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Difference between revisions of "FF:10783-110G9"

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|created_by=
 
|created_by=
 
|creation_date=
 
|creation_date=
|data_phase=1
+
|data_phase=2
|datafreeze_phase=1
+
|datafreeze_phase=2
 
|def=
 
|def=
 
|expression_enrichment_score=chr2:114036488..114036504,-!p1@PAX8!1.78!58.76!PAX8;;chr15:83953397..83953425,-!p1@BNC1!1.46!32.18!BNC1;;chr2:60780607..60780624,-!p2@BCL11A!1.34!63.24!BCL11A;;chr20:50179368..50179392,-!p2@NFATC2!1.33!26.35!NFATC2;;chr4:57522166..57522260,-!p2@HOPX!1.30!21.87!HOPX;;chr9:100615499..100615519,+!p1@FOXE1!1.29!18.61!FOXE1;;chr6:34204921..34204939,+!p3@HMGA1!1.22!463.67!HMGA1;;chr4:57522598..57522664,-!p3@HOPX!1.13!12.45!HOPX;;chr20:42543441..42543497,+!p1@TOX2!1.12!54.94!TOX2;;chr19:45908292..45908374,-!p1@PPP1R13L!1.11!105.07!PPP1R13L;;chr2:60780753..60780800,-!p1@BCL11A!1.08!54.61!BCL11A;;chr11:65667884..65667895,-!p2@FOSL1!1.08!43.06!FOSL1;;chr8:106330656..106330684,+!p1@ZFPM2!1.08!29.38!ZFPM2;;chr12:77459306..77459365,-!p1@E2F7!1.06!133.21!E2F7;;chr17:8027418..8027432,-!p1@HES7!1.04!9.87!HES7;;chrY:21906594..21906622,-!p1@KDM5D!1.03!9.64!KDM5D;;chr13:73633131..73633149,+!p1@KLF5!1.01!101.48!KLF5;;chrY:2803415..2803468,+!p1@ZFY!1.00!9.08!ZFY;;chr3:25470156..25470227,+!p2@RARB!1.00!8.97!RARB;;chr5:50679228..50679288,+!p1@ISL1!0.98!8.63!ISL1;;chr5:2751762..2751784,-!p1@IRX2!0.98!8.52!IRX2;;chr3:25469724..25469773,+!p1@RARB!0.96!11.77!RARB;;chr11:65667846..65667868,-!p1@FOSL1!0.95!213.84!FOSL1;;chr14:36989427..36989442,-!p1@NKX2-1!0.95!7.96!NKX2-1;;chr3:24536253..24536328,-!p1@THRB!0.93!14.69!THRB;;chr19:45971246..45971265,+!p1@FOSB!0.91!137.47!FOSB;;chr4:57522674..57522699,-!p5@HOPX!0.91!7.06!HOPX;;chr19:53496768..53496799,-!p1@ZNF702P!0.90!11.10!ZNF702P;;chr3:32023232..32023273,+!p1@ZNF860!0.90!10.09!ZNF860;;chr6:10415276..10415341,-!p2@TFAP2A!0.90!8.52!TFAP2A;;chr9:14314131..14314147,-!p2@NFIB!0.89!39.47!NFIB;;chrX:55620497..55620512,+!p@chrX:55620497..55620512,+!0.89!6.73!FOXR2;;chr11:46299199..46299233,+!p1@CREB3L1!0.88!35.66!CREB3L1;;chr20:42543506..42543549,+!p2@TOX2!0.88!16.48!TOX2;;chr15:67418119..67418162,+!p5@SMAD3!0.88!7.40!SMAD3;;chr8:67525443..67525459,-!p2@MYBL1!0.87!9.87!MYBL1;;chr14:36989358..36989378,-!p3@NKX2-1!0.86!6.28!NKX2-1;;chrX:66763856..66763896,+!p1@AR!0.84!8.86!AR;;chr8:106330696..106330719,+!p2@ZFPM2!0.83!7.40!ZFPM2;;chr4:53206..53260,+!p1@ZNF595,p1@ZNF718!0.80!54.50!ZNF595;;chr17:17726907..17726958,-!p2@SREBF1!0.80!35.88!SREBF1;;chr12:80084167..80084197,-!p5@PAWR!0.80!13.23!PAWR;;chr4:57522513