FF:583-22A8

Name:	amnion, adult pregnant day17.5
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 amnion dev stage 17.5 days pregnant adult 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

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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs10488

0	0
1	0
10	0
100	0
1000	-0.0355
1001	0.0685
1002	0.0481
1003	-0.138
1004	0
1005	0.0879
1006	-0.0215
1007	-0.0277
1008	0
1009	0.0853
101	-0.101
1010	0
1011	-0.263
1012	0
1013	0.0979
1014	0.476
1015	-0.19
1016	-0.138
1017	0
1018	0.445
1019	0
102	0
1020	0
1021	0
1022	-0.315
1023	0
1024	0.0846
1025	0.512
1026	0.0959
1027	-0.048
1028	0
1029	0.202
103	0.179
1030	0
1031	0.0426
1032	-0.0877
1033	0
1034	0.0959
1035	0
1036	-0.25
1037	0
1038	0.102
1039	0.0409
104	0
1040	0.178
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 no result for this sample

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: CNhs10488

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.827
MA0003.1	MA0003.1	0.234
MA0004.1	MA0004.1	0.884
MA0006.1	MA0006.1	0.0452
MA0007.1	MA0007.1	0.014
MA0009.1	MA0009.1	0.0918
MA0014.1	MA0014.1	0.301
MA0017.1	MA0017.1	8.48255e-13
MA0018.2	MA0018.2	0.0977
MA0019.1	MA0019.1	0.396
MA0024.1	MA0024.1	2.69002e-7
MA0025.1	MA0025.1	0.929
MA0027.1	MA0027.1	0.169
MA0028.1	MA0028.1	0.413
MA0029.1	MA0029.1	1.87786e-4
MA0030.1	MA0030.1	1.04612e-4
MA0031.1	MA0031.1	8.60996e-7
MA0035.2	MA0035.2	0.0467
MA0038.1	MA0038.1	0.00717
MA0039.2	MA0039.2	1.83139e-4
MA0040.1	MA0040.1	0.188
MA0041.1	MA0041.1	0.426
MA0042.1	MA0042.1	0.553
MA0043.1	MA0043.1	0.552
MA0046.1	MA0046.1	9.87144e-29
MA0047.2	MA0047.2	4.31631e-7
MA0048.1	MA0048.1	0.644
MA0050.1	MA0050.1	0.945
MA0051.1	MA0051.1	0.576
MA0052.1	MA0052.1	0.328
MA0055.1	MA0055.1	0.315
MA0057.1	MA0057.1	0.323
MA0058.1	MA0058.1	0.666
MA0059.1	MA0059.1	0.221
MA0060.1	MA0060.1	9.97623e-12
MA0061.1	MA0061.1	0.232
MA0062.2	MA0062.2	0.683
MA0065.2	MA0065.2	4.73482e-7
MA0066.1	MA0066.1	0.787
MA0067.1	MA0067.1	0.133
MA0068.1	MA0068.1	0.744
MA0069.1	MA0069.1	0.186
MA0070.1	MA0070.1	0.643
MA0071.1	MA0071.1	0.543
MA0072.1	MA0072.1	0.906
MA0073.1	MA0073.1	0.616
MA0074.1	MA0074.1	0.174
MA0076.1	MA0076.1	0.349
MA0077.1	MA0077.1	0.0116
MA0078.1	MA0078.1	0.0653
MA0079.2	MA0079.2	0.00792
MA0080.2	MA0080.2	0.904
MA0081.1	MA0081.1	0.518
MA0083.1	MA0083.1	0.172
MA0084.1	MA0084.1	0.38
MA0087.1	MA0087.1	0.159
MA0088.1	MA0088.1	0.617
MA0090.1	MA0090.1	1.1507e-6
MA0091.1	MA0091.1	0.164
MA0092.1	MA0092.1	0.0714
MA0093.1	MA0093.1	0.905
MA0099.2	MA0099.2	2.42319e-26
MA0100.1	MA0100.1	0.234
MA0101.1	MA0101.1	0.242
MA0102.2	MA0102.2	0.19
MA0103.1	MA0103.1	2.35328e-4
MA0104.2	MA0104.2	0.0524
MA0105.1	MA0105.1	0.923
MA0106.1	MA0106.1	0.227
MA0107.1	MA0107.1	0.132
MA0108.2	MA0108.2	0.492
MA0111.1	MA0111.1	0.664
MA0112.2	MA0112.2	0.00729
MA0113.1	MA0113.1	0.013
MA0114.1	MA0114.1	1.3704e-12
MA0115.1	MA0115.1	1.97441e-10
MA0116.1	MA0116.1	0.754
MA0117.1	MA0117.1	0.117
MA0119.1	MA0119.1	0.629
MA0122.1	MA0122.1	0.624
MA0124.1	MA0124.1	0.227
MA0125.1	MA0125.1	0.334
MA0131.1	MA0131.1	0.983
MA0135.1	MA0135.1	0.597
MA0136.1	MA0136.1	0.932
MA0137.2	MA0137.2	2.90568e-7
MA0138.2	MA0138.2	0.716
MA0139.1	MA0139.1	0.662
MA0140.1	MA0140.1	0.481
MA0141.1	MA0141.1	0.347
MA0142.1	MA0142.1	0.113
MA0143.1	MA0143.1	0.225
MA0144.1	MA0144.1	5.24908e-5
MA0145.1	MA0145.1	0.0126
MA0146.1	MA0146.1	0.021
MA0147.1	MA0147.1	0.0365
MA0148.1	MA0148.1	1.44936e-7
MA0149.1	MA0149.1	0.29
MA0150.1	MA0150.1	0.0115
MA0152.1	MA0152.1	0.85
MA0153.1	MA0153.1	3.75339e-17
MA0154.1	MA0154.1	0.0142
MA0155.1	MA0155.1	0.63
MA0156.1	MA0156.1	0.764
MA0157.1	MA0157.1	9.10388e-5
MA0159.1	MA0159.1	0.0189
MA0160.1	MA0160.1	0.202
MA0162.1	MA0162.1	0.507
MA0163.1	MA0163.1	0.324
MA0164.1	MA0164.1	0.0783
MA0258.1	MA0258.1	0.194
MA0259.1	MA0259.1	0.567

