Coexpression cluster:C4719

Full id: C4719_osteosarcoma_myelodysplastic_giant_NK_oral_small_peripheral

Phase1 CAGE Peaks

Hg19::chr8:117768034..117768069,-	p1@EIF3H
Hg19::chr8:118532937..118532997,+	p1@MED30
Hg19::chr8:120845068..120845089,-	p1@TAF2

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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GO ID	GO name	FDR corrected p-value
GO:0006367	transcription initiation from RNA polymerase II promoter	0.000459772037248053
GO:0065003	macromolecular complex assembly	0.000459772037248053
GO:0022607	cellular component assembly	0.000459772037248053
GO:0006352	transcription initiation	0.000536633614484254
GO:0016591	DNA-directed RNA polymerase II, holoenzyme	0.000686881294310163
GO:0003702	RNA polymerase II transcription factor activity	0.00295581685581293
GO:0065004	protein-DNA complex assembly	0.00295581685581293
GO:0044451	nucleoplasm part	0.006631102498811
GO:0043234	protein complex	0.00685229020748069
GO:0005654	nucleoplasm	0.00698684889344578
GO:0016043	cellular component organization and biogenesis	0.00823446397347406
GO:0006366	transcription from RNA polymerase II promoter	0.00824296163660291
GO:0005852	eukaryotic translation initiation factor 3 complex	0.00824296163660291
GO:0031981	nuclear lumen	0.00824296163660291
GO:0042809	vitamin D receptor binding	0.00824296163660291
GO:0016455	RNA polymerase II transcription mediator activity	0.00824296163660291
GO:0010468	regulation of gene expression	0.00824296163660291
GO:0032991	macromolecular complex	0.00824296163660291
GO:0031323	regulation of cellular metabolic process	0.00824296163660291
GO:0019222	regulation of metabolic process	0.00920018719068307
GO:0000119	mediator complex	0.00933805439024332
GO:0046966	thyroid hormone receptor binding	0.00968783702225466
GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	0.00968783702225466
GO:0031974	membrane-enclosed lumen	0.00970343980764691
GO:0043233	organelle lumen	0.00970343980764691
GO:0005669	transcription factor TFIID complex	0.0102824976655482
GO:0030521	androgen receptor signaling pathway	0.0112205646551544
GO:0044428	nuclear part	0.011251545384384
GO:0016251	general RNA polymerase II transcription factor activity	0.0125949339894161
GO:0010467	gene expression	0.013924563945186
GO:0030518	steroid hormone receptor signaling pathway	0.0140986570056485
GO:0050794	regulation of cellular process	0.0140986570056485
GO:0030522	intracellular receptor-mediated signaling pathway	0.0140986570056485
GO:0035257	nuclear hormone receptor binding	0.0140986570056485
GO:0006446	regulation of translational initiation	0.0140986570056485
GO:0051427	hormone receptor binding	0.0140986570056485
GO:0050789	regulation of biological process	0.0161097034051224
GO:0065007	biological regulation	0.0206660733567341
GO:0006413	translational initiation	0.022575564956508
GO:0003743	translation initiation factor activity	0.0266637074945573
GO:0022618	protein-RNA complex assembly	0.030115287626172
GO:0006417	regulation of translation	0.0385757693507559
GO:0003713	transcription coactivator activity	0.0385757693507559
GO:0031326	regulation of cellular biosynthetic process	0.0396046033911602
GO:0008135	translation factor activity, nucleic acid binding	0.0396046033911602
GO:0005667	transcription factor complex	0.0404676791017343
GO:0009889	regulation of biosynthetic process	0.0409184366965092
GO:0022613	ribonucleoprotein complex biogenesis and assembly	0.0453815620915167

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
hematopoietic stem cell	3.11e-47	168
angioblastic mesenchymal cell	3.11e-47	168
hematopoietic cell	2.15e-43	177
hematopoietic oligopotent progenitor cell	3.80e-43	161
hematopoietic multipotent progenitor cell	3.80e-43	161
leukocyte	2.21e-37	136
nongranular leukocyte	1.02e-30	115
hematopoietic lineage restricted progenitor cell	1.09e-30	120
nucleate cell	1.35e-23	55
lymphocyte	3.77e-23	53
common lymphoid progenitor	3.77e-23	53
lymphoid lineage restricted progenitor cell	1.15e-22	52
myeloid cell	7.47e-20	108
common myeloid progenitor	7.47e-20	108
myeloid leukocyte	1.01e-12	72
classical monocyte	6.23e-12	42
CD14-positive, CD16-negative classical monocyte	6.23e-12	42
T cell	2.16e-11	25
pro-T cell	2.16e-11	25
lymphocyte of B lineage	7.85e-11	24
pro-B cell	7.85e-11	24
mature alpha-beta T cell	2.54e-10	18
alpha-beta T cell	2.54e-10	18
immature T cell	2.54e-10	18
mature T cell	2.54e-10	18
immature alpha-beta T cell	2.54e-10	18
granulocyte monocyte progenitor cell	7.18e-10	67
myeloid lineage restricted progenitor cell	1.16e-09	66
macrophage dendritic cell progenitor	4.44e-09	61
monopoietic cell	1.31e-08	59
monocyte	1.31e-08	59
monoblast	1.31e-08	59
promonocyte	1.31e-08	59
B cell	1.92e-08	14
defensive cell	2.27e-08	48
phagocyte	2.27e-08	48
mesenchymal cell	2.96e-07	354

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.43e-10	98
blood island	1.43e-10	98
hemolymphoid system	3.53e-09	108
bone element	2.22e-08	82
immune system	9.04e-08	93
bone marrow	3.61e-07	76
skeletal element	6.27e-07	90

Disease

Ontology term	p-value	n
cancer	2.49e-18	235
disease of cellular proliferation	3.11e-17	239
organ system cancer	2.01e-14	137
hematologic cancer	1.03e-13	51
immune system cancer	1.03e-13	51
leukemia	1.60e-11	39
myeloid leukemia	3.62e-09	31
cell type cancer	3.60e-08	143
carcinoma	7.25e-08	106

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
BRCA1#672	2	13.4561537621492	0.00711980771608456	0.0296438206849049
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0465059791552047
ELK4#2005	3	16.235681658468	0.000233604395574599	0.00256436929466213
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154841373226075
GTF2B#2959	2	21.2958866228828	0.00287818058991141	0.0155909908002986
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157702622438346
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270887702030287
POLR3A#11128	1	113.044036697248	0.0088200988100312	0.0334992472041912
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0278352553890698
SMARCB1#6598	2	12.1684771874383	0.00867500222192174	0.0330153981872781
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331335370731777

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.