Personal tools

FF:10637-108I7: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 66: Line 66:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|top_motifs=NKX6-1,2:3.2117414314;IKZF2:3.16310049102;PAX4:3.02241855323;TOPORS:2.98680204351;CDX1,2,4:2.84866469587;ZBTB16:2.68426571475;FOXD3:2.57939425937;PITX1..3:2.35544591017;POU1F1:2.2946527155;FOXP1:2.20852644902;AIRE:2.15658008838;POU6F1:2.12312647667;AHR_ARNT_ARNT2:1.96977349162;ALX1:1.91033282309;PRDM1:1.86313606459;TEF:1.85532534178;NRF1:1.78788629145;CDC5L:1.65126949963;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.63001132501;FOXM1:1.62521691373;POU3F1..4:1.61957373348;YY1:1.57728739344;BPTF:1.52007532672;BREu{core}:1.47967031619;DBP:1.46568071778;NKX3-1:1.4391506165;ZNF143:1.3920310495;CUX2:1.38851482001;GATA4:1.37983978822;ZNF384:1.35716143038;LHX3,4:1.27882681945;NKX2-3_NKX2-5:1.26704957657;RREB1:1.26494055291;PAX6:1.26289479742;PRRX1,2:1.25654889184;ZFP161:1.23355955952;HOX{A6,A7,B6,B7}:1.19539795513;ATF5_CREB3:1.17786294561;MZF1:1.14075936504;E2F1..5:1.12881877581;HOX{A5,B5}:1.11778514265;SOX5:1.0829503404;OCT4_SOX2{dimer}:1.06297303726;STAT1,3:1.02085057685;ONECUT1,2:1.01674501713;ARID5B:1.01265193867;PATZ1:0.972524354152;GFI1:0.949008389167;POU5F1:0.895582347461;PBX1:0.888216314559;STAT5{A,B}:0.875477331014;RFX1:0.87430472425;NKX2-1,4:0.865578429994;EVI1:0.860694635705;PAX8:0.841858070978;ELK1,4_GABP{A,B1}:0.811064427972;ATF6:0.773605300001;POU2F1..3:0.764303157064;NANOG{mouse}:0.76267294924;FOXN1:0.748733943895;SOX{8,9,10}:0.747648932992;EGR1..3:0.732448001436;HBP1_HMGB_SSRP1_UBTF:0.71412096103;PAX3,7:0.711417635607;RBPJ:0.68706853024;UFEwm:0.685291895262;SOX17:0.672172621052;RFX2..5_RFXANK_RFXAP:0.642436093783;FOXL1:0.631196326422;KLF4:0.607334094389;ATF4:0.603547770947;SOX2:0.602561826611;FOXQ1:0.600260599108;DMAP1_NCOR{1,2}_SMARC:0.583201036821;GFI1B:0.547341925674;TFDP1:0.535601115347;GTF2I:0.468887648819;ALX4:0.437648863746;NFY{A,B,C}:0.436812223766;HOX{A4,D4}:0.409626980158;MAZ:0.389896156763;CREB1:0.389874698481;PDX1:0.383368542295;REST:0.361292757666;T:0.291504523967;FOX{D1,D2}:0.276417065033;FOX{I1,J2}:0.272952780393;GZF1:0.260288145977;HOXA9_MEIS1:0.238054201985;MEF2{A,B,C,D}:0.205866312431;ZIC1..3:0.196808258439;EN1,2:0.190332507887;NANOG:0.16119875593;HMGA1,2:0.147336836378;ADNP_IRX_SIX_ZHX:0.123866100935;ZBTB6:0.0872588931267;MTE{core}:0.032522941174;TAL1_TCF{3,4,12}:0.0189271376356;MYB:0.0167542556532;MYFfamily:-0.00830716633472;GTF2A1,2:-0.0265875794736;RORA:-0.0309548515215;NR6A1:-0.043032023887;MED-1{core}:-0.0645408099156;LEF1_TCF7_TCF7L1,2:-0.121078769203;bHLH_family:-0.141865024534;FOXA2:-0.150563614363;CRX:-0.166819122931;MYBL2:-0.194189634232;SREBF1,2:-0.249012001207;RXR{A,B,G}:-0.251131031644;HMX1:-0.25241335626;FOXP3:-0.254293040134;RUNX1..3:-0.27790784571;TFAP2B:-0.301715366575;PAX2:-0.308191870634;PAX5:-0.309061127456;NHLH1,2:-0.374477862479;JUN:-0.379914955723;TEAD1:-0.380393564904;TLX1..3_NFIC{dimer}:-0.381107220515;SPIB:-0.383550334241;FOXO1,3,4:-0.388687012083;HNF4A_NR2F1,2:-0.395521356721;PAX1,9:-0.411217027759;HNF1A:-0.412881625713;TLX2:-0.421724696887;ZNF423:-0.46433313292;ZNF238:-0.550040497714;XBP1:-0.558767733625;NR1H4:-0.56590200069;IRF1,2:-0.571577051791;NFKB1_REL_RELA:-0.605357767607;SNAI1..3:-0.620196906071;ELF1,2,4:-0.624272744071;NFE2L1:-0.62825035249;GATA6:-0.637595446775;AR:-0.652701081771;MTF1:-0.658449454352;SPI1:-0.662859063606;HIC1:-0.675569623998;ATF2:-0.693050761035;NR3C1:-0.699200601841;CEBPA,B_DDIT3:-0.715886903018;HSF1,2:-0.756911966705;TGIF1:-0.789315448618;NFATC1..3:-0.844192516525;LMO2:-0.849855356259;ZEB1:-0.885313185105;EP300:-0.893445910595;TBP:-0.897496562515;HLF:-0.919875401302;IKZF1:-0.950162727877;GCM1,2:-0.950456733439;NFIL3:-0.950648214695;FOS_FOS{B,L1}_JUN{B,D}:-0.95694705843;NFE2:-0.978863495178;HIF1A:-1.02570857932;TP53:-1.02571983516;NKX3-2:-1.02620438596;FOX{F1,F2,J1}:-1.02928882755;FOSL2:-1.03103100544;ETS1,2:-1.04833153206;NFIX:-1.05610760626;GLI1..3:-1.05769991395;SPZ1:-1.06117324807;BACH2:-1.07777214816;SRF:-1.08187340733;SP1:-1.10293119802;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.1215243404;IRF7:-1.1673377492;HAND1,2:-1.24765038316;NFE2L2:-1.27884941196;XCPE1{core}:-1.2852257834;TFAP2{A,C}:-1.29678778017;NR5A1,2:-1.33411831625;STAT2,4,6:-1.43201951077;NKX2-2,8:-1.45278942757;EBF1:-1.45530073578;SMAD1..7,9:-1.47883299322;MAFB:-1.55484978281;MYOD1:-1.70168503917;RXRA_VDR{dimer}:-1.85006631977;TFAP4:-1.85198804639;HES1:-1.95264498618;TBX4,5:-2.01037339945;ESR1:-2.03513756423;VSX1,2:-2.13531230176;ESRRA:-2.51314983406;ZNF148:-2.61095019281;PPARG:-2.99969170461;TFCP2:-3.01367767276
|comment=
|comment=
|created_by=
|created_by=

Revision as of 18:02, 14 March 2012


Name:neuroectodermal tumor cell line:FU-RPNT-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexmale
age22
cell typeunclassifiable
cell lineFU-RPNT-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: CNhs11744



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: CNhs11744



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: CNhs11744


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)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0005423 (developing anatomical structure)

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