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{{f5samples
{{f5samples
|id=FF:10838-111E1
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
|name=medulloblastoma cell line:D283 Med
|sample_id=10838
|rna_tube_id=111E1
|rna_box=111
|rna_position=E1
|sample_cell_lot=
|sample_cell_catalog=HTB185
|sample_company=ATCC
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=brain
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=6
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=2.18
|rna_od260/280=2.09
|sample_cell_type=neurectodermal cell
|sample_cell_line=D283 Med
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=medulloblastoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=92.0381
|rna_concentration=1.67342
|sample_note=
|profile_hcage=CNhs12805,LSID972,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000030,CL:0000055,CL:0000095,CL:0000123,CL:0000125,CL:0000133,CL:0000144,CL:0000219,CL:0000220,CL:0000221,CL:0000243,CL:0000255,CL:0000333,CL:0000339,CL:0000548,CL:0002319,CL:0002321,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000033,UBERON:0000061,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
|ancestors_in_disease_facet=DOID:0050686,DOID:14566,DOID:162,DOID:3093,DOID:4
|ancestors_in_disease_facet=DOID:0050686,DOID:14566,DOID:162,DOID:3093,DOID:4
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100255
|fonse_cell_line=FF:0100255
|fonse_cell_line_closure=FF:0100255
|fonse_cell_line_closure=FF:0100255
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10838-111E1
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0101359
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0101359
|name=medulloblastoma cell line:D283 Med
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12805,LSID972,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=111
|rna_catalog_number=
|rna_concentration=1.67342
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.18
|rna_od260/280=2.09
|rna_position=E1
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=111E1
|rna_weight_ug=92.0381
|sample_age=6
|sample_cell_catalog=HTB185
|sample_cell_line=D283 Med
|sample_cell_lot=
|sample_cell_type=neurectodermal cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=ATCC
|sample_description=
|sample_dev_stage=
|sample_disease=medulloblastoma
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10838
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=brain
|top_motifs=CRX:3.89411254545;HOX{A6,A7,B6,B7}:2.68923477091;TOPORS:2.26225138659;CDX1,2,4:2.25861044008;ADNP_IRX_SIX_ZHX:2.21370455949;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:2.14898089447;PITX1..3:2.14329702707;LHX3,4:2.10289105939;POU1F1:2.05308904069;BREu{core}:2.00261718331;TFDP1:1.9952104764;FOX{I1,J2}:1.68448098589;E2F1..5:1.65421308718;NANOG:1.64366777861;AHR_ARNT_ARNT2:1.64320420305;NFY{A,B,C}:1.62512883576;bHLH_family:1.57431620853;ZNF143:1.53180533514;YY1:1.47556551787;ZBTB16:1.42265743862;FOXM1:1.40666831641;VSX1,2:1.33792691124;ARID5B:1.31495230201;POU6F1:1.28412449231;IKZF2:1.27117234269;HIF1A:1.24025655951;NRF1:1.18651167492;TEF:1.18065830012;PRRX1,2:1.16769304883;AIRE:1.1496470568;PDX1:1.12963232349;PAX3,7:1.12169099681;ZNF384:1.11958634397;FOXP1:1.11896989519;NKX2-3_NKX2-5:1.09530089262;ZFP161:1.09281343629;PAX4:1.04572460979;NKX2-2,8:1.02470817188;BPTF:1.02002646954;ZIC1..3:1.00790816923;RREB1:0.973499515791;GATA4:0.964793961918;EVI1:0.941426490741;PBX1:0.904851240696;PATZ1:0.872871948206;GFI1:0.843380126