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{{Coexpression_clusters
{
|full_id=C281_Hodgkin_Reticulocytes_chronic_NK_acute_retinoblastoma_small

Latest revision as of 11:13, 17 September 2013


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.valueFDRnGenesnPathwayName
1.73178102544466e-091.82702898184412e-07536DNA replication (KEGG):03030
1.10325843968138e-067.75958435909238e-055128Cell cycle (KEGG):04110
1.90743271438225e-071.50925613525496e-05590Cell cycle (Wikipathways):WP179
4.98652049775905e-084.50923925011639e-06569G1 to S cell cycle control (Wikipathways):WP45
3.02355555239963e-114.78477666167241e-09642DNA Replication (Wikipathways):WP1806
3.24591931887469e-104.10933385769536e-087117Cell Cycle Checkpoints (Reactome):REACT_1538
9.80048795126114e-192.0679029577161e-1613200DNA Replication (Reactome):REACT_383
4.12598982903211e-231.30587578088866e-2017315Cell Cycle, Mitotic (Reactome):REACT_152
4.59313990527007e-060.000290745756003595477Chromosome Maintenance (Reactome):REACT_22172
1.45366014094568e-050.0008365153356532855217IL-4 up reg. targets (Netpath):NetPath_16
3.21151604202121e-242.03288965459943e-2118346{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 IDGO nameFDR corrected p-value
GO:0007049cell cycle2.2622870125023e-16
GO:0005634nucleus4.23132874348546e-16
GO:0000278mitotic cell cycle4.23132874348546e-16
GO:0007067mitosis4.73789433253988e-16
GO:0000087M phase of mitotic cell cycle5.12106063799647e-16
GO:0022403cell cycle phase1.06305146223658e-15
GO:0000279M phase5.36970925071529e-15
GO:0044427chromosomal part1.54973723668964e-14
GO:0005694chromosome8.60797535452794e-14
GO:0022402cell cycle process5.66852759063077e-13
GO:0006260DNA replication1.03837854370626e-12
GO:0051301cell division1.05783228862849e-12
GO:0006259DNA metabolic process1.46945657366705e-10
GO:0043231intracellular membrane-bound organelle1.66140932120097e-09
GO:0043227membrane-bound organelle1.66140932120097e-09
GO:0044424intracellular part1.3146869847198e-08
GO:0043232intracellular non-membrane-bound organelle8.2588349448905e-08
GO:0043228non-membrane-bound organelle8.2588349448905e-08
GO:0043229intracellular organelle1.19354022890078e-07
GO:0043226organelle1.19354022890078e-07
GO:0005622intracellular1.66797348673978e-07
GO:0000775chromosome, pericentric region2.09800396016375e-07
GO:0006270DNA replication initiation8.34699349280514e-07
GO:0044446intracellular organelle part1.14054474853553e-06
GO:0044422organelle part1.14054474853553e-06
GO:0005515protein binding2.15921584624533e-06
GO:0007059chromosome segregation4.82429953233651e-06
GO:0000785chromatin9.46384353276404e-06
GO:0051276chromosome organization and biogenesis1.06858606676366e-05
GO:0005819spindle1.34265301171587e-05
GO:0008094DNA-dependent ATPase activity1.66799956858821e-05
GO:0006996organelle organization and biogenesis1.76202849550051e-05
GO:0051325interphase2.16802053167748e-05
GO:0000070mitotic sister chromatid segregation3.08816827560101e-05
GO:0000819sister chromatid segregation3.34379228715376e-05
GO:0005657replication fork4.40378841206214e-05
GO:0006974response to DNA damage stimulus4.81360124306943e-05
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000108722617716028
GO:0009719response to endogenous stimulus0.000117470101438644
GO:0043283biopolymer metabolic process0.000167176629529225
GO:0006261DNA-dependent DNA replication0.000192833643950437
GO:0000074regulation of progression through cell cycle0.000216788887620517
GO:0051726regulation of cell cycle0.000229491532198212
GO:0044454nuclear chromosome part0.000339765109271521
GO:0051329interphase of mitotic cell cycle0.000676580578926927
GO:0007076mitotic chromosome condensation0.000750958522993768
GO:0042393histone binding0.000750958522993768
GO:0033261regulation of progression through S phase0.000750958522993768
GO:0006268DNA unwinding during replication0.000840195654269063
GO:0000228nuclear chromosome0.000957776371677201
