Coexpression cluster:C281

Full id: C281_Hodgkin_Reticulocytes_chronic_NK_acute_retinoblastoma_small

Phase1 CAGE Peaks

Hg19::chr11:57103327..57103372,-	p1@SSRP1
Hg19::chr11:61891463..61891535,+	p1@INCENP
Hg19::chr11:64851496..64851577,-	p1@CDCA5
Hg19::chr11:71791518..71791605,-	p2@NUMA1
Hg19::chr12:109535416..109535439,+	p3@UNG
Hg19::chr12:2986275..2986363,-	p1@FOXM1
Hg19::chr12:49717021..49717079,+	p1@TROAP
Hg19::chr12:49717081..49717088,+	p2@TROAP
Hg19::chr12:56843161..56843225,-	p1@TIMELESS
Hg19::chr12:6603253..6603303,+	p1@NCAPD2
Hg19::chr15:64673630..64673648,-	p1@KIAA0101
Hg19::chr16:2479390..2479409,+	p2@CCNF
Hg19::chr16:2479428..2479470,+	p1@CCNF
Hg19::chr16:2510094..2510152,+	p1@C16orf59
Hg19::chr16:85722530..85722615,-	p1@GINS2
Hg19::chr16:88870184..88870235,+	p1@CDT1
Hg19::chr17:3627185..3627224,+	p1@GSG2
Hg19::chr17:42219267..42219329,+	p1@C17orf53
Hg19::chr17:43025020..43025149,-	p1@KIF18B
Hg19::chr17:8113886..8113906,-	p1@AURKB
Hg19::chr19:12917412..12917466,+	p1@RNASEH2A
Hg19::chr1:26185844..26185954,-	p1@C1orf135
Hg19::chr1:38158135..38158174,+	p2@CDCA8
Hg19::chr1:38158178..38158237,+	p1@CDCA8
Hg19::chr20:25388293..25388372,+	p1@GINS1
Hg19::chr20:44441242..44441255,+	p3@UBE2C
Hg19::chr20:44441271..44441296,+	p1@UBE2C
Hg19::chr21:34960948..34961024,-	p1@DONSON
Hg19::chr21:37757668..37757731,+	p1@CHAF1B
Hg19::chr22:19467408..19467480,+	p1@CDC45
Hg19::chr22:46692747..46692847,+	p1@GTSE1
Hg19::chr2:10262857..10262873,+	p1@RRM2
Hg19::chr2:234763147..234763211,-	p1@HJURP
Hg19::chr2:25016282..25016339,+	p1@CENPO
Hg19::chr2:25016349..25016364,+	p3@CENPO
Hg19::chr2:27008888..27008968,+	p2@CENPA
Hg19::chr3:127317243..127317288,+	p1@MCM2
Hg19::chr3:48229860..48229918,-	p1@CDC25A
Hg19::chr3:49893958..49894005,-	p1@TRAIP
Hg19::chr4:1723197..1723261,+	p1@TACC3
Hg19::chr6:33359582..33359667,+	p1@KIFC1
Hg19::chr7:73668692..73668763,-	p1@RFC2
Hg19::chr7:99698956..99699038,-	p1@MCM7
Hg19::chr8:120868078..120868182,-	p1@DSCC1
Hg19::chr8:48873479..48873539,+	p1@MCM4
Hg19::chr9:139965000..139965028,-	p1@C9orf140

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

---

p.value	FDR	nGenes	nPathway	Name
1.73178102544466e-09	1.82702898184412e-07	5	36	DNA replication (KEGG):03030
1.10325843968138e-06	7.75958435909238e-05	5	128	Cell cycle (KEGG):04110
1.90743271438225e-07	1.50925613525496e-05	5	90	Cell cycle (Wikipathways):WP179
4.98652049775905e-08	4.50923925011639e-06	5	69	G1 to S cell cycle control (Wikipathways):WP45
3.02355555239963e-11	4.78477666167241e-09	6	42	DNA Replication (Wikipathways):WP1806
3.24591931887469e-10	4.10933385769536e-08	7	117	Cell Cycle Checkpoints (Reactome):REACT_1538
9.80048795126114e-19	2.0679029577161e-16	13	200	DNA Replication (Reactome):REACT_383
4.12598982903211e-23	1.30587578088866e-20	17	315	Cell Cycle, Mitotic (Reactome):REACT_152
4.59313990527007e-06	0.000290745756003595	4	77	Chromosome Maintenance (Reactome):REACT_22172
1.45366014094568e-05	0.000836515335653285	5	217	IL-4 up reg. targets (Netpath):NetPath_16
3.21151604202121e-24	2.03288965459943e-21	18	346	{CDC2,351} (Static Module):NA

