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Difference between revisions of "FF:10486-107A9"

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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=chr11:34642612..34642646,+!p1@EHF!2.00!99.66!EHF;;chr7:101917407..101917443,+!p3@CUX1!1.73!52.56!CUX1;;chr1:201979743..201979762,+!p1@ELF3!1.71!50.87!ELF3;;chr15:67418119..67418162,+!p5@SMAD3!1.68!52.40!SMAD3;;chr8:102504651..102504683,+!p1@GRHL2!1.54!33.54!GRHL2;;chr6:1312325..1312340,+!p1@FOXQ1!1.50!49.03!FOXQ1;;chr7:101917447..101917479,+!p4@CUX1!1.50!30.89!CUX1;;chr15:67418047..67418093,+!p4@SMAD3!1.49!37.55!SMAD3;;chr7:101917482..101917507,+!p6@CUX1!1.42!25.36!CUX1;;chr1:201979703..201979721,+!p2@ELF3!1.42!25.04!ELF3;;chr3:12330560..12330579,+!p1@PPARG!1.27!19.98!PPARG;;chr15:67418099..67418118,+!p16@SMAD3!1.27!17.41!SMAD3;;chr11:65667846..65667868,-!p1@FOSL1!1.25!429.93!FOSL1;;chr1:158985493..158985535,+!p4@IFI16!1.23!24.47!IFI16;;chr2:238592039..238592054,+!p4@LRRFIP1!1.20!14.84!LRRFIP1;;chr15:67418177..67418204,+!p9@SMAD3!1.08!11.15!SMAD3;;chr11:65667884..65667895,-!p2@FOSL1!1.03!38.28!FOSL1;;chr17:70117153..70117174,+!p1@SOX9!1.02!100.14!SOX9;;chr6:10412392..10412409,-!p4@TFAP2A!1.02!10.75!TFAP2A;;chr12:80084737..80084763,-!p3@PAWR!1.00!34.66!PAWR;;chr14:38064429..38064486,-!p1@FOXA1!1.00!8.91!FOXA1;;chr12:26277956..26277980,-!p1@BHLHE41!0.99!31.86!BHLHE41;;chr3:168864315..168864339,-!p2@MECOM!0.97!13.80!MECOM;;chr21:36421535..36421610,-!p2@RUNX1!0.92!27.12!RUNX1;;chr14:37131058..37131139,+!p1@PAX9!0.91!7.06!PAX9;;chr8:102504979..102505010,+!p2@GRHL2!0.88!6.58!GRHL2;;chr7:101917509..101917520,+!p9@CUX1!0.86!6.18!CUX1;;chr3:114343826..114343869,-!p4@ZBTB20!0.85!12.68!ZBTB20;;chr15:41913690..41913753,+!p2@MGA!0.84!14.84!MGA;;chr5:134369905..134369972,-!p1@PITX1!0.84!9.47!PITX1;;chr1:209979467..209979494,-!p1@IRF6!0.82!6.34!IRF6;;chr7:102985288..102985310,-!p2@DNAJC2!0.81!13.48!DNAJC2;;chr3:169381420..169381535,-!p1@MECOM!0.81!6.50!MECOM;;chr6:10412600..10412637,-!p1@TFAP2A!0.80!9.23!TFAP2A;;chr19:45971246..45971265,+!p1@FOSB!0.79!105.20!FOSB;;chr2:46524897..46524911,+!p2@EPAS1!0.79!15.33!EPAS1;;chr4:103423079..103423112,+!p4@NFKB1!0.79!5.14!NFKB1;;chr11:34642656..34642667,+!p2@EHF!0.79!5.14!EHF;;chr10:51572408..51572454,+!p3@NCOA4!0.78!31.86!NCOA4;;chr5:137804484..137804498,+!p2@EGR1!0.77!21.18!EGR1;;chr12:27485762..27485776,+!p3@ARNTL2!0.77!13.96!ARNTL2;;chr13:41593425..41593480,-!p1@ELF1!0.76!33.06!ELF1;;chr6:28048343..28048354,+!p1@ZNF165!0.76!4.81!ZNF165;;chr3:69915385..69915438,+!p3@MITF!0.75!4.57!MITF;;chr11:65479462..65479517,+!p2@KAT5!0.74!20.06!KAT5;;chr1:43148855..43148908,+!p4@YBX1!0.74!7.46!YBX1;;chr14:75988771..75988826,+!p1@BATF!0.74!6.18!BATF;;chr1:158985469..158985489,+!p7@IFI16!0.74!5.46!IFI16;;chr7:27190547..27190591,-!p1@HOXA6!0.73!4.33!HOXA6;;chr9:110252035..110252057,-!p1@KLF4!0.72!77.35!KLF4;;chr20:55204351..55204377,+!p1@TFAP2C!0.71!5.46!TFAP2C;;chr7:17338266..17338282,+!p1@AHR!0.69!47.66!AHR;;chr5:124084493..124084524,-!p2@ZNF608!0.69!9.63!ZNF608;;chr12:26277929..26277955,-!p3@BHLHE41!0.69!5.86!BHLHE41;;chr15:71184890..71184909,-!p3@THAP10!0.69!5.22!THAP10;;chr12:124457746..124457828,+!p1@ZNF664!0.68!164.98!ZNF664;;chr4:56412978..56413003,-!p1@CLOCK!0.68!10.11!CLOCK;;chr15:96875657..96875760,+!p14@NR2F2!0.68!6.74!NR2F2;;chr15:71184837..71184877,-!p2@THAP10!0.67!5.30!THAP10;;chr8:102504690..102504704,+!p3@GRHL2!0.67!3.69!GRHL2;;chr7:102985160..102985273,-!p1@DNAJC2!0.66!103.75!DNAJC2;;chr12:7079780..7079791,-!p2@PHB2!0.65!20.86!PHB2;;chr3:114343768..114343822,-!p1@ZBTB20!0.65!17.49!ZBTB20;;chr14:61116183..61116208,-!p1@SIX1!0.65!15.01!SIX1;;chr12:10875351..10875422,-!p4@CSDA!0.65!7.30!CSDA;;chr12:26277817..26277863,-!p2@BHLHE41!0.65!4.97!BHLHE41;;chr6:34204921..34204939,+!p3@HMGA1!0.64!120.20!HMGA1;;chr15:41952591..41952672,+!p1@MGA!0.64!53.20!MGA;;chr11:67007548..67007610,+!p3@KDM2A!0.64!29.45!KDM2A;;chr7:99156393..99156433,+!p6@ZNF655!0.64!8.51!ZNF655;;chrX:131623044..131623089,-!p1@MBNL3!0.63!15.65!MBNL3;;chr6:126102292..126102329,+!p3@NCOA7!0.63!12.28!NCOA7;;chr5:134369879..134369898,-!p2@PITX1!0.63!3.29!PITX1;;chr6:10413188..10413249,-!p7@TFAP2A!0.63!3.29!TFAP2A;;chr12:57914286..57914304,-!p1@DDIT3!0.62!138.10!DDIT3;;chr6:126240380..126240430,+!p2@NCOA7!0.62!9.23!NCOA7;;chr5:137804405..137804444,+!p3@EGR1!0.62!3.93!EGR1;;chr11:65668011..65668020,-!p3@FOSL1!0.62!3.21!FOSL1;;chr18:55102598..55102623,+!p1@ONECUT2!0.62!3.21!ONECUT2;;chr3:169381183..169381205,-!p4@MECOM!0.62!3.21!MECOM;;chr12:54332608..54332636,+!p1@HOXC13!0.62!3.13!HOXC13;;chr6:21593973..21593988,+!p1@SOX4!0.61!132.56!SOX4;;chr12:27485823..27485868,+!p2@ARNTL2!0.61!14.44!ARNTL2;;chr16:54320646..54320672,-!p2@IRX3!0.61!5.06!IRX3;;chr7:99214559..99214601,+!p1@ZNF498!0.60!44.61!ZNF498;;chr5:137804357..137804390,+!p4@EGR1!0.60!3.69!EGR1;;chr7:99613212..99613236,+!p1@ZKSCAN1!0.59!124.21!ZKSCAN1;;chr11:128392273..128392308,-!p2@ETS1!0.59!14.68!ETS1;;chr12:66218255..66218304,+!p3@HMGA2!0.59!8.91!HMGA2;;chr7:86781858..86781879,+!p3@DMTF1!0.59!5.14!DMTF1;;chr17:38256822..38256851,-!p1@NR1D1!0.58!26.96!NR1D1;;chr14:62162285..62162296,+!p3