FF:1389-42C2

Name:	muscle (biceps femoris), neonate N30
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information strain C57BL/6J tissue muscle (biceps femoris) dev stage 30 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

Download raw sequence, BAM & CTSS
Mm9 BAM CTSS [{{{mm9bam}}} download] [{{{mm9ctss}}} donwload] Mm10 BAM CTSS [{{{mm10bam}}} download] [{{{mm10ctss}}} donwload]

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

CNhs11129

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0
10	0
100	0
1000	1.074
1001	0.642
1002	--0.0962
1003	0.377
1004	0
1005	0.0416
1006	0.954
1007	--0.0837
1008	0
1009	0.103
101	--0.0491
1010	0
1011	--0.108
1012	0
1013	--0.0449
1014	0
1015	--0.264
1016	0.016
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.968
1023	0
1024	0.373
1025	0
1026	0
1027	0.178
1028	0
1029	--0.115
103	0.625
1030	0.0978
1031	--0.0564
1032	0.277
1033	0
1034	0
1035	0.0978
1036	--0.248
1037	0
1038	0.0487
1039	0.551
104	0
1040	0.0739
1041	0.702

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 no result for this sample

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: CNhs11129

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.943
MA0003.1	MA0003.1	0.093
MA0004.1	MA0004.1	0.221
MA0006.1	MA0006.1	0.133
MA0007.1	MA0007.1	0.309
MA0009.1	MA0009.1	0.99
MA0014.1	MA0014.1	0.993
MA0017.1	MA0017.1	0.745
MA0018.2	MA0018.2	0.0147
MA0019.1	MA0019.1	0.115
MA0024.1	MA0024.1	2.30827e-5
MA0025.1	MA0025.1	0.151
MA0027.1	MA0027.1	0.385
MA0028.1	MA0028.1	0.0087
MA0029.1	MA0029.1	0.582
MA0030.1	MA0030.1	0.884
MA0031.1	MA0031.1	0.313
MA0035.2	MA0035.2	0.328
MA0038.1	MA0038.1	0.932
MA0039.2	MA0039.2	0.532
MA0040.1	MA0040.1	0.858
MA0041.1	MA0041.1	0.156
MA0042.1	MA0042.1	0.666
MA0043.1	MA0043.1	0.0734
MA0046.1	MA0046.1	1.1464e-14
MA0047.2	MA0047.2	0.483
MA0048.1	MA0048.1	0.0341
MA0050.1	MA0050.1	0.168
MA0051.1	MA0051.1	0.609
MA0052.1	MA0052.1	3.12094e-65
MA0055.1	MA0055.1	0.177
MA0057.1	MA0057.1	0.683
MA0058.1	MA0058.1	0.205
MA0059.1	MA0059.1	0.0838
MA0060.1	MA0060.1	3.09661e-6
MA0061.1	MA0061.1	0.947
MA0062.2	MA0062.2	6.90819e-7
MA0065.2	MA0065.2	0.00554
MA0066.1	MA0066.1	0.317
MA0067.1	MA0067.1	0.502
MA0068.1	MA0068.1	0.129
MA0069.1	MA0069.1	0.17
MA0070.1	MA0070.1	0.744
MA0071.1	MA0071.1	0.00813
MA0072.1	MA0072.1	0.308
MA0073.1	MA0073.1	0.159
MA0074.1	MA0074.1	0.601
MA0076.1	MA0076.1	9.27111e-4
MA0077.1	MA0077.1	0.239
MA0078.1	MA0078.1	0.0947
MA0079.2	MA0079.2	0.345
MA0080.2	MA0080.2	6.58674e-4
MA0081.1	MA0081.1	0.833
MA0083.1	MA0083.1	5.62276e-7
MA0084.1	MA0084.1	0.945
MA0087.1	MA0087.1	0.861
MA0088.1	MA0088.1	0.691
MA0090.1	MA0090.1	0.0831
MA0091.1	MA0091.1	0.029
MA0092.1	MA0092.1	0.148
MA0093.1	MA0093.1	0.198
MA0099.2	MA0099.2	0.791
MA0100.1	MA0100.1	0.0295
MA0101.1	MA0101.1	0.256
MA0102.2	MA0102.2	0.329
MA0103.1	MA0103.1	0.0123
MA0104.2	MA0104.2	0.0486
MA0105.1	MA0105.1	0.827
MA0106.1	MA0106.1	0.937
MA0107.1	MA0107.1	0.35
MA0108.2	MA0108.2	1.3671e-5
MA0111.1	MA0111.1	0.782
MA0112.2	MA0112.2	3.58765e-7
MA0113.1	MA0113.1	0.078
MA0114.1	MA0114.1	0.781
MA0115.1	MA0115.1	0.844
MA0116.1	MA0116.1	0.484
MA0117.1	MA0117.1	0.575
MA0119.1	MA0119.1	0.474
MA0122.1	MA0122.1	0.239
MA0124.1	MA0124.1	0.222
MA0125.1	MA0125.1	0.606
MA0131.1	MA0131.1	0.51
MA0135.1	MA0135.1	0.714
MA0136.1	MA0136.1	5.71564e-6
MA0137.2	MA0137.2	0.0149
MA0138.2	MA0138.2	0.0043
MA0139.1	MA0139.1	0.524
MA0140.1	MA0140.1	0.817
MA0141.1	MA0141.1	1.21142e-7
MA0142.1	MA0142.1	0.594
MA0143.1	MA0143.1	0.202
MA0144.1	MA0144.1	0.41
MA0145.1	MA0145.1	0.0229
MA0146.1	MA0146.1	0.0697
MA0147.1	MA0147.1	0.117
MA0148.1	MA0148.1	0.586
MA0149.1	MA0149.1	0.328
MA0150.1	MA0150.1	0.0504
MA0152.1	MA0152.1	0.896
MA0153.1	MA0153.1	4.14602e-10
MA0154.1	MA0154.1	0.0414
MA0155.1	MA0155.1	0.153
MA0156.1	MA0156.1	1.60854e-6
MA0157.1	MA0157.1	0.3
MA0159.1	MA0159.1	0.00433
MA0160.1	MA0160.1	2.61104e-4
MA0162.1	MA0162.1	0.222
MA0163.1	MA0163.1	0.0612
MA0164.1	MA0164.1	0.35
MA0258.1	MA0258.1	1.30285e-5
MA0259.1	MA0259.1	0.198

