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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|top_motifs=TFDP1:2.68285363043;BREu{core}:2.67183040206;NKX2-1,4:2.4511143936;POU1F1:2.32842384761;AHR_ARNT_ARNT2:2.1430088239;TEF:2.08615662281;RBPJ:2.0792583225;E2F1..5:2.00640563271;POU6F1:1.96068056979;PAX4:1.92147560743;NKX6-1,2:1.73815610782;PAX3,7:1.468556054;POU3F1..4:1.4656915574;DBP:1.46184939271;PITX1..3:1.41028300962;NFY{A,B,C}:1.39591075555;NKX2-3_NKX2-5:1.39303520961;YY1:1.37093849353;ZNF143:1.27509860856;FOXM1:1.24730656156;ZNF384:1.23952110213;EVI1:1.23266702446;PBX1:1.20080792948;NRF1:1.19909799902;ALX1:1.17796488353;MTE{core}:1.1672394774;CDX1,2,4:1.14627928694;ARID5B:1.14556161082;PRRX1,2:1.07759025112;TFAP2B:1.06344874119;CDC5L:1.04476703861;RREB1:1.02640719071;ZFP161:1.02528790606;MED-1{core}:1.010024316;NKX3-1:1.00481834433;AIRE:0.96878645707;CUX2:0.967210934935;PATZ1:0.966048055653;GFI1:0.958135858569;TOPORS:0.950858715773;FOXP1:0.902073250524;POU5F1:0.885075656413;MZF1:0.877556764756;GATA4:0.863230295524;PAX8:0.859756130273;HOX{A4,D4}:0.854232997824;STAT1,3:0.817828510961;CRX:0.777344955227;ZBTB16:0.770786441105;ATF4:0.76872960717;PDX1:0.764317105438;ZBTB6:0.749073679144;NR1H4:0.748199800266;ELK1,4_GABP{A,B1}:0.744190998004;IKZF2:0.736317869477;RFX1:0.721779383918;FOXD3:0.709529257344;ONECUT1,2:0.701803678463;MYB:0.673538446892;ZIC1..3:0.603250294888;FOXP3:0.588611359212;PRDM1:0.576940030369;KLF4:0.574649373104;REST:0.572187364406;UFEwm:0.52867836745;ESRRA:0.522071692449;TAL1_TCF{3,4,12}:0.489610912466;PAX5:0.434462343072;GTF2I:0.419442609511;LHX3,4:0.415408753418;NFE2L1:0.412228353696;LEF1_TCF7_TCF7L1,2:0.406183283921;SOX{8,9,10}:0.399457101636;HOXA9_MEIS1:0.377498526615;XCPE1{core}:0.375888084324;RFX2..5_RFXANK_RFXAP:0.37558813429;MAZ:0.360423233077;SOX17:0.343554928123;OCT4_SOX2{dimer}:0.320145768409;FOXA2:0.311615981736;HIC1:0.311244397757;ATF5_CREB3:0.309247124352;EGR1..3:0.264836372328;MYFfamily:0.230202498436;NKX3-2:0.21060965;MTF1:0.185474895037;HOX{A6,A7,B6,B7}:0.181026612532;HMGA1,2:0.178005403733;GZF1:0.170285944575;PAX1,9:0.158876215684;CREB1:0.142120259107;HOX{A5,B5}:0.137889684188;BPTF:0.121557544351;SP1:0.117917986594;HAND1,2:0.104933643988;PAX6:0.0819093583911;TGIF1:0.0664311707919;NANOG:0.0434935444909;SREBF1,2:0.0218004199312;GCM1,2:0.00620277836421;NR3C1:-0.00346670830734;PPARG:-0.00989205351553;ADNP_IRX_SIX_ZHX:-0.0212532612267;ZNF423:-0.0280501835423;NFIX:-0.0331792180181;NKX2-2,8:-0.0527018155366;GFI1B:-0.0642477434658;NR6A1:-0.0950894659112;HBP1_HMGB_SSRP1_UBTF:-0.0986565548018;HIF1A:-0.112153047587;SOX2:-0.153535235818;HSF1,2:-0.169129054521;HNF1A:-0.201737265528;FOXN1:-0.203431538583;IKZF1:-0.203438675667;SOX5:-0.213370495536;FOXL1:-0.226893637801;XBP1:-0.241524262031;MYBL2:-0.247250314779;HLF:-0.260545448872;EN1,2:-0.261099435975;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.264096857558;VSX1,2:-0.268009226872;SNAI1..3:-0.271951057154;ATF2:-0.275539561668;LMO2:-0.309737549885;RORA:-0.329623165236;RXR{A,B,G}:-0.336374138941;STAT5{A,B}:-0.341351196692;CEBPA,B_DDIT3:-0.36862612829;NHLH1,2:-0.376024305682;NFIL3:-0.383928196578;GTF2A1,2:-0.396885977613;ALX4:-0.411076674068;MEF2{A,B,C,D}:-0.421823041544;FOXQ1:-0.429956486167;NANOG{mouse}:-0.4315108919;ZEB1:-0.433650687246;DMAP1_NCOR{1,2}_SMARC:-0.439683370269;GATA6:-0.442590789484;HNF4A_NR2F1,2:-0.474797183945;MYOD1:-0.47659296718;FOSL2:-0.488326129099;JUN:-0.523517776348;FOX{I1,J2}:-0.527884523015;MAFB:-0.571682424711;NFKB1_REL_RELA:-0.581541416043;ATF6:-0.593122604958;SPI1:-0.597648405962;NR5A1,2:-0.599007660391;bHLH_family:-0.604750680671;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.621007188636;AR:-0.6230625423;IRF7:-0.628809923876;POU2F1..3:-0.647997364975;IRF1,2:-0.654518984162;FOX{F1,F2,J1}:-0.65667970249;SPIB:-0.697463258238;TEAD1:-0.704662718696;SRF:-0.708022787033;FOS_FOS{B,L1}_JUN{B,D}:-0.725334843798;T:-0.741769616361;RUNX1..3:-0.748032736821;TLX1..3_NFIC{dimer}:-0.787872356219;SMAD1..7,9:-0.795586479042;BACH2:-0.795882782292;TP53:-0.83053265376;ZNF238:-0.854995420348;ELF1,2,4:-0.876237461081;NFE2L2:-0.887732593159;FOX{D1,D2}:-0.888399700454;TFAP2{A,C}:-0.899771141253;RXRA_VDR{dimer}:-0.911367019938;NFATC1..3:-0.949141635333;ESR1:-0.954872627661;NFE2:-0.980203775964;FOXO1,3,4:-0.994353669706;TFAP4:-0.994702458808;TBP:-1.01347696183;TLX2:-1.09847202954;ZNF148:-1.18726990348;ETS1,2:-1.21520282952;STAT2,4,6:-1.22043351943;TFCP2:-1.24399411548;PAX2:-1.26073046047;GLI1..3:-1.30232731491;HES1:-1.35286602091;EP300:-1.40981152803;HMX1:-1.48541983794;TBX4,5:-1.5194940659;EBF1:-1.6140482545;SPZ1:-2.00220964163
|comment=
|comment=
|created_by=
|created_by=

Revision as of 17:55, 14 March 2012


Name:carcinosarcoma cell line:JHUCS-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueuterus
dev stageNA
sexfemale
age56
cell typeunclassifiable
cell lineJHUCS-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: CNhs11747



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: CNhs11747



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: CNhs11747


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
154 (mixed cell type cancer)
162 (cancer)
305 (carcinoma)
4 (disease)
4236 (carcinosarcoma)

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