814;MYB:0.840214374669;MED-1{core}:0.835947152614;MZF1:0.798706528671;SOX{8,9,10}:0.797187835286;ATF4:0.779053533108;RBPJ:0.749323443391;TAL1_TCF{3,4,12}:0.645931836261;POU2F1..3:0.638856669925;ELK1,4_GABP{A,B1}:0.628077948067;FOXD3:0.623002390645;PAX8:0.605708308076;NKX2-1,4:0.601328121216;NKX6-1,2:0.594351423585;TFAP2B:0.580258391417;MYBL2:0.574005425043;FOXN1:0.560196586357;NR6A1:0.552700223819;TLX1..3_NFIC{dimer}:0.551138615493;PAX6:0.533078070295;HMGA1,2:0.452785637659;SOX17:0.431199461324;STAT5{A,B}:0.417533225912;HSF1,2:0.415674317387;UFEwm:0.360569153201;OCT4_SOX2{dimer}:0.354520081587;MYOD1:0.340278109913;RFX1:0.325271968403;RFX2..5_RFXANK_RFXAP:0.299511290001;POU5F1:0.289054033669;KLF4:0.250529672203;TGIF1:0.242198793823;ATF5_CREB3:0.237747553483;MAZ:0.236719526255;PAX5:0.228977426631;CREB1:0.210323355763;GTF2I:0.206679609969;SOX5:0.182780445816;GTF2A1,2:0.180636637563;RXR{A,B,G}:0.169552679734;CDC5L:0.146828996827;SP1:0.134961038921;HOXA9_MEIS1:0.123612368989;TFAP2{A,C}:0.117886059622;HIC1:0.115100373885;T:0.0971767045507;FOXO1,3,4:0.0620806206364;CUX2:0.058630664536;GFI1B:0.0405514343814;FOXP3:0.0387954977942;ZNF423:0.0362550890003;NFIL3:0.00166235105085;MEF2{A,B,C,D}:-0.00158243413551;STAT1,3:-0.0310833902958;SOX2:-0.0363076330851;GATA6:-0.0409591765115;MTE{core}:-0.0578974708418;ALX1:-0.0671942330283;RORA:-0.067459707901;PAX1,9:-0.103995064563;NHLH1,2:-0.106337348207;HOX{A5,B5}:-0.10873780956;EGR1..3:-0.112822564048;TP53:-0.125568225033;ALX4:-0.128610045013;FOXA2:-0.152013158857;ZBTB6:-0.158823726635;REST:-0.169472980165;HNF1A:-0.18631398644;LEF1_TCF7_TCF7L1,2:-0.204388815078;GZF1:-0.211551373024;ONECUT1,2:-0.222791119539;NKX3-1:-0.224498331872;POU3F1..4:-0.230202184041;FOX{F1,F2,J1}:-0.244803808042;HNF4A_NR2F1,2:-0.284665694493;NKX3-2:-0.287160575375;XCPE1{core}:-0.291604400877;JUN:-0.30701841092;AR:-0.315469495727;FOXQ1:-0.334816632536;PAX2:-0.360480760763;FOXL1:-0.385735646228;LMO2:-0.396931661153;HAND1,2:-0.401660648287;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.406418732509;SNAI1..3:-0.428056337803;CEBPA,B_DDIT3:-0.440411011762;MYFfamily:-0.44631360484;ZEB1:-0.470246718653;NFKB1_REL_RELA:-0.480731832735;IKZF1:-0.485881708477;PRDM1:-0.496062188673;TEAD1:-0.530995257023;NR1H4:-0.540249968238;HOX{A4,D4}:-0.540411930912;EN1,2:-0.556094819554;EP300:-0.571061391999;FOX{D1,D2}:-0.582611199585;TBP:-0.622212806404;HES1:-0.627756710815;TBX4,5:-0.658285986619;ATF2:-0.661391563138;HLF:-0.691349200816;NFE2:-0.723325240946;IRF7:-0.741727893526;NR5A1,2:-0.768156167253;DBP:-0.783031102336;SPIB:-0.799535925415;SPI1:-0.804845826529;XBP1:-0.805620975348;ESRRA:-0.80640584513;FOSL2:-0.807847114718;MTF1:-0.844166677221;BACH2:-0.848709188319;FOS_FOS{B,L1}_JUN{B,D}:-0.859318617575;NFE2L2:-0.882605049622;DMAP1_NCOR{1,2}_SMARC:-0.889137355071;HBP1_HMGB_SSRP1_UBTF:-0.88965212655;PPARG:-0.893996166414;RUNX1..3:-0.913947146294;SMAD1..7,9:-0.947245878004;ELF1,2,4:-1.00606556001;NFE2L1:-1.0061438554;NR3C1:-1.01294581497;SPZ1:-1.01611456501;GCM1,2:-1.23462219021;GLI1..3:-1.23562670048;SREBF1,2:-1.2718590306;RXRA_VDR{dimer}:-1.28469896906;SRF:-1.30714716139;IRF1,2:-1.32331825843;ETS1,2:-1.40298331698;NFIX:-1.49883005999;HMX1:-1.52929682334;MAFB:-1.53373402198;NFATC1..3:-1.55716745083;ATF6:-1.57118336089;ZNF238:-1.57174275827;EBF1:-1.65623740507;NANOG{mouse}:-1.65992963252;ESR1:-1.72333673117;TFAP4:-1.73056626625;TLX2:-1.75662504092;ZNF148:-1.83424918951;TFCP2:-2.01833052776;STAT2,4,6:-2.03091061632
}}
}}

