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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;56
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;56
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;56
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;56
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520adult.CNhs10483.56-12G2.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520adult.CNhs10483.56-12G2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520adult.CNhs10483.56-12G2.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520adult.CNhs10483.56-12G2.mm10.nobarcode.ctss.bed.gz

Revision as of 18:47, 4 August 2017


Name:bone (os femoris), adult
Species:Mouse (Mus musculus)
Library ID:CNhs10483
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuebone (os femoris)
dev stageadult
sexmale
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00006018
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10483 CAGE DRX008936 DRR009810
Accession ID Mm9

Library idBAMCTSS
CNhs10483 DRZ001235 DRZ002618
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs10483

00
10
100
1000
10000.693
10010.0264
1002-0.116
1003-0.0139
10040
10050.5
10060.351
1007-0.0321
10080
1009-0.19
101-0.032
10100
10110
10120
10130.104
1014-0.0874
1015-0.0806
1016-0.389
10170
10180
10190
1020
10200
10210
10220.151
10230
10240.136
10250
10260
10270
10280
1029-0.148
1030.275
10300
1031-0.458
1032-0.294
10330
10340
10350
10360.0919
10370
1038-0.109
1039-0.0731
1040
1040-0.216
10410.275



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



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: CNhs10483

Jaspar motifP-value
MA0002.24.08556e-8
MA0003.10.0296
MA0004.10.551
MA0006.10.164
MA0007.10.531
MA0009.10.697
MA0014.10.752
MA0017.10.478
MA0018.20.00909
MA0019.10.273
MA0024.10.614
MA0025.10.809
MA0027.10.582
MA0028.10.816
MA0029.10.724
MA0030.10.922
MA0031.10.898
MA0035.21.94937e-5
MA0038.10.0242
MA0039.20.184
MA0040.10.117
MA0041.10.276
MA0042.10.405
MA0043.10.0532
MA0046.14.74323e-13
MA0047.20.435
MA0048.10.375
MA0050.17.33306e-6
MA0051.11.66842e-5
MA0052.12.25739e-10
MA0055.10.566
MA0057.10.639
MA0058.10.351
MA0059.10.41
MA0060.10.121
MA0061.10.0184
MA0062.20.186
MA0065.20.0341
MA0066.10.222
MA0067.10.751
MA0068.10.0746
MA0069.10.383
MA0070.10.395
MA0071.10.451
MA0072.10.416
MA0073.10.0988
MA0074.10.562
MA0076.10.45
MA0077.10.0928
MA0078.10.825
MA0079.20.331
MA0080.25.93183e-14
MA0081.10.0101
MA0083.10.122
MA0084.10.157
MA0087.10.279
MA0088.10.811
MA0090.10.495
MA0091.10.0523
MA0092.10.743
MA0093.10.461
MA0099.20.0877
MA0100.10.304
MA0101.10.253
MA0102.20.0275
MA0103.10.896
MA0104.20.334
MA0105.15.57347e-4
MA0106.10.864
MA0107.10.0904
MA0108.20.0282
MA0111.10.558
MA0112.26.03827e-6
MA0113.10.589
MA0114.10.95
MA0115.10.697
MA0116.11.64626e-4
MA0117.10.602
MA0119.10.222
MA0122.10.412
MA0124.10.866
MA0125.10.0293
MA0131.10.395
MA0135.10.718
MA0136.13.64724e-14
MA0137.20.588
MA0138.20.572
MA0139.10.617
MA0140.15.67878e-17
MA0141.10.316
MA0142.10.00543
MA0143.10.496
MA0144.10.728
MA0145.10.152
MA0146.10.068
MA0147.10.448
MA0148.10.324
MA0149.10.4
MA0150.10.00242
MA0152.10.269
MA0153.11.60913e-7
MA0154.19.7804e-4
MA0155.10.484
MA0156.16.87285e-8
MA0157.10.931
MA0159.10.00576
MA0160.10.131
MA0162.10.182
MA0163.15.58469e-5
MA0164.10.726
MA0258.10.00191
MA0259.10.26