@HIF1A!0.58!17.57!HIF1A;;chr7:92076740..92076834,+!p1@GATAD1!0.57!84.57!GATAD1;;chr15:41913412..41913456,+!p3@MGA!0.57!6.66!MGA;;chr20:18038521..18038571,-!p1@OVOL2!0.57!2.73!OVOL2;;chr7:17338324..17338341,+!p3@AHR!0.56!10.43!AHR;;chr11:67007611..67007622,+!p6@KDM2A!0.56!3.77!KDM2A;;chr5:2751762..2751784,-!p1@IRX2!0.56!2.65!IRX2;;chr2:214015343..214015366,-!p3@IKZF2!0.56!2.65!IKZF2;;chr14:62162224..62162254,+!p1@HIF1A!0.55!472.54!HIF1A;;chr5:137801160..137801176,+!p1@EGR1!0.55!324.09!EGR1;;chr7:99156249..99156311,+!p1@ZNF655!0.55!72.22!ZNF655;;chr6:15246200..15246214,+!p2@JARID2!0.55!8.26!JARID2;;chr8:128750175..128750201,+!p8@MYC!0.55!4.97!MYC;;chr12:27485889..27485900,+!p4@ARNTL2!0.55!3.21!ARNTL2;;chr7:99156011..99156036,+!p7@ZNF655!0.55!3.13!ZNF655;;chr7:27153454..27153469,-!p2@HOXA3!0.55!2.57!HOXA3;;chr12:27485785..27485816,+!p1@ARNTL2!0.54!21.50!ARNTL2;;chr2:95831389..95831432,-!p1@ZNF514!0.54!13.24!ZNF514;;chr3:168865194..168865245,-!p3@MECOM!0.54!3.37!MECOM;;chr7:99679324..99679368,-!p1@ZNF3!0.53!42.93!ZNF3;;chr22:42666624..42666673,-!p@chr22:42666624..42666673,-!0.53!33.70!TCF20;;chr7:99156314..99156372,+!p4@ZNF655!0.53!9.63!ZNF655;;chr6:31515311..31515330,+!p3@NFKBIL1!0.53!3.69!NFKBIL1;;chr3:101568349..101568365,+!p1@NFKBIZ!0.52!158.16!NFKBIZ;;chr14:62162258..62162269,+!p2@HIF1A!0.52!28.73!HIF1A;;chr16:54320675..54320715,-!p1@IRX3!0.52!5.86!IRX3;;chr5:124084466..124084484,-!p6@ZNF608!0.52!2.33!ZNF608;;chr3:69915369..69915381,+!p4@MITF!0.52!2.33!MITF;;chr7:26191809..26191890,+!p1@NFE2L3!0.51!14.04!NFE2L3;;chr7:99156212..99156244,+!p3@ZNF655!0.51!10.75!ZNF655;;chrX:101186981..101187030,-!p1@ZMAT1!0.51!8.99!ZMAT1;;chr7:99613250..99613264,+!p2@ZKSCAN1!0.51!8.02!ZKSCAN1;;chr8:145159447..145159458,+!p4@MAF1!0.51!6.34!MAF1;;chr14:64970427..64970450,-!p5@ZBTB25!0.51!4.49!ZBTB25;;chr5:134369222..134369237,-!p8@PITX1!0.51!2.25!PITX1;;chr19:36705998..36706021,+!p2@ZNF146!0.50!41.40!ZNF146;;chr6:21597514..21597578,+!p4@SOX4!0.50!4.25!SOX4;;chr8:102504932..102504952,+!p4@GRHL2!0.50!2.17!GRHL2;;chr10:135122868..135122893,+!p3@ZNF511!0.50!2.17!ZNF511;;chr7:101459263..101459310,+!p1@CUX1!0.49!165.70!CUX1;;chr11:67007477..67007493,+!p2@KDM2A!0.49!23.27!KDM2A;;chr7:99156434..99156510,+!p2@ZNF655!0.49!16.45!ZNF655;;chr12:66218598..66218645,+!p2@HMGA2!0.49!12.52!HMGA2;;chr19:45579725..45579743,-!p1@ZNF296!0.49!11.96!ZNF296;;chr17:46682321..46682362,-!p1@HOXB6!0.49!2.09!HOXB6;;chr10:60145155..60145206,+!p1@TFAM!0.48!119.96!TFAM;;chr7:17338239..17338262,+!p2@AHR!0.48!19.98!AHR;;chr18:19749541..19749557,+!p1@GATA6!0.48!8.10!GATA6;;