GO:0032508DNA duplex unwinding0.00100818016843514
GO:0032392DNA geometric change0.00100818016843514
GO:0015630microtubule cytoskeleton0.00103930445808119
GO:0051320S phase0.00130583703614917
GO:0030261chromosome condensation0.00130583703614917
GO:0005874microtubule0.00139015296694561
GO:0003682chromatin binding0.00141128873301318
GO:0031570DNA integrity checkpoint0.00221916089286448
GO:0043234protein complex0.00225183398328797
GO:0044464cell part0.00296865886201738
GO:0000910cytokinesis0.003119778122116
GO:0006334nucleosome assembly0.00497338741349375
GO:0000797condensin core heterodimer0.0055477277281626
GO:0042555MCM complex0.0055477277281626
GO:0016043cellular component organization and biogenesis0.0055477277281626
GO:0006325establishment and/or maintenance of chromatin architecture0.0055477277281626
GO:0006323DNA packaging0.00573896838337752
GO:0031497chromatin assembly0.00624707207923037
GO:0006950response to stress0.00625642725097969
GO:0000075cell cycle checkpoint0.00736081192008598
GO:0042623ATPase activity, coupled0.00927002131673787
GO:0006335DNA replication-dependent nucleosome assembly0.00975672228502966
GO:0008054cyclin catabolic process0.00975672228502966
GO:0007088regulation of mitosis0.00982138043682869
GO:0044430cytoskeletal part0.00982138043682869
GO:0006333chromatin assembly or disassembly0.0119665280658995
GO:0065004protein-DNA complex assembly0.0129432942435279
GO:0007080mitotic metaphase plate congression0.0131832376806434
GO:0005721centric heterochromatin0.0131832376806434
GO:0000796condensin complex0.0131832376806434
GO:0008278cohesin complex0.0131832376806434
GO:0016887ATPase activity0.0150837754738875
GO:0032991macromolecular complex0.0158122035536006
GO:0007017microtubule-based process0.0158122035536006
GO:0004844uracil DNA N-glycosylase activity0.0158122035536006
GO:0051310metaphase plate congression0.0158122035536006
GO:0001833inner cell mass cell proliferation0.0158122035536006
GO:0051319G2 phase0.0158122035536006
GO:0000085G2 phase of mitotic cell cycle0.0158122035536006
GO:0031536positive regulation of exit from mitosis0.0158122035536006
GO:0044428nuclear part0.0179596894477362
GO:0051322anaphase0.0179596894477362
GO:0000090mitotic anaphase0.0179596894477362
GO:0006977DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest0.0179596894477362
GO:0045120pronucleus0.0179596894477362
GO:0031571G1 DNA damage checkpoint0.0179596894477362
GO:0003688DNA replication origin binding0.0179596894477362
GO:0016728oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor0.0179596894477362
GO:0004748ribonucleoside-diphosphate reductase activity0.0179596894477362
GO:0003689DNA clamp loader activity0.019930611063397
GO:0001832blastocyst growth0.019930611063397
GO:0000076DNA replication checkpoint0.019930611063397
GO:0033170DNA-protein loading ATPase activity0.019930611063397
GO:0051303establishment of chromosome localization0.019930611063397
GO:0050000chromosome localization0.019930611063397
GO:0032297negative regulation of DNA replication initiation0.019930611063397
GO:0005678chromatin assembly complex0.019930611063397
GO:0000808origin recognition complex0.0224481117831134
GO:0005664nuclear origin of replication recognition complex0.0224481117831134
GO:0005663DNA replication factor C complex0.0224481117831134
GO:0006281DNA repair0.0224481117831134
GO:0043170macromolecule metabolic process0.0230543629591933
GO:0050794regulation of cellular process0.0242792693903073
GO:0030496midbody0.0242792693903073
GO:0016725oxidoreductase activity, acting on CH or CH2 groups0.0242792693903073
GO:0005881cytoplasmic microtubule0.0242792693903073
GO:0030174regulation of DNA replication initiation0.0242792693903073
GO:0009186deoxyribonucleoside diphosphate metabolic process0.0270695607957624
GO:0031575G1/S transition checkpoint0.0298100699135142
GO:0007090regulation of S phase of mitotic cell cycle0.0325020439979642
