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Difference between revisions of "FF:10070-101I7"

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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=chr1:201979743..201979762,+!p1@ELF3!2.51!318.96!ELF3;;chr1:201979703..201979721,+!p2@ELF3!2.40!251.74!ELF3;;chr3:12330560..12330579,+!p1@PPARG!2.27!208.97!PPARG;;chr5:149546334..149546364,+!p1@CDX1!2.11!127.09!CDX1;;chr16:79634595..79634620,-!p2@MAF!2.01!179.03!MAF;;chr6:34524093..34524135,-!p1@SPDEF!1.97!92.27!SPDEF;;chr4:174451370..174451387,-!p1@HAND2!1.97!91.65!HAND2;;chr6:134210243..134210257,+!p1@TCF21!1.90!77.60!TCF21;;chr11:34642612..34642646,+!p1@EHF!1.89!75.77!EHF;;chr13:28543431..28543487,-!p1@CDX2!1.84!68.44!CDX2;;chr19:46801639..46801699,+!p1@HIF3A!1.83!66.60!HIF3A;;chr19:46367576..46367592,+!p1@FOXA3!1.77!58.05!FOXA3;;chr16:86544113..86544145,+!p1@FOXF1!1.76!70.27!FOXF1;;chrX:2418949..2419024,-!p1@DHRSX,p1@ZBED1!1.72!51.33!ZBED1;;chr7:27192185..27192209,-!p1@HOXA3!1.71!50.72!HOXA3;;chr17:46682321..46682362,-!p1@HOXB6!1.71!50.10!HOXB6;;chr20:42984330..42984364,+!p2@HNF4A!1.71!50.10!HNF4A;;chr16:79634624..79634642,-!p1@MAF!1.69!179.03!MAF;;chr2:60780753..60780800,-!p1@BCL11A!1.68!218.14!BCL11A;;chr19:50922187..50922204,+!p1@SPIB!1.68!46.44!SPIB;;chr13:72441315..72441454,-!p1@DACH1!1.65!84.93!DACH1;;chr8:76319876..76319926,+!p1@HNF4G!1.64!42.77!HNF4G;;chr13:28543253..28543276,-!p5@CDX2!1.62!40.33!CDX2;;chr20:62680984..62680999,-!p1@SOX18!1.61!51.94!SOX18;;chr13:28543285..28543314,-!p2@CDX2!1.61!39.72!CDX2;;chr2:122042770..122042785,-!p1@TFCP2L1!1.60!38.49!TFCP2L1;;chr6:1389789..1389821,+!p1@FOXF2!1.56!47.66!FOXF2;;chr9:20382446..20382493,-!p4@MLLT3!1.54!33.61!MLLT3;;chr16:85932760..85932775,+!p1@IRF8!1.54!33.61!IRF8;;chr19:33793430..33793447,-!p1@CEBPA!1.49!120.98!CEBPA;;chr11:65554528..65554546,+!p1@OVOL1!1.49!29.94!OVOL1;;chr1:214161272..214161322,+!p1@PROX1!1.48!40.33!PROX1;;chr1:199996831..199996843,+!p4@NR5A2!1.46!28.11!NR5A2;;chr19:46800289..46800327,+!p2@HIF3A!1.45!27.50!HIF3A;;chr3:119500941..119500961,+!p1@NR1I2!1.45!26.89!NR1I2;;chr2:176973498..176973524,+!p1@HOXD10!1.44!26.27!HOXD10;;chr13:73633131..73633149,+!p1@KLF5!1.41!254.80!KLF5;;chr6:135502501..135502546,+!p1@MYB!1.40!28.72!MYB;;chr2:70142232..70142251,+!p1@MXD1!1.39!128.32!MXD1;;chr20:50159198..50159299,-!p1@NFATC2!1.39!34.22!NFATC2;;chr17:53342311..53342400,+!p1@HLF!1.38!26.27!HLF;;chr3:141043020..141043049,+!p17@ZBTB38!1.38!23.22!ZBTB38;;chr17:1959369..1959388,+!p2@HIC1!1.37!58.05!HIC1;;chr7:27224842..27224872,-!p1@HOXA11!1.37!22.61!HOXA11;;chr10:101292684..101292706,+!p1@NKX2-3!1.37!22.61!NKX2-3;;chr18:19749541..19749557,+!p1@GATA6!1.36!67.21!GATA6;;chr11:34642656..34642667,+!p2@EHF!1.35!21.39!EHF;;chr13:28543316..28543329,-!p4@CDX2!1.35!21.39!CDX2;;chr14:38064429..38064486,-!p1@FOXA1!1.35!21.39!FOXA1;;chr19:4153613..4153652,+!p1@CREB3L3!1.35!21.39!CREB3L3;;chr20:43029862..43029900,+!p1@HNF4A!1.35!21.39!HNF4A;;chr8:102504651..102504683,+!p1@GRHL2!1.34!20.78!GRHL2;;chr16:79634581..79634592,-!p4@MAF!1.33!20.16!MAF;;chr12:100897130..100897149,+!p3@NR1H4!1.33!20.16!NR1H4;;chr2:177001290..177001315,+!p1@HOXD3!1.33!20.16!HOXD3;;chr1:47903709..47903764,+!p1@BC169308!1.30!21.39!FOXD2;;chr15:42749722..42749739,-!p2@ZFP106!1.29!33.00!ZFP106;;chr18:19749386..19749404,+!p2@GATA6!1.27!25.05!GATA6;;chr1:151804244..151804310,-!p1@RORC!1.27!17.72!RORC;;chr10:114709999..114710031,+!p1