Revision as of 14:48, 21 March 2012


Name:medulloblastoma cell line:D283 Med
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexmale
age6
cell typeneurectodermal cell
cell lineD283 Med
companyATCC
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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.353
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.63
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs12805

Jaspar motifP-value
MA0002.21.66458e-6
MA0003.10.162
MA0004.10.299
MA0006.10.149
MA0007.10.162
MA0009.10.939
MA0014.10.946
MA0017.10.00109
MA0018.20.151
MA0019.10.718
MA0024.11.12948e-4
MA0025.10.811
MA0027.10.92
MA0028.10.523
MA0029.10.853
MA0030.10.704
MA0031.10.236
MA0035.20.272
MA0038.10.121
MA0039.20.362
MA0040.10.245
MA0041.10.169
MA0042.10.482
MA0043.10.196
MA0046.10.0878
MA0047.20.118
MA0048.10.169
MA0050.16.86234e-9
MA0051.11.63775e-4
MA0052.10.153
MA0055.10.302
MA0057.10.328
MA0058.10.255
MA0059.10.252
MA0060.13.9535e-7
MA0061.10.0236
MA0062.20.587
MA0065.20.00451
MA0066.10.0559
MA0067.10.959
MA0068.10.468
MA0069.10.907
MA0070.10.409
MA0071.10.571
MA0072.10.513
MA0073.10.975
MA0074.10.344
MA0076.10.338
MA0077.10.514
MA0078.10.46
MA0079.20.561
MA0080.21.02948e-11
MA0081.10.0904
MA0083.10.00172
MA0084.10.969
MA0087.10.183
MA0088.10.696
MA0090.10.0359
MA0091.10.606
MA0092.10.28
MA0093.10.248
MA0099.21.05399e-20
MA0100.10.56
MA0101.10.0628
MA0102.20.161
MA0103.10.307
MA0104.20.0185
MA0105.10.0381
MA0106.10.712
MA0107.10.0204
MA0108.20.4
MA0111.10.984
MA0112.24.91879e-4
MA0113.10.306
MA0114.10.0272
MA0115.10.798
MA0116.10.0616
MA0117.10.915
MA0119.10.95
MA0122.10.756
MA0124.10.637
MA0125.10.541
MA0131.10.327
MA0135.10.794
MA0136.12.64847e-11
MA0137.28.84362e-4
MA0138.20.148
MA0139.10.688
MA0140.10.324
MA0141.10.0854
MA0142.10.937
MA0143.10.348
MA0144.15.51371e-4
MA0145.10.0307
MA0146.10.0361
MA0147.10.0155
MA0148.10.0666
MA0149.10.0786
MA0150.11.26197e-4
MA0152.10.814
MA0153.10.212
MA0154.10.0347
MA0155.10.264
MA0156.11.28292e-7
MA0157.10.0311
MA0159.10.00456
MA0160.10.0497
MA0162.10.235
MA0163.10.013
MA0164.10.597
MA0258.10.041
MA0259.10.103



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: CNhs12805

Novel motifP-value
10.22
100.207
1000.8
1010.722
1020.969
1030.0324
1040.446
1050.0502
1060.0127
1070.0783
1080.846
1090.0586
110.0994
1100.399
1110.271
1120.223
1130.451
1140.0148
1150.602
1160.675
1170.322
1180.788
1190.378
120.838
1200.353
1210.816
1220.513
1230.893
1240.149
1250.956
1260.534
1270.336
1280.0387
1290.333
130.855
1300.713
1310.42
1320.448
1330.0397
1340.292
1350.00813
1360.659
1370.129
1380.195
1390.0133
140.529
1400.353
1410.965
1420.67
1430.00129
1440.966
1450.414
1460.289
1470.845
1480.0759
1490.0526
150.17
1500.462
1510.134
1520.0226
1530.98
1540.823
1550.909
1560.458
1570.257
1580.884
1590.0789
160.195
1600.508
1610.0918
1620.659
1630.696
1640.516
1650.151
1660.895
1670.587
1680.231
1690.0068
170.295
180.263
190.12
20.103
200.53
210.891
220.153
230.00965
240.563
250.315
260.222
270.0646
280.905
290.41
30.19
300.402
310.329
320.0145
330.435
340.239
350.997
360.199
370.17
380.242
390.326
40.755
400.244
410.0595
420.443
430.135
440.554
450.307
460.208
470.386
480.277
490.213
50.158
500.562
510.243
520.329
530.636
540.283
550.143
560.33
570.878
580.245
590.0302
60.943
600.0554
610.407
620.105
630.196
640.478
650.0518
660.91
670.966
680.495
690.507
70.473
700.0235
710.103
720.0463
730.0216
740.326
750.226
760.885
770.0547
780.737
790.0572
80.291
800.0184
810.53
820.0321
830.792
840.207
850.0467
860.659
870.177
880.918
890.0845
90.0933
900.814
910.257
920.0443
930.801
940.106
950.315
960.224
970.436
980.114
990.58



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: CNhs12805


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)
0000030 (glioblast)
0000055 (non-terminally differentiated cell)
0000095 (neuron associated cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000243 (glial cell (sensu Vertebrata))
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000339 (glioblast (sensu Vertebrata))
0000548 (animal cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3093 (nervous system cancer)
4 (disease)

UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
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

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