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{{f5samples
{{f5samples
|id=FF:10023-101D5
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000119,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000490,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001015,UBERON:0001062,UBERON:0001134,UBERON:0002036,UBERON:0002050,UBERON:0002204,UBERON:0002329,UBERON:0002385,UBERON:0002532,UBERON:0003059,UBERON:0003077,UBERON:0003082,UBERON:0003104,UBERON:0004120,UBERON:0004290,UBERON:0005291,UBERON:0005423,UBERON:0007023,UBERON:0009142
|name=skeletal muscle, adult, pool1
|sample_id=10023
|rna_tube_id=101D5
|rna_box=101
|rna_position=D5
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Ambion
|rna_lot_number=0910061 -14
|rna_catalog_number=Cat:AM6000 Lot:0910061 -14
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=55,79,79 years old adult
|sample_tissue=skeletal muscle
|sample_donor(cell lot)=3 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-ToTALLY-RNA-v1.0
|rna_weight_ug=10
|rna_concentration=1
|sample_note=
|profile_hcage=CNhs10629,LSID657,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|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:10023-101D5
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010023
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010023
|name=skeletal muscle, adult, pool1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10629,LSID657,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:AM6000 Lot:0910061 -14
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_lot_number=0910061 -14
|rna_od260/230=
|rna_od260/280=
|rna_position=D5
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=101D5
|rna_weight_ug=10
|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=Ambion
|sample_description=
|sample_dev_stage=55,79,79 years old adult
|sample_disease=normal
|sample_donor(cell lot)=3 pool
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10023
|sample_note=
|sample_sex=mixed
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=skeletal muscle
|top_motifs=MEF2{A,B,C,D}:7.94112847148;NR1H4:4.79944954124;FOXL1:3.8639796894;NFE2L1:3.71903709557;NR5A1,2:3.68661967348;AR:3.5408665247;ESRRA:3.50270092203;PDX1:3.46119976025;MYOD1:3.2871534463;NKX2-2,8:3.07178063432;TLX2:2.81596630824;HOX{A4,D4}:2.80642997834;MAFB:2.59615221606;SPZ1:2.58014873508;NFIX:2.48063006716;NHLH1,2:2.47500766093;TGIF1:2.40807532562;NR6A1:2.3551834701;SOX5:2.34132470459;SRF:2.25641150569;RORA:2.24994654335;SMAD1..7,9:2.24283925828;RXR{A,B,G}_{NR1H2,PPAR}dimers:2.17747406279;RXR{A,B,G}:2.08012308852;ESR1:2.02000651855;NKX3-2:1.91514384142;IKZF2:1.87666225722;ATF2:1.84036222831;FOX{D1,D2}:1.79331719837;TFAP4:1.77989921921;POU6F1:1.7230746314;HAND1,2:1.71420106306;STAT5{A,B}:1.69581654742;TFAP2{A,C}:1.66921412162;FOXQ1:1.6198897969;HSF1,2:1.54954267298;PATZ1:1.52892243887;NFATC1..3:1.52630459572;EVI1:1.42977058049;FOXO1,3,4:1.41116901982;CUX2:1.39895568459;TBP:1.38139153605;PAX6:1.37459136533;HES1:1.37305026087;YY1:1.36909851296;NKX6-1,2:1.3674591793;GCM1,2:1.36703636086;GATA4:1.34804799248;POU1F1:1.31864559645;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.2668402868;HOX{A6,A7,B6,B7}:1.20726178227;ARID5B:1.1990256978;FOXP3:1.18370179883;GLI1..3:1