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: CNhs10483

Novel motifP-value
10.223
100.116
1000.789
1010.405
1020.321
1030.258
1040.989
1050.324
1060.0874
1070.362
1080.835
1090.0404
110.132
1100.115
1110.197
1120.117
1130.667
1140.14
1150.91
1160.281
1170.0243
1180.382
1190.0711
120.401
1200.646
1210.341
1220.753
1230.97
1240.89
1250.0369
1260.311
1270.156
1280.123
1290.171
130.0809
1300.589
1310.919
1320.711
1330.141
1340.335
1350.973
1360.245
1370.061
1380.444
1390.1
140.306
1400.265
1410.47
1420.893
1430.129
1440.475
1450.0932
1460.612
1470.971
1480.189
1490.175
150.0192
1500.305
1510.0619
1520.219
1530.846
1540.869
1550.582
1560.871
1570.911
1580.0931
1590.995
1600.573
1610.257
1620.587
1630.704
1640.0481
1650.0334
1660.418
1670.762
1680.395
1699.97624e-4
170.242
180.205
190.174
20.746
200.614
210.0786
220.25
230.381
240.275
250.261
260.0489
270.45
280.415
290.111
30.145
300.897
310.395
320.0926
330.361
340.347
350.439
360.146
370.117
380.368
390.911
40.983
400.103
410.344
420.313
430.136
440.318
450.444
460.177
470.181
480.256
490.192
50.0773
500.92
510.717
520.479
530.618
540.719
550.0598
560.257
570.405
580.294
590.0213
60.678
600.157
610.366
620.0742
630.313
640.599
650.196
660.472
670.21
680.658
690.119
70.0623
700.0603
710.0552
720.478
730.0875
740.523
750.119
760.833
770.427
780.0127
790.512
80.0349
800.0139
810.318
820.248
830.237
840.649
850.0456
860.313
870.187
880.807
890.201
90.277
900.79
910.269
920.43
930.281
940.0471
950.0656
960.318
970.961
980.136
990.576



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: CNhs10483


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
0000468 (multi-cellular organism)
0007023 (adult organism)
0000981 (femur)
0001474 (bone element)
0000479 (tissue)
0011216 (organ system subdivision)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0002472 (stylopod)
0008784 (lower limb segment)
0001062 (anatomical entity)
0000480 (anatomical group)
0006058 (multi-limb segment region)
0003608 (hindlimb long bone)
0003826 (upper leg bone)
0008202 (bone of hip region)
0000075 (subdivision of skeletal system)
0004381 (skeleton of limb)
0007273 (pelvic appendage skeleton)
0004765 (skeletal element)
0010912 (subdivision of skeleton)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0002513 (endochondral bone)
0004375 (bone of free limb or fin)
0010740 (bone of appendage girdle complex)
0002529 (limb segment)
0010363 (endochondral element)
0010538 (paired limb/fin segment)
0002428 (limb bone)
0010742 (bone of pelvic complex)
0002495 (long bone)
0003464 (hindlimb bone)
0003606 (limb long bone)
0005893 (leg bone)
0010317 (germ layer / neural crest derived structure)
0010712 (limb skeleton subdivision)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0000978 (leg)
0002103 (hindlimb)
0000376 (hindlimb stylopod)
0001441 (hindlimb skeleton)
0011249 (appendicular skeletal system)
0000154 (posterior region of body)
0010709 (pelvic complex)
0002091 (appendicular skeleton)
0004288 (skeleton)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011464 (mouse bone- os femoris - adult sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0003104 (mesenchyme)
UBERON:0005866 (pre-cartilage condensation)
UBERON:0006234 (femur pre-cartilage condensation)
UBERON:0010316 (germ layer / neural crest)
UBERON:0010882 (limb bone pre-cartilage condensation)
UBERON:0010886 (hindlimb bone pre-cartilage condensation)

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