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{{f5samples
{{f5samples
|id=FF:1389-42C2
|ancestors_in_anatomy_facet=UBERON:0000026,UBERON:0000061,UBERON:0000062,UBERON:0000154,UBERON:0000376,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000978,UBERON:0001048,UBERON:0001062,UBERON:0001374,UBERON:0001383,UBERON:0001630,UBERON:0002050,UBERON:0002101,UBERON:0002103,UBERON:0002204,UBERON:0002472,UBERON:0002529,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003661,UBERON:0003663,UBERON:0004120,UBERON:0004252,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004709,UBERON:0005090,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0006057,UBERON:0006058,UBERON:0008784
|name=muscle (biceps femoris), neonate N30
|sample_id=1389
|rna_tube_id=42C2
|rna_box=42
|rna_position=C2
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=30 days neonate
|sample_tissue=muscle (biceps femoris)
|sample_donor(cell lot)=
|sample_sex=mixture
|sample_age=
|sample_ethnicity=
|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=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=
|rna_concentration=
|sample_note=
|profile_hcage=CNhs11129,LSID735,release008,COMPLETED
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|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
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|sample_description=
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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:1389-42C2
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011490
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011490
|name=muscle (biceps femoris), neonate N30
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11129,LSID735,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=42
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=C2
|rna_rin=
|rna_sample_type=
|rna_tube_id=42C2
|rna_weight_ug=
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_description=
|sample_dev_stage=30 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=1389
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=muscle (biceps femoris)
|top_motifs=MEF2{A,B,C,D}:4.20072134486;NR5A1,2:3.38899024691;NR3C1:3.30764034426;ESRRA:2.74213457338;ESR1:2.67777394108;RXR{A,B,G}:2.47423102242;MAFB:2.39452295705;TGIF1:2.36656236291;NKX2-2,8:2.35425152479;FOXL1:2.30212721473;NFE2L2:2.26746531388;HOX{A4,D4}:2.20547021631;NR1H4:2.18318475289;GCM1,2:2.08923189867;UFEwm:1.9836260544;FOXO1,3,4:1.80726373562;TFAP2{A,C}:1.72183019675;TFAP4:1.69797177025;TAL1_TCF{3,4,12}:1.69731692307;AR:1.69405352715;ALX1:1.68680093918;EVI1:1.54880869076;NFATC1..3:1.51730394481;SRF:1.44237900473;TFCP2:1.37536010676;TEAD1:1.37484972737;NFE2:1.31657662523;YY1:1.28302400513;TLX2:1.2591335154;MYOD1:1.24589270885;NKX2-3_NKX2-5:1.18122675069;RORA:1.17317344344;GTF2A1,2:1.16884351374;NFE2L1:1.15066717398;SOX5:1.10270249238;NHLH1,2:1.02821765608;NR6A1:1.02107835727;ZNF238:0.997578969756;RXRA_VDR{dimer}:0.977814207979;STAT2,4,6:0.963436654271;FOSL2:0.94878741818;HBP1_HMGB_SSRP1_UBTF:0.886609538988;HOX{A5,B5}:0.818221720513;CRX:0.780507707925;SPZ1:0.780136929911;HSF1,2:0.754711149749;SREBF1,2:0.729884399197;GLI1..3:0.713325921712;DMAP1_NCOR{1,2}_SMARC:0.683170503154;FOX{D1,D2}:0.660725991264;HIF1A:0.640509616411;POU3F1..4:0.597