GO:0005856cytoskeleton0.0374383002906492
GO:0010458exit from mitosis0.0374383002906492
GO:0007096regulation of exit from mitosis0.0374383002906492
GO:0009132nucleoside diphosphate metabolic process0.0396538422203975
GO:0001824blastocyst development0.0396538422203975
GO:0030330DNA damage response, signal transduction by p53 class mediator0.0449154254061793
GO:0043596nuclear replication fork0.0464162094595863
GO:0008156negative regulation of DNA replication0.0464162094595863
GO:0000084S phase of mitotic cell cycle0.0464162094595863
GO:0050789regulation of biological process0.0464162094595863
GO:0017111nucleoside-triphosphatase activity0.0468039257702775
GO:0005876spindle microtubule0.0478239994334
GO:0019104DNA N-glycosylase activity0.0478239994334
GO:0005524ATP binding0.0493434192289268
GO:0051053negative regulation of DNA metabolic process0.0493434192289268
GO:0007051spindle organization and biogenesis0.0493434192289268



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 termp-valuen
epithelial cell1.05e-21253
animal cell5.56e-17679
eukaryotic cell5.56e-17679
embryonic cell8.38e-11250
native cell1.20e-09722
migratory neural crest cell8.98e-0941
neurectodermal cell6.73e-0859
neural cell1.73e-0725
ectodermal cell7.36e-0772
Disease
Ontology termp-valuen
cancer8.40e-48235
disease of cellular proliferation1.42e-46239
organ system cancer6.42e-24137
cell type cancer2.61e-23143
hematologic cancer5.17e-2151
immune system cancer5.17e-2151
carcinoma1.35e-18106
leukemia6.87e-1739
myeloid leukemia2.44e-1231


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)
MA0003.16.96095
MA0004.10.623722
MA0006.11.67221
MA0007.10.904552
MA0009.10.282049
MA0014.16.33056
MA0017.10.163868
MA0019.10.637656
MA0024.18.18149
MA0025.10.383675
MA0027.11.77546
MA0028.12.71532
MA0029.10.222602
MA0030.10.215031
MA0031.10.174316
MA0038.13.15106
MA0040.10.226506
MA0041.10.0434336
MA0042.10.0344066
MA0043.10.282278
MA0046.10.274202
MA0048.10.0855519
MA0050.10.324596
MA0051.10.0713589
MA0052.10.2291
MA0055.10.0982142
MA0056.10
MA0057.10.210418
MA0058.10.633056
MA0059.10.0757992
MA0060.126.4223
MA0061.10.190797
MA0063.10
MA0066.10.924061
MA0067.10.537012
MA0068.10.110487
MA0069.10.746822
MA0070.11.34024
MA0071.10.212157
MA0072.10.260306
MA0073.13.17614
MA0074.10.248986
MA0076.11.83077
MA0077.10.254892
MA0078.10.371676
MA0081.10.38039
MA0083.10.287504
MA0084.10.703837
MA0087.10.258584
MA0088.11.33508
MA0089.10
MA0090.10.0971665
MA0091.10.350729
MA0092.10.119932
MA0093.11.31245
MA0095.10
MA0098.10
MA0100.11.98721
MA0101.10.259452
MA0103.10.108723
MA0105.10.655342
MA0106.10.303356
MA0107.10.253705
MA0108.20.172469
MA0109.10
MA0111.10.26112
MA0113.10.0981023
MA0114.10.241927
MA0115.10.471806
MA0116.10.261874
MA0117.10.83365
MA0119.12.04178
MA0122.10.329219
MA0124.10.437263
MA0125.10.36951
MA0130.10
MA0131.10.790153
MA0132.10
MA0133.10
MA0135.10.304312
MA0136.10.262713
MA0139.12.28907
MA0140.10.0574137
MA0141.10.192805
MA0142.10.155551
MA0143.10.0981847
MA0144.10.0453363
MA0145.11.29506
MA0146.13.78728
MA0147.11.56199
MA0148.10.0453767
MA0149.11.64974
MA0062.23.64086
MA0035.20.0571647
MA0039.26.75105
MA0138.20.11686
MA0002.20.229858
MA0137.20.0526133
MA0104.21.70965
MA0047.20.0852269
MA0112.20.266225
MA0065.20.1479
MA0150.10.0929679
MA0151.10
MA0152.10.472076
MA0153.10.356306
MA0154.11.23683
MA0155.10.443381
MA0156.10.505588
MA0157.10.140121
MA0158.10
MA0159.10.444017
MA0160.10.187803
MA0161.10
MA0162.12.66971
MA0163.12.33408
MA0164.10.103984
MA0080.20.440272
MA0018.20.632229
MA0099.20.0598901
MA0079.22.9434
MA0102.20.737926
MA0258.10.0396648
MA0259.11.63407
MA0442.10



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#promotersEnrichmentp-valueq-value
ATF3#46783.906639048001520.0008802442404598030.00656327752048128
BRCA1#672177.459389585539222.82155000628658e-113.2961953143911e-09
CCNT2#905273.719074838651984.04350394519681e-114.60522910068058e-09
CEBPB#1051183.119144723148844.91862943371598e-060.000151981283854397
