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{{f5samples
{{f5samples
|id=FF:10038-101F2
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001896,UBERON:0002028,UBERON:0002050,UBERON:0002298,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0003057,UBERON:0003075,UBERON:0003076,UBERON:0004121,UBERON:0004732,UBERON:0004733,UBERON:0005068,UBERON:0005290,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007023,UBERON:0007135,UBERON:0007284
|name=medulla oblongata, adult, pool1
|sample_id=10038
|rna_tube_id=101F2
|rna_box=101
|rna_position=F2
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Clontech
|rna_lot_number=7060209
|rna_catalog_number=Cat:636562
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=18-64 years old adult
|sample_tissue=medulla oblongata
|sample_donor(cell lot)=29 pool
|sample_sex=mixed
|sample_age=
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=normal
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=50
|rna_concentration=1
|sample_note=
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|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
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|fonse_cell_line_closure=
|fonse_cell_line_closure=
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:10038-101F2
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010038
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010038
|name=medulla oblongata, adult, pool1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10645,LSID658,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:636562
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=7060209
|rna_od260/230=
|rna_od260/280=
|rna_position=F2
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=101F2
|rna_weight_ug=50
|sample_age=
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Clontech
|sample_description=
|sample_dev_stage=18-64 years old adult
|sample_disease=normal
|sample_donor(cell lot)=29 pool
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10038
|sample_note=
|sample_sex=mixed
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=medulla oblongata
|top_motifs=REST:3.58415499794;SOX2:3.46244404202;NHLH1,2:3.41015246727;SOX5:3.39153558314;SOX{8,9,10}:3.35210255535;MYFfamily:3.2706128105;ZFP161:3.0580429424;RREB1:3.02487939223;NANOG:2.95431605146;HIC1:2.92470307892;MTF1:2.895495074;MED-1{core}:2.86976436904;MTE{core}:2.84652658467;NFIX:2.7676877533;ZBTB6:2.74267461608;PRRX1,2:2.73017886349;NKX3-2:2.61138444493;TFAP2B:2.61138237634;SMAD1..7,9:2.58663456567;RFX1:2.5739462341;ATF2:2.56815756673;EBF1:2.4936489516;GCM1,2:2.46741490466;TGIF1:2.44398424379;GTF2I:2.44233508303;PATZ1:2.37744407549;EP300:2.33046092024;JUN:2.2987894095;SOX17:2.29235110262;MAZ:2.28780084001;PAX5:2.22525605292;RFX2..5_RFXANK_RFXAP:2.21918313801;MZF1:2.21703519832;PRDM1:2.20993879805;EGR1..3:2.20236838113;SP1:2.19283879776;LMO2:2.03955708351;RBPJ:2.00326539259;ZNF423:1.99859080903;CUX2:1.98961392554;GFI1B:1.95923814265;TFAP2{A,C}:1.90997537784;POU6F1:1.85567522433;BREu{core}:1.76912463712;LEF1_TCF7_TCF7L1,2:1.72976616178;TLX1..3_NFIC{dimer}:1.55691735372;SREBF1,2:1.52782547665;HOX{A6,A7,B6,B7}:1.51747287525;KLF4:1.47320616979;MAFB:1.41866321716;XBP1:1.41753354761;HBP1_HMGB_SSRP1_UBTF:1.41061495338;FOX{D1,D2}:1.4072144379;FOXP3:1.