
hematopoietic multipotent progenitor cell	4.81e-13	161
hematopoietic lineage restricted progenitor cell	2.05e-12	120
hematopoietic cell	3.59e-12	177
leukocyte	4.72e-12	136
nongranular leukocyte	2.58e-09	115
stuff accumulating cell	9.17e-09	87
dendritic cell	1.18e-07	10
conventional dendritic cell	2.50e-07	8

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.03e-31	108
adult organism	2.85e-31	114
hematopoietic system	1.36e-30	98
blood island	1.36e-30	98
immune system	7.57e-28	93
bone marrow	1.56e-25	76
bone element	3.17e-22	82
skeletal element	4.18e-18	90
skeletal system	1.18e-15	100
lateral plate mesoderm	1.62e-15	203
mesoderm	3.63e-12	315
mesoderm-derived structure	3.63e-12	315
presumptive mesoderm	3.63e-12	315
tissue	6.78e-09	773
musculoskeletal system	3.67e-07	167

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
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00435785936108654
GATA1#2623	4	13.5603081438004	2.95627390049268e-05	0.000615776405850727
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.018674753906845
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00308225519690316
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.000745703451641518
JUNB#3726	4	30.6106326598211	1.13787152942193e-06	4.66580937029043e-05
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00392889507563313
MAFK#7975	4	27.1007331378299	1.85228494563408e-06	6.8623904731138e-05
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00890400361066016
NFE2#4778	4	77.204260651629	2.80776035215453e-08	1.92036465893036e-06
SRF#6722	4	13.7971782621678	2.75840773062708e-05	0.000586373590431429
STAT1#6772	4	20.7065874971992	5.43610708103893e-06	0.000165763967134781
STAT2#6773	4	65.2637711864407	5.50053512607993e-08	3.46902408232284e-06
STAT3#6774	4	10.5194649971542	8.16377768286615e-05	0.00123621397335198
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323594564732372
TAL1#6886	4	29.8686166774402	1.25525650806991e-06	5.04998977065921e-05
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0245255122194849

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.