CHD2#1106296.521231786725851.21757787234564e-182.81957018647243e-16
CTCF#10664171.98096431178860.002725543805451130.0149699221402845
E2F1#1869434.58734209216981.50454397185039e-265.13506757764978e-24
E2F4#18744612.66806031528441.76573713046307e-511.33631753745241e-48
E2F6#1876404.362744114519472.41674140627385e-226.84016411191962e-20
EGR1#1958262.819405575327475.55188025335704e-083.48247941009223e-06
ELF1#1997373.424991836432155.53203736297706e-161.06597869031727e-13
ELK4#2005176.000143221607758.10042517794397e-107.62849689052561e-08
ETS1#2113255.287370066414311.54067483751828e-132.36279793473674e-11
FOS#2353244.69458537855368.28022629338877e-121.04315868981331e-09
GABPB1#2553294.45571372281053.3500796044433e-145.54483302390577e-12
GTF2B#295964.166586513172730.003004892903739890.0159684531610284
GTF2F1#2962195.26203384039995.13746641815713e-104.95888960486056e-08
HDAC2#3066113.20808310006280.0004524793609979790.00420730875919409
HEY1#23462464.040111043105711.25461817719195e-284.69645404328853e-26
HMGN3#9324305.333835471750395.44060644509474e-171.10978807913916e-14
IRF1#3659406.641011959620781.93474408407452e-297.5678927863917e-27
IRF3#36611616.34154859530079.3341582565583e-161.76283933843887e-13
MAX#4149314.348461321287413.50041690683563e-156.24923147577788e-13
MXI1#4601286.063565339244794.94337318434796e-171.01430442436172e-14
MYC#4609364.087003203868237.36533682248907e-181.60590482756563e-15
NANOG#7992374.45029237754540.0009036676684637660.0065819197731144
NFKB1#4790293.459866071774372.34035757418545e-112.79023521336021e-09
NFYA#48002510.01390255425575.08776226885587e-201.2928486705524e-17
NFYB#4801279.83726995316271.15547122494712e-213.1508161687272e-19
NR2C2#718253.545066402743570.01306506352065560.0463470048243522
NRF1#4899174.512494578501865.70518661524608e-083.57006581731387e-06
PAX5#5079192.754820545486491.47724405940275e-050.000350401754076684
PBX3#5090104.764024497118293.49622827593698e-050.00068149045336055
POLR2A#5430462.147453176558075.35449299434509e-161.03367448028911e-13
POU2F2#5452163.167347498345231.71364315144799e-050.00039205077129042
REST#5978183.776098193267492.99108731249004e-071.50911192187994e-05
RFX5#5993266.809688728414628.224990812016e-171.66474770429484e-14
RXRA#625673.054833042911580.007352158876692580.030396742841649
SETDB1#986976.135656157523330.0001316759889185950.00173113149630779
SIN3A#25942465.408884726815141.84636119222069e-348.84550993368518e-32
SIX5#147912155.571755007214892.87913874308864e-081.96019798689331e-06
SMARCB1#6598114.364779860711562.96036183323798e-050.000613690411872849
SP1#6667445.450625666047823.87370492437202e-311.61826347438596e-28
SP2#6668179.66543518250784.73722805592909e-136.91959945361088e-11
SREBF1#672055.109331460922640.00288702855915930.0156186674794114
SRF#672292.699447920858920.005195387322461680.0240770791875477
TAF1#6872463.343046285745297.65155694296417e-252.42157865323102e-22
TAF7#6879256.213624676589083.81299227824374e-156.7840732631601e-13
TBP#6908453.626188715637778.29246962520681e-252.60860613008125e-22
TCF7L2#6934112.57547700422850.002728843984758630.0149856839270274
TFAP2C#7022184.229698151684445.35084286782104e-083.39511955207996e-06
THAP1#5514596.137441335340481.27803550244023e-050.000313472874211731
TRIM28#10155104.041418488100550.0001376742215399870.00179911887179863
USF1#7391212.904162713507981.61975465913921e-066.1447714074043e-05
USF2#7392102.824390735884690.002255529731620.0128108151860268
YY1#7528313.309702027075427.08853204881519e-129.0063162852337e-10
ZBTB33#1000964.130181525649720.003137552918294680.0164747556175856
ZBTB7A#51341243.835778769326555.85386447540758e-105.62439514210757e-08
ZEB1#693582.937118611746760.00520134483610080.0241036186421233
ZNF143#7702154.402459745291716.12780371364921e-072.81063545037246e-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

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