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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|top_motifs=MYB:2.12624025534;E2F1..5:1.75324808807;NFY{A,B,C}:1.33489119083;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.21022376933;bHLH_family:1.13279903785;YY1:1.06653108576;EP300:1.05569388078;ELK1,4_GABP{A,B1}:0.953035414514;BREu{core}:0.945066593907;NRF1:0.936691468057;HBP1_HMGB_SSRP1_UBTF:0.906302498831;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.891038838446;SPIB:0.859059981313;ELF1,2,4:0.857523098169;HIF1A:0.823036870189;ZNF143:0.807474864577;TEF:0.805602661482;SPI1:0.725748955664;PAX8:0.720399714416;PITX1..3:0.710945131674;FOXP1:0.708416259787;DMAP1_NCOR{1,2}_SMARC:0.697543621606;POU5F1:0.654171802531;RUNX1..3:0.62899880336;NANOG{mouse}:0.59009013131;NANOG:0.587599189126;MYOD1:0.553150462497;FOXA2:0.523702872002;VSX1,2:0.51521243888;NKX2-2,8:0.503642181705;NR5A1,2:0.491609171838;ETS1,2:0.425378685853;NKX3-1:0.407238499901;TLX2:0.385698222515;CEBPA,B_DDIT3:0.372622048165;NR6A1:0.367192622365;POU2F1..3:0.354693767216;PBX1:0.34769536293;FOXQ1:0.294835965378;POU3F1..4:0.288452662781;TFDP1:0.286518365425;GATA6:0.281166829808;NFIL3:0.268763932995;CRX:0.256104428371;RFX2..5_RFXANK_RFXAP:0.237839734555;GFI1:0.219484906947;OCT4_SOX2{dimer}:0.202747472133;RBPJ:0.200835448283;CUX2:0.198071036394;HOX{A6,A7,B6,B7}:0.188677185404;FOXD3:0.169794191914;POU1F1:0.168950293125;PAX4:0.164824070734;FOXP3:0.146018900838;PAX5:0.144131290864;HAND1,2:0.14227786506;DBP:0.0983103862964;ZNF238:0.094355380958;TOPORS:0.093388437846;SOX{8,9,10}:0.0864377217255;MTF1:0.0734435365819;ONECUT1,2:0.061832007506;IRF7:0.0597757023907;HOXA9_MEIS1:0.0462277377229;AHR_ARNT_ARNT2:0.0391719458656;NKX2-3_NKX2-5:0.0259282557579;AIRE:0.0166023573604;PDX1:0.0158545787439;HLF:-0.00368067901915;PRRX1,2:-0.00402001736586;ATF5_CREB3:-0.00592425028821;ALX1:-0.00858037462466;IRF1,2:-0.0255094123408;ARID5B:-0.0516649899989;PAX2:-0.0528110943743;REST:-0.0567300090631;CDX1,2,4:-0.0684361361346;AR:-0.0801437482117;BPTF:-0.0813257165345;STAT1,3:-0.0852808793551;EN1,2:-0.0872851547187;IKZF1:-0.0993325194871;LHX3,4:-0.101900806663;HOX{A4,D4}:-0.109315083936;ZNF423:-0.121975672243;HNF1A:-0.146391586424;SNAI1..3:-0.157650242084;PAX6:-0.173935016684;FOXM1:-0.18057553789;ZEB1:-0.184253202001;NKX2-1,4:-0.195591793986;PRDM1:-0.199856303762;HOX{A5,B5}:-0.214047903448;GCM1,2:-0.21743472348;MEF2{A,B,C,D}:-0.225681821917;NKX6-1,2:-0.265557577685;ATF4:-0.266274311597;SREBF1,2:-0.274133640816;FOX{I1,J2}:-0.276667457066;ZBTB16:-0.279170585272;HNF4A_NR2F1,2:-0.281821581435;TBP:-0.285833022075;CREB1:-0.315522223076;PAX3,7:-0.318961046535;IKZF2:-0.32686001174;RFX1:-0.33381017432;KLF4:-0.339540103