..57522548,-!p4@HOPX!0.80!5.38!HOPX;;chr5:321810..321877,+!p1@AHRR!0.78!17.16!AHRR;;chr11:120107344..120107351,+!p1@POU2F3!0.77!6.06!POU2F3;;chr14:33403881..33403924,+!p1@NPAS3!0.77!4.93!NPAS3;;chr20:30433396..30433414,-!p1@FOXS1!0.77!4.93!FOXS1;;chr7:63505799..63505904,+!p1@ZNF727!0.77!4.82!ZNF727;;chr17:7590797..7590815,-!p1@TP53!0.76!228.97!TP53;;chr11:65686732..65686756,+!p2@DRAP1!0.76!21.98!DRAP1;;chr11:46299539..46299620,+!p2@CREB3L1!0.76!8.52!CREB3L1;;chr11:31832658..31832681,-!p1@PAX6!0.76!4.71!PAX6;;chr15:96869255..96869291,+!p6@NR2F2!0.75!8.86!NR2F2;;chr15:83953373..83953386,-!p2@BNC1!0.75!4.60!BNC1;;chr4:109089095..109089144,-!p6@LEF1!0.75!4.60!LEF1;;chr15:67418047..67418093,+!p4@SMAD3!0.74!5.83!SMAD3;;chr3:24536332..24536358,-!p2@THRB!0.74!4.49!THRB;;chr17:41622765..41622821,-!p2@ETV4!0.73!6.95!ETV4;;chr3:169381420..169381535,-!p1@MECOM!0.73!5.27!MECOM;;chr17:41622731..41622764,-!p5@ETV4!0.73!4.37!ETV4;;chr19:22605136..22605154,-!p1@ZNF98!0.73!4.37!ZNF98;;chr6:34204672..34204692,+!p1@HMGA1!0.72!542.61!HMGA1;;chr19:22817119..22817145,+!p1@ZNF492!0.72!7.51!ZNF492;;chr3:25469815..25469866,+!p3@RARB!0.72!4.26!RARB;;chr11:65686802..65686818,+!p6@DRAP1!0.71!7.74!DRAP1;;chr10:28032421..28032494,-!p2@MKX!0.71!4.15!MKX;;chr14:36989379..36989390,-!p8@NKX2-1!0.71!4.15!NKX2-1;;chr19:46271505..46271575,-!p2@SIX5!0.70!11.21!SIX5;;chr1:59249645..59249656,-!p4@JUN!0.70!11.10!JUN;;chr5:150284532..150284549,-!p1@ZNF300!0.70!8.97!ZNF300;;chr13:72441315..72441454,-!p1@DACH1!0.70!8.75!DACH1;;chr17:7388010..7388017,-!p5@ZBTB4!0.70!7.18!ZBTB4;;chr3:24536485..24536500,-!p3@THRB!0.70!4.04!THRB;;chr20:55204351..55204377,+!p1@TFAP2C!0.69!5.16!TFAP2C;;chr8:93115584..93115642,-!p5@RUNX1T1!0.69!3.92!RUNX1T1;;chr9:127533519..127533573,-!p2@NR6A1!0.67!4.60!NR6A1;;chr17:5015129..5015187,-!p1@ZNF232!0.66!21.98!ZNF232;;chr12:26277956..26277980,-!p1@BHLHE41!0.66!14.69!BHLHE41;;chr9:14314106..14314119,-!p5@NFIB!0.66!6.95!NFIB;;chr4:109088940..109089037,-!p4@LEF1!0.66!3.59!LEF1;;chr12:80084737..80084763,-!p3@PAWR!0.65!14.80!PAWR;;chr15:96875657..96875760,+!p14@NR2F2!0.65!6.17!NR2F2;;chr19:13136057..13136085,+!p11@NFIX!0.65!3.48!NFIX;;chr12:115121962..115121987,-!p1@TBX3!0.64!32.85!TBX3;;chr18:3448455..3448480,+!p5@TGIF1!0.64!6.84!TGIF1;;chr9:14313893..14313908,-!p7@NFIB!0.64!5.16!NFIB;;chrX:55620469..55620479,+!p@chrX:55620469..55620479,+!0.64!3.36!FOXR2;;chr19:58545454..58545498,+!p1@ZSCAN1!0.64!3.36!ZSCAN1;;chr14:36989336..36989354,-!p5@NKX2-1!0.64!3.36!NKX2-1;;chr5:176738887..176738934,-!p1@MXD3!0.63!25.34!MXD3;;chr13:36871902..36872023,-!p1@CCDC169-SOHLH2,p1@CCDC169,p1@