chr8:123793988..123794016,+!p1@ZHX2!0.48!4.17!ZHX2;;chr19:58874112..58874125,-!p1@ZNF497,p5@A1BG!0.48!3.21!ZNF497;;chr19:50431973..50431998,+!p5@ATF5!0.48!2.81!ATF5;;chr20:22565370..22565388,-!p2@FOXA2!0.48!2.01!FOXA2;;chr3:181429704..181429722,+!p1@SOX2!0.48!2.01!SOX2;;chr17:17740287..17740307,-!p1@SREBF1!0.47!70.77!SREBF1;;chr19:36706024..36706049,+!p1@ZNF146!0.47!48.14!ZNF146;;chr10:45496346..45496409,+!p1@ZNF22!0.47!37.71!ZNF22;;chr3:141747459..141747475,-!p1@TFDP2!0.47!21.75!TFDP2;;chr11:129765427..129765492,-!p1@NFRKB!0.47!20.86!NFRKB;;chr12:48298785..48298828,-!p1@VDR!0.47!13.56!VDR;;chr15:57025759..57025811,-!p2@ZNF280D!0.47!13.40!ZNF280D;;chr8:57123815..57123867,-!p1@PLAG1!0.47!10.35!PLAG1;;chr15:61521417..61521460,-!p2@RORA!0.47!5.38!RORA;;chr7:74072256..74072279,+!p3@GTF2I!0.47!4.81!GTF2I;;chr3:23986876..23986885,+!p4@NR1D2!0.47!3.05!NR1D2;;chr11:128392085..128392232,-!p1@ETS1!0.46!88.99!ETS1;;chr19:44716678..44716732,+!p1@ZNF227!0.46!17.65!ZNF227;;chr12:6798616..6798684,-!p2@ZNF384!0.46!17.33!ZNF384;;chr10:97889784..97889827,+!p1@ZNF518A!0.46!12.12!ZNF518A;;chr7:99156145..99156207,+!p5@ZNF655!0.46!8.18!ZNF655;;chr3:107241882..107241904,+!p2@BBX!0.46!5.86!BBX;;chr13:45011349..45011391,-!p4@TSC22D1!0.46!5.78!TSC22D1;;chr14:64970670..64970712,-!p3@ZBTB25!0.46!4.97!ZBTB25;;chr6:21597600..21597664,+!p3@SOX4!0.46!3.69!SOX4;;chr5:16465902..16465917,-!p1@ZNF622!0.45!60.74!ZNF622;;chr11:128392309..128392350,-!p3@ETS1!0.45!5.38!ETS1;;chr7:99070527..99070542,+!p2@ZNF789!0.45!4.97!ZNF789;;chr6:126240442..126240459,+!p4@NCOA7!0.45!2.57!NCOA7;;chr10:135122906..135122921,+!p4@ZNF511!0.45!1.85!ZNF511;;chr14:75745523..75745537,+!p1@FOS!0.44!305.16!FOS;;chr11:65101305..65101359,+!p1@DPF2!0.44!98.86!DPF2;;chr10:104154246..104154347,+!p3@NFKB2!0.44!14.68!NFKB2;;chr3:23986824..23986848,+!p2@NR1D2!0.44!13.48!NR1D2;;chr10:96122645..96122675,-!p2@NOC3L!0.44!11.31!NOC3L;;chr7:86781916..86781963,+!p2@DMTF1!0.44!10.35!DMTF1;;chr1:43148792..43148849,+!p2@YBX1!0.44!8.83!YBX1;;chr6:21597499..21597513,+!p16@SOX4!0.44!1.77!SOX4;;chr12:69753448..69753577,+!p1@YEATS4!0.43!47.74!YEATS4;;chr7:99097863..99097936,-!p1@ZNF394!0.43!24.07!ZNF394;;chr16:68564003..68564050,+!p2@ZFP90!0.43!5.86!ZFP90;;chr11:67007445..67007459,+!p4@KDM2A!0.43!3.45!KDM2A;;chr19:33865009..33865090,+!p3@CEBPG!0.43!2.57!CEBPG;;chr8:128747757..128747800,+!p7@MYC!0.43!2.57!MYC;;chr12:54410664..54410684,+!p1@HOXC4,p1@HOXC5,p1@HOXC6!0.43!1.69!HOXC5;;chr14:100705200..100705237,+!p3@YY1!0.42!17.97!YY1;;chr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Line 45: Line 45:
 
