FF:508-5B2

Name:	liver, adult pregnant day01
Species:	Mouse (Mus musculus)
Library ID:	CNhs10466
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain C57BL/6J tissue liver dev stage 1 day pregnant adult 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  DRS008877 Library accession numbers Library id Method Exp. accession id Run accession id CNhs10466 CAGE DRX009014 DRR009888 Accession ID Mm9 Library id BAM CTSS CNhs10466 DRZ001313 DRZ002696 Accession ID Mm10 Library id BAM CTSS CNhs10466

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.
Analyst:NA

link to dataset.
data

CNhs10466

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0
10	0
100	0
1000	0.0773
1001	0.03
1002	--0.116
1003	0.112
1004	0
1005	0
1006	--0.143
1007	--0.228
1008	0
1009	0.00269
101	0.0309
1010	0
1011	--0.224
1012	0
1013	0.466
1014	--0.0874
1015	--0.382
1016	--0.318
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.736
1023	0
1024	0
1025	0.437
1026	0
1027	--0.048
1028	0
1029	--0.0989
103	--0.0848
1030	0
1031	--0.417
1032	--0.397
1033	0.0463
1034	0.816
1035	0
1036	--0.183
1037	0
1038	--0.14
1039	0.803
104	0
1040	--0.19
1041	0

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: CNhs10466

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.216
MA0003.1	MA0003.1	0.4
MA0004.1	MA0004.1	0.427
MA0006.1	MA0006.1	0.273
MA0007.1	MA0007.1	0.0722
MA0009.1	MA0009.1	0.983
MA0014.1	MA0014.1	0.114
MA0017.1	MA0017.1	4.99121e-23
MA0018.2	MA0018.2	2.1753e-4
MA0019.1	MA0019.1	0.596
MA0024.1	MA0024.1	3.16662e-4
MA0025.1	MA0025.1	0.0011
MA0027.1	MA0027.1	0.883
MA0028.1	MA0028.1	0.318
MA0029.1	MA0029.1	0.235
MA0030.1	MA0030.1	0.00618
MA0031.1	MA0031.1	0.00221
MA0035.2	MA0035.2	0.0457
MA0038.1	MA0038.1	0.465
MA0039.2	MA0039.2	0.26
MA0040.1	MA0040.1	0.291
MA0041.1	MA0041.1	0.864
MA0042.1	MA0042.1	0.945
MA0043.1	MA0043.1	0.315
MA0046.1	MA0046.1	1.74228e-96
MA0047.2	MA0047.2	3.20453e-7
MA0048.1	MA0048.1	0.261
MA0050.1	MA0050.1	0.00108
MA0051.1	MA0051.1	9.61359e-4
MA0052.1	MA0052.1	0.0109
MA0055.1	MA0055.1	0.226
MA0057.1	MA0057.1	0.459
MA0058.1	MA0058.1	0.298
MA0059.1	MA0059.1	0.0546
MA0060.1	MA0060.1	2.36029e-5
MA0061.1	MA0061.1	0.611
MA0062.2	MA0062.2	0.44
MA0065.2	MA0065.2	3.90538e-15
MA0066.1	MA0066.1	0.0629
MA0067.1	MA0067.1	0.155
MA0068.1	MA0068.1	0.462
MA0069.1	MA0069.1	0.307
MA0070.1	MA0070.1	0.462
MA0071.1	MA0071.1	9.60444e-5
MA0072.1	MA0072.1	1.49741e-4
MA0073.1	MA0073.1	0.832
MA0074.1	MA0074.1	0.226
MA0076.1	MA0076.1	0.716
MA0077.1	MA0077.1	0.0602
MA0078.1	MA0078.1	0.847
MA0079.2	MA0079.2	0.375
MA0080.2	MA0080.2	0.894
MA0081.1	MA0081.1	0.857
MA0083.1	MA0083.1	0.00162
MA0084.1	MA0084.1	0.488
MA0087.1	MA0087.1	0.376
MA0088.1	MA0088.1	0.205
MA0090.1	MA0090.1	0.707
MA0091.1	MA0091.1	0.798
MA0092.1	MA0092.1	0.118
MA0093.1	MA0093.1	0.446
MA0099.2	MA0099.2	0.63
MA0100.1	MA0100.1	0.314
MA0101.1	MA0101.1	0.96
MA0102.2	MA0102.2	0.304
MA0103.1	MA0103.1	0.115
MA0104.2	MA0104.2	0.548
MA0105.1	MA0105.1	0.203
MA0106.1	MA0106.1	0.125
MA0107.1	MA0107.1	0.703
MA0108.2	MA0108.2	0.00302
MA0111.1	MA0111.1	0.606
MA0112.2	MA0112.2	6.71493e-6
MA0113.1	MA0113.1	0.315
MA0114.1	MA0114.1	4.44663e-22
MA0115.1	MA0115.1	4.69992e-10
MA0116.1	MA0116.1	0.153
MA0117.1	MA0117.1	0.644
MA0119.1	MA0119.1	0.0192
MA0122.1	MA0122.1	0.586
MA0124.1	MA0124.1	0.578
MA0125.1	MA0125.1	0.369
MA0131.1	MA0131.1	0.898
MA0135.1	MA0135.1	0.772
MA0136.1	MA0136.1	0.873
MA0137.2	MA0137.2	0.00754
MA0138.2	MA0138.2	0.361
MA0139.1	MA0139.1	0.208
MA0140.1	MA0140.1	0.686
MA0141.1	MA0141.1	3.72461e-6
MA0142.1	MA0142.1	0.242
MA0143.1	MA0143.1	0.296
MA0144.1	MA0144.1	0.112
MA0145.1	MA0145.1	0.0383
MA0146.1	MA0146.1	0.103
MA0147.1	MA0147.1	0.437
MA0148.1	MA0148.1	1.36926e-10
MA0149.1	MA0149.1	0.00917
MA0150.1	MA0150.1	0.00614
MA0152.1	MA0152.1	0.984
MA0153.1	MA0153.1	4.37719e-65
MA0154.1	MA0154.1	0.144
MA0155.1	MA0155.1	0.941
MA0156.1	MA0156.1	0.923
MA0157.1	MA0157.1	0.00151
MA0159.1	MA0159.1	3.47374e-4
MA0160.1	MA0160.1	9.14822e-5
MA0162.1	MA0162.1	0.433
MA0163.1	MA0163.1	0.0116
MA0164.1	MA0164.1	0.774
MA0258.1	MA0258.1	0.00145
MA0259.1	MA0259.1	0.836

