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FF:1525-43A6

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Name:bone (os femoris), neonate N16
Species:Mouse (Mus musculus)
Library ID:CNhs11225
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuebone (os femoris)
dev stage16 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

Accession numbers
MethodSample accession id
CAGE  SAMD00005320
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11225 CAGE DRX008938 DRR009812
Accession ID Mm9

Library idBAMCTSS
CNhs11225 DRZ001237 DRZ002620
Accession ID Mm10

Library idBAMCTSS
CNhs11225 DRZ012587 DRZ013970
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data

CNhs11225

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.5
1001 0.477
1002 -0.0184
1003 0.202
1004 0
1005 0.159
1006 0.471
1007 0.0255
1008 0
1009 0.0308
101 -0.0109
1010 0
1011 0
1012 0.275
1013 -0.125
1014 0.0867
1015 -0.117
1016 -0.0563
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.159
1022 0.488
1023 0
1024 0.159
1025 0
1026 0
1027 0.0867
1028 0
1029 0.436
103 0.942
1030 0.843
1031 0.0391
1032 5.473114e-4
1033 0
1034 0
1035 0.159
1036 0.0137
1037 0
1038 -0.0249
1039 0.204
104 0
1040 0.0629
1041 0.159



Repeat families with enriched expression in this sample
Summary:Ranked list of repeat family expression in this sample relative to

the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA



link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs
Summary:Association of JASPAR motif to the promoter expression in this

sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon



link to dataset.
data

library id: CNhs11225
Jaspar motif P-value
MA0002.2 0.141
MA0003.1 0.0829
MA0004.1 0.31
MA0006.1 0.0721
MA0007.1 0.901
MA0009.1 0.456
MA0014.1 0.521
MA0017.1 0.607
MA0018.2 1.78397e-4
MA0019.1 0.0666
MA0024.1 0.188
MA0025.1 0.134
MA0027.1 0.227
MA0028.1 0.034
MA0029.1 0.957
MA0030.1 0.594
MA0031.1 0.386
MA0035.2 0.0475
MA0038.1 0.598
MA0039.2 0.748
MA0040.1 0.639
MA0041.1 0.0825
MA0042.1 0.993
MA0043.1 0.00132
MA0046.1 6.0018e-17
MA0047.2 0.311
MA0048.1 0.75
MA0050.1 0.928
MA0051.1 0.826
MA0052.1 1.32842e-23
MA0055.1 0.304
MA0057.1 0.421
MA0058.1 0.141
MA0059.1 0.16
MA0060.1 0.14
MA0061.1 0.0828
MA0062.2 0.00917
MA0065.2 0.26
MA0066.1 0.142
MA0067.1 0.282
MA0068.1 0.107
MA0069.1 0.0816
MA0070.1 0.54
MA0071.1 0.753
MA0072.1 0.4
MA0073.1 0.891
MA0074.1 0.836
MA0076.1 0.008
MA0077.1 0.125
MA0078.1 0.225
MA0079.2 0.802
MA0080.2 0.0341
MA0081.1 0.144
MA0083.1 0.00131
MA0084.1 0.547
MA0087.1 0.179
MA0088.1 0.97
MA0090.1 0.867
MA0091.1 0.0438
MA0092.1 0.423
MA0093.1 0.279
MA0099.2 0.645
MA0100.1 0.771
MA0101.1 0.854
MA0102.2 0.516
MA0103.1 0.015
MA0104.2 0.0826
MA0105.1 0.0186
MA0106.1 0.471
MA0107.1 0.576
MA0108.2 0.0539
MA0111.1 0.884
MA0112.2 1.99088e-7
MA0113.1 0.499
MA0114.1 0.293
MA0115.1 0.171
MA0116.1 0.014
MA0117.1 0.943
MA0119.1 0.136
MA0122.1 0.753
MA0124.1 0.644
MA0125.1 0.417
MA0131.1 0.847
MA0135.1 0.148
MA0136.1 0.967
MA0137.2 0.00154
MA0138.2 0.419
MA0139.1 0.776
MA0140.1 3.68197e-13
MA0141.1 0.0179
MA0142.1 0.714
MA0143.1 0.16
MA0144.1 0.26
MA0145.1 0.161
MA0146.1 0.289
MA0147.1 0.206
MA0148.1 0.545
MA0149.1 0.254
MA0150.1 0.107
MA0152.1 0.123
MA0153.1 4.31841e-12
MA0154.1 0.00197
MA0155.1 0.331
MA0156.1 0.931
MA0157.1 0.327
MA0159.1 0.145
MA0160.1 0.189
MA0162.1 0.198
MA0163.1 3.88134e-4
MA0164.1 0.805
MA0258.1 1.73013e-4
MA0259.1 0.355



