FF:324-5I8

Name:	whole body, embryo E11
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 11 days embryo 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

CAGE Accession numbers
Method Sample accession id CAGE  DRS009005 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

CNhs11014

0	0
1	0.00413
10	0
100	0.227
1000	-0.0157
1001	-0.0239
1002	0.156
1003	-0.121
1004	0.116
1005	-0.223
1006	-0.105
1007	0.231
1008	0
1009	-0.108
101	0.194
1010	0
1011	-0.117
1012	0
1013	-0.4
1014	0.193
1015	0.4
1016	0.105
1017	0
1018	0.0429
1019	0
102	0
1020	0
1021	0.0019
1022	-0.252
1023	0
1024	-0.0576
1025	0.21
1026	0
1027	0.3
1028	0
1029	-0.115
103	-0.0802
1030	0
1031	-0.0459
1032	-0.396
1033	0.0344
1034	0
1035	0
1036	0.0745
1037	0
1038	-0.0517
1039	-0.062
104	0
1040	-0.00315
1041	0

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: CNhs11014

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.52861e-4
MA0003.1	MA0003.1	0.0789
MA0004.1	MA0004.1	0.963
MA0006.1	MA0006.1	0.238
MA0007.1	MA0007.1	0.199
MA0009.1	MA0009.1	0.537
MA0014.1	MA0014.1	0.241
MA0017.1	MA0017.1	8.41182e-4
MA0018.2	MA0018.2	0.0472
MA0019.1	MA0019.1	0.605
MA0024.1	MA0024.1	6.95345e-6
MA0025.1	MA0025.1	0.0661
MA0027.1	MA0027.1	0.236
MA0028.1	MA0028.1	0.0474
MA0029.1	MA0029.1	0.701
MA0030.1	MA0030.1	0.0688
MA0031.1	MA0031.1	0.0085
MA0035.2	MA0035.2	0.0366
MA0038.1	MA0038.1	1.06987e-4
MA0039.2	MA0039.2	4.70676e-4
MA0040.1	MA0040.1	0.412
MA0041.1	MA0041.1	0.762
MA0042.1	MA0042.1	0.328
MA0043.1	MA0043.1	0.00391
MA0046.1	MA0046.1	5.63481e-13
MA0047.2	MA0047.2	0.0131
MA0048.1	MA0048.1	0.0675
MA0050.1	MA0050.1	4.28676e-7
MA0051.1	MA0051.1	8.05779e-6
MA0052.1	MA0052.1	0.00354
MA0055.1	MA0055.1	0.0665
MA0057.1	MA0057.1	0.0285
MA0058.1	MA0058.1	0.678
MA0059.1	MA0059.1	0.478
MA0060.1	MA0060.1	1.88308e-20
MA0061.1	MA0061.1	0.116
MA0062.2	MA0062.2	0.168
MA0065.2	MA0065.2	0.00283
MA0066.1	MA0066.1	0.244
MA0067.1	MA0067.1	0.715
MA0068.1	MA0068.1	0.183
MA0069.1	MA0069.1	0.708
MA0070.1	MA0070.1	0.729
MA0071.1	MA0071.1	0.138
MA0072.1	MA0072.1	0.17
MA0073.1	MA0073.1	0.869
MA0074.1	MA0074.1	0.48
MA0076.1	MA0076.1	0.036
MA0077.1	MA0077.1	0.00727
MA0078.1	MA0078.1	0.0211
MA0079.2	MA0079.2	0.124
MA0080.2	MA0080.2	1.2062e-9
MA0081.1	MA0081.1	0.353
MA0083.1	MA0083.1	0.919
MA0084.1	MA0084.1	0.857
MA0087.1	MA0087.1	0.222
MA0088.1	MA0088.1	0.717
MA0090.1	MA0090.1	0.196
MA0091.1	MA0091.1	0.927
MA0092.1	MA0092.1	0.268
MA0093.1	MA0093.1	0.948
MA0099.2	MA0099.2	5.43705e-6
MA0100.1	MA0100.1	0.295
MA0101.1	MA0101.1	0.53
MA0102.2	MA0102.2	0.545
MA0103.1	MA0103.1	0.00411
MA0104.2	MA0104.2	0.22
MA0105.1	MA0105.1	0.354
MA0106.1	MA0106.1	0.204
MA0107.1	MA0107.1	0.261
MA0108.2	MA0108.2	0.255
MA0111.1	MA0111.1	0.665
MA0112.2	MA0112.2	2.04525e-4
MA0113.1	MA0113.1	0.339
MA0114.1	MA0114.1	0.00514
MA0115.1	MA0115.1	0.535
MA0116.1	MA0116.1	0.0466
MA0117.1	MA0117.1	0.804
MA0119.1	MA0119.1	0.0318
MA0122.1	MA0122.1	0.737
MA0124.1	MA0124.1	0.847
MA0125.1	MA0125.1	0.245
MA0131.1	MA0131.1	0.173
MA0135.1	MA0135.1	0.847
MA0136.1	MA0136.1	5.42465e-4
MA0137.2	MA0137.2	0.252
MA0138.2	MA0138.2	0.00573
MA0139.1	MA0139.1	0.0477
MA0140.1	MA0140.1	0.167
MA0141.1	MA0141.1	0.0199
MA0142.1	MA0142.1	0.0172
MA0143.1	MA0143.1	9.66636e-5
MA0144.1	MA0144.1	0.158
MA0145.1	MA0145.1	0.0102
MA0146.1	MA0146.1	0.278
MA0147.1	MA0147.1	0.268
MA0148.1	MA0148.1	0.00101
MA0149.1	MA0149.1	0.00404
MA0150.1	MA0150.1	0.0264
MA0152.1	MA0152.1	0.221
MA0153.1	MA0153.1	2.82423e-8
MA0154.1	MA0154.1	0.00558
MA0155.1	MA0155.1	0.574
MA0156.1	MA0156.1	0.0396
MA0157.1	MA0157.1	0.0248
MA0159.1	MA0159.1	0.047
MA0160.1	MA0160.1	0.103
MA0162.1	MA0162.1	0.701
MA0163.1	MA0163.1	0.0752
MA0164.1	MA0164.1	0.241
MA0258.1	MA0258.1	0.0129
MA0259.1	MA0259.1	0.269

