Coexpression cluster:C3382

Full id: C3382_Hodgkin_acute_chronic_CD19_CD133_thymus_granulocyte

Phase1 CAGE Peaks

Hg19::chr13:51483881..51483935,+	p1@RNASEH2B
Hg19::chr13:51484119..51484151,+	p3@RNASEH2B
Hg19::chr13:51484154..51484216,+	p2@RNASEH2B

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><br>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	2.21e-33	172
angioblastic mesenchymal cell	2.21e-33	172
hematopoietic oligopotent progenitor cell	5.68e-30	165
hematopoietic multipotent progenitor cell	5.68e-30	165
hematopoietic cell	2.24e-29	182
lymphocyte	1.08e-25	53
common lymphoid progenitor	1.08e-25	53
lymphoid lineage restricted progenitor cell	3.20e-25	52
hematopoietic lineage restricted progenitor cell	9.32e-21	124
leukocyte	1.60e-20	140
nongranular leukocyte	2.77e-20	119
lymphocyte of B lineage	2.50e-13	24
pro-B cell	2.50e-13	24
T cell	3.58e-12	25
pro-T cell	3.58e-12	25
mature alpha-beta T cell	6.00e-10	18
alpha-beta T cell	6.00e-10	18
immature T cell	6.00e-10	18
mature T cell	6.00e-10	18
immature alpha-beta T cell	6.00e-10	18
B cell	1.42e-09	14
myeloid cell	2.73e-09	112
common myeloid progenitor	2.73e-09	112

Disease

Ontology term	p-value	n
hematologic cancer	1.38e-20	51
immune system cancer	1.38e-20	51
leukemia	1.68e-16	39
myeloid leukemia	4.25e-13	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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189539499970104
CTCF#10664	3	5.36025637307503	0.006492509252767	0.027876631057792
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00171407753618706
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324230149218586
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00436203520128119
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321145080824115
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00913394525511385
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0460876630224287
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108478804155645
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293711156020727
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000735838223946095
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0269019113240467
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172560947992594
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00164994172666726
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275874120064985
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0389997766671592
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00614003487022933
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328483607602039
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0139807014838548
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242300221505449
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109105364695531

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.