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FF:1350-25C3

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Name:bone (os femoris), neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11195
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 stage20 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  SAMD00004931
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11195 CAGE DRX008939 DRR009813
Accession ID Mm9

Library idBAMCTSS
CNhs11195 DRZ001238 DRZ002621
Accession ID Mm10

Library idBAMCTSS
CNhs11195 DRZ012588 DRZ013971
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

CNhs11195

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.535
1001 0.304
1002 --0.0587
1003 0.116
1004 0
1005 0.172
1006 0.368
1007 0.0791
1008 0
1009 0.2
101 0.00531
1010 0
1011 0
1012 0
1013 --0.118
1014 0.207
1015 --0.182
1016 --0.072
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.172
1022 0.522
1023 0
1024 0.172
1025 0
1026 0
1027 0
1028 0
1029 0.0728
103 1.192
1030 0.39
1031 0.0306
1032 0.0115
1033 0.00808
1034 0
1035 0.172
1036 0.163
1037 0
1038 --0.113
1039 0.0859
104 0
1040 0.0576
1041 0.172



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: CNhs11195

Jaspar motif P-value
MA0002.2 0.00741
MA0003.1 0.0732
MA0004.1 0.323
MA0006.1 0.0902
MA0007.1 0.668
MA0009.1 0.443
MA0014.1 0.744
MA0017.1 0.792
MA0018.2 4.83997e-4
MA0019.1 0.247
MA0024.1 0.19
MA0025.1 0.121
MA0027.1 0.0906
MA0028.1 0.0682
MA0029.1 0.571
MA0030.1 0.566
MA0031.1 0.456
MA0035.2 0.426
MA0038.1 0.0424
MA0039.2 0.591
MA0040.1 0.498
MA0041.1 0.106
MA0042.1 0.592
MA0043.1 0.00939
MA0046.1 1.95212e-6
MA0047.2 0.438
MA0048.1 0.92
MA0050.1 0.647
MA0051.1 0.803
MA0052.1 1.27095e-5
MA0055.1 0.326
MA0057.1 0.334
MA0058.1 0.22
MA0059.1 0.464
MA0060.1 0.0589
MA0061.1 0.107
MA0062.2 0.0166
MA0065.2 0.18
MA0066.1 0.235
MA0067.1 0.184
MA0068.1 0.422
MA0069.1 0.331
MA0070.1 0.665
MA0071.1 0.885
MA0072.1 0.75
MA0073.1 0.806
MA0074.1 0.979
MA0076.1 0.0169
MA0077.1 0.43
MA0078.1 0.323
MA0079.2 0.0676
MA0080.2 0.00702
MA0081.1 0.426
MA0083.1 0.0988
MA0084.1 0.814
MA0087.1 0.477
MA0088.1 0.752
MA0090.1 0.717
MA0091.1 0.151
MA0092.1 0.521
MA0093.1 0.268
MA0099.2 0.702
MA0100.1 0.732
MA0101.1 0.901
MA0102.2 0.791
MA0103.1 0.0102
MA0104.2 0.152
MA0105.1 0.00169
MA0106.1 0.435
MA0107.1 0.815
MA0108.2 0.493
MA0111.1 0.648
MA0112.2 1.84616e-7
MA0113.1 0.883
MA0114.1 0.391
MA0115.1 0.302
MA0116.1 0.00488
MA0117.1 0.874
MA0119.1 0.106
MA0122.1 0.707
MA0124.1 0.929
MA0125.1 0.355
MA0131.1 0.931
MA0135.1 0.0936
MA0136.1 0.896
MA0137.2 0.0406
MA0138.2 0.846
MA0139.1 0.832
MA0140.1 9.46226e-9
MA0141.1 0.0762
MA0142.1 0.904
MA0143.1 0.371
MA0144.1 0.49
MA0145.1 0.229
MA0146.1 0.644
MA0147.1 0.308
MA0148.1 0.503
MA0149.1 0.342
MA0150.1 0.232
MA0152.1 0.0214
MA0153.1 1.58027e-6
MA0154.1 0.00411
MA0155.1 0.503
MA0156.1 0.819
MA0157.1 0.706
MA0159.1 0.15
MA0160.1 0.6
MA0162.1 0.149
MA0163.1 2.12311e-5
MA0164.1 0.961
MA0258.1 8.20917e-4
MA0259.1 0.852



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: CNhs11195

Novel motif P-value
1 0.0937
10 0.0733
100 0.537
101 0.871
102 0.891
103 0.167
104 0.627
105 0.288
106 0.0854
107 0.115
108 0.905
109 0.0794
11 0.223
110 0.197
111 0.349
112 0.381
113 0.909
114 0.388
115 0.931
116 0.446
117 0.117
118 0.399
119 0.804
12 0.841
120 0.519
121 0.895
122 0.893
123 0.534
124 0.195
125 0.394
126 0.374
127 0.137
128 0.164
129 0.827
13 0.0137
130 0.608
131 0.713
132 0.539
133 0.772
134 0.874
135 0.78
136 0.195
137 0.4
138 0.566
139 0.765
14 0.876
140 0.18
141 0.335
142 0.757
143 0.174
144 0.15
145 0.363
146 0.903
147 0.993
148 0.416
149 0.92
15 0.418
150 0.408
151 0.202
152 0.271
153 0.975
154 0.864
155 0.651
156 0
157 0.629
158 0.724
159 0.381
160 0.0752
161 0.766
162 0.754
163 0.455
164 0.24
165 0.742
166 0.957
167 0.411
168 0.844
169 0.00298
17 0.268
18 0.785
19 0.041
2 0.606
20 0.268
21 0.5
22 0.454
23 0.646
24 0.816
25 0.507
26 0.0073
27 0.75
28 0.512
29 0.22
3 0.0849
30 0.636
31 0.425
32 0.00169
33 0.961
34 0.365
35 0.709
36 0.878
37 0.0661
38 0.0662
39 0.616
4 0.856
40 0.686
41 0.937
42 0.361
43 0.184
44 0.619
45 0.651
46 0.0635
47 0.373
48 0.544
49 0.33
5 6.92008e-5
50 0.281
51 0.733
52 0.286
53 0.68
54 0.675
55 0.912
56 0.297
57 0.531
58 0.768
59 0.0142
6 0.672
60 0.143
61 0.708
62 0.279
63 0.203
64 0.699
65 0.17
66 0.515
67 0.123
68 0.649
69 0.584
7 0.0859
70 0.359
71 0.0156
72 0.959
73 0.219
74 0.899
75 0.213
76 0.764
77 0.737
78 0.015
79 0.87
8 0.155
80 0.328
81 0.411
82 0.562
83 0.594
84 0.371
85 0.0366
86 0.766
87 0.131
88 0.39
89 0.551
9 0.464
90 0.958
91 0.231
92 0.311
93 0.792
94 0.453
95 0.393
96 0.745
97 0.706
98 0.681
99 0.658



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: CNhs11195


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)
0000308 (mouse neonate N20 sample)
0011467 (mouse bone- os femoris - neonate N20 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)