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{{f5samples
{{f5samples
|id=FF:10069-101I6
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,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:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001004,UBERON:0001015,UBERON:0001062,UBERON:0001103,UBERON:0001134,UBERON:0001443,UBERON:0001630,UBERON:0001774,UBERON:0002036,UBERON:0002050,UBERON:0002100,UBERON:0002204,UBERON:0002329,UBERON:0002385,UBERON:0002426,UBERON:0002532,UBERON:0003059,UBERON:0003077,UBERON:0003082,UBERON:0003104,UBERON:0003830,UBERON:0003831,UBERON:0003897,UBERON:0003898,UBERON:0004120,UBERON:0004290,UBERON:0004830,UBERON:0005090,UBERON:0005175,UBERON:0005177,UBERON:0005181,UBERON:0005291,UBERON:0005423,UBERON:0005482,UBERON:0009142
|name=diaphragm, fetal, donor1
|sample_id=10069
|rna_tube_id=101I6
|rna_box=101
|rna_position=I6
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Biochain
|rna_lot_number=A912092
|rna_catalog_number=Cat:RtHFN: Diaphragm
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=36 weeks fetus
|sample_tissue=diaphragm
|sample_donor(cell lot)=1
|sample_sex=male
|sample_age=
|sample_ethnicity=A?
|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=10
|rna_concentration=2
|sample_note=
|profile_hcage=CNhs11779,LSID820,release009,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
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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:10069-101I6
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010069
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010069
|name=diaphragm, fetal, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11779,LSID820,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:RtHFN: Diaphragm
|rna_concentration=2
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=A912092
|rna_od260/230=
|rna_od260/280=
|rna_position=I6
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=101I6
|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=Biochain
|sample_description=
|sample_dev_stage=36 weeks fetus
|sample_disease=normal
|sample_donor(cell lot)=1
|sample_ethnicity=A?
|sample_experimental_condition=
|sample_id=10069
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=diaphragm
|top_motifs=MEF2{A,B,C,D}:6.20431999248;NR1H4:4.51449731561;FOXL1:3.73293352504;TAL1_TCF{3,4,12}:3.68545634184;IKZF2:3.57578959382;SOX5:3.40472679666;NR5A1,2:3.36043991811;ESR1:3.28954075946;NR6A1:3.27502461839;HOX{A4,D4}:3.0038738266;SMAD1..7,9:2.89565982482;SPZ1:2.83125764952;SRF:2.60227227693;ZNF384:2.58342389552;NFE2L1:2.53320788184;GCM1,2:2.49356183782;MYBL2:2.45474000104;GLI1..3:2.30996233198;MAFB:2.20421851982;NKX2-2,8:2.18365651657;TBP:2.15176692038;FOXP3:2.12671194158;AR:2.03332867695;PDX1:1.93397193215;TFAP2{A,C}:1.88548263071;TFAP4:1.86544450228;TLX2:1.85495390667;PAX5:1.83061187502;ALX1:1.72175896499;TOPORS:1.71619505732;GATA4:1.71291875308;ATF2:1.67506916237;TGIF1:1.61480945446;RORA:1.612022436;HIC1:1.60193468607;PATZ1:1.59883984216;ESRRA:1.57982678519;MAZ:1.55955335729;NANOG{mouse}:1.54397455041;FOXM1:1.52181672296;NKX3-1:1.51568675368;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.49903024276;UFEwm:1.48965890529;IKZF1:1.48295555108;NFATC1..3:1.46927876976;POU1F1:1.43303064483;RXR{A,B,G}:1.42914958675;HOX{A6,A7,B6,B7}:1.4250568207;HMGA1,2:1.41642815434;EVI1:1.