@TCF7L2!1.25!383.73!TCF7L2;;chr14:75745523..75745537,+!p1@FOS!1.24!1896.03!FOS;;chr18:72922811..72922827,+!p1@TSHZ1!1.24!80.66!TSHZ1;;chr6:1389824..1389840,+!p3@FOXF2!1.24!16.50!FOXF2;;chr11:65554563..65554576,+!p2@OVOL1!1.23!15.89!OVOL1;;chr13:72441074..72441172,-!p2@DACH1!1.23!15.89!DACH1;;chr1:200011711..200011752,+!p3@NR5A2!1.23!15.89!NR5A2;;chr7:113726357..113726443,+!p1@FOXP2!1.22!26.89!FOXP2;;chr1:209979467..209979494,-!p1@IRF6!1.22!17.72!IRF6;;chr12:48298765..48298783,-!p2@VDR!1.21!31.77!VDR;;chr17:46687959..46688007,-!p2@HOXB7!1.21!20.78!HOXB7;;chr4:94749897..94749909,+!p1@ATOH1!1.21!15.28!ATOH1;;chr13:28543388..28543406,-!p3@CDX2!1.19!14.66!CDX2;;chr11:113930425..113930471,+!p1@ZBTB16!1.18!20.16!ZBTB16;;chr3:18486354..18486377,-!p2@SATB1!1.18!17.72!SATB1;;chr12:54410664..54410684,+!p1@HOXC4,p1@HOXC5,p1@HOXC6!1.18!14.05!HOXC5;;chr7:27205136..27205164,-!p1@HOXA9!1.18!14.05!HOXA9;;chr19:57352087..57352102,-!p1@PEG3,p1@ZIM2!1.18!14.05!PEG3;;chr2:46524897..46524911,+!p2@EPAS1!1.17!38.49!EPAS1;;chr14:75746722..75746777,+!p2@FOS!1.17!17.72!FOS;;chr2:145277882..145277967,-!p3@ZEB2!1.16!23.22!ZEB2;;chr9:110251836..110251887,-!p4@KLF4!1.16!17.72!KLF4;;chr9:110250697..110250738,-!p2@KLF4!1.16!15.89!KLF4;;chr4:41750731..41750748,-!p1@PHOX2B!1.16!13.44!PHOX2B;;chr15:96873984..96873999,+!p3@NR2F2!1.15!96.54!NR2F2;;chr4:174451350..174451363,-!p3@HAND2!1.14!12.83!HAND2;;chr8:10588010..10588030,-!p1@SOX7!1.14!12.83!SOX7;;chr3:18466787..18466839,-!p1@SATB1!1.12!54.38!SATB1;;chr8:55370487..55370503,+!p1@SOX17!1.12!12.22!SOX17;;chr11:47279248..47279264,+!p3@NR1H3!1.11!13.44!NR1H3;;chr1:27240455..27240474,-!p1@NR0B2!1.10!11.61!NR0B2;;chr17:36105042..36105060,-!p1@HNF1B!1.10!11.61!HNF1B;;chr1:61548225..61548299,+!p1@NFIA!1.08!146.04!NFIA;;chr5:133451294..133451310,+!p2@TCF7!1.08!11.00!TCF7;;chr7:156803329..156803362,-!p1@MNX1!1.08!11.00!MNX1;;chr2:176994408..176994492,+!p1@HOXD8!1.08!11.00!HOXD8;;chr4:149363494..149363543,-!p1@NR3C2!1.08!11.00!NR3C2;;chr2:200323414..200323455,-!p1@SATB2!1.07!23.22!SATB2;;chrX:131623044..131623089,-!p1@MBNL3!1.06!43.99!MBNL3;;chr1:61548374..61548415,+!p4@NFIA!1.06!19.55!NFIA;;chr3:71355163..71355209,-!p5@FOXP1!1.06!14.66!FOXP1;;chr13:73636621..73636647,+!p4@KLF5!1.06!10.39!KLF5;;chr8:25902876..25902936,-!p1@EBF2!1.06!10.39!EBF2;;chr5:158526917..158526932,-!p1@EBF1!1.05!25.66!EBF1;;chr10:70320074..70320106,+!p1@TET1!1.05!20.78!TET1;;chr10:114710060..114710069,+!p5@TCF7L2!1.05!17.72!TCF7L2;;chr3:12329397..12329433,+!p2@PPARG!1.04!23.22!PPARG;;chr19:58373157..58373159,+!p4@ZNF587!1.03!17.72!ZNF587;;chr20:6748325..6748352,+!p1@BMP2!1.03!14.05!BMP2;;chr3:141043050..141043063,+!p22@ZBTB38!1.03!9.78!ZBTB38;;chr11:34645791..34645836,+!p3@EHF!1.03!9.78!EHF;;chr5:134369879..134369898,-!p2@PITX1!1.03!9.78!PITX1;;chr2:43453734..43453751,-!p1@ZFP36L2!1.02!1027.75!ZFP36L2;;chr17:38256822..38256851,-!p1@NR1D1!1.02!75.16!NR1D1;;chr2:19558373..19558392,-!p1@OSR1!1.02!26.27!OSR1;;chr3:114819124..114819200,-!p3@ZBTB20!1.02!22.61!ZBTB20;;chr4:38665810..38665827,+!p1@KLF3!1.01!136.26!KLF3;;chr2:60780607..60780624,-!p2@BCL11A!1.01!28.72!BCL11A;;chr6:7108179..7108199,+!p4@RREB1!1.01!18.94!RREB1;;chr3:24536253..24536328,-!p1@THRB!1.01!17.72!THRB;;chr2:70166212..70166223,+!p16@MXD1!1.01!9.17!MXD1;;chr7:27213893..27213954,-!p1@HOXA10!1.01!9.17!HOXA10;;chr7:27224795..27224840,-!p2@HOXA11!1.01!9.17!HOXA11;;chr1:40105299..40105326,-!p1@HEYL!1.01!9.17!HEYL;;chr11:16