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

---

GO ID	GO name	FDR corrected p-value
GO:0007049	cell cycle	2.2622870125023e-16
GO:0005634	nucleus	4.23132874348546e-16
GO:0000278	mitotic cell cycle	4.23132874348546e-16
GO:0007067	mitosis	4.73789433253988e-16
GO:0000087	M phase of mitotic cell cycle	5.12106063799647e-16
GO:0022403	cell cycle phase	1.06305146223658e-15
GO:0000279	M phase	5.36970925071529e-15
GO:0044427	chromosomal part	1.54973723668964e-14
GO:0005694	chromosome	8.60797535452794e-14
GO:0022402	cell cycle process	5.66852759063077e-13
GO:0006260	DNA replication	1.03837854370626e-12
GO:0051301	cell division	1.05783228862849e-12
GO:0006259	DNA metabolic process	1.46945657366705e-10
GO:0043231	intracellular membrane-bound organelle	1.66140932120097e-09
GO:0043227	membrane-bound organelle	1.66140932120097e-09
GO:0044424	intracellular part	1.3146869847198e-08
GO:0043232	intracellular non-membrane-bound organelle	8.2588349448905e-08
GO:0043228	non-membrane-bound organelle	8.2588349448905e-08
GO:0043229	intracellular organelle	1.19354022890078e-07
GO:0043226	organelle	1.19354022890078e-07
GO:0005622	intracellular	1.66797348673978e-07
GO:0000775	chromosome, pericentric region	2.09800396016375e-07
GO:0006270	DNA replication initiation	8.34699349280514e-07
GO:0044446	intracellular organelle part	1.14054474853553e-06
GO:0044422	organelle part	1.14054474853553e-06
GO:0005515	protein binding	2.15921584624533e-06
GO:0007059	chromosome segregation	4.82429953233651e-06
GO:0000785	chromatin	9.46384353276404e-06
GO:0051276	chromosome organization and biogenesis	1.06858606676366e-05
GO:0005819	spindle	1.34265301171587e-05
GO:0008094	DNA-dependent ATPase activity	1.66799956858821e-05
GO:0006996	organelle organization and biogenesis	1.76202849550051e-05
GO:0051325	interphase	2.16802053167748e-05
GO:0000070	mitotic sister chromatid segregation	3.08816827560101e-05
GO:0000819	sister chromatid segregation	3.34379228715376e-05
GO:0005657	replication fork	4.40378841206214e-05
GO:0006974	response to DNA damage stimulus	4.81360124306943e-05
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.000108722617716028
GO:0009719	response to endogenous stimulus	0.000117470101438644
GO:0043283	biopolymer metabolic process	0.000167176629529225
GO:0006261	DNA-dependent DNA replication	0.000192833643950437
GO:0000074	regulation of progression through cell cycle	0.000216788887620517
GO:0051726	regulation of cell cycle	0.000229491532198212
GO:0044454	nuclear chromosome part	0.000339765109271521
GO:0051329	interphase of mitotic cell cycle	0.000676580578926927
GO:0007076	mitotic chromosome condensation	0.000750958522993768
GO:0042393	histone binding	0.000750958522993768
GO:0033261	regulation of progression through S phase	0.000750958522993768
GO:0006268	DNA unwinding during replication	0.000840195654269063
GO:0000228	nuclear chromosome	0.000957776371677201
GO:0032508	DNA duplex unwinding	0.00100818016843514
GO:0032392	DNA geometric change	0.00100818016843514
GO:0015630	microtubule cytoskeleton	0.00103930445808119
GO:0051320	S phase	0.00130583703614917
GO:0030261	chromosome condensation	0.00130583703614917
GO:0005874	microtubule	0.00139015296694561
GO:0003682	chromatin binding	0.00141128873301318
GO:0031570	DNA integrity checkpoint	0.00221916089286448
GO:0043234	protein complex	0.00225183398328797
GO:0044464	cell part	0.00296865886201738
GO:0000910	cytokinesis	0.003119778122116
GO:0006334	nucleosome assembly	0.00497338741349375
GO:0000797	condensin core heterodimer	0.0055477277281626
GO:0042555	MCM complex	0.0055477277281626
GO:0016043	cellular component organization and biogenesis	0.0055477277281626
GO:0006325	establishment and/or maintenance of chromatin architecture	0.0055477277281626
GO:0006323	DNA packaging	0.00573896838337752
GO:0031497	chromatin assembly	0.00624707207923037
GO:0006950	response to stress	0.00625642725097969
GO:0000075	cell cycle checkpoint	0.00736081192008598
