Coexpression cluster:C1426

Full id: C1426_CD14_bile_mucinous_lung_large_glioblastoma_nonsmall

Phase1 CAGE Peaks

Hg19::chr16:83986837..83986852,+	p1@OSGIN1
Hg19::chr1:94374914..94374922,-	p7@GCLM
Hg19::chr1:94374946..94374994,-	p1@GCLM
Hg19::chr20:633833..633851,-	p1@SRXN1
Hg19::chr4:139092367..139092379,-	p@chr4:139092367..139092379 -
Hg19::chr4:139163058..139163082,-	p8@SLC7A11

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:0006979	response to oxidative stress	0.00267447141343291
GO:0035226	glutamate-cysteine ligase catalytic subunit binding	0.00267447141343291
GO:0015327	cystine:glutamate antiporter activity	0.00267447141343291
GO:0035229	positive regulation of glutamate-cysteine ligase activity	0.00267447141343291
GO:0032542	sulfiredoxin activity	0.00267447141343291
GO:0035227	regulation of glutamate-cysteine ligase activity	0.00267447141343291
GO:0051409	response to nitrosative stress	0.00267447141343291
GO:0017109	glutamate-cysteine ligase complex	0.00416010516649996
GO:0004357	glutamate-cysteine ligase activity	0.00416010516649996
GO:0005294	neutral L-amino acid secondary active transmembrane transporter activity	0.00534823430200747
GO:0015184	L-cystine transmembrane transporter activity	0.00534823430200747
GO:0051900	regulation of mitochondrial depolarization	0.00534823430200747
GO:0000099	sulfur amino acid transmembrane transporter activity	0.00534823430200747
GO:0051351	positive regulation of ligase activity	0.00534823430200747
GO:0051882	mitochondrial depolarization	0.00623933116986053
GO:0051340	regulation of ligase activity	0.00660605893926391
GO:0006534	cysteine metabolic process	0.00660605893926391
GO:0005313	L-glutamate transmembrane transporter activity	0.0078802164471195
GO:0006750	glutathione biosynthetic process	0.0078802164471195
GO:0015172	acidic amino acid transmembrane transporter activity	0.00802058041895813
GO:0051899	membrane depolarization	0.00802058041895813
GO:0051881	regulation of mitochondrial membrane potential	0.00894971234644914
GO:0043524	negative regulation of neuron apoptosis	0.00894971234644914
GO:0005829	cytosol	0.0108478504797685
GO:0042221	response to chemical stimulus	0.0111896010626077
GO:0006536	glutamate metabolic process	0.0115131714638974
GO:0015175	neutral amino acid transmembrane transporter activity	0.0117791598889394
GO:0006749	glutathione metabolic process	0.0126936457064729
GO:0043523	regulation of neuron apoptosis	0.0161219563560019
GO:0016667	oxidoreductase activity, acting on sulfur group of donors	0.0169452130303383
GO:0005275	amine transmembrane transporter activity	0.0169452130303383
GO:0000096	sulfur amino acid metabolic process	0.0169452130303383
GO:0051402	neuron apoptosis	0.0169975821508008
GO:0042391	regulation of membrane potential	0.0170468221915915
GO:0015179	L-amino acid transmembrane transporter activity	0.0170932013623182
GO:0065008	regulation of biological quality	0.0200632651173214
GO:0035150	regulation of tube size	0.0206031839965857
GO:0050880	regulation of blood vessel size	0.0206031839965857
GO:0003018	vascular process in circulatory system	0.0206031839965857
GO:0044272	sulfur compound biosynthetic process	0.0210205779842032
GO:0009653	anatomical structure morphogenesis	0.0211854925063784
GO:0015300	solute:solute antiporter activity	0.0223308459100891
GO:0030308	negative regulation of cell growth	0.0223308459100891
GO:0045792	negative regulation of cell size	0.0223308459100891
GO:0048523	negative regulation of cellular process	0.0223308459100891
GO:0009069	serine family amino acid metabolic process	0.0223308459100891
GO:0048519	negative regulation of biological process	0.0230630761274883
GO:0045926	negative regulation of growth	0.0230630761274883
GO:0006950	response to stress	0.0230630761274883
GO:0015171	amino acid transmembrane transporter activity	0.0230630761274883
GO:0042493	response to drug	0.0230630761274883
GO:0006865	amino acid transport	0.0251250696915076
GO:0009064	glutamine family amino acid metabolic process	0.0284879107806133
GO:0035239	tube morphogenesis	0.0284879107806133
GO:0015837	amine transport	0.0284879107806133
GO:0006790	sulfur metabolic process	0.0286428388044346
GO:0015297	antiporter activity	0.029769822580319
GO:0046943	carboxylic acid transmembrane transporter activity	0.0302525219420084
GO:0046942	carboxylic acid transport	0.0302525219420084
GO:0015849	organic acid transport	0.0302525219420084
GO:0005342	organic acid transmembrane transporter activity	0.0302525219420084
GO:0016491	oxidoreductase activity	0.0303262360818528
GO:0046982	protein heterodimerization activity	0.0310591708125885
GO:0035295	tube development	0.0340499713122673
GO:0048869	cellular developmental process	0.0381580052831729
GO:0030154	cell differentiation	0.0381580052831729
GO:0008015	blood circulation	0.0436428645669278
GO:0003013	circulatory system process	0.0436428645669278
GO:0001558	regulation of cell growth	0.0436428645669278
GO:0048856	anatomical structure development	0.0438016778475504