419037..16419064,-!p3@SOX6!1.01!9.17!SOX6;;chr11:47400078..47400106,-!p1@SPI1!1.01!9.17!SPI1;;chr12:121416340..121416360,+!p1@HNF1A!1.01!9.17!HNF1A;;chr10:111967345..111967422,+!p1@MXI1!1.00!150.92!MXI1;;chr12:52445218..52445237,+!p1@NR4A1!1.00!115.48!NR4A1;;chr3:114866084..114866118,-!p2@ZBTB20!1.00!33.61!ZBTB20;;chr17:38256799..38256815,-!p3@NR1D1!1.00!16.50!NR1D1;;chr8:60031682..60031710,-!p2@TOX!1.00!14.66!TOX;;chr15:96874012..96874042,+!p2@NR2F2!0.99!80.66!NR2F2;;chr20:51588873..51588953,+!p1@TSHZ2!0.99!11.61!TSHZ2;;chr8:48650715..48650735,-!p1@CEBPD!0.98!1113.30!CEBPD;;chr15:61521417..61521460,-!p2@RORA!0.98!19.55!RORA;;chr17:46806035..46806059,-!p2@HOXB13!0.98!8.55!HOXB13;;chr1:209979411..209979433,-!p2@IRF6!0.98!8.55!IRF6;;chr1:6479968..6479986,-!p1@HES2!0.98!8.55!HES2;;chr21:39870339..39870443,-!p1@ERG!0.98!8.55!ERG;;chr7:114054885..114054910,+!p4@FOXP2!0.98!8.55!FOXP2;;chr2:177001268..177001287,+!p3@HOXD3!0.98!8.55!HOXD3;;chr4:109087445..109087463,-!p1@LEF1!0.98!8.55!LEF1;;chr13:73636252..73636307,+!p2@KLF5!0.97!9.78!KLF5;;chr12:115121962..115121987,-!p1@TBX3!0.96!70.27!TBX3;;chr2:10183651..10183713,+!p1@KLF11!0.96!60.49!KLF11;;chr10:114710098..114710130,+!p2@TCF7L2!0.95!61.10!TCF7L2;;chr10:111967317..111967328,+!p5@MXI1!0.95!7.94!MXI1;;chr12:100867627..100867652,+!p1@NR1H4!0.95!7.94!NR1H4;;chr21:40177845..40177863,+!p1@ETS2!0.94!476.60!ETS2;;chr5:124084493..124084524,-!p2@ZNF608!0.94!17.72!ZNF608;;chr3:71179699..71179744,-!p2@FOXP1!0.93!58.66!FOXP1;;chr13:41593425..41593480,-!p1@ELF1!0.93!49.49!ELF1;;chr13:37494365..37494381,-!p1@SMAD9!0.93!13.44!SMAD9;;chr6:21597600..21597664,+!p3@SOX4!0.93!12.83!SOX4;;chr6:1312325..1312340,+!p1@FOXQ1!0.92!12.22!FOXQ1;;chr5:71803177..71803255,-!p1@ZNF366!0.92!7.33!ZNF366;;chr6:391743..391759,+!p1@IRF4!0.92!7.33!IRF4;;chr7:27205106..27205134,-!p2@HOXA9!0.92!7.33!HOXA9;;chr22:38380543..38380569,-!p1@SOX10!0.92!7.33!SOX10;;chr3:18465604..18465618,-!p9@SATB1!0.92!7.33!SATB1;;chr3:71294213..71294240,-!p30@FOXP1!0.92!7.33!FOXP1;;chr4:149363475..149363492,-!p2@NR3C2!0.92!7.33!NR3C2;;chr16:52581025..52581072,-!p1@TOX3!0.92!7.33!TOX3;;chr17:46690839..46690884,-!p1@HOXB8!0.92!7.33!HOXB8;;chr11:71955210..71955227,-!p1@PHOX2A!0.92!7.33!PHOX2A;;chr1:221052840..221052875,+!p4@HLX!0.91!8.55!HLX;;chr2:145277640..145277771,-!p1@ZEB2!0.90!96.54!ZEB2;;chr10:114710218..114710229,+!p4@TCF7L2!0.90!14.05!TCF7L2;;chr18:19749517..19749531,+!p3@GATA6!0.90!12.83!GATA6;;chr5:134369905..134369972,-!p1@PITX1!0.90!11.00!PITX1;;chr5:88178983..88179012,-!p1@MEF2C!0.89!54.38!MEF2C;;chr3:71179746..71179783,-!p7@FOXP1!0.89!23.83!FOXP1;;chr11:47279504..47279563,+!p1@NR1H3!0.89!15.89!NR1H3;;chr8:71316428..71316459,-!p2@NCOA2!0.89!11.61!NCOA2;;chr5:88179195..88179224,-!p3@MEF2C!0.89!11.00!MEF2C;;chr7:137620650..137620677,-!p3@CREB3L2!0.89!6.72!CREB3L2;;chr7:15726243..15726293,-!p2@MEOX2!0.89!6.72!MEOX2;;chr7:27239740..27239759,-!p2@HOXA13!0.89!6.72!HOXA13;;chr16:79634464..79634493,-!p5@MAF!0.89!6.72!MAF;;chr20:30433396..30433414,-!p1@FOXS1!0.89!6.72!FOXS1;;chr11:113930401..113930422,+!p3@ZBTB16!0.89!6.72!ZBTB16;;chr2:176969228..176969260,+!p1@HOXD11!0.89!6.72!HOXD11;;chr2:5832508..5832524,+!p1@SOX11!0.89!6.72!SOX11;;chr2:60780730..60780742,-!p5@BCL11A!0.89!6.72!BCL11A;;chr6:144289132..144289134,-!p3@PLAGL1!0.88!15.89!PLAGL1;;chr7:99613250..99613264,+!p2@ZKSCAN1!0.87!19.55!ZKSC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Line 44: Line 44:
 
