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Difference between revisions of "FF:11674-122G9"

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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=chr6:134210243..134210257,+!p1@TCF21!2.33!212.51!TCF21;;chr19:46801639..46801699,+!p1@HIF3A!1.79!61.00!HIF3A;;chr15:57511609..57511651,+!p2@TCF12!1.63!68.21!TCF12;;chr15:42749722..42749739,-!p2@ZFP106!1.58!65.59!ZFP106;;chr6:1389789..1389821,+!p1@FOXF2!1.57!49.19!FOXF2;;chr14:61116183..61116208,-!p1@SIX1!1.51!114.78!SIX1;;chr16:86544113..86544145,+!p1@FOXF1!1.50!37.39!FOXF1;;chr2:239756671..239756732,+!p1@TWIST2!1.49!93.79!TWIST2;;chr19:13134772..13134822,+!p2@NFIX!1.47!41.32!NFIX;;chr17:59477233..59477263,+!p1@TBX2!1.44!80.02!TBX2;;chr17:1959369..1959388,+!p2@HIC1!1.36!56.41!HIC1;;chr17:46671108..46671147,-!p1@HOXB5!1.33!20.33!HOXB5;;chr1:170633348..170633399,+!p2@PRRX1!1.32!26.89!PRRX1;;chr17:46655704..46655718,-!p2@HOXB4!1.30!28.20!HOXB4;;chr1:170632285..170632309,+!p1@PRRX1!1.30!21.64!PRRX1;;chr11:46299199..46299233,+!p1@CREB3L1!1.27!89.20!CREB3L1;;chr7:19157248..19157268,-!p1@TWIST1!1.27!47.88!TWIST1;;chr2:239756739..239756755,+!p2@TWIST2!1.25!28.20!TWIST2;;chr15:96876966..96877017,+!p12@NR2F2!1.24!23.61!NR2F2;;chr7:27183291..27183324,-!p1@HOXA5!1.22!15.74!HOXA5;;chr3:25470156..25470227,+!p2@RARB!1.22!15.74!RARB;;chr12:66218255..66218304,+!p3@HMGA2!1.21!40.67!HMGA2;;chr7:27183263..27183284,-!p2@HOXA5!1.21!15.09!HOXA5;;chr17:59477275..59477286,+!p3@TBX2!1.20!19.68!TBX2;;chr5:92918956..92918969,+!p4@NR2F1!1.20!16.40!NR2F1;;chr12:66218598..66218645,+!p2@HMGA2!1.19!66.25!HMGA2;;chr11:47279504..47279563,+!p1@NR1H3!1.18!32.14!NR1H3;;chr11:46299539..46299620,+!p2@CREB3L1!1.18!23.61!CREB3L1;;chr5:92918919..92918942,+!p1@NR2F1!1.17!61.65!NR2F1;;chr14:75745523..75745537,+!p1@FOS!1.15!1547.91!FOS;;chr15:57511589..57511608,+!p4@TCF12!1.15!13.12!TCF12;;chr15:96873984..96873999,+!p3@NR2F2!1.13!90.51!NR2F2;;chr3:12329358..12329393,+!p3@PPARG!1.13!30.83!PPARG;;chr20:50179368..50179392,-!p2@NFATC2!1.12!15.74!NFATC2;;chr1:170633262..170633285,+!p3@PRRX1!1.11!13.77!PRRX1;;chr17:59477197..59477212,+!p2@TBX2!1.09!19.68!TBX2;;chr9:132427972..132428056,+!p1@PRRX2!1.08!14.43!PRRX2;;chr7:27183114..27183138,-!p3@HOXA5!1.08!11.15!HOXA5;;chr11:113930425..113930471,+!p1@ZBTB16!1.06!15.09!ZBTB16;;chr3:12329397..12329433,+!p2@PPARG!1.03!22.30!PPARG;;chr3:141105705..141105770,+!p4@ZBTB38!1.03!11.81!ZBTB38;;chr5:2751762..2751784,-!p1@IRX2!1.03!9.84!IRX2;;chr7:27183191..27183214,-!p4@HOXA5!1.03!9.84!HOXA5;;chr17:46675558..46675577,-!p2@HOXB6!1.03!9.84!HOXB6;;chr9:102584262..102584276,+!p1@NR4A3!1.02!21.64!NR4A3;;chr1:170632959..170632987,+!p4@PRRX1!1.02!10.49!PRRX1;;chr5:137801160..137801176,+!p1@EGR1!1.01!927.44!EGR1;;chr8:49833948..49833973,-!p2@SNAI2!1.01!59.69!SNAI2;;chr6:1389989..1390019,+!p2@FOXF2!1.01!9.18!FOXF2;;chr6:1610293..1610310,+!p1@FOXC1!1.00!15.09!FOXC1;;chr8:48650715..48650735,-!p1@CEBPD!0.99!1147.82!CEBPD;;chr19:45971246..45971265,+!p1@FOSB!0.99!165.94!FOSB;;chr7:19157043..19157088,-!p2@TWIST1!0.99!22.30!TWIST1;;chr15:96874145..96874166,+!p7@NR2F2!0.99!17.05!NR2F2;;chr12:66218836..66218888,+!p1@HMGA2!0.98!81.99!HMGA2;;chr11:47279248..47279264,+!p3@NR1H3!0.98!9.84!NR1H3;;chr14:61116168..61116180,-!p2@SIX1!0.98!9.84!SIX1;;chr3:12330560..12330579,+!p1@PPARG!0.98!9.84!PPARG;;chrY:21906594..21906622,-!p1@KDM5D!0.98!8.53!KDM5D;;chr12:52445218..52445237,+!p1@NR4A1!0.95!102.98!NR4A1;;chr15:96874012..96874042,+!p2@NR2F2!0.94!71.49!NR2F2;;chr17:17726907..17726958,-!p2@SREBF1!0.94!49.19!SREBF1;;chr2:19558373..19558392,-!p1@OSR1!0.94!21.64!OSR1;;chr19:3574330..3574393,+!p2@HMG20B!0.91!7.21!HMG20B;;chr1:170632250..170632277,+!p7@PRRX1!0.91!7.21!PRRX1;;chr14:29235961..29236008,+!p1@FOXG1!0.91!7.21!FOXG1;;chr9:132427883..132427951,+!p2@PRRX2!0.91!7.21!PRRX2;;chr8:25902876..25902936,-!p1@EBF2!0.91!7.21!EBF2;;chr8:49833978..49833996,-!p1@SNAI2!0.90!148.23!SNAI2;;chr21:47063625..47063658,+!p1@PCBP3!0.90!31.48!PCBP3;;chr5:92919100..92919135,+!p3@NR2F1!0.90!8.53!NR2F1;;chr6:85473156..85473210,-!p2@TBX18!0.90!8.53!TBX18;;chr12:66218183..66218209,+!p4@HMGA2!0.88!13.12!HMGA2;;chr12:66218904..66218913,+!p11@HMGA2!0.88!6.56!HMGA2;;chr15:80843484..80843499,+!p5@ARNT2!0.88!6.56!ARNT2;;chr7:14028488..14028516,-!p2@ETV1!0.87!7.21!ETV1;;chr20:42543441..42543497,+!p1@TOX2!0.85!28.86!TOX2;;chr5:137804484..137804498,+!p2@EGR1!0.85!25.58!EGR1;;chr9:128509663..128509715,+!p1@PBX3!0.85!21.64!PBX3;;chr14:73360799..73360817,-!p1@DPF3!0.84!21.64!DPF3;;chr20:42543506..42543549,+!p2@TOX2!0.84!15.09!TOX2;;chr12:115122318..115122331,-!p2@TBX3!0.84!5.90!TBX3;;chrY:2803415..2803468,+!p1@ZFY!0.84!5.90!ZFY;;chr7:27142290..27142310,-!p1@HOXA2!0.84!5.90!HOXA2;;chr1:164528410..164528428,+!p1@PBX1!0.83!45.91!PBX1;;chr1:164528445..164528459,+!p2@PBX1!0.83!19.02!PBX1;;chr17:1958388..1958404,+!p1@HIC1!0.82!38.04!HIC1;;chr17:7492684..7492778,-!p2@SOX15!0.82!12.46!SOX15;;chr9:73029219..73029289,-!p2@KLF9!0.81!17.71!KLF9;;chr14:75746722..75746777,+!p2@FOS!0.81!7.21!FOS;;chr5:137804357..137804390,+!p4@EGR1!0.81!6.56!EGR1;;chr2:66662281..66662308,+!p1@MEIS1!0.80!19.68!MEIS1;;chr2:223163706..223163730,-!p1@PAX3!0.80!5.25!PAX3;;chr6:1389824..1389840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Line 45: Line 45:
 
|is_obsolete=
 
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|library_id=CNhs12894
 
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Revision as of 09:59, 27 November 2014


Name:"Smooth Muscle Cells - Tracheal, donor3"
Species:Human (Homo sapiens)
Library ID:CNhs12894
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexNA
ageNA
cell typesmooth muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2587
catalog numberSC3415
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005738
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12894 CAGE DRX008506 DRR009378
Accession ID Hg19

Library idBAMCTSS
CNhs12894 DRZ000803 DRZ002188
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: "CNhs12894This 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: "CNhs12894This 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: "CNhs12894


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)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0002600 (smooth muscle cell of trachea)

UBERON: Anatomy
0000468 (multi-cellular organism)
0003126 (trachea)
0002100 (trunk)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0000464 (anatomical space)
0001005 (respiratory airway)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0007196 (tracheobronchial tree)
0000065 (respiratory tract)
0001558 (lower respiratory tract)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000167 (smooth muscle cell sample)
0000184 (human smooth muscle cell of trachea 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:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)
CL:0000514 (smooth muscle myoblast)