38730560875;AHR_ARNT_ARNT2:1.35392709462;OCT4_SOX2{dimer}:1.34745985186;GATA4:1.34605089707;POU5F1:1.30412371673;GTF2A1,2:1.24381680572;RORA:1.23662664479;ZIC1..3:1.19798005938;TFDP1:1.17826629499;VSX1,2:1.16673614366;NKX2-3_NKX2-5:1.14233501837;AR:1.13962550917;MYBL2:1.12104154453;FOX{F1,F2,J1}:1.10814611329;DBP:1.05670072317;NR3C1:0.998294678153;XCPE1{core}:0.987653180773;NRF1:0.984855387267;PAX6:0.975117845816;PDX1:0.923241000531;FOXM1:0.914393155918;ESRRA:0.896802553824;STAT1,3:0.884271548373;FOXO1,3,4:0.835405631591;TFCP2:0.761635082658;ZNF238:0.741818853328;MYOD1:0.728328752178;ZNF143:0.673722276227;STAT2,4,6:0.672287386176;T:0.665143257914;GZF1:0.625318071459;IRF7:0.625130024952;HMX1:0.614552827391;MEF2{A,B,C,D}:0.605308691194;GFI1:0.59874027186;PBX1:0.583264525845;SPZ1:0.580739155677;ADNP_IRX_SIX_ZHX:0.526257398826;NFIL3:0.505402783343;TFAP4:0.464336719705;FOX{I1,J2}:0.463956412285;CREB1:0.453218466018;HAND1,2:0.40360308197;NR5A1,2:0.374290033989;NFY{A,B,C}:0.343471682015;BPTF:0.333052400437;ONECUT1,2:0.313583694541;HOX{A4,D4}:0.313149000964;ARID5B:0.289275500641;NFATC1..3:0.2814166976;FOXQ1:0.23856193396;FOXP1:0.238475304261;PAX2:0.228752696267;IRF1,2:0.216128077388;TBP:0.199409504034;ATF4:0.198937324716;NFE2L2:0.187787672851;CDC5L:0.165532116744;TLX2:0.148709477757;ZEB1:0.129349167988;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.127834358037;FOXN1:0.117221776473;TOPORS:0.08857388183;FOXA2:0.0806876198223;SRF:0.0499987863096;CRX:0.0244216103191;bHLH_family:0.0111404180859;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.00437207446018;ATF5_CREB3:-0.00489913700247;TBX4,5:-0.00723989527587;ZNF384:-0.0551272518252;HSF1,2:-0.0717769970342;ETS1,2:-0.0849209663344;POU3F1..4:-0.100721279227;ZNF148:-0.143403562249;NR1H4:-0.189070020044;ESR1:-0.219813863862;ALX4:-0.233063310658;HOXA9_MEIS1:-0.233273893374;IKZF1:-0.252337468544;NFE2:-0.252875025595;GATA6:-0.302264741663;HMGA1,2:-0.329784838562;SPI1:-0.343552115257;YY1:-0.34451883368;TP53:-0.361475135406;ATF6:-0.363001945731;SNAI1..3:-0.363437052403;PAX3,7:-0.399829757129;TEAD1:-0.403654990222;HNF1A:-0.423083934191;LHX3,4:-0.426826887382;CEBPA,B_DDIT3:-0.45365361893;NANOG{mouse}:-0.459876724859;SPIB:-0.467161703902;RXR{A,B,G}:-0.471358352235;HNF4A_NR2F1,2:-0.521664254796;FOXD3:-0.533439644552;NFE2L1:-0.564267389197;NKX6-1,2:-0.603332294592;IKZF2:-0.611531723702;HES1:-0.711611995634;TAL1_TCF{3,4,12}:-0.721716025571;PAX8:-0.778640301153;FOSL2:-0.803461116824;HLF:-0.803798401788;HIF1A:-0.853311018349;BACH2:-0.864410011729;GLI1..3:-0.871486327981;NFKB1_REL_RELA:-0.893597978827;DMAP1_NCOR{1,2}_SMARC:-0.896767542553;ELF1,2,4:-0.904258150044;ELK1,4_GABP{A,B1}:-0.931169937396;FOS_FOS{B,L1}_JUN{B,D}:-0.954850609313;RUNX1..3:-1.01652115817;POU1F1:-1.02603610691;POU2F1..3:-1.05161871728;UFEwm:-1.05601588329;PAX1,9:-1.15528178864;E2F1..5:-1.20356233528;PPARG:-1.2275104024;NKX3-1:-1.23902852528;PITX1..3:-1.25075002642;ALX1:-1.3019696105;NKX2-1,4:-1.3889518943;MYB:-1.42279868789;RXRA_VDR{dimer}:-1.44795979644;TEF:-1.59787639003;FOXL1:-1.70295170797;NR6A1:-1.70572976721;EN1,2:-1.77326551253;PAX4:-1.99947616148;EVI1:-2.07549256779;HOX{A5,B5}:-2.17264788732;ZBTB16:-2.34034874236;AIRE:-2.35447164693;NKX2-2,8:-2.53967771606;CDX1,2,4:-2.66159934993;STAT5{A,B}:-2.829037075
}}
}}