FANTOM5 phase1 novel unique motifs
Summary: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 in

169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon



link to dataset.
data

library id: CNhs11225
Novel motif P-value
1 0.179
10 0.202
100 0.659
101 0.911
102 0.869
103 0.267
104 0.691
105 0.246
106 0.0447
107 0.118
108 0.99
109 0.051
11 0.298
110 0.161
111 0.615
112 0.418
113 0.989
114 0.435
115 0.829
116 0.672
117 0.212
118 0.501
119 0.158
12 0.316
120 0.419
121 0.584
122 0.893
123 0.7
124 0.0948
125 0.0912
126 0.285
127 0.0792
128 0.0924
129 0.892
13 0.00959
130 0.755
131 0.858
132 0.768
133 0.623
134 0.503
135 0.777
136 0.448
137 0.0679
138 0.309
139 0.469
14 0.293
140 0.0996
141 0.701
142 0.239
143 0.733
144 0.0391
145 0.353
146 0.991
147 0.762
148 0.417
149 0.877
15 0.321
150 0.239
151 0.185
152 0.178
153 0.819
154 0.616
155 0.356
156 3.49556e-26
157 0.886
158 0.101
159 0.0141
160 0.0835
161 0.992
162 0.696
163 0.451
164 0.406
165 0.117
166 0.899
167 0.928
168 0.372
169 5.92162e-4
17 0.218
18 0.802
19 0.0309
2 0.578
20 0.369
21 0.35
22 0.159
23 0.581
24 0.95
25 0.577
26 0.0112
27 0.818
28 0.608
29 0.269
3 0.13
30 0.684
31 0.349
32 0.00116
33 0.602
34 0.171
35 0.611
36 0.411
37 0.0563
38 0.982
39 0.282
4 0.623
40 0.482
41 0.588
42 0.592
43 0.207
44 0.802
45 0.41
46 0.163
47 0.768
48 0.733
49 0.304
5 0.0226
50 0.284
51 0.685
52 0.29
53 0.563
54 0.528
55 0.854
56 0.409
57 0.306
58 0.389
59 0.0152
6 0.766
60 0.104
61 0.672
62 0.163
63 0.117
64 0.762
65 0.867
66 0.362
67 0.145
68 0.277
69 0.131
7 0.0542
70 0.424
71 0.0404
72 0.976
73 0.13
74 0.777
75 0.382
76 0.947
77 0.623
78 0.00798
79 0.885
8 0.248
80 0.0728
81 0.355
82 0.414
83 0.474
84 0.946
85 0.0797
86 0.597
87 0.00655
88 0.375
89 0.339
9 0.191
90 0.706
91 0.0401
92 0.598
93 0.302
94 0.133
95 0.105
96 0.188
97 0.435
98 0.629
99 0.837



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11225


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)
Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji



link to source data

data

UBERON: Anatomy
0000468 (multi-cellular 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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000306 (mouse neonate N16 sample)
0011462 (mouse bone- os femoris - neonate N16 sample)

Ancestor terms (development)
Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship

Analyst: Hideya Kawaji

link to source data

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)
FF:0000294 (mouse embryonic day 11 sample)