526;NHLH1,2:-0.369183756759;POU6F1:-0.375598552275;ZFP161:-0.376727130712;NFKB1_REL_RELA:-0.377668241048;MZF1:-0.396248060271;FOX{F1,F2,J1}:-0.428833070205;MYBL2:-0.436745829896;EBF1:-0.448505887404;FOXN1:-0.492744382888;SP1:-0.494073583656;FOS_FOS{B,L1}_JUN{B,D}:-0.495629814988;TGIF1:-0.50151455551;STAT5{A,B}:-0.503516977125;NFE2:-0.510605060022;GATA4:-0.511301438835;RORA:-0.51219162525;HSF1,2:-0.517009157769;FOSL2:-0.517522136314;HES1:-0.517898992445;BACH2:-0.586536035042;UFEwm:-0.597445328423;HIC1:-0.600679103732;LMO2:-0.604367155018;MYFfamily:-0.615287400212;ESRRA:-0.621020668459;ZNF384:-0.637481830736;TFAP2B:-0.64274476932;LEF1_TCF7_TCF7L1,2:-0.65670991321;ALX4:-0.657344607364;SOX17:-0.657703680293;ADNP_IRX_SIX_ZHX:-0.666740043789;PPARG:-0.677918895494;NFIX:-0.70977176692;NKX3-2:-0.71141937957;XBP1:-0.712942742295;SOX5:-0.763281963561;NFE2L2:-0.782637124075;T:-0.783483689804;GTF2A1,2:-0.802434056168;GTF2I:-0.816613769554;ZNF148:-0.822158957924;TP53:-0.851525798993;ATF2:-0.858487429773;ATF6:-0.864179314951;ESR1:-0.877262514368;EVI1:-0.881862114929;GZF1:-0.912408757234;MTE{core}:-0.92086415089;NR3C1:-0.928347183336;RREB1:-0.934575147945;MED-1{core}:-0.956489243866;NFE2L1:-0.976837710407;FOX{D1,D2}:-0.98401615716;FOXL1:-0.986286389159;STAT2,4,6:-0.992187144066;RXRA_VDR{dimer}:-0.994530807788;NR1H4:-0.999540003067;TFAP2{A,C}:-1.00293971155;FOXO1,3,4:-1.00608115397;SRF:-1.01687067241;ZIC1..3:-1.01714050609;TEAD1:-1.03791213683;XCPE1{core}:-1.04341144588;PATZ1:-1.04899156582;MAFB:-1.12335408241;TLX1..3_NFIC{dimer}:-1.12910460208;SOX2:-1.16223171981;HMGA1,2:-1.17114692759;TAL1_TCF{3,4,12}:-1.17284027015;MAZ:-1.18427185311;TFAP4:-1.2226421821;ZBTB6:-1.2306375551;RXR{A,B,G}:-1.24282110954;EGR1..3:-1.24473999066;GFI1B:-1.30083365055;PAX1,9:-1.32553013507;CDC5L:-1.36499331047;SMAD1..7,9:-1.38427945786;TFCP2:-1.42652040703;SPZ1:-1.46998970392;HMX1:-1.49533187031;JUN:-1.51322175239;NFATC1..3:-1.53330777443;TBX4,5:-1.63661162985;GLI1..3:-1.7244774484
|comment=
|comment=
|created_by=
|created_by=

Revision as of 18:02, 14 March 2012


Name:myelodysplastic syndrome cell line:SKM-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
age76
cell typemyeloid cell
cell lineSKM-1
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: CNhs11934



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: CNhs11934



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: CNhs11934


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
1287 (cardiovascular system disease)
225 (syndrome)
4 (disease)
7 (disease of anatomical entity)
74 (hematopoietic system disease)

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

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