FF:11343-117G2: Difference between revisions

Revision as of 18:05, 27 November 2014

Name:	"Endothelial Cells - Thoracic, donor2"
Species:	Human (Homo sapiens)
Library ID:	CNhs11978
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	internal thoracic artery
dev stage	50 years old adult
sex	male
age	50
cell type	blood vessel endothelial cell
cell line	NA
company	Cell Applications
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	1555
catalog number	CA308-R10a
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004966

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11978		CAGE		DRX008230		DRR009102

Accession ID Hg19

Library id		BAM		CTSS
CNhs11978		DRZ000527		DRZ001912

Download raw sequence, BAM & CTSS

Hg19

BAM	CTSS
[{{{hg19bam}}} download]	[{{{hg19ctss}}} donwload]

Hg38

BAM	CTSS
[{{{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. dataNo results for this sample

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. 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 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 Analyst: Michiel de Hoon link to dataset. data
library id: "CNhs11978This 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 in169 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: "CNhs11978This 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: "CNhs11978

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000051 human thoracic endothelial cell sample

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)
0000076 (squamous epithelial cell)
0002139 (endothelial cell of vascular tree)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000115 (endothelial cell)
0000071 (blood vessel endothelial cell)
1000413 (endothelial cell of artery)
0002544 (aortic endothelial cell)
0002545 (thoracic aorta endothelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000947 (aorta)
0001637 (artery)
0002100 (trunk)
0000483 (epithelium)
0000479 (tissue)
0000055 (vessel)
0000064 (organ part)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0003914 (epithelial tube)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0006914 (squamous epithelium)
0009569 (subdivision of trunk)
0004573 (systemic artery)
0000487 (simple squamous epithelium)
0005800 (segment of aorta)
0003509 (arterial blood vessel)
0004638 (blood vessel endothelium)
0003915 (endothelial tube)
0004700 (arterial system endothelium)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0002049 (vasculature)
0001986 (endothelium)
0010317 (germ layer / neural crest derived structure)
0007798 (vascular system)
0004852 (cardiovascular system endothelium)
0001515 (thoracic aorta)
0001917 (endothelium of artery)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0010191 (aortic system)
0000915 (thoracic segment of trunk)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000046 (human endothelial cell sample)
0000047 (human endothelial cell of the artery sample)
0000048 (human endothelial cell of the aorta sample)
0000001 (sample)
0000051 (human thoracic endothelial 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:0002546 (embryonic blood vessel endothelial progenitor cell)
CL:0000222 (mesodermal cell)