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: CNhs11014

Novel motif	Logo	P-value
1	1	0.131
10	10	0.505
100	100	0.774
101	101	0.553
102	102	0.767
103	103	0.056
104	104	0.697
105	105	0.0727
106	106	0.00537
107	107	0.0819
108	108	0.98
109	109	0.0308
11	11	0.155
110	110	0.486
111	111	0.0387
112	112	0.0466
113	113	0.422
114	114	0.0784
115	115	0.257
116	116	0.848
117	117	0.848
118	118	0.968
119	119	0.00719
12	12	0.591
120	120	0.544
121	121	0.684
122	122	0.77
123	123	0.199
124	124	0.14
125	125	0.999
126	126	0.66
127	127	0.0979
128	128	0.0226
129	129	0.263
13	13	0.158
130	130	0.976
131	131	0.113
132	132	0.207
133	133	0.198
134	134	0.995
135	135	0.292
136	136	0.391
137	137	0.552
138	138	0.645
139	139	0.00658
14	14	0.17
140	140	0.0188
141	141	0.0689
142	142	0.938
143	143	0.697
144	144	0.953
145	145	0.513
146	146	0.351
147	147	0.516
148	148	0.246
149	149	0.0728
15	15	0.092
150	150	0.543
151	151	0.119
152	152	0.0294
153	153	0.186
154	154	0.741
155	155	0.631
156	156	3.6311e-7
157	157	0.924
158	158	0.511
159	159	0.0182
160	160	0.58
161	161	0.647
162	162	0.695
163	163	0.115
164	164	0.128
165	165	0.676
166	166	0.617
167	167	0.797
168	168	0.804
169	169	0.00853
17	17	0.0677
18	18	0.94
19	19	0.0625
2	2	0.312
20	20	0.482
21	21	0.594
22	22	0.152
23	23	0.0686
24	24	0.233
25	25	0.648
26	26	0.158
27	27	0.361
28	28	0.381
29	29	0.939
3	3	0.326
30	30	0.482
31	31	0.47
32	32	0.0502
33	33	0.497
34	34	0.535
35	35	0.978
36	36	0.439
37	37	0.134
38	38	0.109
39	39	0.362
4	4	0.478
40	40	0.17
41	41	0.621
42	42	0.653
43	43	0.153
44	44	0.866
45	45	0.314
46	46	0.31
47	47	0.151
48	48	0.149
49	49	0.137
5	5	0.241
50	50	0.589
51	51	0.582
52	52	0.166
53	53	0.325
54	54	0.587
55	55	0.79
56	56	0.317
57	57	0.717
58	58	0.193
59	59	0.0538
6	6	0.555
60	60	0.054
61	61	0.714
62	62	0.146
63	63	0.0702
64	64	0.48
65	65	0.0754
66	66	0.229
67	67	0.914
68	68	0.218
69	69	0.235
7	7	0.248
70	70	4.32794e-4
71	71	0.373
72	72	0.303
73	73	0.0866
74	74	0.544
75	75	0.384
76	76	0.863
77	77	0.212
78	78	0.381
79	79	0.337
8	8	0.373
80	80	0.588
81	81	0.323
82	82	0.094
83	83	0.793
84	84	0.99
85	85	0.0151
86	86	0.457
87	87	0.662
88	88	0.924
89	89	0.148
9	9	0.398
90	90	0.321
91	91	0.555
92	92	0.086
93	93	0.296
94	94	0.714
95	95	0.0996
96	96	0.339
97	97	0.391
98	98	0.146
99	99	0.444

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: CNhs11014

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011311 mouse whole body- embryo E11 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)
0000922 (embryo)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000294 (mouse embryonic day 11 sample)
0011311 (mouse whole body- embryo E11 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}}}