GO:0042623	ATPase activity, coupled	0.00927002131673787
GO:0006335	DNA replication-dependent nucleosome assembly	0.00975672228502966
GO:0008054	cyclin catabolic process	0.00975672228502966
GO:0007088	regulation of mitosis	0.00982138043682869
GO:0044430	cytoskeletal part	0.00982138043682869
GO:0006333	chromatin assembly or disassembly	0.0119665280658995
GO:0065004	protein-DNA complex assembly	0.0129432942435279
GO:0007080	mitotic metaphase plate congression	0.0131832376806434
GO:0005721	centric heterochromatin	0.0131832376806434
GO:0000796	condensin complex	0.0131832376806434
GO:0008278	cohesin complex	0.0131832376806434
GO:0016887	ATPase activity	0.0150837754738875
GO:0032991	macromolecular complex	0.0158122035536006
GO:0007017	microtubule-based process	0.0158122035536006
GO:0004844	uracil DNA N-glycosylase activity	0.0158122035536006
GO:0051310	metaphase plate congression	0.0158122035536006
GO:0001833	inner cell mass cell proliferation	0.0158122035536006
GO:0051319	G2 phase	0.0158122035536006
GO:0000085	G2 phase of mitotic cell cycle	0.0158122035536006
GO:0031536	positive regulation of exit from mitosis	0.0158122035536006
GO:0044428	nuclear part	0.0179596894477362
GO:0051322	anaphase	0.0179596894477362
GO:0000090	mitotic anaphase	0.0179596894477362
GO:0006977	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	0.0179596894477362
GO:0045120	pronucleus	0.0179596894477362
GO:0031571	G1 DNA damage checkpoint	0.0179596894477362
GO:0003688	DNA replication origin binding	0.0179596894477362
GO:0016728	oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor	0.0179596894477362
GO:0004748	ribonucleoside-diphosphate reductase activity	0.0179596894477362
GO:0003689	DNA clamp loader activity	0.019930611063397
GO:0001832	blastocyst growth	0.019930611063397
GO:0000076	DNA replication checkpoint	0.019930611063397
GO:0033170	DNA-protein loading ATPase activity	0.019930611063397
GO:0051303	establishment of chromosome localization	0.019930611063397
GO:0050000	chromosome localization	0.019930611063397
GO:0032297	negative regulation of DNA replication initiation	0.019930611063397
GO:0005678	chromatin assembly complex	0.019930611063397
GO:0000808	origin recognition complex	0.0224481117831134
GO:0005664	nuclear origin of replication recognition complex	0.0224481117831134
GO:0005663	DNA replication factor C complex	0.0224481117831134
GO:0006281	DNA repair	0.0224481117831134
GO:0043170	macromolecule metabolic process	0.0230543629591933
GO:0050794	regulation of cellular process	0.0242792693903073
GO:0030496	midbody	0.0242792693903073
GO:0016725	oxidoreductase activity, acting on CH or CH2 groups	0.0242792693903073
GO:0005881	cytoplasmic microtubule	0.0242792693903073
GO:0030174	regulation of DNA replication initiation	0.0242792693903073
GO:0009186	deoxyribonucleoside diphosphate metabolic process	0.0270695607957624
GO:0031575	G1/S transition checkpoint	0.0298100699135142
GO:0007090	regulation of S phase of mitotic cell cycle	0.0325020439979642
GO:0005856	cytoskeleton	0.0374383002906492
GO:0010458	exit from mitosis	0.0374383002906492
GO:0007096	regulation of exit from mitosis	0.0374383002906492
GO:0009132	nucleoside diphosphate metabolic process	0.0396538422203975
GO:0001824	blastocyst development	0.0396538422203975
GO:0030330	DNA damage response, signal transduction by p53 class mediator	0.0449154254061793
GO:0043596	nuclear replication fork	0.0464162094595863
GO:0008156	negative regulation of DNA replication	0.0464162094595863
GO:0000084	S phase of mitotic cell cycle	0.0464162094595863
GO:0050789	regulation of biological process	0.0464162094595863
GO:0017111	nucleoside-triphosphatase activity	0.0468039257702775
GO:0005876	spindle microtubule	0.0478239994334
GO:0019104	DNA N-glycosylase activity	0.0478239994334
GO:0005524	ATP binding	0.0493434192289268
GO:0051053	negative regulation of DNA metabolic process	0.0493434192289268
GO:0007051	spindle organization and biogenesis	0.0493434192289268

