FF:1525-43A6

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 strain C57BL/6J tissue bone (os femoris) dev stage 16 days neonate sex mixture age NA cell type CELL MIXTURE - tissue sample cell line NA company NA collaboration FANTOM5 OSC CORE (contact: Al Forrest) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type NA extraction protocol (Details) NA

Accession numbers
Method Sample accession id CAGE  SAMD00005320 Library accession numbers Library id Method Exp. accession id Run accession id CNhs11225 CAGE DRX008938 DRR009812 Accession ID Mm9 Library id BAM CTSS CNhs11225 DRZ001237 DRZ002620 Accession ID Mm10 Library id BAM CTSS CNhs11225 DRZ012587 DRZ013970

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download donwload

Relative expression to median (log10)

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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

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 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

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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: CNhs11225

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

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: CNhs11225

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

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: CNhs11225

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011462 mouse bone- os femoris - neonate N16 sample

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)