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Difference between revisions of "FF:10706-109H4"

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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=chr3:189349162..189349207,+!p2@TP63!1.76!56.93!TP63;;chrX:2418949..2419024,-!p1@DHRSX,p1@ZBED1!1.53!32.93!ZBED1;;chr6:45296048..45296082,+!p1@RUNX2!1.45!31.21!RUNX2;;chr20:30433396..30433414,-!p1@FOXS1!1.30!18.86!FOXS1;;chrX:66763856..66763896,+!p1@AR!1.23!22.98!AR;;chr20:42543441..42543497,+!p1@TOX2!1.22!69.11!TOX2;;chr1:151804244..151804310,-!p1@RORC!1.21!15.09!RORC;;chr3:21792585..21792625,-!p2@ZNF385D!1.20!16.46!ZNF385D;;chr3:114343768..114343822,-!p1@ZBTB20!1.18!61.22!ZBTB20;;chr3:189348969..189349018,+!p4@TP63!1.16!13.38!TP63;;chr17:70117153..70117174,+!p1@SOX9!1.14!132.05!SOX9;;chr1:119530493..119530572,-!p1@TBX15!1.14!12.86!TBX15;;chr20:42543506..42543549,+!p2@TOX2!1.12!29.67!TOX2;;chr3:141087339..141087387,+!p2@ZBTB38!1.10!117.81!ZBTB38;;chr4:111558135..111558198,-!p2@PITX2!1.10!11.66!PITX2;;chr5:134369905..134369972,-!p1@PITX1!1.08!17.15!PITX1;;chr12:66218598..66218645,+!p2@HMGA2!1.07!50.59!HMGA2;;chr6:126240380..126240430,+!p2@NCOA7!1.05!27.10!NCOA7;;chr2:176969228..176969260,+!p1@HOXD11!1.05!10.12!HOXD11;;chr12:66218836..66218888,+!p1@HMGA2!1.03!91.57!HMGA2;;chr9:14180778..14180808,-!p15@NFIB!1.03!9.77!NFIB;;chr3:193853927..193853944,+!p1@HES1!1.02!313.82!HES1;;chr3:114343826..114343869,-!p4@ZBTB20!1.01!18.86!ZBTB20;;chr12:26277817..26277863,-!p2@BHLHE41!1.01!12.52!BHLHE41;;chr3:21792682..21792720,-!p1@ZNF385D!1.00!8.92!ZNF385D;;chr5:158526917..158526932,-!p1@EBF1!0.97!21.26!EBF1;;chr19:45971246..45971265,+!p1@FOSB!0.96!157.25!FOSB;;chr3:141087393..141087426,+!p3@ZBTB38!0.96!33.27!ZBTB38;;chr20:50179368..50179392,-!p2@NFATC2!0.96!10.63!NFATC2;;chr7:14028488..14028516,-!p2@ETV1!0.96!8.92!ETV1;;chr14:75745523..75745537,+!p1@FOS!0.94!965.48!FOS;;chr1:158969752..158969780,+!p6@IFI16!0.94!13.55!IFI16;;chr6:28321971..28321995,-!p1@ZNF323!0.94!7.72!ZNF323;;chr12:26277956..26277980,-!p1@BHLHE41!0.92!27.61!BHLHE41;;chr17:38256799..38256815,-!p3@NR1D1!0.92!13.72!NR1D1;;chr6:10412600..10412637,-!p1@TFAP2A!0.92!12.52!TFAP2A;;chr3:157823517..157823562,-!p1@SHOX2!0.91!7.72!SHOX2;;chr7:26191809..26191890,+!p1@NFE2L3!0.90!35.67!NFE2L3;;chr7:17338266..17338282,+!p1@AHR!0.89!77.34!AHR;;chr2:178128149..178128198,-!p2@NFE2L2!0.89!38.41!NFE2L2;;chr12:66218255..66218304,+!p3@HMGA2!0.89!19.04!HMGA2;;chr5:124082322..124082364,-!p1@ZNF608!0.89!18.01!ZNF608;;chr3:5021268..5021282,+!p4@BHLHE40!0.89!14.40!BHLHE40;;chr17:38256822..38256851,-!p1@NR1D1!0.88!54.88!NR1D1;;chr8:116681409..116681431,-!p2@TRPS1!0.88!19.04!TRPS1;;chrX:66763815..66763854,+!p2@AR!0.87!8.57!AR;;chr12:125003087..125003141,-!p4@NCOR2!0.87!8.40!NCOR2;;chr10:63809013..63809041,+!p3@ARID5B!0.86!36.36!ARID5B;;chr7:14029283..14029311,-!p1@ETV1!0.86!35.16!ETV1;;chr3:71179699..71179744,-!p2@FOXP1!0.84!47.16!FOXP1;;chr11:46299199..46299233,+!p1@CREB3L1!0.83!31.90!CREB3L1;;chr16:86544113..86544145,+!p1@FOXF1!0.83!7.37!FOXF1;;chr12:77459306..77459365,-!p1@E2F7!0.82!74.94!E2F7;;chr19:13134772..13134822,+!p2@NFIX!0.82!8.40!NFIX;;chr9:16728327..16728338,-!p5@BNC2!0.82!5.66!BNC2;;chr6:35310395..35310410,+!p2@PPARD!0.81!22.64!PPARD;;chr5:124084493..124084524,-!p2@ZNF608!0.80!12.69!ZNF608;;chr9:16728161..16728185,-!p4@BNC2!0.80!5.32!BNC2;;chr15:80843484..80843499,+!p5@ARNT2!0.80!5.32!ARNT2;;chr2:101436564..101436