Revision as of 14:00, 21 March 2012


Name:medulla oblongata, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemedulla oblongata
dev stage18-64 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number7060209
catalog numberCat:636562
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-Neural0.138
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-penis0.113
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-lymphoma-0.36
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0.0508
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0.447
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
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: CNhs10645

Jaspar motifP-value
MA0002.20.0156
MA0003.10.445
MA0004.10.366
MA0006.10.691
MA0007.10.332
MA0009.10.162
MA0014.10.65
MA0017.10.016
MA0018.20.0396
MA0019.10.385
MA0024.10.987
MA0025.10.186
MA0027.10.524
MA0028.10.077
MA0029.10.187
MA0030.10.00887
MA0031.10.301
MA0035.20.132
MA0038.10.017
MA0039.20.623
MA0040.10.182
MA0041.10.102
MA0042.10.502
MA0043.10.351
MA0046.10.563
MA0047.20.627
MA0048.10.0753
MA0050.10.569
MA0051.10.817
MA0052.10.0456
MA0055.19.32654e-4
MA0057.10.899
MA0058.10.489
MA0059.10.0599
MA0060.10.0577
MA0061.10.00592
MA0062.20.0223
MA0065.20.00301
MA0066.10.0134
MA0067.10.705
MA0068.10.21
MA0069.10.639
MA0070.10.0337
MA0071.10.0555
MA0072.10.98
MA0073.10.701
MA0074.10.187
MA0076.10.187
MA0077.10.027
MA0078.10.935
MA0079.20.244
MA0080.21.16513e-4
MA0081.10.104
MA0083.10.792
MA0084.10.229
MA0087.10.122
MA0088.10.143
MA0090.10.377
MA0091.10.546
MA0092.10.401
MA0093.10.46
MA0099.21.63686e-9
MA0100.10.624
MA0101.10.0113
MA0102.20.509
MA0103.10.0766
MA0104.20.251
MA0105.18.13862e-6
MA0106.10.0171
MA0107.10.0102
MA0108.21.25356e-4
MA0111.10.373
MA0112.20.00139
MA0113.10.591
MA0114.10.0151
MA0115.10.483
MA0116.10.00115
MA0117.10.789
MA0119.10.0672
MA0122.10.415
MA0124.10.593
MA0125.10.117
MA0131.10.773
MA0135.10.00528
MA0136.12.41919e-6
MA0137.20.29
MA0138.20.117
MA0139.10.442
MA0140.10.0757
MA0141.10.0218
MA0142.10.473
MA0143.10.108
MA0144.10.748
MA0145.10.621
MA0146.10.0291
MA0147.10.118
MA0148.10.468
MA0149.10.00735
MA0150.10.00502
MA0152.10.903
MA0153.10.675
MA0154.10.0315
MA0155.10.946
MA0156.19.37318e-4
MA0157.10.948
MA0159.10.017
MA0160.10.0901
MA0162.10.183
MA0163.11.1616e-9
MA0164.10.556
MA0258.10.0222
MA0259.10.428



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: CNhs10645

Novel motifP-value
10.0208
100.0193
1000.209
1010.994
1020.846
1030.122
1040.214
1050.653
1060.0809
1070.261
1080.815
1090.011
110.012
1100.0325
1110.0267
1120.345
1130.606
1140.0431
1150.826
1160.214
1170.00647
1180.0898
1190.115
120.839
1200.0754
1210.921
1220.548
1230.49
1240.157
1250.277
1260.126
1270.447
1280.264
1290.478
130.00358
1300.97
1310.0396
1320.679
1330.00248
1340.236
1350.0765
1360.0151
1370.808
1380.803
1390.0496
140.879
1400.113
1410.26
1420.854
1430.00671
1440.959
1450.141
1460.986
1470.96
1480.163
1490.324
150.048
1500.163
1510.778
1520.288
1530.75
1540.66
1550.165
1560.392
1570.419
1580.824
1590.0384
160.0568
1600.184
1610.217
1620.951
1630.924
1640.00495
1650.148
1660.896
1670.219
1680.982
1690.0129
170.159
180.0845
190.392
20.746
200.0978
210.0654
220.454
230.633
240.205
250.554
261.66736e-4
270.873
280.813
290.00509
30.0236
300.372
310.957
320.0209
330.116
340.882
350.324
360.0915
370.0492
380.368
390.481
40.916
400.105
410.407
420.162
430.127
440.0397
450.974
460.026
470.0473
480.0412
490.152
50.567
500.615
510.444
520.956
530.755
540.581
550.472
560.576
570.18
580.336
590.197
60.661
600.191
610.0781
620.174
630.237
640.145
650.353
660.263
670.467
680.502
690.511
70.124
700.00697
710.00577
720.508
730.0854
740.518
750.0125
760.138
770.379
780.00144
790.128
80.0438
800.697
810.417
820.473
830.296
840.521
850.36
860.161
870.0185
880.827
890.328
90.815
900.0123
910.321
920.481
930.876
940.035
950.0454
960.994
970.833
980.179
990.902



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: CNhs10645


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

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
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)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001896 (medulla oblongata)
0002028 (hindbrain)
0002050 (embryonic structure)
0002298 (brainstem)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0004121 (ectoderm-derived structure)
0004732 (segmental subdivision of nervous system)
0004733 (segmental subdivision of hindbrain)
0005068 (neural rod)
0005290 (myelencephalon)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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