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>

---

Cell Type

Ontology term	p-value	n
epithelial cell	1.05e-21	253
animal cell	5.56e-17	679
eukaryotic cell	5.56e-17	679
embryonic cell	8.38e-11	250
native cell	1.20e-09	722
migratory neural crest cell	8.98e-09	41
neurectodermal cell	6.73e-08	59
neural cell	1.73e-07	25
ectodermal cell	7.36e-07	72

Disease

Ontology term	p-value	n
cancer	8.40e-48	235
disease of cellular proliferation	1.42e-46	239
organ system cancer	6.42e-24	137
cell type cancer	2.61e-23	143
hematologic cancer	5.17e-21	51
immune system cancer	5.17e-21	51
carcinoma	1.35e-18	106
leukemia	6.87e-17	39
myeloid leukemia	2.44e-12	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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ATF3#467	8	3.90663904800152	0.000880244240459803	0.00656327752048128
BRCA1#672	17	7.45938958553922	2.82155000628658e-11	3.2961953143911e-09
CCNT2#905	27	3.71907483865198	4.04350394519681e-11	4.60522910068058e-09
CEBPB#1051	18	3.11914472314884	4.91862943371598e-06	0.000151981283854397
CHD2#1106	29	6.52123178672585	1.21757787234564e-18	2.81957018647243e-16
CTCF#10664	17	1.9809643117886	0.00272554380545113	0.0149699221402845
E2F1#1869	43	4.5873420921698	1.50454397185039e-26	5.13506757764978e-24
E2F4#1874	46	12.6680603152844	1.76573713046307e-51	1.33631753745241e-48
E2F6#1876	40	4.36274411451947	2.41674140627385e-22	6.84016411191962e-20
EGR1#1958	26	2.81940557532747	5.55188025335704e-08	3.48247941009223e-06
ELF1#1997	37	3.42499183643215	5.53203736297706e-16	1.06597869031727e-13
ELK4#2005	17	6.00014322160775	8.10042517794397e-10	7.62849689052561e-08
ETS1#2113	25	5.28737006641431	1.54067483751828e-13	2.36279793473674e-11
FOS#2353	24	4.6945853785536	8.28022629338877e-12	1.04315868981331e-09
GABPB1#2553	29	4.4557137228105	3.3500796044433e-14	5.54483302390577e-12
GTF2B#2959	6	4.16658651317273	0.00300489290373989	0.0159684531610284
GTF2F1#2962	19	5.2620338403999	5.13746641815713e-10	4.95888960486056e-08
HDAC2#3066	11	3.2080831000628	0.000452479360997979	0.00420730875919409
HEY1#23462	46	4.04011104310571	1.25461817719195e-28	4.69645404328853e-26
HMGN3#9324	30	5.33383547175039	5.44060644509474e-17	1.10978807913916e-14
IRF1#3659	40	6.64101195962078	1.93474408407452e-29	7.5678927863917e-27
IRF3#3661	16	16.3415485953007	9.3341582565583e-16	1.76283933843887e-13
MAX#4149	31	4.34846132128741	3.50041690683563e-15	6.24923147577788e-13
MXI1#4601	28	6.06356533924479	4.94337318434796e-17	1.01430442436172e-14
MYC#4609	36	4.08700320386823	7.36533682248907e-18	1.60590482756563e-15