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: CNhs10466

Novel motif	Logo	P-value
1	1	0.0869
10	10	0.213
100	100	0.498
101	101	0.642
102	102	0.216
103	103	0.0127
104	104	0.807
105	105	0.646
106	106	0.0966
107	107	0.156
108	108	0.741
109	109	0.0295
11	11	0.0472
110	110	0.0732
111	111	0.0338
112	112	0.0155
113	113	0.996
114	114	0.00434
115	115	0.365
116	116	0.843
117	117	0.0722
118	118	0.435
119	119	0.0606
12	12	0.478
120	120	0.696
121	121	0.517
122	122	0.358
123	123	0.418
124	124	0.484
125	125	0.339
126	126	0.261
127	127	0.774
128	128	0.0349
129	129	0.652
13	13	9.49059e-5
130	130	0.74
131	131	0.475
132	132	0.498
133	133	0.743
134	134	0.718
135	135	0.369
136	136	0.441
137	137	0.802
138	138	0.499
139	139	0.341
14	14	0.461
140	140	0.0487
141	141	0.532
142	142	0.265
143	143	0.869
144	144	0.491
145	145	0.0639
146	146	0.42
147	147	0.408
148	148	0.661
149	149	0.0909
15	15	0.138
150	150	0.218
151	151	0.445
152	152	0.0648
153	153	0.423
154	154	0.958
155	155	0.439
156	156	0.101
157	157	0.745
158	158	0.567
159	159	0.375
160	160	0.336
161	161	0.88
162	162	0.615
163	163	0.211
164	164	0.0336
165	165	0.566
166	166	0.276
167	167	0.264
168	168	0.952
169	169	0.00228
17	17	0.0635
18	18	0.871
19	19	0.0473
2	2	0.736
20	20	0.522
21	21	0.573
22	22	0.123
23	23	0.256
24	24	0.148
25	25	0.554
26	26	0.00637
27	27	0.698
28	28	0.462
29	29	0.197
3	3	0.0638
30	30	0.777
31	31	0.405
32	32	0.178
33	33	0.313
34	34	0.854
35	35	0.46
36	36	0.0718
37	37	0.0652
38	38	0.254
39	39	0.317
4	4	0.934
40	40	0.103
41	41	0.933
42	42	0.358
43	43	0.0808
44	44	0.0591
45	45	0.652
46	46	0.155
47	47	0.328
48	48	0.102
49	49	0.0417
5	5	0.184
50	50	0.666
51	51	0.308
52	52	0.452
53	53	0.671
54	54	0.331
55	55	0.659
56	56	0.457
57	57	0.902
58	58	0.243
59	59	0.316
6	6	0.786
60	60	0.146
61	61	0.169
62	62	0.0729
63	63	0.0842
64	64	0.432
65	65	0.158
66	66	0.514
67	67	0.93
68	68	0.184
69	69	0.899
7	7	0.194
70	70	0.0152
71	71	0.0443
72	72	0.65
73	73	0.0484
74	74	0.591
75	75	0.0173
76	76	0.871
77	77	0.416
78	78	0.0295
79	79	0.947
8	8	0.00709
80	80	0.543
81	81	0.559
82	82	0.0201
83	83	0.306
84	84	0.274
85	85	0.0449
86	86	0.0893
87	87	0.135
88	88	0.826
89	89	0.0544
9	9	0.774
90	90	0.149
91	91	0.652
92	92	0.25
93	93	0.115
94	94	0.822
95	95	0.205
96	96	0.308
97	97	0.232
98	98	0.334
99	99	0.0826

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: CNhs10466

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011379 mouse liver- adult pregnant day01 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)
0007023 (adult organism)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000317 (mouse pregnant tissue sample)
0000318 (mouse pregnant day 1 sample)
0011379 (mouse liver- adult pregnant day01 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:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)