FF:11830-124G3

Name:	Mouse hepatic Sinusoidal Endothelial Cells, donor1
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 liver dev stage NA sex male age NA cell type hepatic sinusoidal endothelial cell cell line NA company NA collaboration Soichi Kojima (RIKEN ASI) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

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

CNhs13209

0	0
1	0
10	0
100	0
1000	0
1001	-0.0275
1002	-0.0941
1003	-0.121
1004	0
1005	0
1006	0
1007	-0.175
1008	0
1009	0.605
101	-0.0411
1010	0
1011	0.00303
1012	0
1013	-0.0181
1014	0
1015	-0.242
1016	-0.183
1017	0
1018	0
1019	0
102	0.078
1020	0.199
1021	0.199
1022	0.219
1023	0.521
1024	1.071
1025	0.221
1026	0
1027	0
1028	0
1029	-0.0206
103	-0.0788
1030	0
1031	0.42
1032	-0.142
1033	0.434
1034	0.334
1035	0
1036	0.386
1037	0
1038	0.253
1039	-0.027
104	0
1040	0.425
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: CNhs13209

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.263
MA0003.1	MA0003.1	0.342
MA0004.1	MA0004.1	0.938
MA0006.1	MA0006.1	0.295
MA0007.1	MA0007.1	0.61
MA0009.1	MA0009.1	0.707
MA0014.1	MA0014.1	0.352
MA0017.1	MA0017.1	0.466
MA0018.2	MA0018.2	3.84935e-5
MA0019.1	MA0019.1	0.193
MA0024.1	MA0024.1	0.777
MA0025.1	MA0025.1	4.29731e-6
MA0027.1	MA0027.1	0.322
MA0028.1	MA0028.1	0.0821
MA0029.1	MA0029.1	0.486
MA0030.1	MA0030.1	0.0604
MA0031.1	MA0031.1	0.0157
MA0035.2	MA0035.2	0.564
MA0038.1	MA0038.1	0.167
MA0039.2	MA0039.2	0.00124
MA0040.1	MA0040.1	0.288
MA0041.1	MA0041.1	0.535
MA0042.1	MA0042.1	0.853
MA0043.1	MA0043.1	6.36573e-6
MA0046.1	MA0046.1	3.66825e-7
MA0047.2	MA0047.2	0.1
MA0048.1	MA0048.1	0.392
MA0050.1	MA0050.1	1.68011e-9
MA0051.1	MA0051.1	6.37324e-12
MA0052.1	MA0052.1	2.50566e-4
MA0055.1	MA0055.1	0.00178
MA0057.1	MA0057.1	0.882
MA0058.1	MA0058.1	0.644
MA0059.1	MA0059.1	0.00923
MA0060.1	MA0060.1	0.766
MA0061.1	MA0061.1	8.89864e-6
MA0062.2	MA0062.2	3.01688e-4
MA0065.2	MA0065.2	0.548
MA0066.1	MA0066.1	0.0172
MA0067.1	MA0067.1	0.00184
MA0068.1	MA0068.1	2.84187e-5
MA0069.1	MA0069.1	0.778
MA0070.1	MA0070.1	0.432
MA0071.1	MA0071.1	0.719
MA0072.1	MA0072.1	0.977
MA0073.1	MA0073.1	0.82
MA0074.1	MA0074.1	0.368
MA0076.1	MA0076.1	0.0733
MA0077.1	MA0077.1	0.509
MA0078.1	MA0078.1	0.137
MA0079.2	MA0079.2	0.0629
MA0080.2	MA0080.2	6.3141e-6
MA0081.1	MA0081.1	0.0466
MA0083.1	MA0083.1	2.01785e-5
MA0084.1	MA0084.1	0.73
MA0087.1	MA0087.1	0.138
MA0088.1	MA0088.1	0.384
MA0090.1	MA0090.1	0.0745
MA0091.1	MA0091.1	0.0146
MA0092.1	MA0092.1	0.481
MA0093.1	MA0093.1	0.79
MA0099.2	MA0099.2	6.36128e-4
MA0100.1	MA0100.1	0.221
MA0101.1	MA0101.1	2.39453e-10
MA0102.2	MA0102.2	0.0772
MA0103.1	MA0103.1	0.0116
MA0104.2	MA0104.2	0.0491
MA0105.1	MA0105.1	0.795
MA0106.1	MA0106.1	0.726
MA0107.1	MA0107.1	1.17997e-11
MA0108.2	MA0108.2	2.84228e-6
MA0111.1	MA0111.1	0.142
MA0112.2	MA0112.2	0.0442
MA0113.1	MA0113.1	0.937
MA0114.1	MA0114.1	0.0828
MA0115.1	MA0115.1	0.253
MA0116.1	MA0116.1	0.00194
MA0117.1	MA0117.1	0.322
MA0119.1	MA0119.1	0.572
MA0122.1	MA0122.1	0.886
MA0124.1	MA0124.1	0.513
MA0125.1	MA0125.1	0.0951
MA0131.1	MA0131.1	0.866
MA0135.1	MA0135.1	0.0927
MA0136.1	MA0136.1	8.43568e-7
MA0137.2	MA0137.2	2.67507e-13
MA0138.2	MA0138.2	0.0276
MA0139.1	MA0139.1	0.419
MA0140.1	MA0140.1	0.599
MA0141.1	MA0141.1	0.0329
MA0142.1	MA0142.1	0.0249
MA0143.1	MA0143.1	0.014
MA0144.1	MA0144.1	1.03229e-8
MA0145.1	MA0145.1	0.0262
MA0146.1	MA0146.1	0.951
MA0147.1	MA0147.1	0.0061
MA0148.1	MA0148.1	0.291
MA0149.1	MA0149.1	0.302
MA0150.1	MA0150.1	0.468
MA0152.1	MA0152.1	0.0125
MA0153.1	MA0153.1	1.37063e-5
MA0154.1	MA0154.1	0.436
MA0155.1	MA0155.1	0.622
MA0156.1	MA0156.1	8.10408e-10
MA0157.1	MA0157.1	0.0403
MA0159.1	MA0159.1	0.833
MA0160.1	MA0160.1	0.278
MA0162.1	MA0162.1	0.909
MA0163.1	MA0163.1	0.0951
MA0164.1	MA0164.1	0.795
MA0258.1	MA0258.1	0.0155
MA0259.1	MA0259.1	0.77