NANOG#79923	7	4.4502923775454	0.000903667668463766	0.0065819197731144
NFKB1#4790	29	3.45986607177437	2.34035757418545e-11	2.79023521336021e-09
NFYA#4800	25	10.0139025542557	5.08776226885587e-20	1.2928486705524e-17
NFYB#4801	27	9.8372699531627	1.15547122494712e-21	3.1508161687272e-19
NR2C2#7182	5	3.54506640274357	0.0130650635206556	0.0463470048243522
NRF1#4899	17	4.51249457850186	5.70518661524608e-08	3.57006581731387e-06
PAX5#5079	19	2.75482054548649	1.47724405940275e-05	0.000350401754076684
PBX3#5090	10	4.76402449711829	3.49622827593698e-05	0.00068149045336055
POLR2A#5430	46	2.14745317655807	5.35449299434509e-16	1.03367448028911e-13
POU2F2#5452	16	3.16734749834523	1.71364315144799e-05	0.00039205077129042
REST#5978	18	3.77609819326749	2.99108731249004e-07	1.50911192187994e-05
RFX5#5993	26	6.80968872841462	8.224990812016e-17	1.66474770429484e-14
RXRA#6256	7	3.05483304291158	0.00735215887669258	0.030396742841649
SETDB1#9869	7	6.13565615752333	0.000131675988918595	0.00173113149630779
SIN3A#25942	46	5.40888472681514	1.84636119222069e-34	8.84550993368518e-32
SIX5#147912	15	5.57175500721489	2.87913874308864e-08	1.96019798689331e-06
SMARCB1#6598	11	4.36477986071156	2.96036183323798e-05	0.000613690411872849
SP1#6667	44	5.45062566604782	3.87370492437202e-31	1.61826347438596e-28
SP2#6668	17	9.6654351825078	4.73722805592909e-13	6.91959945361088e-11
SREBF1#6720	5	5.10933146092264	0.0028870285591593	0.0156186674794114
SRF#6722	9	2.69944792085892	0.00519538732246168	0.0240770791875477
TAF1#6872	46	3.34304628574529	7.65155694296417e-25	2.42157865323102e-22
TAF7#6879	25	6.21362467658908	3.81299227824374e-15	6.7840732631601e-13
TBP#6908	45	3.62618871563777	8.29246962520681e-25	2.60860613008125e-22
TCF7L2#6934	11	2.5754770042285	0.00272884398475863	0.0149856839270274
TFAP2C#7022	18	4.22969815168444	5.35084286782104e-08	3.39511955207996e-06
THAP1#55145	9	6.13744133534048	1.27803550244023e-05	0.000313472874211731
TRIM28#10155	10	4.04141848810055	0.000137674221539987	0.00179911887179863
USF1#7391	21	2.90416271350798	1.61975465913921e-06	6.1447714074043e-05
USF2#7392	10	2.82439073588469	0.00225552973162	0.0128108151860268
YY1#7528	31	3.30970202707542	7.08853204881519e-12	9.0063162852337e-10
ZBTB33#10009	6	4.13018152564972	0.00313755291829468	0.0164747556175856
ZBTB7A#51341	24	3.83577876932655	5.85386447540758e-10	5.62439514210757e-08
ZEB1#6935	8	2.93711861174676	0.0052013448361008	0.0241036186421233
ZNF143#7702	15	4.40245974529171	6.12780371364921e-07	2.81063545037246e-05

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

---