.16266494615;BPTF:1.16098199012;FOX{F1,F2,J1}:1.14850451471;POU3F1..4:1.10880089968;MTF1:1.09038928986;UFEwm:1.02721790148;TFCP2:1.00924977493;GTF2A1,2:0.992661725573;RREB1:0.989763978833;STAT2,4,6:0.983410558029;TLX1..3_NFIC{dimer}:0.972702705279;FOXM1:0.953672221865;LMO2:0.948526721194;HIC1:0.933309682992;PAX1,9:0.915737126536;ZNF423:0.882579180557;ALX4:0.878687935716;MAZ:0.850713235121;MYBL2:0.756223010045;EN1,2:0.752096333372;TEAD1:0.745389816878;IKZF1:0.709449773568;TFAP2B:0.690756274676;LEF1_TCF7_TCF7L1,2:0.680223012289;TBX4,5:0.674717660743;ZIC1..3:0.65583877547;IRF7:0.654399922835;NR3C1:0.639786897769;MYFfamily:0.62373291495;MED-1{core}:0.614301731934;RFX2..5_RFXANK_RFXAP:0.609044896646;ATF4:0.57650955933;SREBF1,2:0.565816001166;KLF4:0.530140824838;NKX2-1,4:0.521162114957;MTE{core}:0.519990993944;MZF1:0.500609784639;PBX1:0.492579157707;bHLH_family:0.479144623901;TP53:0.478230757145;ZBTB16:0.46809468577;GFI1B:0.449640911061;CDX1,2,4:0.422081366599;REST:0.420605209421;PPARG:0.399161589704;SNAI1..3:0.387069031573;EGR1..3:0.379037423282;ZNF238:0.35590460711;JUN:0.349451544471;DMAP1_NCOR{1,2}_SMARC:0.349302485212;GTF2I:0.344186303116;SP1:0.297569996932;ZNF384:0.292003337706;XBP1:0.284373933871;HMX1:0.2436941172;HNF4A_NR2F1,2:0.23847185036;ALX1:0.234402691845;PAX5:0.226382094609;ZFP161:0.20258500328;FOSL2:0.20058807087;RXRA_VDR{dimer}:0.184530874744;NFE2L2:0.123784563426;HMGA1,2:0.100889366495;ZNF148:0.1002359861;TEF:0.0867792229707;RBPJ:0.0676979977482;EP300:0.0673385880823;FOXA2:0.0669961028744;NANOG{mouse}:0.0562242851893;TAL1_TCF{3,4,12}:0.0483090244245;NFE2:0.0449240229532;PAX2:0.0359761414503;CEBPA,B_DDIT3:0.0315410125232;ZNF143:0.0294035069586;SOX{8,9,10}:0.0261638042258;HLF:0.0085376706691;BREu{core}:-0.0171651001091;PAX3,7:-0.0291010359768;ATF5_CREB3:-0.0348208735992;ZBTB6:-0.0381120171425;LHX3,4:-0.101125298696;ETS1,2:-0.155550906697;SOX17:-0.176995620099;NKX2-3_NKX2-5:-0.184125607147;ATF6:-0.190872537134;FOXN1:-0.192946746868;FOX{I1,J2}:-0.194954234649;NKX3-1:-0.204146809591;ZEB1:-0.215101761785;SPI1:-0.224703866598;CRX:-0.253605201899;IRF1,2:-0.275727666611;HNF1A:-0.294951463604;PRDM1:-0.324282524928;NFKB1_REL_RELA:-0.338895247863;STAT1,3:-0.361242915572;GZF1:-0.396132840642;HOX{A5,B5}:-0.43745760284;NFIL3:-0.448804981764;FOS_FOS{B,L1}_JUN{B,D}:-0.464467262692;SPIB:-0.467806277027;NRF1:-0.511474368602;BACH2:-0.589417966393;T:-0.649643162635;PITX1..3:-0.680436242592;ELF1,2,4:-0.685344922779;EBF1:-0.700607703341;GATA6:-0.706621817034;NANOG:-0.773405349523;HBP1_HMGB_SSRP1_UBTF:-0.785446293272;AHR_ARNT_ARNT2:-0.807705421297;PAX4:-0.812889197401;RUNX1..3:-0.818998441277;CREB1:-0.845375117909;TOPORS:-0.8544630775;NFY{A,B,C}:-0.862222990676;E2F1..5:-0.87025801861;TFDP1:-0.923697806177;HOXA9_MEIS1:-0.948638603929;FOXP1:-0.99315643176;PRRX1,2:-1.06973431544;CDC5L:-1.12493468093;OCT4_SOX2{dimer}:-1.14689585632;ONECUT1,2:-1.15688336308;XCPE1{core}:-1.24799380652;ADNP_IRX_SIX_ZHX:-1.25254288845;MYB:-1.25470719103;RFX1:-1.28115550972;GFI1:-1.315990732;SOX2:-1.32813318954;FOXD3:-1.39414290465;HIF1A:-1.44059983554;ELK1,4_GABP{A,B1}:-1.45562233041;VSX1,2:-1.61198434344;DBP:-1.71340317384;AIRE:-1.82489173902;POU5F1:-2.01468768523;POU2F1..3:-2.13134231287;PAX8:-2.35739812734
}}
}}

