FF:657-19C2

Name:	whole body, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain C57BL/6J tissue whole body dev stage 0 day neonate sex female 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

CAGE Accession numbers
Method Sample accession id CAGE  DRS009014 Library accession numbers Library id Method Exp. accession id Run accession id {{{library_id}}} {{{accession_numbers}}} Accession ID Mm9 Library id BAM CTSS {{{library_id}}} Accession ID Mm10 Library id BAM CTSS {{{library_id}}}

Download raw sequence, BAM & CTSS
Mm9 BAM CTSS [{{{mm9bam}}} download] [{{{mm9ctss}}} donwload] Mm10 BAM CTSS [{{{mm10bam}}} download] [{{{mm10ctss}}} 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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs10525

0	0
1	0.129
10	0
100	0.0845
1000	0.206
1001	0.0695
1002	-0.00451
1003	0.0873
1004	0
1005	0.022
1006	0.237
1007	-0.00118
1008	0
1009	0.17
101	-0.016
1010	0
1011	0.0845
1012	0
1013	-0.0543
1014	0.23
1015	-0.0624
1016	0.222
1017	0.0845
1018	0.0845
1019	0
102	0
1020	0
1021	0
1022	0.406
1023	0
1024	0.311
1025	0.585
1026	0.126
1027	0.107
1028	0
1029	-0.0207
103	0.573
1030	0
1031	0.361
1032	0.0108
1033	0
1034	0.155
1035	0.0845
1036	-0.00681
1037	0
1038	0.0206
1039	0.0904
104	0
1040	0.252
1041	0.155

Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data

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

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JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10525

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.679
MA0003.1	MA0003.1	0.0265
MA0004.1	MA0004.1	0.153
MA0006.1	MA0006.1	0.215
MA0007.1	MA0007.1	0.211
MA0009.1	MA0009.1	0.519
MA0014.1	MA0014.1	0.213
MA0017.1	MA0017.1	0.13
MA0018.2	MA0018.2	8.60808e-4
MA0019.1	MA0019.1	0.763
MA0024.1	MA0024.1	0.0282
MA0025.1	MA0025.1	0.456
MA0027.1	MA0027.1	0.206
MA0028.1	MA0028.1	1.57843e-8
MA0029.1	MA0029.1	0.292
MA0030.1	MA0030.1	0.00827
MA0031.1	MA0031.1	0.245
MA0035.2	MA0035.2	0.0744
MA0038.1	MA0038.1	0.144
MA0039.2	MA0039.2	0.308
MA0040.1	MA0040.1	0.212
MA0041.1	MA0041.1	0.281
MA0042.1	MA0042.1	0.415
MA0043.1	MA0043.1	0.0142
MA0046.1	MA0046.1	3.34964e-26
MA0047.2	MA0047.2	0.0533
MA0048.1	MA0048.1	0.00158
MA0050.1	MA0050.1	0.0793
MA0051.1	MA0051.1	0.0822
MA0052.1	MA0052.1	2.60886e-19
MA0055.1	MA0055.1	1.03463e-5
MA0057.1	MA0057.1	0.488
MA0058.1	MA0058.1	0.0293
MA0059.1	MA0059.1	0.00348
MA0060.1	MA0060.1	0.0795
MA0061.1	MA0061.1	0.717
MA0062.2	MA0062.2	3.43294e-14
MA0065.2	MA0065.2	0.0915
MA0066.1	MA0066.1	0.84
MA0067.1	MA0067.1	0.191
MA0068.1	MA0068.1	0.882
MA0069.1	MA0069.1	0.431
MA0070.1	MA0070.1	0.191
MA0071.1	MA0071.1	0.287
MA0072.1	MA0072.1	0.793
MA0073.1	MA0073.1	0.924
MA0074.1	MA0074.1	0.949
MA0076.1	MA0076.1	1.35763e-9
MA0077.1	MA0077.1	0.718
MA0078.1	MA0078.1	0.0489
MA0079.2	MA0079.2	0.0148
MA0080.2	MA0080.2	4.95348e-5
MA0081.1	MA0081.1	0.0389
MA0083.1	MA0083.1	2.20393e-8
MA0084.1	MA0084.1	0.887
MA0087.1	MA0087.1	0.122
MA0088.1	MA0088.1	0.0716
MA0090.1	MA0090.1	0.0473
MA0091.1	MA0091.1	0.353
MA0092.1	MA0092.1	0.0727
MA0093.1	MA0093.1	0.113
MA0099.2	MA0099.2	0.116
MA0100.1	MA0100.1	0.0155
MA0101.1	MA0101.1	0.0903
MA0102.2	MA0102.2	0.325
MA0103.1	MA0103.1	0.541
MA0104.2	MA0104.2	0.0379
MA0105.1	MA0105.1	0.77
MA0106.1	MA0106.1	0.308
MA0107.1	MA0107.1	0.303
MA0108.2	MA0108.2	2.33065e-57
MA0111.1	MA0111.1	0.93
MA0112.2	MA0112.2	0.334
MA0113.1	MA0113.1	0.483
MA0114.1	MA0114.1	0.0316
MA0115.1	MA0115.1	0.817
MA0116.1	MA0116.1	0.793
MA0117.1	MA0117.1	0.562
MA0119.1	MA0119.1	0.262
MA0122.1	MA0122.1	0.571
MA0124.1	MA0124.1	0.853
MA0125.1	MA0125.1	0.00939
MA0131.1	MA0131.1	0.193
MA0135.1	MA0135.1	0.0196
MA0136.1	MA0136.1	6.19661e-13
MA0137.2	MA0137.2	0.00438
MA0138.2	MA0138.2	7.81506e-7
MA0139.1	MA0139.1	0.406
MA0140.1	MA0140.1	0.136
MA0141.1	MA0141.1	0.42
MA0142.1	MA0142.1	0.447
MA0143.1	MA0143.1	0.753
MA0144.1	MA0144.1	0.356
MA0145.1	MA0145.1	0.015
MA0146.1	MA0146.1	0.609
MA0147.1	MA0147.1	0.0255
MA0148.1	MA0148.1	0.00893
MA0149.1	MA0149.1	0.00875
MA0150.1	MA0150.1	0.583
MA0152.1	MA0152.1	0.99
MA0153.1	MA0153.1	9.36347e-12
MA0154.1	MA0154.1	0.156
MA0155.1	MA0155.1	0.048
MA0156.1	MA0156.1	3.20817e-11
MA0157.1	MA0157.1	0.174
MA0159.1	MA0159.1	0.244
MA0160.1	MA0160.1	0.593
MA0162.1	MA0162.1	0.712
MA0163.1	MA0163.1	0.999
MA0164.1	MA0164.1	0.297
MA0258.1	MA0258.1	0.699
MA0259.1	MA0259.1	0.0706

FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10525

Novel motif	Logo	P-value
1	1	0.671
10	10	0.114
100	100	0.67
101	101	0.164
102	102	0.2
103	103	0.18
104	104	0.792
105	105	0.541
106	106	0.053
107	107	0.012
108	108	0.376
109	109	0.709
11	11	0.658
110	110	0.456
111	111	0.0454
112	112	0.614
113	113	0.469
114	114	0.895
115	115	0.813
116	116	0.103
117	117	0.0112
118	118	0.402
119	119	0.593
12	12	0.653
120	120	0.788
121	121	0.651
122	122	0.281
123	123	0.194
124	124	0.454
125	125	0.101
126	126	0.163
127	127	0.768
128	128	0.152
129	129	0.804
13	13	0.135
130	130	0.664
131	131	0.181
132	132	0.555
133	133	0.151
134	134	0.237
135	135	0.398
136	136	0.736
137	137	0.875
138	138	0.81
139	139	0.968
14	14	0.293
140	140	0.775
141	141	0.593
142	142	0.337
143	143	0.201
144	144	0.842
145	145	0.586
146	146	0.21
147	147	0.74
148	148	0.8
149	149	0.332
15	15	0.188
150	150	0.915
151	151	0.529
152	152	0.1
153	153	0.323
154	154	0.479
155	155	0.0855
156	156	0.856
157	157	0.0483
158	158	0.00651
159	159	0.0974
160	160	0.307
161	161	0.0632
162	162	0.222
163	163	0.692
164	164	0.123
165	165	0.781
166	166	0.166
167	167	0.0118
168	168	0.0031
169	169	0.172
17	17	0.489
18	18	0.549
19	19	0.257
2	2	0.0135
20	20	0.00823
21	21	0.185
22	22	0.519
23	23	0.133
24	24	0.292
25	25	0.642
26	26	0.691
27	27	0.309
28	28	0.962
29	29	0.0402
3	3	0.637
30	30	0.0996
31	31	0.473
32	32	0.0932
33	33	0.395
34	34	0.218
35	35	0.393
36	36	0.0684
37	37	0.821
38	38	0.972
39	39	0.669
4	4	0.658
40	40	0.473
41	41	0.359
42	42	0.696
43	43	0.634
44	44	0.652
45	45	0.135
46	46	0.867
47	47	0.979
48	48	0.782
49	49	0.855
5	5	0.94
50	50	0.522
51	51	0.649
52	52	0.0797
53	53	0.242
54	54	0.333
55	55	0.66
56	56	0.405
57	57	0.301
58	58	0.942
59	59	0.063
6	6	0.65
60	60	0.236
61	61	0.314
62	62	0.942
63	63	0.488
64	64	0.897
65	65	0.557
66	66	0.493
67	67	0.443
68	68	0.562
69	69	0.814
7	7	0.961
70	70	0.279
71	71	0.653
72	72	0.853
73	73	0.881
74	74	0.845
75	75	0.12
76	76	0.00774
77	77	0.146
78	78	0.519
79	79	0.925
8	8	0.743
80	80	0.554
81	81	0.332
82	82	0.622
83	83	0.885
84	84	0.181
85	85	0.261
86	86	0.629
87	87	0.351
88	88	0.308
89	89	0.302
9	9	0.294
90	90	0.0187
91	91	0.539
92	92	0.369
93	93	0.0464
94	94	0.432
95	95	0.237
96	96	0.878
97	97	0.7
98	98	0.836
99	99	0.133

de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10525

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011398 mouse whole body- neonate N00 sample

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000468 (multi-cellular organism)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011398 (mouse whole body- neonate N00 sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
FF:0000294 (mouse embryonic day 11 sample)

{{{1}}} Accession numbers
Method Sample accession id {{{2}}}  Library accession numbers Library id Method Exp. accession id Run accession id {{{4}}} {{{3}}} Accession ID Library id BAM CTSS {{{4}}} Accession ID Library id BAM CTSS {{{4}}}