SOHLH2!0.63!7.96!SOHLH2;;chr20:50159198..50159299,-!p1@NFATC2!0.63!5.16!NFATC2;;chr5:43067636..43067674,+!p6@ZNF131!0.63!4.71!ZNF131;;chr14:37131058..37131139,+!p1@PAX9!0.63!3.25!PAX9;;chr19:13135582..13135600,+!p3@NFIX!0.63!3.25!NFIX;;chr20:32274179..32274213,-!p1@E2F1!0.62!24.89!E2F1;;chr11:65687362..65687436,+!p3@DRAP1!0.62!16.82!DRAP1;;chr5:138647473..138647476,+!p6@MATR3!0.62!9.19!MATR3;;chr9:99180617..99180658,-!p1@ZNF367!0.62!7.74!ZNF367;;chr19:9811125..9811144,-!p2@ZNF812!0.62!3.14!ZNF812;;chr15:96874012..96874042,+!p2@NR2F2!0.61!32.85!NR2F2;;chr12:80084303..80084332,-!p1@PAWR!0.61!21.42!PAWR;;chr3:114343768..114343822,-!p1@ZBTB20!0.61!15.81!ZBTB20;;chr20:31350184..31350200,+!p1@DNMT3B!0.61!7.18!DNMT3B;;chr5:134369905..134369972,-!p1@PITX1!0.61!5.16!PITX1;;chr14:36988564..36988601,-!p7@NKX2-1!0.61!3.03!NKX2-1;;chr19:12203100..12203132,+!p1@ZNF788!0.60!6.73!ZNF788;;chr10:8096772..8096787,+!p2@GATA3!0.60!3.70!GATA3;;chr17:17740287..17740307,-!p1@SREBF1!0.59!92.17!SREBF1;;chr6:31126291..31126399,+!p1@TCF19!0.59!33.19!TCF19;;chr1:59249688..59249703,-!p3@JUN!0.59!21.08!JUN;;chr10:94449703..94449718,+!p1@HHEX!0.59!13.12!HHEX;;chr9:14314066..14314075,-!p11@NFIB!0.59!2.92!NFIB;;chr17:41277372..41277418,-!p1@BRCA1!0.58!12.11!BRCA1;;chr3:21792585..21792625,-!p2@ZNF385D!0.58!3.25!ZNF385D;;chr10:28034739..28034756,-!p1@MKX!0.58!2.80!MKX;;chr17:41622925..41622976,-!p3@ETV4!0.57!4.37!ETV4;;chr6:32095523..32095564,-!p2@ATF6B!0.57!3.92!ATF6B;;chr12:80084137..80084165,-!p10@PAWR!0.57!3.70!PAWR;;chr14:36989940..36989957,-!p2@NKX2-1!0.57!2.69!NKX2-1;;chr3:24536231..24536249,-!p4@THRB!0.57!2.69!THRB;;chr14:62162285..62162296,+!p3@HIF1A!0.56!16.71!HIF1A;;chr1:41827095..41827155,+!p1@FOXO6!0.56!3.81!FOXO6;;chr19:48774586..48774670,+!p1@ZNF114!0.56!3.48!ZNF114;;chr19:20278012..20278034,+!p1@ZNF486!0.55!26.80!ZNF486;;chr20:2489542..2489583,-!p1@ZNF343!0.55!21.53!ZNF343;;chr18:3450293..3450304,+!p4@TGIF1!0.55!7.40!TGIF1;;chr15:83953474..83953483,-!p3@BNC1!0.55!2.58!BNC1;;chr14:36989913..36989931,-!p6@NKX2-1!0.55!2.58!NKX2-1;;chr9:100616439..100616476,+!p3@FOXE1!0.55!2.58!FOXE1;;chr3:42947600..42947680,+!p1@ZNF662!0.54!3.92!ZNF662;;chr5:134369222..134369237,-!p8@PITX1!0.54!2.47!PITX1;;chr6:28321971..28321995,-!p1@ZNF323!0.54!2.47!ZNF323;;chr7:101917407..101917443,+!p3@CUX1!0.54!2.47!CUX1;;chr9:100615546..100615558,+!p4@FOXE1!0.54!2.47!FOXE1;;chr11:65688877..65688891,+!p13@DRAP1!0.54!2.47!DRAP1;;chr11:65686952..65686975,+!p5@DRAP1!0.53!16.48!DRAP1;;chr5:43120995..43121052,+!p1@ZNF131!0.53!15.14!ZNF131;;chr19:13134772..13134822,+!p2@NFIX!0.53!3.92!NFIX;;chr3:25470062..