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FF:1985-43F5

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Name:bone (os femoris), neonate N02
Species:Mouse (Mus musculus)
Library ID:CNhs11227
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 stage2 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  SAMD00005623
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11227 CAGE DRX008937 DRR009811
Accession ID Mm9

Library idBAMCTSS
CNhs11227 DRZ001236 DRZ002619
Accession ID Mm10

Library idBAMCTSS
CNhs11227 DRZ012586 DRZ013969
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.
Analyst:NA

link to dataset.
data

CNhs11227

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.354
1001 0.348
1002 0.0712
1003 0.283
1004 0
1005 0.144
1006 0.454
1007 0.0472
1008 0
1009 0.237
101 0.00728
1010 0
1011 --0.026
1012 0
1013 --0.0774
1014 0.462
1015 2.684411e-4
1016 0.209
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0164
1022 0.418
1023 0
1024 0.274
1025 0
1026 0.0651
1027 0.239
1028 0
1029 0.262
103 0.957
1030 0.0651
1031 0.262
1032 0.137
1033 --0.0419
1034 0
1035 0.0977
1036 --0.0113
1037 0
1038 0.111
1039 0.067
104 0
1040 0.232
1041 0.0651



Repeat families with enriched expression in this sampleSummary: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 motifsSummary: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: CNhs11227

Jaspar motif P-value
MA0002.2 0.64
MA0003.1 0.0471
MA0004.1 0.0879
MA0006.1 0.0795
MA0007.1 0.894
MA0009.1 0.255
MA0014.1 0.408
MA0017.1 0.00612
MA0018.2 1.48201e-4
MA0019.1 0.112
MA0024.1 0.856
MA0025.1 0.0271
MA0027.1 0.0621
MA0028.1 3.10538e-6
MA0029.1 0.284
MA0030.1 0.433
MA0031.1 0.139
MA0035.2 0.568
MA0038.1 0.996
MA0039.2 0.477
MA0040.1 0.169
MA0041.1 0.102
MA0042.1 0.76
MA0043.1 0.0148
MA0046.1 3.04597e-16
MA0047.2 0.0168
MA0048.1 0.343
MA0050.1 0.0181
MA0051.1 0.0538
MA0052.1 7.64668e-36
MA0055.1 0.0181
MA0057.1 0.41
MA0058.1 0.114
MA0059.1 0.0843
MA0060.1 0.0109
MA0061.1 0.338
MA0062.2 8.54191e-11
MA0065.2 0.903
MA0066.1 0.899
MA0067.1 0.0129
MA0068.1 0.0402
MA0069.1 0.107
MA0070.1 0.812
MA0071.1 0.224
MA0072.1 0.132
MA0073.1 0.824
MA0074.1 0.811
MA0076.1 3.56e-7
MA0077.1 0.295
MA0078.1 0.175
MA0079.2 0.0577
MA0080.2 0.0713
MA0081.1 0.823
MA0083.1 4.62437e-8
MA0084.1 0.818
MA0087.1 0.644
MA0088.1 0.383
MA0090.1 0.0745
MA0091.1 0.0354
MA0092.1 0.231
MA0093.1 0.147
MA0099.2 0.61
MA0100.1 0.0744
MA0101.1 0.557
MA0102.2 0.654
MA0103.1 1.58556e-6
MA0104.2 0.0481
MA0105.1 0.505
MA0106.1 0.886
MA0107.1 0.84
MA0108.2 1.75486e-5
MA0111.1 0.958
MA0112.2 0.00476
MA0113.1 0.707
MA0114.1 0.00213
MA0115.1 0.101
MA0116.1 0.54
MA0117.1 0.701
MA0119.1 0.41
MA0122.1 0.858
MA0124.1 0.937
MA0125.1 0.669
MA0131.1 0.464
MA0135.1 0.934
MA0136.1 0.00125
MA0137.2 0.00125
MA0138.2 0.771
MA0139.1 0.0472
MA0140.1 0.0138
MA0141.1 0.872
MA0142.1 0.215
MA0143.1 0.851
MA0144.1 0.112
MA0145.1 0.107
MA0146.1 0.415
MA0147.1 0.134
MA0148.1 0.0415
MA0149.1 0.0423
MA0150.1 0.259
MA0152.1 0.0678
MA0153.1 1.51683e-13
MA0154.1 0.0893
MA0155.1 0.0795
MA0156.1 9.54522e-5
MA0157.1 0.519
MA0159.1 0.727
MA0160.1 0.439
MA0162.1 0.269
MA0163.1 0.124
MA0164.1 0.537
MA0258.1 0.219
MA0259.1 0.366



FANTOM5 phase1 novel unique motifsSummary: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: CNhs11227

Novel motif P-value
1 0.828
10 0.717
100 0.731
101 0.693
102 0.781
103 0.313
104 0.778
105 0.103
106 0.14
107 0.0862
108 0.699
109 0.234
11 0.876
110 0.621
111 0.778
112 0.444
113 0.976
114 0.826
115 1
116 0.473
117 0.614
118 0.888
119 0.685
12 0.123
120 0.259
121 0.683
122 0.864
123 0.953
124 0.0785
125 0.38
126 0.782
127 0.174
128 0.492
129 0.717
13 0.0845
130 0.857
131 0.771
132 0.798
133 0.647
134 0.857
135 0.678
136 0.36
137 0.325
138 0.167
139 0.946
14 0.695
140 0.239
141 0.944
142 0.487
143 0.996
144 0.00131
145 0.614
146 0.543
147 0.772
148 0.819
149 0.869
15 0.213
150 0.208
151 0.756
152 0.027
153 0.236
154 0.624
155 0.946
156 6.70933e-17
157 0.704
158 0.858
159 0.104
160 0.0584
161 0.208
162 0.582
163 0.465
164 0.605
165 0.822
166 0.276
167 0.314
168 0.132
169 0.00227
17 0.586
18 0.445
19 0.0302
2 0.227
20 0.785
21 0.999
22 0.177
23 0.656
24 0.514
25 0.597
26 0.0419
27 0.648
28 0.302
29 0.331
3 0.96
30 0.634
31 0.913
32 0.00912
33 0.32
34 0.0689
35 0.0427
36 0.0727
37 0.211
38 0.419
39 0.245
4 0.977
40 0.0725
41 0.292
42 0.691
43 0.567
44 0.167
45 0.237
46 0.381
47 0.669
48 0.533
49 0.677
5 0.075
50 0.0477
51 0.989
52 0.174
53 0.671
54 0.523
55 0.997
56 0.71
57 0.89
58 0.805
59 0.0132
6 0.318
60 0.158
61 0.97
62 0.912
63 0.21
64 0.566
65 0.377
66 0.701
67 0.224
68 0.449
69 0.39
7 0.277
70 0.515
71 0.19
72 0.307
73 0.139
74 0.988
75 0.378
76 0.615
77 0.356
78 0.0379
79 0.444
8 0.903
80 0.642
81 0.563
82 0.961
83 0.772
84 0.809
85 0.103
86 0.971
87 0.0168
88 0.711
89 0.264
9 0.182
90 0.0403
91 0.0209
92 0.392
93 0.108
94 0.569
95 0.305
96 0.488
97 0.443
98 0.563
99 0.59



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs11227


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)
0000307 (mouse neonate N2 sample)
0011463 (mouse bone- os femoris - neonate N2 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)