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: CNhs11129

Novel motif	Logo	P-value
1	1	0.201
10	10	0.678
100	100	0.418
101	101	0.394
102	102	0.574
103	103	0.784
104	104	0.999
105	105	0.0893
106	106	0.18
107	107	0.253
108	108	0.763
109	109	0.0667
11	11	0.162
110	110	0.391
111	111	0.438
112	112	0.733
113	113	0.649
114	114	0.168
115	115	0.431
116	116	0.38
117	117	0.881
118	118	0.486
119	119	0.0465
12	12	0.117
120	120	0.892
121	121	0.563
122	122	0.97
123	123	0.665
124	124	0.227
125	125	0.474
126	126	0.893
127	127	0.171
128	128	0.469
129	129	0.338
13	13	0.00372
130	130	0.721
131	131	0.708
132	132	0.896
133	133	0.726
134	134	0.473
135	135	0.478
136	136	0.292
137	137	0.899
138	138	0.23
139	139	0.0864
14	14	0.124
140	140	0.06
141	141	0.09
142	142	0.978
143	143	0.733
144	144	0.106
145	145	0.923
146	146	0.761
147	147	0.797
148	148	0.851
149	149	0.0608
15	15	0.847
150	150	0.454
151	151	0.257
152	152	0.0387
153	153	0.363
154	154	0.934
155	155	0.681
156	156	0.115
157	157	0.283
158	158	0.981
159	159	0.338
160	160	0.239
161	161	0.126
162	162	0.511
163	163	0.402
164	164	0.727
165	165	0.00975
166	166	0.801
167	167	0.191
168	168	0.0819
169	169	5.68599e-4
17	17	0.131
18	18	0.975
19	19	0.0232
2	2	0.359
20	20	0.914
21	21	0.823
22	22	0.0514
23	23	0.399
24	24	0.926
25	25	0.727
26	26	0.368
27	27	0.863
28	28	0.79
29	29	0.988
3	3	0.563
30	30	0.803
31	31	0.213
32	32	0.0295
33	33	0.796
34	34	0.171
35	35	0.767
36	36	0.197
37	37	0.00948
38	38	0.701
39	39	0.338
4	4	0.705
40	40	0.573
41	41	0.397
42	42	0.571
43	43	0.271
44	44	0.562
45	45	0.31
46	46	0.408
47	47	0.99
48	48	0.671
49	49	0.669
5	5	0.145
50	50	0.317
51	51	0.879
52	52	0.34
53	53	0.692
54	54	0.383
55	55	0.308
56	56	0.456
57	57	0.365
58	58	0.683
59	59	0.00747
6	6	0.52
60	60	0.0993
61	61	0.777
62	62	0.305
63	63	0.0709
64	64	0.724
65	65	0.453
66	66	0.738
67	67	0.273
68	68	0.587
69	69	0.0159
7	7	0.136
70	70	0.116
71	71	0.104
72	72	0.652
73	73	0.0239
74	74	0.151
75	75	0.586
76	76	0.536
77	77	0.436
78	78	0.0172
79	79	0.0755
8	8	0.363
80	80	0.469
81	81	0.152
82	82	0.106
83	83	0.413
84	84	0.581
85	85	0.00135
86	86	0.194
87	87	0.319
88	88	0.812
89	89	0.0782
9	9	0.462
90	90	0.326
91	91	0.192
92	92	0.484
93	93	0.294
94	94	0.237
95	95	0.149
96	96	0.399
97	97	0.911
98	98	0.662
99	99	0.68

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: CNhs11129

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000026 (appendage)
0000061 (anatomical structure)
0000062 (organ)
0000154 (posterior region of body)
0000376 (hindlimb stylopod)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000978 (leg)
0001048 (primordium)
0001062 (anatomical entity)
0001374 (biceps femoris)
0001383 (muscle of leg)
0001630 (muscle organ)
0002050 (embryonic structure)
0002101 (limb)
0002103 (hindlimb)
0002204 (musculoskeletal system)
0002472 (stylopod)
0002529 (limb segment)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003102 (surface structure)
0003661 (limb muscle)
0003663 (hindlimb muscle)
0004120 (mesoderm-derived structure)
0004252 (hindlimb stylopod muscle)
0004347 (limb bud)
0004357 (paired limb/fin bud)
0004708 (paired limb/fin)
0004709 (pelvic appendage)
0005090 (muscle structure)
0005423 (developing anatomical structure)
0005732 (limb/fin field)
0005733 (limb field)
0006058 (multi-limb segment region)
0008784 (lower limb segment)

FF: FANTOM5
NA

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

link to source data
data
NA