190627376;ARID5B:0.596163363496;PAX5:0.595053011247;PDX1:0.584889377888;MTF1:0.571953613059;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.566882872904;GFI1B:0.536259457181;POU1F1:0.521236267983;PAX2:0.518179690153;TLX1..3_NFIC{dimer}:0.51315870662;NANOG{mouse}:0.511095849399;FOX{I1,J2}:0.488093155974;SOX{8,9,10}:0.458276796775;TBP:0.441011152496;HES1:0.440789328349;IKZF1:0.429360686863;SMAD1..7,9:0.408461449116;ZNF143:0.390709041962;IKZF2:0.378274973828;GATA4:0.37115280818;PAX1,9:0.370034128095;ATF6:0.367677471518;ZNF148:0.353314174114;MYFfamily:0.347496817587;HLF:0.339645063685;TOPORS:0.338186220821;KLF4:0.332222246512;CEBPA,B_DDIT3:0.299853197841;PATZ1:0.282972564562;RFX2..5_RFXANK_RFXAP:0.279768891754;TFAP2B:0.260356191622;FOXP1:0.253765621986;ALX4:0.237677727368;TP53:0.22862049169;HIC1:0.202225332249;MYBL2:0.181752774203;MAZ:0.148226507309;POU6F1:0.14624251047;SP1:0.137302791001;SPI1:0.131536527526;ATF4:0.130534768027;RBPJ:0.124831523751;EBF1:0.117684789356;BACH2:0.0868993871524;GFI1:0.0805024795352;FOXA2:0.0758668830705;NFIL3:0.0658228961236;PRDM1:0.0109435588883;EP300:-0.00133002353441;LMO2:-0.00389169833011;IRF1,2:-0.0175932413691;FOS_FOS{B,L1}_JUN{B,D}:-0.0459206041379;NKX2-1,4:-0.0498276461204;FOXP3:-0.0653560887536;MZF1:-0.0668384787868;PAX4:-0.0757020531131;HMX1:-0.0840121981695;ATF2:-0.0916034072701;IRF7:-0.0986592207803;CREB1:-0.115629465753;SPIB:-0.158933235764;STAT5{A,B}:-0.15969980685;MTE{core}:-0.160480336429;PBX1:-0.171624805402;PITX1..3:-0.206371293766;EN1,2:-0.209525381738;NFKB1_REL_RELA:-0.239805646263;RREB1:-0.255148322923;GTF2I:-0.264683090283;ZIC1..3:-0.323158140819;ETS1,2:-0.325203863226;HAND1,2:-0.350634542264;ZBTB6:-0.367584914804;STAT1,3:-0.377564184181;RUNX1..3:-0.378372444535;XCPE1{core}:-0.393093380449;TEF:-0.397320392096;HNF4A_NR2F1,2:-0.401803600447;ZNF384:-0.407683306245;JUN:-0.407999426968;MED-1{core}:-0.435214756697;ZFP161:-0.440317338521;REST:-0.451435815671;HMGA1,2:-0.511737354976;GATA6:-0.538796046025;PPARG:-0.541593118442;VSX1,2:-0.554432737303;NRF1:-0.569738417238;LHX3,4:-0.573788013215;ATF5_CREB3:-0.580336996637;EGR1..3:-0.583900333105;ELF1,2,4:-0.596462701828;LEF1_TCF7_TCF7L1,2:-0.6339367901;CDC5L:-0.635126635526;ZNF423:-0.643743751019;MYB:-0.647535527565;FOXM1:-0.700637685492;OCT4_SOX2{dimer}:-0.702387252203;ZBTB16:-0.743133649926;RFX1:-0.770858082115;FOXN1:-0.773608290323;HNF1A:-0.789519456557;CUX2:-0.790754679387;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.791464881797;FOX{F1,F2,J1}:-0.80671988623;AHR_ARNT_ARNT2:-0.80700663441;HOXA9_MEIS1:-0.822575539269;PAX8:-0.823291980498;NFIX:-0.869227856303;ELK1,4_GABP{A,B1}:-0.898942956943;AIRE:-0.905522756454;BREu{core}:-0.910537319112;SOX2:-0.94533760696;NKX3-2:-0.961595685663;SOX17:-0.968296281643;bHLH_family:-0.999087728225;NKX6-1,2:-1.02242216813;BPTF:-1.02994092063;CDX1,2,4:-1.0388529874;ZEB1:-1.05455418763;SNAI1..3:-1.05766123964;E2F1..5:-1.13307147504;NKX3-1:-1.15338053762;FOXQ1:-1.16917610721;NFY{A,B,C}:-1.19611831769;POU5F1:-1.24390515438;PRRX1,2:-1.25676058644;NANOG:-1.39489016779;TFDP1:-1.40480661771;T:-1.41929695485;POU2F1..3:-1.42565043587;DBP:-1.45674560816;TBX4,5:-1.46217298311;ONECUT1,2:-1.58140674465;PAX6:-1.72907971366;FOXD3:-1.83219006557;ADNP_IRX_SIX_ZHX:-2.49146135094;GZF1:-3.06302761893
}}
}}

