Coexpression cluster:C109

Full id: C109_Reticulocytes_non_acute_Hodgkin_Burkitt_retinoblastoma_lymphoma

Phase1 CAGE Peaks

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Hg19::chr10:129924611..129924662,-	p1@MKI67
Hg19::chr10:129924668..129924722,-	p2@MKI67
Hg19::chr10:13203543..13203587,+	p1@MCM10
Hg19::chr10:14920843..14920886,+	p1@SUV39H2
Hg19::chr10:27444268..27444301,+	p1@MASTL
Hg19::chr10:5454505..5454540,+	p3@NET1
Hg19::chr10:58120996..58121039,-	p1@ZWINT
Hg19::chr10:62538228..62538244,+	p1@CDK1
Hg19::chr10:62538248..62538260,+	p2@CDK1
Hg19::chr10:70231639..70231735,-	p1@DNA2
Id	Short description

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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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p.value	FDR	nGenes	nPathway	Name

p.value	FDR	nGenes	nPathway	Name
8.82e-20	1.12e-17	15	90	Cell cycle (Wikipathways)
2.10e-9	1.21e-7	5	13	{RAD51,13} (Static Module)
2.51e-9	1.22e-7	6	28	Homologous recombination (KEGG)
2.40e-9	1.22e-7	9	114	Oocyte meiosis (KEGG)
4.20e-7	1.56e-5	5	34	{PCNA,34} (Static Module)
2.31e-10	1.63e-8	7	36	DNA replication (KEGG)
3.94e-8	1.78e-6	7	73	DNA damage response (Wikipathways)
5.55e-7	1.95e-5	7	107	DNA Repair (Reactome)
7.05e-5	2.03e-3	6	154	Integrated Breast Cancer Pathway (Wikipathways)
9.67e-52	2.04e-49	38	200	DNA Replication (Reactome)

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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 ID	GO name	FDR corrected p-value
GO:0000019	regulation of mitotic recombination	2.37e-2
GO:0000070	mitotic sister chromatid segregation	3.70e-15
GO:0000074	regulation of progression through cell cycle	5.92e-18
GO:0000075	cell cycle checkpoint	7.78e-18
GO:0000076	DNA replication checkpoint	7.98e-4
GO:0000077	DNA damage checkpoint	4.13e-4
GO:0000079	regulation of cyclin-dependent protein kinase activity	1.31e-4
GO:0000080	G1 phase of mitotic cell cycle	5.76e-3
GO:0000085	G2 phase of mitotic cell cycle	2.93e-2
GO:0000086	G2/M transition of mitotic cell cycle	5.76e-3

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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

Ontology term	p-value	n
neural cell	1.00e-07	25
native cell	1.05e-07	722
epithelial cell	1.18e-13	253
animal cell	7.43e-12	679
eukaryotic cell	7.43e-12	679
neurectodermal cell	9.93e-07	59

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Disease

Ontology term	p-value	n

Ontology term	p-value	n
cell type cancer	1.42e-28	143
carcinoma	1.66e-22	106
leukemia	1.75e-19	39
disease of cellular proliferation	1.76e-57	239
cancer	3.38e-59	235
hematologic cancer	3.48e-24	51
immune system cancer	3.48e-24	51
myeloid leukemia	7.75e-15	31
organ system cancer	8.61e-30	137

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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

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Motifs	-log10(p-value)

Motifs	-log10(p-value)
motif37_GCTCGCA	8.29
motif82_TTGAATCGCGG	8.13
motif92_GCGKWWNAA	7.06
motif107_CGTCTGCGTA	7.04
motif117_SKSNGCGCTSN	6.77
motif46_CGNAGT	6.26
motif73_GAGCKMGC	6.01
motif139_CGTTCGAATT	5.50
motif3_CGCTNA	5.02
motif114_AAACCCGCTC	4.82