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: CNhs13209

Novel motif	Logo	P-value
1	1	0.118
10	10	0.257
100	100	0.884
101	101	0.368
102	102	0.749
103	103	0.172
104	104	0.78
105	105	0.551
106	106	0.141
107	107	0.33
108	108	0.715
109	109	0.949
11	11	0.261
110	110	0.849
111	111	0.0917
112	112	0.628
113	113	0.858
114	114	0.0392
115	115	0.376
116	116	0.325
117	117	0.51
118	118	0.304
119	119	0.414
12	12	0.802
120	120	0.96
121	121	0.065
122	122	0.752
123	123	0.156
124	124	0.173
125	125	0.233
126	126	0.617
127	127	0.477
128	128	0.108
129	129	0.418
13	13	0.0632
130	130	0.14
131	131	0.953
132	132	0.71
133	133	0.912
134	134	0.877
135	135	0.0378
136	136	0.0207
137	137	0.574
138	138	0.126
139	139	0.0657
14	14	0.916
140	140	0.287
141	141	0.961
142	142	0.666
143	143	0.36
144	144	0.702
145	145	0.91
146	146	0.75
147	147	0.959
148	148	0.907
149	149	0.576
15	15	0.529
150	150	0.299
151	151	0.188
152	152	0.00872
153	153	0.346
154	154	0.96
155	155	0.269
156	156	2.80876e-40
157	157	0.236
158	158	0.976
159	159	0.0605
160	160	0.148
161	161	0.201
162	162	0.528
163	163	0.552
164	164	0.966
165	165	0.166
166	166	0.658
167	167	0.278
168	168	0.703
169	169	0.365
17	17	0.872
18	18	0.0308
19	19	0.92
2	2	0.974
20	20	0.275
21	21	0.29
22	22	0.931
23	23	0.851
24	24	0.676
25	25	0.536
26	26	0.323
27	27	0.157
28	28	0.912
29	29	0.193
3	3	0.375
30	30	0.823
31	31	0.335
32	32	0.0309
33	33	0.362
34	34	0.731
35	35	3.04646e-4
36	36	0.274
37	37	0.412
38	38	0.595
39	39	0.843
4	4	0.495
40	40	0.375
41	41	0.603
42	42	0.411
43	43	0.289
44	44	0.0679
45	45	0.795
46	46	0.257
47	47	0.272
48	48	0.347
49	49	0.19
5	5	0.638
50	50	0.513
51	51	0.428
52	52	0.52
53	53	0.789
54	54	0.586
55	55	0.272
56	56	0.809
57	57	0.0833
58	58	0.492
59	59	0.445
6	6	0.28
60	60	0.568
61	61	0.983
62	62	0.137
63	63	0.772
64	64	0.129
65	65	0.547
66	66	0.755
67	67	0.441
68	68	0.658
69	69	0.141
7	7	0.818
70	70	0.297
71	71	0.194
72	72	0.685
73	73	0.0714
74	74	0.0934
75	75	0.783
76	76	0.456
77	77	0.238
78	78	0.448
79	79	0.548
8	8	0.011
80	80	0.792
81	81	0.258
82	82	0.129
83	83	0.744
84	84	0.613
85	85	0.448
86	86	0.945
87	87	0.0186
88	88	0.758
89	89	0.554
9	9	0.901
90	90	0.131
91	91	0.279
92	92	0.417
93	93	0.538
94	94	0.00747
95	95	0.287
96	96	0.0524
97	97	0.572
98	98	0.556
99	99	0.988

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: CNhs13209

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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002262 (endothelial cell of sinusoid)
0002321 (embryonic cell)
0002371 (somatic cell)
1000398 (endothelial cell of hepatic sinusoid)

UBERON: Anatomy
0000015 (anatomical boundary)
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000353 (parenchyma)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001009 (circulatory system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001280 (liver parenchyma)
0001281 (hepatic sinusoid)
0001555 (digestive tract)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003497 (abdomen blood vessel)
0003513 (trunk blood vessel)
0003835 (abdominal segment blood vessel)
0003894 (liver primordium)
0003909 (sinusoid)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004647 (liver lobule)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0006965 (vascular cord)
0007026 (primitive gut)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

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