Revision as of 15:31, 21 March 2012


Name:muscle (biceps femoris), neonate N30
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuemuscle (biceps femoris)
dev stage30 days neonate
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} 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

CNhs11129

00
10
100
1000
10001.074
10010.642
1002-0.0962
10030.377
10040
10050.0416
10060.954
1007-0.0837
10080
10090.103
101-0.0491
10100
1011-0.108
10120
1013-0.0449
10140
1015-0.264
10160.016
10170
10180
10190
1020
10200
10210
10220.968
10230
10240.373
10250
10260
10270.178
10280
1029-0.115
1030.625
10300.0978
1031-0.0564
10320.277
10330
10340
10350.0978
1036-0.248
10370
10380.0487
10390.551
1040
10400.0739
10410.702



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: CNhs11129

Jaspar motifP-value
MA0002.20.943
MA0003.10.093
MA0004.10.221
MA0006.10.133
MA0007.10.309
MA0009.10.99
MA0014.10.993
MA0017.10.745
MA0018.20.0147
MA0019.10.115
MA0024.12.30827e-5
MA0025.10.151
MA0027.10.385
MA0028.10.0087
MA0029.10.582
MA0030.10.884
MA0031.10.313
MA0035.20.328
MA0038.10.932
MA0039.20.532
MA0040.10.858
MA0041.10.156
MA0042.10.666
MA0043.10.0734
MA0046.11.1464e-14
MA0047.20.483
MA0048.10.0341
MA0050.10.168
MA0051.10.609
MA0052.13.12094e-65
MA0055.10.177
MA0057.10.683
MA0058.10.205
MA0059.10.0838
MA0060.13.09661e-6
MA0061.10.947
MA0062.26.90819e-7
MA0065.20.00554
MA0066.10.317
MA0067.10.502
MA0068.10.129
MA0069.10.17
MA0070.10.744
MA0071.10.00813
MA0072.10.308
MA0073.10.159
MA0074.10.601
MA0076.19.27111e-4
MA0077.10.239
MA0078.10.0947
MA0079.20.345
MA0080.26.58674e-4
MA0081.10.833
MA0083.15.62276e-7
MA0084.10.945
MA0087.10.861
MA0088.10.691
MA0090.10.0831
MA0091.10.029
MA0092.10.148
MA0093.10.198
MA0099.20.791
MA0100.10.0295
MA0101.10.256
MA0102.20.329
MA0103.10.0123
MA0104.20.0486
MA0105.10.827
MA0106.10.937
MA0107.10.35
MA0108.21.3671e-5
MA0111.10.782
MA0112.23.58765e-7
MA0113.10.078
MA0114.10.781
MA0115.10.844
MA0116.10.484
MA0117.10.575
MA0119.10.474
MA0122.10.239
MA0124.10.222
MA0125.10.606
MA0131.10.51
MA0135.10.714
MA0136.15.71564e-6
MA0137.20.0149
MA0138.20.0043
MA0139.10.524
MA0140.10.817
MA0141.11.21142e-7
MA0142.10.594
MA0143.10.202
MA0144.10.41
MA0145.10.0229
MA0146.10.0697
MA0147.10.117
MA0148.10.586
MA0149.10.328
MA0150.10.0504
MA0152.10.896
MA0153.14.14602e-10
MA0154.10.0414
MA0155.10.153
MA0156.11.60854e-6
MA0157.10.3
MA0159.10.00433
MA0160.12.61104e-4
MA0162.10.222
MA0163.10.0612
MA0164.10.35
MA0258.11.30285e-5
MA0259.10.198



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: CNhs11129

Novel motifP-value
10.201
100.678
1000.418
1010.394
1020.574
1030.784
1040.999
1050.0893
1060.18
1070.253
1080.763
1090.0667
110.162
1100.391
1110.438
1120.733
1130.649
1140.168
1150.431
1160.38
1170.881
1180.486
1190.0465
120.117
1200.892
1210.563
1220.97
1230.665
1240.227
1250.474
1260.893
1270.171
1280.469
1290.338
130.00372
1300.721
1310.708
1320.896
1330.726
1340.473
1350.478
1360.292
1370.899
1380.23
1390.0864
140.124
1400.06
1410.09
1420.978
1430.733
1440.106
1450.923
1460.761
1470.797
1480.851
1490.0608
150.847
1500.454
1510.257
1520.0387
1530.363
1540.934
1550.681
1560.115
1570.283
1580.981
1590.338
1600.239
1610.126
1620.511
1630.402
1640.727
1650.00975
1660.801
1670.191
1680.0819
1695.68599e-4
170.131
180.975
190.0232
20.359
200.914
210.823
220.0514
230.399
240.926
250.727
260.368
270.863
280.79
290.988
30.563
300.803
310.213
320.0295
330.796
340.171
350.767
360.197
370.00948
380.701
390.338
40.705
400.573
410.397
420.571
430.271
440.562
450.31
460.408
470.99
480.671
490.669
50.145
500.317
510.879
520.34
530.692
540.383
550.308
560.456
570.365
580.683
590.00747
60.52
600.0993
610.777
620.305
630.0709
640.724
650.453
660.738
670.273
680.587
690.0159
70.136
700.116
710.104
720.652
730.0239
740.151
750.586
760.536
770.436
780.0172
790.0755
80.363
800.469
810.152
820.106
830.413
840.581
850.00135
860.194
870.319
880.812
890.0782
90.462
900.326
910.192
920.484
930.294
940.237
950.149
960.399
970.911
980.662
990.68



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: CNhs11129


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
0000026 (appendage)
0000061 (anatomical structure)
0000062 (organ)
0000154 (posterior region of body)
0000376 (hindlimb stylopod)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000978 (leg)
0001048 (primordium)
0001062 (anatomical entity)
0001374 (biceps femoris)
0001383 (muscle of leg)
0001630 (muscle organ)
0002050 (embryonic structure)
0002101 (limb)
0002103 (hindlimb)
0002204 (musculoskeletal system)
0002472 (stylopod)
0002529 (limb segment)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003102 (surface structure)
0003661 (limb muscle)
0003663 (hindlimb muscle)
0004120 (mesoderm-derived structure)
0004252 (hindlimb stylopod muscle)
0004347 (limb bud)
0004357 (paired limb/fin bud)
0004708 (paired limb/fin)
0004709 (pelvic appendage)
0005090 (muscle structure)
0005423 (developing anatomical structure)
0005732 (limb/fin field)
0005733 (limb field)
0006058 (multi-limb segment region)
0008784 (lower limb segment)

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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