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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
ATF3#467	25	3.20902493228696	2.99036018049575e-07	1.50947427206764e-05
BCL3#602	13	2.5663562082777	0.00188248528005793	0.0110913280020292
BCLAF1#9774	42	5.19663542642924	8.8765288503037e-19	2.0739503279572e-16
BRCA1#672	69	7.95835379647108	2.08531332636188e-43	1.30411999096951e-40
CCNT2#905	103	3.72930721386944	2.08502963204116e-38	1.13415838406639e-35
CEBPB#1051	58	2.64186607027337	1.29244564773917e-12	1.79496982718393e-10
CHD2#1106	127	7.50680514247338	2.23159292065808e-88	3.06664911895538e-85
CTCF#10664	60	1.83780218505429	6.84688254025659e-07	3.09693185630948e-05
CTCFL#140690	30	3.38510989010989	4.97262058296064e-09	4.00412892107808e-07
E2F1#1869	162	4.542840301774	7.18484573172608e-95	1.087504497646e-91
E2F4#1874	173	12.5232824831098	8.58749244045613e-188	3.09265214823724e-184
E2F6#1876	146	4.18574135330182	7.93067246808312e-73	9.10188463619927e-70
EGR1#1958	109	3.10692297905317	4.98344976916624e-34	2.34444374072952e-31
ELF1#1997	152	3.69846222707855	1.401575159797e-70	1.50906297024782e-67
ELK4#2005	65	6.03039604457384	1.61182012092964e-33	7.44853458450311e-31
EP300#2033	39	1.50962129898688	0.00504822920127289	0.0235140491281661
ETS1#2113	112	6.2264069902095	5.55822721625236e-66	5.6358805071668e-63
FOS#2353	99	5.09027186046026	2.66269186441772e-48	1.85392583751948e-45
FOSL2#2355	21	2.0316240725474	0.00164723367542335	0.0103052256995052
FOXA1#3169	47	2.97615273269209	6.5599742044369e-12	8.41667255451087e-10
GABPB1#2553	107	4.32138383126567	1.48721583193014e-46	9.83059077664253e-44
GATA1#2623	60	4.64924850644586	8.6134245134183e-25	2.70143376203271e-22
GATA3#2625	18	2.80147025388405	8.86092084179814e-05	0.00129811433833154
GTF2B#2959	51	9.30934472371735	1.59091594665046e-34	7.656851177522e-32
GTF2F1#2962	81	5.89664303438497	2.33394101551043e-42	1.41717712627264e-39
HDAC2#3066	42	3.2197488567903	1.01353963542501e-11	1.26618499981044e-09
HEY1#23462	174	4.01702469428796	3.1669055009569e-104	5.60590582397352e-101
HMGN3#9324	92	4.29957937456145	4.96750252920554e-38	2.66051793152665e-35
HNF4A#3172	22	2.90805935991418	7.84466453758008e-06	0.000222270461106979
HNF4G#3174	16	2.62888434527514	0.00044341949353159	0.00412968507980611
IRF1#3659	145	6.32793568152438	5.35057396385227e-97	8.59705529555027e-94
IRF3#3661	59	15.8396296027308	3.15371845060316e-53	2.49523637320109e-50
IRF4#3662	20	2.5045157356279	0.000160425289468072	0.00199697935718189
JUN#3725	29	2.07355455187288	0.00014349990315681	0.00186753724433572
JUNB#3726	18	3.14852221643875	1.98785029278891e-05	0.000444749564542805
JUND#3727	71	2.83783508498767	1.82185029473507e-17	3.83613352685153e-15
MAFF#23764	11	3.53982240793941	0.000328020801771982	0.0033425860587632
MAX#4149	122	4.49835298342211	5.21955440039163e-58	4.74021775671741e-55
MXI1#4601	115	6.54617564175611	1.00771093762089e-70	1.09629502723113e-67
MYC#4609	101	3.014002680186	1.8584620883681e-29	7.29683917470211e-27
NANOG#79923	29	4.84627757685353	2.37708926970677e-12	3.22416657453124e-10
NFKB1#4790	119	3.73188312845181	3.61329131684236e-47	2.43463568928838e-44
NFYA#4800	112	11.7923716478915	9.53009508608791e-96	1.46369647161167e-92
NFYB#4801	113	10.8220379294264	1.00395280161665e-92	1.45627537011169e-89
NR2C2#7182	22	4.10012251380171	2.65575752648744e-08	1.8295821920107e-06