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr20:62680984..62680999,-!p1@SOX18!2.49!400.21!SOX18;;chr8:55370487..55370503,+!p1@SOX17!2.27!184.71!SOX17;;chr21:39870339..39870443,-!p1@ERG!2.10!124.76!ERG;;chr8:10588010..10588030,-!p1@SOX7!1.93!84.25!SOX7;;chr22:19748231..19748317,+!p1@TBX1!1.92!81.82!TBX1;;chr2:177053386..177053402,+!p1@HOXD1!1.88!75.34!HOXD1;;chr17:6926362..6926377,+!p1@BCL6B!1.88!74.53!BCL6B;;chr1:6479968..6479986,-!p1@HES2!1.85!70.48!HES2;;chr19:13213511..13213545,-!p2@LYL1!1.65!47.80!LYL1;;chr12:96588368..96588394,+!p3@ELK3!1.53!86.69!ELK3;;chr18:53068911..53068935,-!p4@TCF4!1.46!31.60!TCF4;;chr6:126070769..126070801,+!p1@HEY2!1.44!30.79!HEY2;;chr10:94449703..94449718,+!p1@HHEX!1.43!97.22!HHEX;;chr16:86600426..86600441,+!p1@FOXC2!1.43!62.38!FOXC2;;chr19:13213662..13213686,-!p1@LYL1!1.38!34.03!LYL1;;chr19:13213399..13213414,-!p6@LYL1!1.31!19.44!LYL1;;chr7:27205136..27205164,-!p1@HOXA9!1.26!17.01!HOXA9;;chr1:209979467..209979494,-!p1@IRF6!1.17!15.39!IRF6;;chr17:46655672..46655697,-!p3@HOXB4!1.17!13.77!HOXB4;;chr17:46688334..46688385,-!p1@HOXB7!1.14!18.63!HOXB7;;chr20:62680671..62680679,-!p2@SOX18!1.09!11.34!SOX18;;chr6:34204921..34204939,+!p3@HMGA1!1.07!327.30!HMGA1;;chr11:65429891..65429915,-!p7@RELA!1.06!10.53!RELA;;chr17:41622925..41622976,-!p3@ETV4!1.05!15.39!ETV4;;chr20:48599506..48599526,+!p1@SNAI1!1.01!60.76!SNAI1;;chr3:128206762..128206781,-!p2@GATA2!1.00!57.52!GATA2;;chr18:22932080..22932170,-!p1@ZNF521!1.00!38.89!ZNF521;;chr17:46682321..46682362,-!p1@HOXB6!1.00!8.91!HOXB6;;chr7:27205106..27205134,-!p2@HOXA9!1.00!8.91!HOXA9;;chr18:19749541..19749557,+!p1@GATA6!0.98!27.54!GATA6;;chr3:169381420..169381535,-!p1@MECOM!0.97!9.72!MECOM;;chr6:21593973..21593988,+!p1@SOX4!0.95!292.46!SOX4;;chr1:151032860..151032918,+!p1@MLLT11!0.94!93.98!MLLT11;;chr5:92918919..92918942,+!p1@NR2F1!0.93!34.84!NR2F1;;chr16:86601052..86601066,+!p4@FOXC2!0.92!7.29!FOXC2;;chr19:13213555..13213568,-!p5@LYL1!0.92!7.29!LYL1;;chr13:79177703..79177729,-!p2@POU4F1!0.92!7.29!POU4F1;;chr19:49865646..49865718,-!p1@TEAD2!0.91!63.19!TEAD2;;chr22:38597987..38598021,+!p2@MAFF!0.90!44.56!MAFF;;chr10:94449675..94449694,+!p2@HHEX!0.90!19.44!HHEX;;chr17:46655704..46655718,-!p2@HOXB4!0.90!10.53!HOXB4;;chr17:46687959..46688007,-!p2@HOXB7!0.90!9.72!HOXB7;;chr2:46524537..46524553,+!p1@EPAS1!0.89!703.20!EPAS1;;chr12:124873357..124873401,-!p1@NCOR2!0.89!81.82!NCOR2;;chr12:66218255..66218304,+!p3@HMGA2!0.88!18.63!HMGA2;;chr6:21594845..21594908,+!p6@SOX4!0.87!10.53!SOX4;;chr6:28321971..28321995,-!p1@ZNF323!0.87!6.48!ZNF323;;chr14:74256787..74256858,-!p6@C14orf43!0.87!6.48!C14orf43;;chr1:47695003..47695042,-!p2@TAL1!0.87!6.48!TAL1;;chr17:46690839..46690884,-!p1@HOXB8!0.87!6.48!HOXB8;;chr17:46691732..46691766,-!p4@HOXB8!0.87!6.48!HOXB8;;chr20:42543506..42543549,+!p2@TOX2!0.85!15.39!TOX2;;chr17:1958388..1958404,+!p1@HIC1!0.84!40.51!HIC1;;chr2:46602901..46602926,+!p7@EPAS1!0.84!8.10!EPAS1;;chr20:42543441..42543497,+!p1@TOX2!0.82!26.73!TOX2;;chr14:24837368..24837401,+!p1@NFATC4!0.82!13.77!NFATC4;;chr6:21597600..21597664,+!p3@SOX4!0.82!9.72!SOX4;;chr19:53496768..53496799,-!p1@ZNF702P!0.82!8.91!ZNF702P;;chr16:30406423..30406447,+!p4@ZNF48!0.82!5.67!ZNF48;;chr16:86600870..86600921,+!p2@FOXC2!0.82!5.67!FOXC2;;chr2:176994408..176994492,+!p1@HOXD8!0.82!5.67!HOXD8;;chr6:21597765..21597779,+!p2@SOX4!0.81!47.80!SOX4;;chr1:935467..935484,-!p1@HES4!0.80!25.11!HES4;;chr2:46602879..46602899,+!p8@EPAS1!0.80!6.48!EPAS1;;chr12:124873852..124873881,-!p3@NCOR2!0.79!34.03!NCOR2;;chr7:26191809..26191890,+!p1@NFE2L3!0.79!27.54!NFE2L3;;chr17:38498594..38498661,+!p2@RARA!0.79!18.63!RARA;;chr6:85474299..85474324,-!p1@TBX18!0.79!9.72!TBX18;;chr19:49864746..49864780,-!p2@TEAD2!0.79!7.29!TEAD2;;chr17:3571863..3571881,-!p1@TAX1BP3!0.77!379.96!TAX1BP3;;chr6:21597370..21597408,+!p5@SOX4!0.77!8.10!SOX4;;chr3:25469724..25469773,+!p1@RARB!0.77!7.29!RARB;;chr3:169381183..169381205,-!p4@MECOM!0.77!4.86!MECOM;;chr7:27183291..27183324,-!p1@HOXA5!0.77!4.86!HOXA5;;chr8:55370720..55370733,+!p2@SOX17!0.77!4.86!SOX17;;chr16:86601088..86601105,+!p5@FOXC2!0.77!4.86!FOXC2;;chr19:13213465..13213478,-!p7@LYL1!0.77!4.86!LYL1;;chr19:9732460..9732472,-!p2@ZNF561!0.77!4.86!ZNF561;;chr9:16705069..16705086,-!p3@BNC2!0.77!4.86!BNC2;;chr4:2263809..2263854,-!p1@MXD4!0.76!204.16!MXD4;;chr14:74226961..74227020,-!p1@C14orf43!0.75!34.03!C14orf43;;chr3:168864315..168864339,-!p2@MECOM!0.75!8.10!MECOM;;chr1:935496..935509,-!p3@HES4!0.75!7.29!HES4;;chr19:1652555..1652568,-!p2@TCF3!0.74!20.25!TCF3;;chr1:23885981..23886002,-!p1@ID3!0.72!841.74!ID3;;chr12:66218598..66218645,+!p2@HMGA2!0.72!21.87!HMGA2;;chr6:126240380..126240430,+!p2@NCOA7!0.72!12.15!NCOA7;;chr12:80084137..80084165,-!p10@PAWR!0.72!5.67!PAWR;;chr12:66218836..66218888,+!p1@HMGA2!0.71!43.75!HMGA2;;chr3:178789522..178789564,-!p2@ZMAT3!0.71!34.03!ZMAT3;;chr13:72441315..72441454,-!p1@DACH1!0.71!8.91!DACH1;;chr3:170076314..170076334,+!p2@SKIL!0.71!5.67!SKIL;;chr3:25469815..25469866,+!p3@RARB!0.70!4.05!RARB;;chr3:25470062..25470084,+!p4@RARB!0.70!4.05!RARB;;chr3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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11978
-|library_id_phase_based=1:CNhs11978
+|library_id_phase_based=2:CNhs11978
-|name=Endothelial Cells - Thoracic, donor2
+|name="Endothelial Cells - Thoracic, donor2"
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
-|profile_hcage=CNhs11978,LSID836,release011,COMPLETED
+|profile_hcage="CNhs11978,LSID836,release011,COMPLETED"
-|profile_rnaseq=,,,
+|profile_rnaseq=
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FF:11343-117G2: Difference between revisions

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Revision as of 18:05, 27 November 2014

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0