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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|top_motifs=HBP1_HMGB_SSRP1_UBTF:3.2872623684;PDX1:2.00811885541;CDX1,2,4:1.48587891535;AIRE:1.39976003818;PAX4:1.37354642507;NKX6-1,2:1.34128812378;NKX2-3_NKX2-5:1.33197744756;ZNF148:1.32957027134;POU1F1:1.3276919437;FOXD3:1.133492663;RXR{A,B,G}:1.12267838824;RBPJ:1.04453803248;NFY{A,B,C}:0.970479639428;XCPE1{core}:0.967286151607;HSF1,2:0.944246020282;STAT1,3:0.919760787989;EN1,2:0.884387219211;GFI1:0.867658218383;GFI1B:0.862422405422;EVI1:0.829231246785;TEF:0.824838607509;ONECUT1,2:0.822091690224;ZNF384:0.773898687234;TP53:0.725780010081;ZNF143:0.720273457668;FOX{I1,J2}:0.713264021182;NRF1:0.702448412387;MYB:0.697084668436;LMO2:0.690243843022;POU5F1:0.689589763773;PITX1..3:0.685112224933;E2F1..5:0.656635010874;ZBTB16:0.65615934004;PAX8:0.628894587304;FOXQ1:0.624094619765;HOXA9_MEIS1:0.619573516319;PBX1:0.595979331749;PPARG:0.578039920521;NKX3-1:0.561322941457;HOX{A5,B5}:0.553988585303;OCT4_SOX2{dimer}:0.532881349349;GZF1:0.509687305461;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.500902395433;ZIC1..3:0.489553190151;PRRX1,2:0.485294120372;TEAD1:0.485113497665;bHLH_family:0.48198365126;TAL1_TCF{3,4,12}:0.46702500888;NR6A1:0.451496614146;LHX3,4:0.450833794569;MZF1:0.450476926969;GATA4:0.438001166455;NR3C1:0.437115673149;HMGA1,2:0.424060666572;HOX{A6,A7,B6,B7}:0.418663452315;NFIX:0.412923568901;FOXL1:0.40060005516;GCM1,2:0.39750611034;SREBF1,2:0.394912179799;STAT5{A,B}:0.373082848216;VSX1,2:0.346945067987;CDC5L:0.34554581681;UFEwm:0.306709953598;HOX{A4,D4}:0.300838092338;ALX4:0.273626968154;FOXP1:0.270582021995;CUX2:0.266795655376;TOPORS:0.246916493842;PRDM1:0.231033030098;IKZF2:0.219831570253;SP1:0.178522343832;IRF7:0.178346099155;BACH2:0.139771938244;FOSL2:0.131523093538;KLF4:0.121129399388;HES1:0.0990019886885;ELK1,4_GABP{A,B1}:0.0935854123893;ARID5B:0.0667275482118;POU3F1..4:0.0664315822972;TFDP1:0.0531244412446;PAX3,7:0.0280837127459;SOX{8,9,10}:0.0241472566283;MEF2{A,B,C,D}:0.00320479588323;ZBTB6:-0.000887851895816;RREB1:-0.00504723342436;RFX2..5_RFXANK_RFXAP:-0.0268629132074;MTF1:-0.027100415493;ESR1:-0.0377064222059;FOXM1:-0.0398772004491;IRF1,2:-0.0558486375921;GTF2I:-0.0616117305391;CRX:-0.0710500553672;NFE2:-0.0829917310284;FOXP3:-0.09008295751;RFX1:-0.101991040604;NKX2-2,8:-0.126237191336;HAND1,2:-0.134039773413;FOS_FOS{B,L1}_JUN{B,D}:-0.163552790605;DBP:-0.164197850031;MAZ:-0.175022773003;ZFP161:-0.178587867426;GTF2A1,2:-0.180014925805;NFIL3:-0.188684077184;DMAP1_NCOR{1,2}_SMARC:-0.193321477033;MYBL2:-0.193411063294;NFKB1_REL_RELA:-0.200211626713;HLF:-0.203698343436;CEBPA,B_DDIT3:-0.222945723012;SRF:-0.228999788514;FOX{D1,D2}:-0.268750008076;HNF1A:-0.280183759325;SPIB:-0.301410