25470084,+!p4@RARB!0.53!2.35!RARB;;chr3:69788576..69788648,+!p1@MITF!0.52!15.47!MITF;;chr19:58400372..58400411,-!p1@ZNF814!0.52!15.25!ZNF814;;chr10:94449675..94449694,+!p2@HHEX!0.52!7.51!HHEX;;chr21:36421535..36421610,-!p2@RUNX1!0.51!9.98!RUNX1;;chr8:28243813..28243839,-!p4@ZNF395!0.51!4.60!ZNF395;;chr3:168864315..168864339,-!p2@MECOM!0.51!4.15!MECOM;;chr4:149363475..149363492,-!p2@NR3C2!0.51!2.24!NR3C2;;chr19:58740449..58740456,+!p3@ZNF544!0.51!2.24!ZNF544;;chr11:65668011..65668020,-!p3@FOSL1!0.51!2.24!FOSL1;;chr14:37051600..37051611,-!p2@NKX2-8!0.51!2.24!NKX2-8;;chr1:8938709..8938720,-!p3@ENO1!0.50!138.26!ENO1;;chr19:20188776..20188826,+!p1@ZNF90!0.50!7.06!ZNF90;;chr11:65687222..65687240,+!p7@DRAP1!0.50!3.03!DRAP1;;chr14:36988882..36988895,-!p13@NKX2-1!0.50!2.13!NKX2-1;;chr4:149366111..149366128,-!p7@NR3C2!0.50!2.13!NR3C2;;chr6:28321909..28321965,-!p3@ZNF323!0.50!2.13!ZNF323;;chr15:96869114..96869160,+!p11@NR2F2!0.49!3.14!NR2F2;;chrX:66763815..66763854,+!p2@AR!0.49!3.03!AR;;chr11:6947720..6947812,+!p1@ZNF215!0.49!2.92!ZNF215;;chr11:19263192..19263222,-!p2@E2F8!0.49!2.69!E2F8;;chr2:60778035..60778060,-!p4@BCL11A!0.49!2.69!BCL11A;;chr13:73636516..73636532,+!p3@KLF5!0.49!2.47!KLF5;;chr1:212782094..212782109,+!p1@ATF3!0.48!74.01!ATF3;;chr19:53193731..53193767,-!p1@ZNF83!0.48!24.11!ZNF83;;chr15:96873984..96873999,+!p3@NR2F2!0.48!19.85!NR2F2;;chr3:150126759..150126784,+!p2@TSC22D2!0.48!11.89!TSC22D2;;chr3:12329358..12329393,+!p3@PPARG!0.48!6.17!PPARG;;chr15:96874063..96874074,+!p10@NR2F2!0.48!4.37!NR2F2;;chr19:22605097..22605121,-!p2@ZNF98!0.48!2.02!ZNF98;;chr3:111314186..111314204,-!p1@ZBED2!0.48!2.02!ZBED2;;chr7:57509877..57509895,+!p1@ZNF716!0.48!2.02!ZNF716;;chr8:67525473..67525518,-!p1@MYBL1!0.47!5.49!MYBL1;;chr12:26277929..26277955,-!p3@BHLHE41!0.47!3.14!BHLHE41;;chr17:1958388..1958404,+!p1@HIC1!0.46!16.37!HIC1;;chr11:128392273..128392308,-!p2@ETS1!0.46!10.65!ETS1;;chr17:4890695..4890773,-!p2@CAMTA2!0.46!7.62!CAMTA2;;chr17:41623009..41623053,-!p4@ETV4!0.46!3.59!ETV4;;chr9:14082760..14082775,-!p6@NFIB!0.46!3.59!NFIB;;chr19:37464063..37464127,+!p2@ZNF568!0.46!2.69!ZNF568;;chrX:55620481..55620492,+!p@chrX:55620481..55620492,+!0.46!1.91!FOXR2;;chr8:93115508..93115552,-!p6@RUNX1T1!0.46!1.91!RUNX1T1;;chr12:80084120..80084136,-!p15@PAWR!0.46!1.91!PAWR;;chr14:36989412..36989423,-!p12@NKX2-1!0.46!1.91!NKX2-1;;chr2:95963052..95963106,+!p1@KCNIP3!0.46!1.91!KCNIP3;;chr3:141868293..141868355,-!p2@TFDP2!0.45!21.98!TFDP2;;chr3:141868357..141868393,-!p3@TFDP2!0.45!16.37!TFDP2;;chr5:92918894..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Line 45: Line 45:
 
