Coexpression cluster:C4505

Full id: C4505_acute_pineal_skin_occipital_parietal_colon_brain

Phase1 CAGE Peaks

Hg19::chr5:53606354..53606372,-	p3@ARL15
Hg19::chr5:53606375..53606394,-	p2@ARL15
Hg19::chr5:53606396..53606431,-	p1@ARL15

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	2.59e-14	72
leukocyte	1.46e-12	136
myeloid lineage restricted progenitor cell	6.30e-12	66
hematopoietic lineage restricted progenitor cell	7.43e-11	120
nongranular leukocyte	7.61e-11	115
hematopoietic stem cell	8.89e-11	168
angioblastic mesenchymal cell	8.89e-11	168
monopoietic cell	1.25e-10	59
monocyte	1.25e-10	59
monoblast	1.25e-10	59
promonocyte	1.25e-10	59
granulocyte monocyte progenitor cell	1.98e-10	67
hematopoietic oligopotent progenitor cell	2.37e-10	161
hematopoietic multipotent progenitor cell	2.37e-10	161
defensive cell	7.23e-10	48
phagocyte	7.23e-10	48
macrophage dendritic cell progenitor	7.70e-10	61
myeloid cell	1.53e-09	108
common myeloid progenitor	1.53e-09	108
hematopoietic cell	4.47e-08	177
classical monocyte	2.79e-07	42
CD14-positive, CD16-negative classical monocyte	2.79e-07	42

Uber Anatomy

Ontology term	p-value	n
adult organism	1.95e-33	114
central nervous system	2.54e-13	81
neural tube	3.78e-12	56
neural rod	3.78e-12	56
future spinal cord	3.78e-12	56
neural keel	3.78e-12	56
regional part of forebrain	9.50e-12	41
forebrain	9.50e-12	41
anterior neural tube	9.50e-12	41
future forebrain	9.50e-12	41
nervous system	2.88e-11	89
hemolymphoid system	4.47e-11	108
hematopoietic system	5.07e-11	98
blood island	5.07e-11	98
regional part of nervous system	7.51e-11	53
regional part of brain	7.51e-11	53
brain	2.90e-10	68
future brain	2.90e-10	68
regional part of cerebral cortex	1.00e-09	22
brain grey matter	1.73e-09	34
gray matter	1.73e-09	34
telencephalon	2.86e-09	34
cerebral hemisphere	3.20e-09	32
regional part of telencephalon	4.69e-09	32
neocortex	1.03e-08	20
immune system	1.05e-08	93
cerebral cortex	8.52e-08	25
pallium	8.52e-08	25
bone element	1.71e-07	82
bone marrow	2.30e-07	76

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	0.0190887939637891
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115637757637286
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662410102836328
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327183371104982
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323925285417586
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.032209607035187
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464484894481245
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168160459757916
FOS#2353	3	8.9979553088944	0.00137249927241713	0.0090090158702767
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00583330340088889
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00389146251873891
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00438524642590589
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000853596024186725
GTF2B#2959	3	31.9438299343242	3.06634405746243e-05	0.000629414125427121
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435547563975368
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109073853878457
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000759618320988073
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157442252821277
MAFF#23764	3	56.3153564899452	5.59409009993116e-06	0.00016924715409812
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722551107103632
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270620829026488
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00200153105049291
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00246544991484137
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309845534057887
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.0013726561212539
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885084726774585
RDBP#7936	3	153.638403990025	2.75057764221434e-07	1.4054186808964e-05
REST#5978	3	9.65002871612802	0.00111263624711459	0.00770472198729616
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486240602808303
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277953952752161
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203792732672368
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247634794701469
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545062731892067
TAL1#6886	3	29.8686166774402	3.75103522793067e-05	0.000721728754918664
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631413084148581
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.0061658619919108
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330900106760918

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.