40747776993;KLF4:1.40342566236;NHLH1,2:1.38167217708;FOXP1:1.35204661901;XBP1:1.30618499179;NFIX:1.28124385792;EGR1..3:1.18817908945;RREB1:1.17590295285;ZBTB16:1.17423168966;ZNF423:1.1658551324;MYOD1:1.16430090355;HES1:1.16248508762;MTE{core}:1.15802918104;NKX2-1,4:1.15749469192;GFI1B:1.10134732319;TFAP2B:1.10086959285;GTF2A1,2:1.08595055854;HSF1,2:1.05637604662;MED-1{core}:1.05290719867;MZF1:1.04283607204;POU3F1..4:1.04204330644;LHX3,4:1.02705586706;TLX1..3_NFIC{dimer}:1.0207301289;TEAD1:0.973131910637;YY1:0.967447832494;EP300:0.927942906838;ZIC1..3:0.907616723624;BPTF:0.907354785303;NKX6-1,2:0.877974856517;TFCP2:0.876821706571;FOXQ1:0.87335830542;TBX4,5:0.860212054943;HAND1,2:0.819688010447;MTF1:0.817665486516;GTF2I:0.815506072422;RBPJ:0.796801770853;PRDM1:0.749824793886;FOXO1,3,4:0.728837091473;RXRA_VDR{dimer}:0.703899725214;STAT5{A,B}:0.678494682844;PBX1:0.677316604147;SP1:0.648610456663;SOX{8,9,10}:0.640235376914;LMO2:0.622240295135;PAX6:0.607282711053;CDX1,2,4:0.580624076013;HOX{A5,B5}:0.569983706359;PAX3,7:0.565452145056;POU6F1:0.553686777636;MYFfamily:0.551347414392;ATF6:0.53440004617;ZFP161:0.517264362773;PAX1,9:0.469765492902;NR3C1:0.453729583755;ZNF148:0.444501103383;LEF1_TCF7_TCF7L1,2:0.439474074823;IRF7:0.424403829155;ZNF238:0.402127026901;ARID5B:0.39753697501;AIRE:0.392803689357;BREu{core}:0.389721454564;NKX2-3_NKX2-5:0.365852738835;NKX3-2:0.343408642408;HOXA9_MEIS1:0.334170171693;STAT2,4,6:0.31563026156;CUX2:0.27752746599;HMX1:0.273068000674;SOX17:0.235950636003;REST:0.2194778563;JUN:0.2104578428;CREB1:0.187422388472;GZF1:0.104216687388;FOXA2:0.0988130909681;FOX{F1,F2,J1}:-0.0119007800841;ALX4:-0.0422194978551;SOX2:-0.0510147820771;POU5F1:-0.063793675955;EN1,2:-0.0897422998529;GFI1:-0.129024513457;SNAI1..3:-0.140887629501;ETS1,2:-0.146350108879;FOX{D1,D2}:-0.147474536538;PITX1..3:-0.154374706267;PAX2:-0.160425435884;SPI1:-0.188352477462;ATF4:-0.190036374567;DMAP1_NCOR{1,2}_SMARC:-0.194082904248;GATA6:-0.214169388144;STAT1,3:-0.219895146193;TP53:-0.240946614476;ONECUT1,2:-0.248728628151;SREBF1,2:-0.248814562864;IRF1,2:-0.259654715474;T:-0.259750284534;XCPE1{core}:-0.264837328814;ZNF143:-0.2895633842;HNF4A_NR2F1,2:-0.296396348241;RFX2..5_RFXANK_RFXAP:-0.353372309214;ZBTB6:-0.364514735941;NANOG:-0.419226901886;FOX{I1,J2}:-0.432144483933;SPIB:-0.467286790361;HBP1_HMGB_SSRP1_UBTF:-0.503472794372;FOSL2:-0.50501981333;PPARG:-0.544275571944;HNF1A:-0.574685988342;HLF:-0.599841325009;NFKB1_REL_RELA:-0.60102243285;DBP:-0.606951397759;PAX4:-0.621181433029;E2F1..5:-0.683137940518;NRF1:-0.686696593479;CDC5L:-0.691525625351;ELF1,2,4:-0.755284726655;FOXN1:-0.7556840131;CEBPA,B_DDIT3:-0.76031910521;ZEB1:-0.764563072054;AHR_ARNT_ARNT2:-0.828000128646;ATF5_CREB3:-0.839420466236;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.843566440145;RFX1:-0.854314711121;FOS_FOS{B,L1}_JUN{B,D}:-0.884356399199;VSX1,2:-0.899966956696;NFE2:-0.926768560501;TEF:-0.932308713956;RUNX1..3:-0.951791959845;NFIL3:-0.989996626028;NFY{A,B,C}:-1.01758415021;FOXD3:-1.01971823109;BACH2:-1.02532736365;NFE2L2:-1.05560419757;EBF1:-1.09760588894;ADNP_IRX_SIX_ZHX:-1.23844507176;PAX8:-1.24413558269;CRX:-1.34410130667;OCT4_SOX2{dimer}:-1.40533768076;bHLH_family:-1.4196924695;PRRX1,2:-1.45863059703;HIF1A:-1.47581487769;TFDP1:-1.47865591231;POU2F1..3:-1.87648666219;MYB:-1.90566371241;ELK1,4_GABP{A,B1}:-2.11824610611
}}
}}