|is_obsolete=
 
|is_obsolete=
 
|library_id=CNhs11273
 
|library_id=CNhs11273
|library_id_phase_based=1:CNhs11273
+
|library_id_phase_based=2:CNhs11273
 
|name=squamous cell lung carcinoma cell line:EBC-1
 
|name=squamous cell lung carcinoma cell line:EBC-1
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
|profile_hcage=CNhs11273,LSID758,release008,COMPLETED
+
|profile_hcage="CNhs11273,LSID758,release008,COMPLETED"
|profile_rnaseq=,,,
+
|profile_rnaseq=
|profile_srnaseq=,,,
+
|profile_srnaseq=",,,"
 
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Revision as of 07:47, 27 November 2014


Name:squamous cell lung carcinoma cell line:EBC-1
Species:Human (Homo sapiens)
Library ID:CNhs11273
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexmale
age69
cell typeunclassifiable
cell lineEBC-1
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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  SAMD00004799
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11273 CAGE DRX008017 DRR008889
Accession ID Hg19

Library idBAMCTSS
CNhs11273 DRZ000314 DRZ001699
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: "CNhs11273This 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: "CNhs11273This 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: "CNhs11273


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000082 (epithelial cell of lung)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
0050615 (respiratory system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
1324 (lung cancer)
305 (carcinoma)
1749 (squamous cell carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002048 (lung)
0002100 (trunk)
0000483 (epithelium)
0000479 (tissue)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0004802 (respiratory tract epithelium)
0000025 (tube)
0005911 (endo-epithelium)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0004807 (respiratory system epithelium)
0000117 (respiratory tube)
0000171 (respiration organ)
0000115 (lung epithelium)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0102024 (squamous cell carcinoma cell line sample)
0100353 (lung cell line sample)
0101120 (epithelial cell line sample)
0100762 (lung cancer cell line sample)
0102202 (lung squamous cell carcinoma cell line sample)
0103001 (EBC-1 cell 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
UBERON:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)