NR3C1#2908	28	2.39568373298769	1.56205385861904e-05	0.000365865312716559
NRF1#4899	80	5.58184203323927	5.01013411436673e-40	2.89090274458755e-37
PAX5#5079	83	3.16327965193006	3.41061327980397e-24	1.04765011861602e-21
PBX3#5090	26	3.25587045631627	1.275059606794e-07	7.29276836111493e-06
POLR2A#5430	175	2.14745317655807	7.45180401329323e-59	7.1399904527003e-56
POLR3A#11128	5	9.6894888597641	0.000187157979374115	0.00226364704202121
POU2F2#5452	89	4.63111452079477	5.24579633641302e-39	2.92976322769326e-36
RDBP#7936	7	6.145536159601	0.000166674082182185	0.00204310733204522
REST#5978	61	3.36372429533605	3.52846814894721e-18	7.87413856854483e-16
RFX5#5993	98	6.74683006322925	1.02937066149038e-58	9.68526509147688e-56
RXRA#6256	31	3.55607503607504	8.26773034892817e-10	7.7720386130667e-08
SETDB1#9869	41	9.44640613313388	8.16302694049053e-28	2.96020267582601e-25
SIN3A#25942	173	5.34706890136582	1.05891772484641e-123	2.30400642219239e-120
SIX5#147912	50	4.88191867298829	2.65798444302232e-21	7.15456797022701e-19
SMARCB1#6598	34	3.5462419231963	1.16953039463378e-10	1.25922252458925e-08
SMARCC1#6599	12	2.99405892477473	0.000776284295806765	0.00608529276962867
SP1#6667	148	4.81920253694202	2.50216627875889e-83	3.18687492667439e-80
SP2#6668	64	9.56471972346318	1.06359170007262e-44	6.81475175238556e-42
SPI1#6688	54	2.53161982548701	5.43673498928498e-11	6.09235156165165e-09
SREBF1#6720	25	6.71512134864119	8.55049267509536e-14	1.35099077835746e-11
SRF#6722	59	4.65162009981658	2.36652336745363e-24	7.31234715897897e-22
STAT1#6772	32	3.78634742805928	8.87395170813282e-11	9.68429093464664e-09
STAT2#6773	19	7.0857808716707	4.01443221402395e-11	4.58211241530543e-09
STAT3#6774	39	2.34433791365152	3.99638107446564e-07	1.93320075514644e-05
TAF1#6872	175	3.34304628574529	1.55290626467304e-92	2.22169832022175e-89
TAF7#6879	105	6.85984164295435	9.11257895869824e-65	9.0638917511189e-62
TAL1#6886	21	3.58423400129282	5.08385600166115e-07	2.37775565139941e-05
TBP#6908	175	3.70677068709639	2.13192217071704e-100	3.71093032645861e-97
TCF12#6938	38	2.30919809304619	8.47043702266688e-07	3.68141478239828e-05
TCF7L2#6934	56	3.44645650020395	4.94469186355296e-17	1.01258563438747e-14
TFAP2A#7020	38	3.58690346386119	5.35713562656047e-12	6.96754530139912e-10
TFAP2C#7022	58	3.58248719641082	1.82590427657175e-18	4.13656435446589e-16
THAP1#55145	30	5.37756764620308	6.86188160132018e-14	1.09411916421417e-11
TRIM28#10155	41	4.35549443917579	1.07666014070838e-15	2.02239763373097e-13
USF1#7391	88	3.19892535082457	2.18067284018526e-26	7.3943925570165e-24
USF2#7392	37	2.74692173284329	1.62547353457485e-08	1.1821924127957e-06
WRNIP1#56897	8	5.02034122740005	0.000226010408440665	0.00249490551179946
YY1#7528	146	4.09731959702093	1.5434855608852e-71	1.71489455843924e-68
ZBTB33#10009	44	7.96141657896669	6.83557709403704e-27	2.35610837004665e-24
ZBTB7A#51341	69	2.89875281281964	2.20434489150265e-17	4.60439152247289e-15
ZEB1#6935	38	3.66720238095238	2.77963020458267e-12	3.71705248318066e-10
ZNF143#7702	64	4.93746342481478	4.65397501926886e-28	1.69357664472969e-25
ZNF263#10127	59	2.77193518047789	9.55797559135582e-14	1.50109084629415e-11
ZZZ3#26009	4	5.47230199851962	0.00649622629937089	0.0278239574507872

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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