Revision as of 14:01, 21 March 2012


Name:diaphragm, fetal, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuediaphragm
dev stage36 weeks fetus
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberA912092
catalog numberCat:RtHFN: Diaphragm
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
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-penis0.603
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-0.253
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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: CNhs11779

Jaspar motifP-value
MA0002.24.36784e-4
MA0003.10.229
MA0004.10.00726
MA0006.10.947
MA0007.10.403
MA0009.10.0629
MA0014.10.412
MA0017.10.934
MA0018.20.381
MA0019.10.621
MA0024.10.0199
MA0025.10.163
MA0027.10.929
MA0028.13.30551e-10
MA0029.10.756
MA0030.10.278
MA0031.10.102
MA0035.20.0463
MA0038.10.0133
MA0039.23.14907e-4
MA0040.10.526
MA0041.10.683
MA0042.10.834
MA0043.10.0108
MA0046.15.58323e-4
MA0047.20.135
MA0048.10.0642
MA0050.10.00798
MA0051.10.016
MA0052.12.1144e-24
MA0055.10.00334
MA0057.10.738
MA0058.10.00149
MA0059.10.00197
MA0060.12.34876e-6
MA0061.12.40422e-6
MA0062.23.32754e-19
MA0065.20.253
MA0066.10.552
MA0067.10.0659
MA0068.10.0189
MA0069.10.517
MA0070.10.277
MA0071.10.235
MA0072.10.645
MA0073.10.294
MA0074.10.68
MA0076.14.5515e-14
MA0077.10.401
MA0078.10.694
MA0079.20.704
MA0080.21.1842e-7
MA0081.10.02
MA0083.10.00154
MA0084.10.145
MA0087.10.335
MA0088.10.115
MA0090.10.368
MA0091.10.0104
MA0092.10.192
MA0093.10.00459
MA0099.26.66126e-20
MA0100.10.0357
MA0101.12.3876e-5
MA0102.20.00771
MA0103.10.0271
MA0104.22.89158e-4
MA0105.16.93453e-6
MA0106.17.79244e-4
MA0107.11.80682e-5
MA0108.29.88476e-13
MA0111.10.676
MA0112.20.0356
MA0113.10.0599
MA0114.10.413
MA0115.10.704
MA0116.10.00358
MA0117.10.286
MA0119.10.0783
MA0122.10.275
MA0124.10.646
MA0125.10.912
MA0131.10.211
MA0135.10.39
MA0136.17.12446e-13
MA0137.20.201
MA0138.20.447
MA0139.10.00257
MA0140.10.127
MA0141.10.178
MA0142.14.27514e-4
MA0143.10.0923
MA0144.10.438
MA0145.10.445
MA0146.10.155
MA0147.12.39298e-4
MA0148.10.263
MA0149.10.101
MA0150.11.94337e-7
MA0152.10.0476
MA0153.10.772
MA0154.10.0741
MA0155.10.0956
MA0156.11.88442e-16
MA0157.10.122
MA0159.10.958
MA0160.10.911
MA0162.10.437
MA0163.10.137
MA0164.10.813
MA0258.10.0121
MA0259.10.0951



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: CNhs11779

Novel motifP-value
10.667
100.2
1000.845
1010.276
1020.491
1030.48
1040.735
1050.808
1060.667
1070.0998
1080.106
1090.00657
110.721
1100.637
1110.959
1120.728
1130.00192
1140.306
1150.087
1160.0621
1170.0222
1180.0194
1190.232
120.729
1200.291
1210.85
1220.00187
1230.354
1240.323
1250.867
1260.603
1270.543
1280.358
1290.719
130.432
1300.464
1310.274
1320.0224
1330.0374
1340.841
1350.0837
1360.0799
1370.698
1380.951
1390.135
140.934
1400.511
1410.699
1420.387
1430.0501
1440.504
1450.946
1460.587
1470.0115
1480.23
1490.196
150.233
1500.665
1510.539
1520.797
1530.372
1540.66
1550.401
1560.798
1570.902
1580.53
1590.968
160.595
1600.437
1610.141
1620.559
1630.184
1640.317
1650.0351
1660.0253
1670.333
1680.379
1690.848
170.62
180.32
190.0261
20.0637
200.0247
210.489
220.982
230.353
240.0114
250.567
260.241
270.482
280.398
290.026
30.647
300.189
310.256
325.7549e-8
330.179
340.246
350.864
360.149
370.21
380.838
390.101
40.708
400.162
410.34
420.216
430.657
440.0799
450.463
460.762
470.207
480.204
490.953
50.696
500.826
510.912
520.222
530.644
540.854
550.255
560.345
570.866
580.623
590.79
60.629
600.223
610.33
620.965
630.547
640.424
650.689
660.00464
670.482
680.36
690.514
70.954
700.719
710.147
720.366
730.185
740.406
750.0525
760.251
770.433
780.641
790.132
80.993
800.151
810.727
820.592
830.687
840.903
850.00377
860.87
870.00286
880.928
890.36
90.767
900.699
910.0534
920.234
930.896
940.0921
950.00116
960.884
970.944
980.806
990.0609



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: CNhs11779


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)
0000062 (organ)
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)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001004 (respiratory system)
0001015 (musculature)
0001062 (anatomical entity)
0001103 (diaphragm)
0001134 (skeletal muscle tissue)
0001443 (chest)
0001630 (muscle organ)
0001774 (muscle of trunk)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002100 (trunk)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002426 (chest muscle)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0003830 (thoracic segment muscle)
0003831 (respiratory system muscle)
0003897 (axial muscle)
0003898 (skeletal muscle of trunk)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0004830 (respiratory system skeletal muscle)
0005090 (muscle structure)
0005175 (chest organ)
0005177 (trunk region element)
0005181 (thoracic segment organ)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
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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