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: CNhs10488

Novel motif	Logo	P-value
1	1	0.826
10	10	0.605
100	100	0.305
101	101	0.493
102	102	0.564
103	103	0.196
104	104	0.498
105	105	0.79
106	106	0.0384
107	107	0.0546
108	108	0.785
109	109	0.126
11	11	0.334
110	110	0.366
111	111	0.271
112	112	0.0874
113	113	0.595
114	114	0.0725
115	115	0.484
116	116	0.563
117	117	0.185
118	118	0.216
119	119	0.006
12	12	0.784
120	120	0.543
121	121	0.38
122	122	0.493
123	123	0.483
124	124	0.184
125	125	0.07
126	126	0.392
127	127	0.682
128	128	0.0156
129	129	0.443
13	13	5.37441e-4
130	130	0.0337
131	131	0.504
132	132	0.732
133	133	0.528
134	134	0.806
135	135	0.0846
136	136	0.00273
137	137	0.54
138	138	0.0441
139	139	0.0488
14	14	0.467
140	140	0.0875
141	141	0.1
142	142	0.817
143	143	0.776
144	144	0.652
145	145	0.246
146	146	0.258
147	147	0.462
148	148	0.743
149	149	0.0185
15	15	0.179
150	150	0.0783
151	151	0.765
152	152	0.0178
153	153	0.641
154	154	0.971
155	155	0.414
156	156	0.0684
157	157	0.587
158	158	0.195
159	159	0.115
160	160	0.345
161	161	0.0809
162	162	0.889
163	163	0.733
164	164	0.0288
165	165	0.505
166	166	0.0288
167	167	0.243
168	168	0.29
169	169	0.0212
17	17	0.0198
18	18	0.896
19	19	0.0135
2	2	0.132
20	20	0.506
21	21	0.221
22	22	0.0448
23	23	0.0476
24	24	0.296
25	25	0.598
26	26	0.0947
27	27	0.709
28	28	0.307
29	29	0.453
3	3	0.18
30	30	0.386
31	31	0.766
32	32	0.0832
33	33	0.539
34	34	0.763
35	35	0.289
36	36	0.572
37	37	0.0804
38	38	0.483
39	39	0.754
4	4	0.118
40	40	0.316
41	41	0.516
42	42	0.62
43	43	0.0702
44	44	0.482
45	45	0.098
46	46	0.51
47	47	0.564
48	48	0.411
49	49	0.123
5	5	0.851
50	50	0.374
51	51	0.687
52	52	0.19
53	53	0.884
54	54	0.333
55	55	0.468
56	56	0.415
57	57	0.394
58	58	0.705
59	59	0.124
6	6	0.856
60	60	0.0549
61	61	0.26
62	62	0.508
63	63	0.825
64	64	0.921
65	65	0.404
66	66	0.196
67	67	0.544
68	68	0.0821
69	69	0.148
7	7	0.319
70	70	0.0163
71	71	0.502
72	72	0.583
73	73	0.0503
74	74	0.799
75	75	0.26
76	76	0.609
77	77	0.0448
78	78	6.05475e-4
79	79	0.532
8	8	0.442
80	80	0.821
81	81	0.339
82	82	0.139
83	83	0.661
84	84	0.443
85	85	0.159
86	86	0.464
87	87	0.15
88	88	0.601
89	89	0.649
9	9	0.704
90	90	0.435
91	91	0.414
92	92	0.0507
93	93	0.247
94	94	0.14
95	95	0.188
96	96	0.917
97	97	0.382
98	98	0.401
99	99	0.593

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: CNhs10488

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)<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
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000158 (membranous layer)
0000305 (amnion)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004871 (somatic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0005631 (extraembryonic membrane)
0007023 (adult organism)

FF: FANTOM5
NA

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
NA