Coexpression cluster:C3467

Full id: C3467_acute_non_diffuse_chronic_myeloma_merkel_B

Phase1 CAGE Peaks

Hg19::chr14:96000839..96000849,-	p9@SNHG10
Hg19::chr14:96000850..96000861,-	p8@SNHG10
Hg19::chr14:96000869..96000881,-	p7@SNHG10

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
lymphocyte	5.76e-19	53
common lymphoid progenitor	5.76e-19	53
lymphoid lineage restricted progenitor cell	2.89e-18	52
lymphocyte of B lineage	5.08e-14	24
pro-B cell	5.08e-14	24
B cell	3.13e-09	14
hematopoietic cell	1.61e-08	182
hematopoietic stem cell	1.71e-07	172
angioblastic mesenchymal cell	1.71e-07	172
connective tissue cell	1.83e-07	365
mesenchymal cell	2.07e-07	358
hematopoietic oligopotent progenitor cell	2.29e-07	165
hematopoietic multipotent progenitor cell	2.29e-07	165
motile cell	2.45e-07	390

Uber Anatomy

Ontology term	p-value	n
connective tissue	4.19e-09	375

Disease

Ontology term	p-value	n
hematologic cancer	2.73e-18	51
immune system cancer	2.73e-18	51
leukemia	1.10e-13	39
organ system cancer	1.09e-11	137
cancer	2.33e-11	235
disease of cellular proliferation	9.58e-11	239
myeloid leukemia	1.07e-09	31

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
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00659493016545353
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324468256106461
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321344759108543
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00913902814062031
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046114373221569
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00255390028990009
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00896226406852398
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0153842760323384
GATA1#2623	3	13.5603081438004	0.000400961596378263	0.00387310656346184
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00433231020356386
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127833287439324
IRF3#3661	3	46.9819522114896	9.63568551583244e-06	0.000253422654139518
IRF4#3662	3	21.9145126867441	9.49854535978121e-05	0.00136416196208772
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186174126604174
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00719254931970797
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293899515413742
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269145176555013
NFYA#4800	3	18.4255806998305	0.000159813550781416	0.00199245164498751
NFYB#4801	3	16.7597932535365	0.000212364992329618	0.00245344993737976
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000604311810007916
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00470315671851533
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172637118895136
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.0013643495789165
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.0048391560114158
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275989490640455
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239366513492266
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0245983464349772
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000938973354993235
SREBF1#6720	3	47.0058494404883	9.62099323994382e-06	0.000254381496958606
SREBF2#6721	3	436.943262411348	1.19027063774682e-08	8.90477615584817e-07
SRF#6722	3	13.7971782621678	0.000380661502580019	0.00374490454671765
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189926637978129
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00421060531367357
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388353731951731

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.