647,+!p1@NPAS2!0.79!114.55!NPAS2;;chr3:5021191..5021202,+!p3@BHLHE40!0.79!14.75!BHLHE40;;chr17:17726907..17726958,-!p2@SREBF1!0.78!34.13!SREBF1;;chr9:16705069..16705086,-!p3@BNC2!0.78!4.97!BNC2;;chr8:11561684..11561751,+!p1@GATA4!0.78!4.97!GATA4;;chr11:66886717..66886762,+!p1@KDM2A!0.76!108.55!KDM2A;;chr14:62162258..62162269,+!p2@HIF1A!0.76!50.59!HIF1A;;chr21:47063625..47063658,+!p1@PCBP3!0.76!22.64!PCBP3;;chr17:41623692..41623715,-!p1@ETV4!0.76!22.12!ETV4;;chr17:53342311..53342400,+!p1@HLF!0.76!5.49!HLF;;chr6:10412392..10412409,-!p4@TFAP2A!0.76!5.49!TFAP2A;;chr3:21792631..21792665,-!p3@ZNF385D!0.76!4.80!ZNF385D;;chr2:46524897..46524911,+!p2@EPAS1!0.75!13.89!EPAS1;;chr2:231090433..231090469,+!p1@SP140!0.75!4.63!SP140;;chr16:67198683..67198698,+!p2@HSF4!0.75!4.63!HSF4;;chr1:158979686..158979745,+!p1@IFI16!0.74!166.69!IFI16;;chr6:168227552..168227609,+!p1@MLLT4!0.74!40.99!MLLT4;;chr6:45390025..45390076,+!p2@RUNX2!0.74!11.66!RUNX2;;chr2:157189180..157189290,-!p1@NR4A2!0.73!25.04!NR4A2;;chr16:79633894..79633954,-!p3@MAF!0.73!8.92!MAF;;chr6:126240442..126240459,+!p4@NCOA7!0.73!5.83!NCOA7;;chr16:79634624..79634642,-!p1@MAF!0.72!18.52!MAF;;chr12:66218212..66218244,+!p5@HMGA2!0.72!6.52!HMGA2;;chr12:26277929..26277955,-!p3@BHLHE41!0.72!6.35!BHLHE41;;chr5:176738887..176738934,-!p1@MXD3!0.71!31.04!MXD3;;chr14:62162285..62162296,+!p3@HIF1A!0.71!24.18!HIF1A;;chr17:56065729..56065781,-!p2@VEZF1!0.71!19.89!VEZF1;;chr3:114866084..114866118,-!p2@ZBTB20!0.71!16.81!ZBTB20;;chr9:14314522..14314556,-!p3@NFIB!0.71!10.46!NFIB;;chr8:116681194..116681214,-!p1@TRPS1!0.70!42.87!TRPS1;;chr1:158979872..158979898,+!p3@IFI16!0.70!13.72!IFI16;;chr6:45389835..45389861,+!p7@RUNX2!0.70!6.86!RUNX2;;chr1:41827095..41827155,+!p1@FOXO6!0.70!5.66!FOXO6;;chr1:8938709..8938720,-!p3@ENO1!0.69!218.48!ENO1;;chr5:92918894..92918912,+!p2@NR2F1!0.69!14.23!NR2F1;;chr7:14029312..14029325,-!p4@ETV1!0.69!4.97!ETV1;;chr5:134369879..134369898,-!p2@PITX1!0.69!3.94!PITX1;;chr12:24102576..24102623,-!p2@SOX5!0.69!3.94!SOX5;;chr6:85473156..85473210,-!p2@TBX18!0.68!4.80!TBX18;;chr8:116681221..116681236,-!p3@TRPS1!0.67!12.18!TRPS1;;chr6:168227611..168227624,+!p2@MLLT4!0.67!5.66!MLLT4;;chr12:66218183..66218209,+!p4@HMGA2!0.66!7.55!HMGA2;;chr1:158979792..158979814,+!p2@IFI16!0.65!39.10!IFI16;;chr5:92918919..92918942,+!p1@NR2F1!0.65!17.66!NR2F1;;chr9:109625401..109625458,+!p1@ZNF462!0.65!10.12!ZNF462;;chr3:24536253..24536328,-!p1@THRB!0.65!7.20!THRB;;chr16:79634595..79634620,-!p2@MAF!0.65!6.86!MAF;;chr17:41622925..41622976,-!p3@ETV4!0.65!5.49!ETV4;;chr5:124081979..124082021,-!p7@ZNF608!0.65!3.43!ZNF608;;chr5:124082470..124082483,-!p8@ZNF608!0.65!3.43!ZNF608;;chrX:66763914..66763933,+!p3@AR!0.65!3.43!AR;;chr2:46524537..46524553,+!p1@EPAS1!0.64!395.45!EPAS1;;chr3:5021113..5021180,+!p1@BHLHE40!0.64!276.61!BHLHE40;;chr8:72756063..72756125,-!p1@MSC!0.64!7.55!MSC;;chr6:126112074..126112144,+!p1@NCOA7!0.63!51.96!NCOA7;;chr3:168865194..168865245,-!p3@MECOM!0.63!4.46!MECOM;;chr6:126240356..126240379,+!p7@NCOA7!0.63!4.12!NCOA7;;chr1:44513995..44514031,+!p1@KLF17!0.63!3.26!KLF17;;chr2:176969179..176969226,+!p2@HOXD11!0.63!3.26!HOXD11;;chr5:137801160..137801176,+!p1@EGR1!0.62!377.45!EGR1;;chr6:91006518..91006570,-!p1@BACH2!0.62!8.23!BACH2;;chr5:158526459..158526481,-!p2@EBF1!0.62!4.46!EBF1;;chr10:64134120..64134183,+!p1@ZNF365!0.62!3.94!ZNF365;;chr12:26278008..26278024,-!p4@BHLHE41!0.62!3.94!BHLHE41;;chr10:31288398..31288455,-!p2@ZNF438!0.62!3.77!ZNF438;;chr9:73028814..73028895,-!p1@KLF9!0.61!36.87!KLF9;;chr1:59249645..59249656,-!p4@JUN!0.61!8.75!JUN;;chr8:72756267..72756296,-!p4@MSC!0.61!4.80!MSC;;chr15:67418047..67418093,+!p4@SMAD3!0.61!4.12!SMAD3;;chr5:92919100..92919135,+!p3@NR2F1!0.61!3.94!NR2F1;;chr16:67198633..67198671,+!p1@HSF4!0.61!3.09!HSF4;;chr1:8935472..8935488,-!p20@ENO1!0.61!3.09!ENO1;;chrX:66764343..66764362,+!p4@AR!0.61!3.09!AR;;chr12:66218904..66218913,+!p11@HMGA2!0.61!3.09!HMGA2;;chr7:28725740..28725778,+!p1@CREB5!0.60!31.73!CREB5;;chr9:73029219..73029289,-!p2@KLF9!0.60!10.46!KLF9;;chr2:121493425..121493474,+!p1@GLI2!0.60!7.37!GLI2;;chr17:41622765..41622821,-!p2@ETV4!0.60!4.97!ETV4;;chr1:158985493..158985535,+!p4@IFI16!0.60!4.97!IFI16;;chr8:116681247..116681261,-!p8@TRPS1!0.60!4.12!TRPS1;;chr15:67418119..67418162,+!p5@SMAD3!0.60!3.43!SMAD3;;chr18:53068911..53068935,-!p4@TCF4!0.60!3.43!TCF4;;chr1:8938736..8938756,-!p1@ENO1!0.59!3899.98!ENO1;;chr8:103667935..103667960,-!p1@KLF10!0.59!157.25!KLF10;;chr3:69788576..69788648,+!p1@MITF!0.59!18.52!MITF;;chr5:124080203..124080258,-!p5@ZNF608!0.59!3.43!ZNF608;;chr6:45295979..45295986,+!p28@RUNX2!0.59!2.92!RUNX2;;chr8:10588010..10588030,-!p1@SOX7!0.59!2.92!SOX7;;chr2:121493492..121493537,+!p2@GLI2!0.58!5.14!GLI2;;chr6:1312325..1312340,+!p1@FOXQ1!0.58!4.97!FOXQ1;;chr5:124082279..124082319,-!p3@ZNF608!0.58!3.60!ZNF608;;chr9:14314566..14314618,-!p1@NFIB!0.57!40.13!NFIB;;chr6:31126291..31126399,+!p1@TCF19!0.57!31.55!TCF19;;chr1:120190786..120190915,-!p1@ZNF697!0.57!24.01!ZNF697;;chr1:59249688..59249703,-!p3@JUN!0.57!19.72!JUN;;chr1:935467..935484,-!p1@HES4!0.57!14.40!HES4;;chr3:71179746..71179783,-!p7@FOXP1!0.57!10.80!FOXP1;;chr7:17338324..17338341,+!p3@AHR!0.57!10.80!AHR;;chr19:13134457..13134462,+!p5@NFIX!0.57!5.49!NFIX;;chr12:66218573..66218596,+!p7@HMGA2!0.57!4.46!HMGA2;;chr15:67418177..67418204,+!p9@SMAD3!0.57!2.74!SMAD3;;chr9:16728047..16728061,-!p8@BNC2!0.57!2.74!BNC2;;chr9:14314131..14314147,-!p2@NFIB!0.56!18.18!NFIB;;chr3:114819124..114819200,-!p3@ZBTB20!0.56!7.03!ZBTB20;;chr3:125094150..125094176,-!p2@ZNF148!0.56!6.69!ZNF148;;chr3:168864315..168864339,-!p2@MECOM!0.56!4.80!MECOM;;chr13:45010939..45011033,-!p1@TSC22D1!0.55!214.53!TSC22D1;;chr6:144329384..144329405,-!p1@PLAGL1!0.55!36.87!PLAGL1;;chrX:128657413..128657456,-!p2@SMARCA1!0.55!27.27!SMARCA1;;chr11:67007548..67007610,+!p3@KDM2A!0.55!23.84!KDM2A;;chr6:35310363..35310382,+!p3@PPARD!0.55!11.32!PPARD;;chr16:29819446..29819471,+!p9@MAZ!0.55!9.09!MAZ;;chr3:114866124..114866149,-!p5@ZBTB20!0.55!4.80!ZBTB20;;chr1:120190761..120190782,-!p2@ZNF697!0.55!3.77!ZNF697;;chr1:3569072..3569093,+!p1@TP73!0.55!2.57!TP73;;chr7:17338239..17338262,+!p2@AHR!0.54!22.98!AHR;;chr2:178128199..178128245,-!p3@NFE2L2!0.54!16.63!NFE2L2;;chr10:70320074..70320106,+!p1@TET1!0.54!5.66!TET1;;chr21:36260295..36260310,-!p3@RUNX1!0.54!4.46!RUNX1;;chr8:116681275..116681290,-!p11@TRPS1!0.54!3.26!TRPS1;;chr5:137804405..137804444,+!p3@EGR1!0.54!3.09!EGR1;;chr2:121493717..121493755,+!p3@GLI2!0.54!2.74!GLI2;;chr10:114709999..114710031,+!p1@TCF7L2!0.53!73.40!TCF7L2;;chr10:111985713..111985774,+!p2@MXI1!0.53!29.32!MXI1;;chr2:148778590..148778647,+!p2@MBD5!0.53!22.64!MBD5;;chr9:95640300..95640345,-!p1@ZNF484!0.53!16.81!ZNF484;;chr5:137804484..137804498,+!p2@EGR1!0.53!11.83!EGR1;;chr11:65667884..65667895,-!p2@FOSL1!0.53!11.49!FOSL1;;chr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Line 45: Line 45:
 
|is_obsolete=
 
|is_obsolete=
 
|library_id=CNhs11933
 
|library_id=CNhs11933
|library_id_phase_based=1:CNhs11933
+
|library_id_phase_based=2:CNhs11933
 
|name=pleomorphic hepatocellular carcinoma cell line:SNU-387
 
|name=pleomorphic hepatocellular carcinoma cell line:SNU-387
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
|profile_hcage=CNhs11933,LSID835,release010,COMPLETED
+
|profile_hcage="CNhs11933,LSID835,release010,COMPLETED"
|profile_rnaseq=,,,
+
|profile_rnaseq=
|profile_srnaseq=,,,
+
|profile_srnaseq=",,,"
 
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Revision as of 08:09, 27 November 2014


Name:pleomorphic hepatocellular carcinoma cell line:SNU-387
Species:Human (Homo sapiens)
Library ID:CNhs11933
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexfemale
age41
cell typehepatocyte
cell lineSNU-387
companyATCC
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  SAMD00005502
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11933 CAGE DRX007986 DRR008858
Accession ID Hg19

Library idBAMCTSS
CNhs11933 DRZ000283 DRZ001668
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: "CNhs11933This 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: "CNhs11933This 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: "CNhs11933


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
7 (disease of anatomical entity)
305 (carcinoma)
5662 (pleomorphic carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0100224 (liver cell line sample)
0100578 (hepatoma cell line sample)
0103191 (SNU-387 cell 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

CL:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)
UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)