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
animal cell	3.16e-22	679
eukaryotic cell	3.16e-22	679
epithelial cell	1.98e-16	254
somatic cell	6.48e-13	591
native cell	1.13e-11	722
monopoietic cell	3.71e-11	63
monocyte	3.71e-11	63
monoblast	3.71e-11	63
promonocyte	3.71e-11	63
embryonic cell	4.46e-11	248
mesodermal cell	5.30e-11	119
CD14-positive, CD16-negative classical monocyte	1.57e-10	42
classical monocyte	3.08e-10	45
macrophage dendritic cell progenitor	4.20e-10	65
myeloid lineage restricted progenitor cell	4.33e-10	70
myeloid leukocyte	4.21e-09	76
lining cell	3.47e-08	57
barrier cell	3.47e-08	57
granulocyte monocyte progenitor cell	7.47e-08	71
squamous epithelial cell	8.01e-08	62

Uber Anatomy

Ontology term	p-value	n
mesoderm	2.14e-19	448
mesoderm-derived structure	2.14e-19	448
presumptive mesoderm	2.14e-19	448
anatomical system	1.69e-11	625
musculoskeletal system	2.74e-11	167
anatomical group	2.96e-11	626
multi-cellular organism	3.33e-11	659
trunk	5.49e-11	216
epithelial tube	4.91e-10	118
germ layer	1.14e-08	604
embryonic tissue	1.14e-08	604
presumptive structure	1.14e-08	604
epiblast (generic)	1.14e-08	604
embryonic structure	1.90e-08	605
developing anatomical structure	1.90e-08	605
immune system	2.62e-08	115
bone marrow	5.53e-08	80
lateral plate mesoderm	6.39e-08	216
skeletal element	7.15e-08	101
skeletal system	7.15e-08	101
trunk mesenchyme	1.05e-07	143
artery	1.45e-07	42
arterial blood vessel	1.45e-07	42
arterial system	1.45e-07	42
unilaminar epithelium	1.55e-07	138
embryo	2.47e-07	612
bone element	3.83e-07	86
mesenchyme	7.09e-07	238
entire embryonic mesenchyme	7.09e-07	238
organ	7.49e-07	511

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
BCLAF1#9774	3	10.8263238050609	0.00177235104699106	0.0108896676665902
CCNT2#905	4	4.22413438464176	0.00710980547887581	0.0296116196525886
CTCF#10664	4	3.57350424871668	0.0131663500723851	0.0466049969567812
CTCFL#140690	3	9.87323717948718	0.00231276002785771	0.0131187456305361
E2F1#1869	5	4.08949101239944	0.00174981759776199	0.0107588131456885
E2F4#1874	3	6.33403015764222	0.00819717536837434	0.0323620170219115
E2F6#1876	5	4.18096310974782	0.00157359875958697	0.0099748167548254
EGR1#1958	5	4.15681591234178	0.00161796681886444	0.010133663364041
ELF1#1997	5	3.54841496567295	0.00344683777572169	0.0175311332647608
FOS#2353	4	5.99863687259627	0.00189982371188635	0.0111840194265091
FOSL1#8061	3	19.8567898581865	0.000301402757252219	0.00311049432457159
GTF2B#2959	3	15.9719149671621	0.000571165371589299	0.00486716222612719
HDAC2#3066	4	8.9437468244175	0.000409407956530718	0.00390307234797915
HEY1#23462	5	3.36675920258809	0.00442382704520303	0.0209504408821457
HNF4A#3172	3	11.5661451814768	0.00146348715008573	0.00937700211458919
JUN#3725	3	6.25641459616817	0.00848634685095487	0.0324143502456525
JUND#3727	4	4.66310929458068	0.00491764340826023	0.0229919312344566
MAFF#23764	4	37.5435709932968	1.44675523683818e-06	5.6232850829975e-05
MAFK#7975	4	18.0671554252199	2.61700332070418e-05	0.000564238666001288
NFE2#4778	3	38.6021303258145	4.21574363639564e-05	0.000754822646393835
REST#5978	4	6.43335247741868	0.00145495422303207	0.00932518957344256
SIN3A#25942	5	4.50740393901261	0.00109611006120864	0.00766088728384988
SMC3#9126	3	7.52246642246642	0.00503954071682855	0.0234819573893485
STAT1#6772	3	10.3532937485996	0.00201668045992093	0.0117219551732904
STAT2#6773	2	21.7545903954802	0.00337914239989322	0.0172557330873483
STAT3#6774	3	5.25973249857712	0.0137766205807855	0.048471111603445
TAF1#6872	5	2.78587190478774	0.0107863634029041	0.039792193833836
TAF7#6879	3	5.71653470246196	0.0109272937988966	0.04021267220095
TBP#6908	5	3.08897557258032	0.00664544827578693	0.0282879141012803
TCF7L2#6934	4	7.18011770875823	0.000955329712067973	0.00687572736535504

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.