|is_obsolete=
 
|is_obsolete=
 
|library_id=CNhs11872
 
|library_id=CNhs11872
|library_id_phase_based=1:CNhs11872
+
|library_id_phase_based=2:CNhs11872
 
|name=thyroid carcinoma cell line:TCO-1
 
|name=thyroid carcinoma cell line:TCO-1
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
|profile_hcage=CNhs11872,LSID830,release010,COMPLETED
+
|profile_hcage="CNhs11872,LSID830,release010,COMPLETED"
|profile_rnaseq=,,,
+
|profile_rnaseq=
|profile_srnaseq=,,,
+
|profile_srnaseq=",,,"
 
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Revision as of 08:18, 27 November 2014


Name:thyroid carcinoma cell line:TCO-1
Species:Human (Homo sapiens)
Library ID:CNhs11872
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethyroid
dev stageNA
sexmale
ageunknown
cell typeunclassifiable
cell lineTCO-1
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005528
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11872 CAGE DRX008026 DRR008898
Accession ID Hg19

Library idBAMCTSS
CNhs11872 DRZ000323 DRZ001708
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
No results for this sample

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: "CNhs11872This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifsSummary:Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: "CNhs11872This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: "CNhs11872


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0002046 (thyroid gland)
0004119 (endoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0101610 (thyroid cancer cell line sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0007123 (pharyngeal pouch 2)
UBERON:0010316 (germ layer / neural crest)