Coexpression cluster:C600

Full id: C600_Reticulocytes_CD34_HES3GFP_Hep2_Mesenchymal_iPS_CD4

Phase1 CAGE Peaks

Hg19::chr17:77429187..77429190,+	p@chr17:77429187..77429190 +
Hg19::chr18:23751305..23751327,-	p1@ENST00000307796
Hg19::chr1:120904659..120904667,+	p1@ENST00000401004
Hg19::chr1:120905986..120906002,+	p1@HIST2H2BA
Hg19::chr1:149804218..149804222,+	p11@HIST2H4A p11@HIST2H4B
Hg19::chr1:149812975..149812992,+	p@chr1:149812975..149812992 +
Hg19::chr1:149822620..149822635,+	p1@HIST2H2AA3 p1@HIST2H2AA4
Hg19::chr1:149824160..149824183,+	p1@HIST2H3A p1@HIST2H3C p1@HIST2H3D
Hg19::chr21:44985053..44985072,+	p1@uc002zdj.1
Hg19::chr22:51142547..51142550,-	p@chr22:51142547..51142550 -
Hg19::chr2:175366659..175366666,+	p1@ENST00000313760 p1@ENST00000545980
Hg19::chr6:27776055..27776066,+	p19@HIST1H3H
Hg19::chr6:27791862..27791877,+	p10@HIST1H4C p10@HIST1H4F p9@HIST1H4A p9@HIST1H4B p9@HIST1H4D p9@HIST1H4E p9@HIST1H4H p9@HIST1H4I p9@HIST1H4J p9@HIST1H4K p9@HIST1H4L p9@HIST2H4A p9@HIST2H4B p9@HIST4H4
Hg19::chr6:32146268..32146280,+	p2@RNF5
Hg19::chrX:57301700..57301701,+	p@chrX:57301700..57301701 +

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0000786	nucleosome	1.02889990100262e-05
GO:0006334	nucleosome assembly	1.82795360157763e-05
GO:0031497	chromatin assembly	1.82795360157763e-05
GO:0006333	chromatin assembly or disassembly	2.69989057737589e-05
GO:0065004	protein-DNA complex assembly	2.69989057737589e-05
GO:0000785	chromatin	3.35101398552361e-05
GO:0006325	establishment and/or maintenance of chromatin architecture	6.68254071514103e-05
GO:0006323	DNA packaging	6.68254071514103e-05
GO:0044427	chromosomal part	6.68254071514103e-05
GO:0005694	chromosome	8.42194242363336e-05
GO:0051276	chromosome organization and biogenesis	8.42194242363336e-05
GO:0065003	macromolecular complex assembly	0.000215905675290121
GO:0022607	cellular component assembly	0.000247612823251949
GO:0006259	DNA metabolic process	0.000826583373718418
GO:0006996	organelle organization and biogenesis	0.00139878014476753
GO:0043234	protein complex	0.00791414839995249
GO:0043232	intracellular non-membrane-bound organelle	0.00791414839995249
GO:0043228	non-membrane-bound organelle	0.00791414839995249
GO:0043283	biopolymer metabolic process	0.00941767443590979
GO:0016043	cellular component organization and biogenesis	0.00998393556166264
GO:0003677	DNA binding	0.0115816774323599
GO:0032991	macromolecular complex	0.0148845201490435
GO:0044446	intracellular organelle part	0.0163198533038729
GO:0044422	organelle part	0.0163198533038729
GO:0043170	macromolecule metabolic process	0.0277801155833588
GO:0048015	phosphoinositide-mediated signaling	0.0348538768688054
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0394742815323511
GO:0044237	cellular metabolic process	0.0398442130585918
GO:0005634	nucleus	0.0398442130585918
GO:0044238	primary metabolic process	0.0398442130585918
GO:0003676	nucleic acid binding	0.0439843809381516

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>

---

Cell Type

Ontology term	p-value	n
native cell	1.29e-15	722
hematopoietic oligopotent progenitor cell	5.42e-13	165
hematopoietic multipotent progenitor cell	5.42e-13	165
hematopoietic stem cell	1.04e-12	172
angioblastic mesenchymal cell	1.04e-12	172
animal cell	1.33e-12	679
eukaryotic cell	1.33e-12	679
hematopoietic cell	2.42e-12	182
CD14-positive, CD16-negative classical monocyte	1.91e-11	42
classical monocyte	3.34e-11	45
somatic cell	3.00e-10	591
myeloid cell	3.36e-10	112
common myeloid progenitor	3.36e-10	112
hematopoietic lineage restricted progenitor cell	1.19e-09	124
leukocyte	4.48e-09	140
stem cell	5.16e-08	444
multi fate stem cell	2.22e-07	430
somatic stem cell	2.29e-07	436
motile cell	4.70e-07	390
granulocyte monocyte progenitor cell	8.71e-07	71

Uber Anatomy

Ontology term	p-value	n
larynx	1.94e-07	9
bone marrow	4.43e-07	80

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

---

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

---

No analysis results for this cluster

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

---

This analysis result is provided for C0 - C305 clusters.