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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|top_motifs=NKX3-1:1.89309627834;TFDP1:1.41392330972;ONECUT1,2:1.38782918422;ELK1,4_GABP{A,B1}:1.38502203263;PPARG:1.36293837478;HOXA9_MEIS1:1.34249890343;PITX1..3:1.25758767804;ADNP_IRX_SIX_ZHX:1.25727297222;FOXD3:1.23236386507;FOX{I1,J2}:1.01677171561;TEF:0.99127957233;ZBTB16:0.918324222395;POU1F1:0.906153899015;ELF1,2,4:0.888960053344;E2F1..5:0.861784775579;ZNF143:0.743892472368;EN1,2:0.734099204139;GATA4:0.703579230626;GFI1:0.622047351086;FOXP1:0.600735918532;PAX4:0.556469946298;RBPJ:0.53728133798;POU3F1..4:0.514608799538;ARID5B:0.512053209305;RXR{A,B,G}:0.498686429319;NFE2:0.495518291724;BACH2:0.494701601562;PRDM1:0.46353299965;bHLH_family:0.424862925758;TOPORS:0.421199583386;MYB:0.418725622826;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.4176366208;PAX8:0.413434320784;ZNF384:0.385834317535;AIRE:0.376051015903;NFE2L1:0.359461670118;TP53:0.358267220419;NR3C1:0.357617448494;FOS_FOS{B,L1}_JUN{B,D}:0.28973831165;EVI1:0.28378939581;CEBPA,B_DDIT3:0.28351518588;GFI1B:0.280056408786;OCT4_SOX2{dimer}:0.27153634552;TEAD1:0.271165102251;PAX3,7:0.269055875847;HOX{A4,D4}:0.266936159686;UFEwm:0.256489849426;BREu{core}:0.247936073179;HOX{A5,B5}:0.244159544417;POU2F1..3:0.240953423456;HIC1:0.237026285448;NKX2-1,4:0.200084510974;CDC5L:0.187136055302;PRRX1,2:0.1852483001;NR6A1:0.183108038113;FOXA2:0.179172104538;TFAP2B:0.17471198954;IKZF2:0.161821260803;VSX1,2:0.130855369069;FOSL2:0.130788575564;YY1:0.125583903868;PBX1:0.109474706915;T:0.101552054206;POU6F1:0.0862363846602;NKX3-2:0.0795884611144;NRF1:0.0778057255659;ZFP161:0.0598003126447;HMGA1,2:0.0468975116738;GCM1,2:0.0349826640297;ZBTB6:0.025507533005;CDX1,2,4:0.0199525791906;TFAP2{A,C}:0.019564887173;ALX4:0.00827918868555;STAT5{A,B}:0.00782594433377;NFIX:0.00699615455887;FOXM1:0.00309886643282;AHR_ARNT_ARNT2:-0.0114955509381;HBP1_HMGB_SSRP1_UBTF:-0.0261704345056;CRX:-0.0367224694902;NFE2L2:-0.0378634186312;TLX1..3_NFIC{dimer}:-0.0414808224761;HES1:-0.067691073432;MYBL2:-0.0773887826131;NFY{A,B,C}:-0.0799900078151;DMAP1_NCOR{1,2}_SMARC:-0.0835461797387;GTF2A1,2:-0.084392590119;PDX1:-0.0882542813568;KLF4:-0.106929114071;NKX6-1,2:-0.116094947919;CUX2:-0.129470226796;RUNX1..3:-0.138334410017;ZIC1..3:-0.14676388637;MED-1{core}:-0.158737835255;MTE{core}:-0.164260801745;MYOD1:-0.173170662728;SPI1:-0.182639916331;PAX5:-0.183935091193;SRF:-0.195602642224;MZF1:-0.195688299048;GTF2I:-0.197936782685;LEF1_TCF7_TCF7L1,2:-0.209897960688;HNF1A:-0.213777735932;SMAD1..7,9:-0.214364023967;HLF:-0.217715538731;IKZF1:-0.222042063714;NANOG:-0.231732152931;ESRRA:-0.232382991653;ETS1,2:-0.234758191645;NKX2-2,8:-0.24013618662;FOXO1,3,4:-0.249824598067;TBX4,5:-0.25267061478;NR5A1,2:-0.27485881409;RFX1:-0.276482019766;SPIB:-0.279782551119;FOXQ1:-0.281528570042;POU5F1:-0.295299130969;EGR1..3:-0.301932986586;REST:-0.310279417488;BPTF:-0.339064399557;MEF2{A,B,C,D}:-0.342150069794;PAX6:-0.352409640182;MYFfamily:-0.354762004774;NFKB1_REL_RELA:-0.355820452189;LHX3,4:-0.359763165035;IRF1,2:-0.364078018361;NFIL3:-0.390503696949;GZF1:-0.399705861567;XCPE1{core}:-0.405396079785;JUN:-0.41596515999;MAZ:-0.424483279585;HNF4A_NR2F1,2:-0.425685946206;XBP1:-0.437406516876;NHLH1,2:-0.443686061734;SOX2:-0.44511288432;FOX{F1,F2,J1}:-0.4472114206;GATA6:-0.447758767969;SNAI1..3:-0.457212583653;MTF1:-0.460218665811;SOX5:-0.460415205888;STAT2,4,6:-0.466225265603;SOX17:-0.47720631992;TAL1_TCF{3,4,12}:-0.483887822252;IRF7:-0.501992959573;TFAP4:-0.507984505537;HIF1A:-0.510232217163;PAX1,9:-0.511238946655;ATF5_CREB3:-0.524647756271;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.525646451179;ALX1:-0.528533306647;NFATC1..3:-0.54082283278;DBP:-0.549435078362;AR:-0.557041877531;ZEB1:-0.599128937235;PAX2:-0.621341601017;SOX{8,9,10}:-0.632224699444;ATF2:-0.639289506646;CREB1:-0.642082286779;ATF4:-0.644381310394;NR1H4:-0.666935042167;ZNF148:-0.671864717292;FOX{D1,D2}:-0.675925619359;PATZ1:-0.680838404334;TLX2:-0.683440108108;RREB1:-0.694386746781;SPZ1:-0.711846262561;ZNF238:-0.715457358286;LMO2:-0.742447079881;MAFB:-0.764107947195;HSF1,2:-0.811146191188;STAT1,3:-0.81148757203;FOXL1:-0.812618809124;FOXN1:-0.826614061803;NANOG{mouse}:-0.832563912623;NKX2-3_NKX2-5:-0.83578480045;RXRA_VDR{dimer}:-0.839497071233;FOXP3:-0.880870832234;EBF1:-0.894243394455;HOX{A6,A7,B6,B7}:-0.904449206953;ZNF423:-0.907271121197;TGIF1:-0.910279016372;EP300:-0.92708006317;SP1:-0.964212839355;SREBF1,2:-0.970106641128;TBP:-0.99568003738;HAND1,2:-1.01417731417;ATF6:-1.07004612305;HMX1:-1.16467694969;TFCP2:-1.2253511723;RFX2..5_RFXANK_RFXAP:-1.24320286911;RORA:-1.28602599888;GLI1..3:-1.37509557356;ESR1:-2.17856354522
|comment=
|comment=
|created_by=
|created_by=

Revision as of 17:57, 14 March 2012


Name:fibrosarcoma cell line:HT-1080
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepelvis
dev stageNA
sexmale
age35
cell typeunclassifiable
cell lineHT-1080
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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>data



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 no result for this sample


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: CNhs11860



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: CNhs11860



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: CNhs11860


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

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
NA