Revision as of 14:00, 21 March 2012


Name:skeletal muscle, 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
tissueskeletal muscle
dev stage55,79,79 years old adult
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -14
catalog numberCat:AM6000 Lot:0910061 -14
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-penis-0.042
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-0.47
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
C115-pituitary-Neural-caudate-putamen-amygdala-medulla-hippocampus0
C116-myeloma-xeroderma-tonsil-CD19-spleen-lymph-trachea0
C117-serous-clear-kidney-neuroectodermal-mesothelioma-endometrial-Intestinal0
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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: CNhs10629

Jaspar motifP-value
MA0002.20.0244
MA0003.10.184
MA0004.10.993
MA0006.10.351
MA0007.10.485
MA0009.10.127
MA0014.10.449
MA0017.10.0949
MA0018.20.125
MA0019.10.101
MA0024.19.08118e-4
MA0025.10.243
MA0027.10.651
MA0028.11.53694e-7
MA0029.10.968
MA0030.10.01
MA0031.10.0367
MA0035.20.486
MA0038.10.00528
MA0039.20.00161
MA0040.10.375
MA0041.10.213
MA0042.10.243
MA0043.10.032
MA0046.10.615
MA0047.20.146
MA0048.11.46164e-5
MA0050.10.0039
MA0051.10.197
MA0052.13.12138e-44
MA0055.11.12303e-5
MA0057.10.98
MA0058.10.952
MA0059.10.554
MA0060.13.76103e-5
MA0061.10.0102
MA0062.21.95594e-15
MA0065.20.0308
MA0066.10.281
MA0067.10.706
MA0068.10.0415
MA0069.10.71
MA0070.10.621
MA0071.10.142
MA0072.10.631
MA0073.10.568
MA0074.10.53
MA0076.14.47677e-8
MA0077.10.131
MA0078.10.263
MA0079.20.961
MA0080.25.33263e-6
MA0081.10.0217
MA0083.10.00425
MA0084.10.834
MA0087.10.371
MA0088.10.208
MA0090.10.141
MA0091.10.00252
MA0092.10.129
MA0093.10.983
MA0099.21.86655e-5
MA0100.10.0422
MA0101.10.0222
MA0102.20.0481
MA0103.10.625
MA0104.20.34
MA0105.10.0325
MA0106.10.436
MA0107.10.00997
MA0108.25.62196e-17
MA0111.10.923
MA0112.23.28312e-4
MA0113.16.38467e-4
MA0114.10.131
MA0115.10.0493
MA0116.10.0799
MA0117.10.744
MA0119.10.165
MA0122.10.103
MA0124.10.633
MA0125.10.358
MA0131.10.0245
MA0135.10.971
MA0136.13.6327e-8
MA0137.20.551
MA0138.20.855
MA0139.10.131
MA0140.10.388
MA0141.10.00142
MA0142.10.0552
MA0143.10.423
MA0144.10.424
MA0145.10.0797
MA0146.10.395
MA0147.10.276
MA0148.10.153
MA0149.10.214
MA0150.10.921
MA0152.10.729
MA0153.10.2
MA0154.10.993
MA0155.10.115
MA0156.19.14842e-12
MA0157.10.0783
MA0159.10.13
MA0160.10.0146
MA0162.10.565
MA0163.10.0824
MA0164.10.637
MA0258.10.00704
MA0259.10.254



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: CNhs10629

Novel motifP-value
10.568
100.656
1000.427
1010.0996
1020.678
1030.562
1040.987
1050.478
1060.157
1070.0661
1080.251
1090.56
110.735
1100.315
1110.755
1120.191
1130.895
1140.679
1150.524
1160.424
1170.218
1180.0572
1190.0778
120.963
1200.172
1210.962
1220.295
1230.0641
1240.263
1250.694
1260.607
1270.788
1280.064
1290.902
130.608
1300.872
1310.154
1320.389
1330.00154
1340.124
1350.0561
1360.496
1370.757
1380.918
1390.00829
140.205
1400.355
1410.928
1420.785
1430.0241
1440.585
1450.836
1460.318
1470.00153
1480.28
1490.0792
150.874
1500.644
1510.147
1520.414
1530.125
1540.986
1550.546
1560.219
1570.505
1580.492
1590.586
160.543
1600.717
1610.2
1620.771
1630.49
1640.113
1650.0174
1660.427
1670.388
1680.597
1690.128
170.863
180.64
190.0208
20.141
200.0255
210.417
220.0552
230.181
240.242
250.706
260.343
270.648
280.609
290.0975
30.896
300.153
310.494
320.556
330.346
340.328
350.451
360.05
370.472
380.961
390.0405
40.996
400.0387
410.395
420.399
430.687
440.0203
450.13
460.869
470.409
480.442
490.923
50.388
500.502
510.909
520.0701
530.644
540.488
550.195
560.824
570.766
580.58
590.516
60.815
600.0617
610.791
620.223
630.205
640.613
650.344
660.0273
670.549
680.373
690.515
70.229
700.314
710.376
720.356
730.537
740.414
750.399
760.184
770.0783
780.123
790.0231
80.672
800.575
810.485
820.381
830.632
840.302
850.0132
860.375
870.461
880.992
890.128
90.376
900.993
910.311
920.177
930.862
940.518
950.0582
960.406
970.94
980.1
990.438



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: CNhs10629


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
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature 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)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0007023 (adult organism)
0009142 (entire embryonic mesenchyme)

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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