676756;TFAP2{A,C}:-0.325999183783;PATZ1:-0.32731246142;POU2F1..3:-0.345824744484;TBX4,5:-0.354808680714;STAT2,4,6:-0.360276448756;EGR1..3:-0.362102301582;MED-1{core}:-0.378575528123;TGIF1:-0.378710136158;RORA:-0.380582433497;HNF4A_NR2F1,2:-0.390017247355;SNAI1..3:-0.399017697978;ADNP_IRX_SIX_ZHX:-0.402696111604;TFAP2B:-0.41261819306;AHR_ARNT_ARNT2:-0.423234122907;EP300:-0.423809472283;REST:-0.425275314664;FOXN1:-0.432979636275;RUNX1..3:-0.436520997882;NANOG{mouse}:-0.475356601567;SOX2:-0.480215003148;EBF1:-0.485617144401;ZEB1:-0.49434215903;BPTF:-0.499112576503;FOXA2:-0.499624041522;NKX3-2:-0.502162508513;TLX2:-0.504233764693;NHLH1,2:-0.513347507377;MTE{core}:-0.515967913594;ETS1,2:-0.519093307132;NFE2L2:-0.52592155496;PAX5:-0.530789496984;MYOD1:-0.53129010876;NR1H4:-0.539535636611;ELF1,2,4:-0.548900855249;PAX2:-0.552214758091;FOXO1,3,4:-0.554666393398;NKX2-1,4:-0.559761979417;SPI1:-0.586044402876;CREB1:-0.59357165036;GATA6:-0.594140014488;ZNF238:-0.608837871307;ATF4:-0.611789513021;TLX1..3_NFIC{dimer}:-0.616382439368;YY1:-0.617506318307;HIC1:-0.624919680713;HIF1A:-0.639527719429;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.643796860174;ATF5_CREB3:-0.663610192491;XBP1:-0.680809538935;GLI1..3:-0.7052729336;NFATC1..3:-0.708222912339;SOX5:-0.760556952226;MAFB:-0.791847324166;TBP:-0.80421499101;TFCP2:-0.816257770664;ALX1:-0.831821553253;SMAD1..7,9:-0.831975866674;LEF1_TCF7_TCF7L1,2:-0.84511309129;MYFfamily:-0.854636786963;NANOG:-0.87079400366;NFE2L1:-0.877299384056;ATF6:-0.882512269194;AR:-0.883328892571;ATF2:-0.891181025241;BREu{core}:-0.902481136382;SOX17:-0.91699502511;IKZF1:-0.961687297635;NR5A1,2:-0.970483588974;ZNF423:-1.01463823562;JUN:-1.08933493638;RXRA_VDR{dimer}:-1.11121128454;FOX{F1,F2,J1}:-1.15837766714;PAX6:-1.15914190913;PAX1,9:-1.38288670449;ESRRA:-1.54273253681;T:-1.57401783415;POU6F1:-1.62574295292;SPZ1:-1.6604107306;TFAP4:-1.78570121965;HMX1:-1.93147977078
|comment=
|comment=
|created_by=
|created_by=

Revision as of 17:57, 14 March 2012


Name:epithelioid sarcoma cell line:HS-ES-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexunknown
ageNA
cell typeunclassifiable
cell lineHS-ES-1
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
Download raw sequence, BAM & CTSS
CollapseHg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
CollapseHg38
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: CNhs11247



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: CNhs11247



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: CNhs11247


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

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3350 (mesenchymal cell neoplasm)
4 (disease)
6193 (epithelioid sarcoma)

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