|is_obsolete=
 
|is_obsolete=
 
|library_id=CNhs11780
 
|library_id=CNhs11780
|library_id_phase_based=1:CNhs11780
+
|library_id_phase_based=2:CNhs11780
|name=colon, fetal, donor1
+
|name="colon, fetal, donor1"
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
|profile_hcage=CNhs11780,LSID820,release009,COMPLETED
+
|profile_hcage="CNhs11780,LSID820,release009,COMPLETED"
|profile_rnaseq=,,,
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|profile_rnaseq=
|profile_srnaseq=,,,
+
|profile_srnaseq=",,,"
 
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Revision as of 07:06, 27 November 2014


Name:"colon, fetal, donor1"
Species:Human (Homo sapiens)
Library ID:CNhs11780
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecolon
dev stage37 weeks fetus
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB207218
catalog numberCat:RtHFN: Colon
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005845
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11780 CAGE DRX008639 DRR009511
Accession ID Hg19

Library idBAMCTSS
CNhs11780 DRZ000936 DRZ002321
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. <br>Analyst:NA <br><br>link to dataset.<br>dataNo results for this sample

Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



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


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: "CNhs11780This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: "CNhs11780This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: "CNhs11780


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0001155 (colon)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0000059 (large intestine)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000999 (fetal tissue sample)
0000004 (tissue sample)
0010070 (human colon - fetal sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA