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Difference between revisions of "FF:10549-107H9"

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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=chr13:72441074..72441172,-!p2@DACH1!2.32!209.83!DACH1;;chr7:96654133..96654150,-!p1@DLX5!2.09!122.21!DLX5;;chr13:72440772..72440847,-!p5@DACH1!2.03!106.63!DACH1;;chr11:31832658..31832681,-!p1@PAX6!1.77!57.84!PAX6;;chr3:181429704..181429722,+!p1@SOX2!1.71!50.51!SOX2;;chr10:114886432..114886455,+!p20@TCF7L2!1.62!40.78!TCF7L2;;chr10:114886551..114886601,+!p11@TCF7L2!1.59!38.26!TCF7L2;;chr13:72440434..72440479,-!p6@DACH1!1.59!37.91!DACH1;;chr3:181429741..181429767,+!p2@SOX2!1.56!35.28!SOX2;;chr13:72440901..72440968,-!p4@DACH1!1.55!34.59!DACH1;;chr7:15726296..15726315,-!p1@MEOX2!1.55!34.36!MEOX2;;chr13:72440880..72440895,-!p7@DACH1!1.54!33.44!DACH1;;chr6:19837592..19837621,+!p1@ID4!1.44!155.54!ID4;;chr7:27183263..27183284,-!p2@HOXA5!1.44!26.57!HOXA5;;chr7:27153454..27153469,-!p2@HOXA3!1.43!26.11!HOXA3;;chr13:72441315..72441454,-!p1@DACH1!1.41!48.68!DACH1;;chr7:27183291..27183324,-!p1@HOXA5!1.40!24.28!HOXA5;;chr12:66218598..66218645,+!p2@HMGA2!1.38!103.20!HMGA2;;chr7:15726243..15726293,-!p2@MEOX2!1.35!21.53!MEOX2;;chr11:31832610..31832639,-!p5@PAX6!1.35!21.42!PAX6;;chr14:38064429..38064486,-!p1@FOXA1!1.33!20.27!FOXA1;;chr5:92918919..92918942,+!p1@NR2F1!1.30!83.27!NR2F1;;chr17:41622834..41622883,-!p6@ETV4!1.30!23.14!ETV4;;chr17:46690839..46690884,-!p1@HOXB8!1.29!18.44!HOXB8;;chr8:99956662..99956684,+!p1@OSR2!1.28!27.37!OSR2;;chr3:32023232..32023273,+!p1@ZNF860!1.27!25.08!ZNF860;;chr11:31832207..31832226,-!p12@PAX6!1.26!17.07!PAX6;;chr12:66218443..66218461,+!p8@HMGA2!1.24!20.73!HMGA2;;chr9:126774018..126774055,+!p1@LHX2!1.24!16.26!LHX2;;chr11:31832581..31832601,-!p7@PAX6!1.23!16.04!PAX6;;chr17:41623692..41623715,-!p1@ETV4!1.21!63.68!ETV4;;chr17:46703687..46703740,-!p1@HOXB9!1.21!15.12!HOXB9;;chr13:72441047..72441060,-!p11@DACH1!1.21!15.12!DACH1;;chr12:66218255..66218304,+!p3@HMGA2!1.20!39.74!HMGA2;;chr10:114886405..114886424,+!p26@TCF7L2!1.20!14.78!TCF7L2;;chr19:38720294..38720348,-!p1@DPF1!1.19!17.98!DPF1;;chr11:31832549..31832562,-!p10@PAX6!1.19!14.55!PAX6;;chr17:41623009..41623053,-!p4@ETV4!1.18!22.56!ETV4;;chr12:66218378..66218401,+!p6@HMGA2!1.18!21.99!HMGA2;;chr11:31832807..31832823,-!p4@PAX6!1.18!13.97!PAX6;;chr11:31832862..31832884,-!p2@PAX6!1.16!13.40!PAX6;;chr14:37131058..37131139,+!p1@PAX9!1.14!12.94!PAX9;;chr17:41622765..41622821,-!p2@ETV4!1.13!18.90!ETV4;;chr2:171572786..171572840,+!p2@SP5!1.13!12.48!SP5;;chr2:172967621..172967637,-!p1@DLX2!1.11!31.61!DLX2;;chr22:19748231..19748317,+!p1@TBX1!1.09!11.22!TBX1;;chr13:72440745..72440757,-!p18@DACH1!1.09!11.22!DACH1;;chr12:66218836..66218888,+!p1@HMGA2!1.08!102.51!HMGA2;;chr17:46675558..46675577,-!p2@HOXB6!1.08!11.00!HOXB6;;chr9:126773880..126773895,+!p2@LHX2!1.08!11.00!LHX2;;chr5:172662197..172662216,-!p1@NKX2-5!1.07!10.88!NKX2-5;;chr10:114889045..114889074,+!p12@TCF7L2!1.07!10.65!TCF7L2;;chr7:27142290..27142310,-!p1@HOXA2!1.06!10.42!HOXA2;;chr17:41622925..41622976,-!p3@ETV4!1.05!15.58!ETV4;;chr7:15726176..15726191,-!p3@MEOX2!1.05!10.31!MEOX2;;chr17:46682321..46682362,-!p1@HOXB6!1.04!9.96!HOXB6;;chrY:21906594..21906622,-!p1@KDM5D!1.04!9.85!KDM5D;;chr5:92918768..92918783,+!p8@NR2F1!1.04!9.85!NR2F1;;chr1:8763440..8763460,-!p2@RERE!1.03!49.82!RERE;;chr11:31832687..31832704,-!p6@PAX6!1.03!9.74!PAX6;;chr10:114886387..114886398,+!p36@TCF7L2!1.03!9.62!TCF7L2;;chr12:66218420..66218439,+!p12@HMGA2!1.03!9.62!HMGA2;;chr7:27170359..27170381,-!p1@HOXA4!1.03!9.62!HOXA4;;chr8:77593474..77593612,+!p1@ZFHX4!1.01!39.63!ZFHX4;;chr7:96654026..96654061,-!p2@DLX5!1.01!9.28!DLX5;;chr5:124082279..124082319,-!p3@ZNF608!1.00!10.88!ZNF608;;chr13:72440583..72440605,-!p10@DACH1!1.00!9.05!DACH1;;chr2:172967242..172967265,-!p2@DLX2!1.00!8.93!DLX2;;chr12:66218183..66218209,+!p4@HMGA2!0.99!17.30!HMGA2;;chr12:54378923..54378966,+!p1@HOXC10!0.99!8.82!HOXC10;;chr20:50418972..50419029,-!p1@SALL4!0.99!8.82!SALL4;;chr7:27153428..27153440,-!p3@HOXA3!0.99!8.82!HOXA3;;chr13:72440693..72440706,-!p15@DACH1!0.99!8.70!DACH1;;chr13:72440540..72440579,-!p9@DACH1!0.97!8.36!DACH1;;chr17:46692318..46692362,-!p5@HOXB8!0.97!8.36!HOXB8;;chr9:126774058..126774081,+!p3@LHX2!0.97!8.36!LHX2;;chr3:189507432..189507459,+!p1@TP63!0.96!8.02!TP63;;chr5:92919375..92919438,+!p6@NR2F1!0.95!8.59!NR2F1;;chr15:37390850..37390909,-!p3@MEIS2!0.94!15.46!MEIS2;;chr19:21265028..21265052,+!p2@ZNF714!0.94!14.20!ZNF714;;chr17:46703942..46703964,-!p4@HOXB9!0.94!7.79!HOXB9;;chr20:50418947..50418964,-!p4@SALL4!0.94!7.79!SALL4;;chr17:46655730..46655791,-!p1@HOXB4!0.93!19.13!HOXB4;;chr5:92920456..92920488,+!p9@NR2F1!0.93!8.82!NR2F1;;chr12:66218152..66218174,+!p10@HMGA2!0.93!8.02!HMGA2;;chr7:15726220..15726236,-!p4@MEOX2!0.93!7.44!MEOX2;;chr1:8763463..8763499,-!p6@RERE!0.92!21.07!RERE;;chr1:247171316..247171336,-!p3@ZNF695!0.92!11.22!ZNF695;;chr2:45168875..45168916,+!p1@SIX3!0.92!7.33!SIX3;;chr12:66218212..66218244,+!p5@HMGA2!0.91!10.54!HMGA2;;chr5:92918956..92918969,+!p4@NR2F1!0.91!7.90!NR2F1;;chr7:20826426..20826432,-!p2@SP8!0.91!7.10!SP8;;chr2:45168834..45168847,+!p2@SIX3!0.91!7.10!SIX3;;chr9:96717629..9671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Line 45: Line 45:
 
|is_obsolete=
 
|is_obsolete=
 
|library_id=CNhs11286
 
|library_id=CNhs11286
|library_id_phase_based=1:CNhs11286
+
|library_id_phase_based=2:CNhs11286
 
|name=gastric cancer cell line:AZ521
 
|name=gastric cancer cell line:AZ521
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 
|profile_cagescan=,,,
 
|profile_cagescan=,,,
|profile_hcage=CNhs11286,LSID759,release008,COMPLETED
+
|profile_hcage="CNhs11286,LSID759,release008,COMPLETED"
|profile_rnaseq=,,,
+
|profile_rnaseq=
|profile_srnaseq=,,,
+
|profile_srnaseq=",,,"
 
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Revision as of 07:54, 27 November 2014


Name:gastric cancer cell line:AZ521
Species:Human (Homo sapiens)
Library ID:CNhs11286
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuestomach
dev stageNA
sexunknown
ageunknown
cell typeunclassifiable
cell lineAZ521
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  SAMD00005896
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11286 CAGE DRX007892 DRR008764
Accession ID Hg19

Library idBAMCTSS
CNhs11286 DRZ000189 DRZ001574
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: "CNhs11286This 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: "CNhs11286This 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: "CNhs11286


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

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
3119 (gastrointestinal system cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000945 (stomach)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100787 (gastric 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:0010316 (germ layer / neural crest)