FF:11714-123C4: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse hepatocyte, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs13078
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	liver
dev stage	NA
sex	NA
age	NA
cell type	hepatocyte
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNA2060
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004776

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13078		CAGE		DRX008857		DRR009729

Accession ID Mm9

Library id		BAM		CTSS
CNhs13078		DRZ001154		DRZ002539

Accession ID Mm10

Library id		BAM		CTSS
CNhs13078		DRZ012504		DRZ013889

Download raw sequence, BAM & CTSS

Mm9

Fasta	BAM	CTSS
download	download	donwload

Mm10

BAM	CTSS
download	donwload

Relative expression to median (log10)

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

CNhs13078

0	0
1	0
10	0
100	0
1000	0
1001	-0.0394
1002	-0.116
1003	0.00925
1004	0
1005	0
1006	-0.143
1007	-0.481
1008	0
1009	-0.19
101	0.0841
1010	0
1011	-0.126
1012	0
1013	0.306
1014	-0.0874
1015	-0.303
1016	-0.379
1017	0
1018	0
1019	0
102	0
1020	0.289
1021	0
1022	0.303
1023	0
1024	-0.0776
1025	0
1026	0
1027	-0.048
1028	0
1029	-0.176
103	-0.0887
1030	0
1031	-0.775
1032	-0.43
1033	0.225
1034	0.285
1035	0
1036	0.0729
1037	0
1038	-0.219
1039	0.505
104	0
1040	-0.538
1041	0

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

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

JASPAR motifsSummary: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 Analyst: Michiel de Hoon link to dataset. data

library id: CNhs13078

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.089
MA0003.1	MA0003.1	0.68
MA0004.1	MA0004.1	0.197
MA0006.1	MA0006.1	0.57
MA0007.1	MA0007.1	0.038
MA0009.1	MA0009.1	0.982
MA0014.1	MA0014.1	0.214
MA0017.1	MA0017.1	8.66483e-14
MA0018.2	MA0018.2	0.514
MA0019.1	MA0019.1	0.998
MA0024.1	MA0024.1	1.64244e-4
MA0025.1	MA0025.1	0.019
MA0027.1	MA0027.1	0.845
MA0028.1	MA0028.1	0.981
MA0029.1	MA0029.1	0.337
MA0030.1	MA0030.1	0.0459
MA0031.1	MA0031.1	0.00211
MA0035.2	MA0035.2	0.0284
MA0038.1	MA0038.1	0.0033
MA0039.2	MA0039.2	0.471
MA0040.1	MA0040.1	0.78
MA0041.1	MA0041.1	0.314
MA0042.1	MA0042.1	0.792
MA0043.1	MA0043.1	0.37
MA0046.1	MA0046.1	5.458e-63
MA0047.2	MA0047.2	1.08072e-5
MA0048.1	MA0048.1	0.246
MA0050.1	MA0050.1	0.553
MA0051.1	MA0051.1	0.243
MA0052.1	MA0052.1	0.548
MA0055.1	MA0055.1	0.297
MA0057.1	MA0057.1	0.42
MA0058.1	MA0058.1	0.134
MA0059.1	MA0059.1	0.00703
MA0060.1	MA0060.1	1.94261e-9
MA0061.1	MA0061.1	0.333
MA0062.2	MA0062.2	0.587
MA0065.2	MA0065.2	6.37281e-12
MA0066.1	MA0066.1	0.0171
MA0067.1	MA0067.1	0.508
MA0068.1	MA0068.1	0.431
MA0069.1	MA0069.1	0.126
MA0070.1	MA0070.1	0.317
MA0071.1	MA0071.1	3.38577e-5
MA0072.1	MA0072.1	0.00241
MA0073.1	MA0073.1	0.919
MA0074.1	MA0074.1	0.165
MA0076.1	MA0076.1	0.601
MA0077.1	MA0077.1	0.165
MA0078.1	MA0078.1	0.478
MA0079.2	MA0079.2	0.0959
MA0080.2	MA0080.2	0.00182
MA0081.1	MA0081.1	0.164
MA0083.1	MA0083.1	0.159
MA0084.1	MA0084.1	0.534
MA0087.1	MA0087.1	0.481
MA0088.1	MA0088.1	0.959
MA0090.1	MA0090.1	0.354
MA0091.1	MA0091.1	0.846
MA0092.1	MA0092.1	0.306
MA0093.1	MA0093.1	0.239
MA0099.2	MA0099.2	1.48312e-6
MA0100.1	MA0100.1	0.961
MA0101.1	MA0101.1	0.508
MA0102.2	MA0102.2	0.272
MA0103.1	MA0103.1	0.0355
MA0104.2	MA0104.2	0.118
MA0105.1	MA0105.1	0.0621
MA0106.1	MA0106.1	0.11
MA0107.1	MA0107.1	0.803
MA0108.2	MA0108.2	0.46
MA0111.1	MA0111.1	0.741
MA0112.2	MA0112.2	2.20028e-5
MA0113.1	MA0113.1	0.175
MA0114.1	MA0114.1	1.33348e-14
MA0115.1	MA0115.1	1.07137e-9
MA0116.1	MA0116.1	0.049
MA0117.1	MA0117.1	0.213
MA0119.1	MA0119.1	0.113
MA0122.1	MA0122.1	0.458
MA0124.1	MA0124.1	0.807
MA0125.1	MA0125.1	0.249
MA0131.1	MA0131.1	0.871
MA0135.1	MA0135.1	0.874
MA0136.1	MA0136.1	0.0147
MA0137.2	MA0137.2	0.048
MA0138.2	MA0138.2	0.478
MA0139.1	MA0139.1	0.165
MA0140.1	MA0140.1	0.902
MA0141.1	MA0141.1	1.84412e-5
MA0142.1	MA0142.1	0.305
MA0143.1	MA0143.1	0.167
MA0144.1	MA0144.1	0.12
MA0145.1	MA0145.1	0.148
MA0146.1	MA0146.1	0.0664
MA0147.1	MA0147.1	0.0639
MA0148.1	MA0148.1	3.21286e-7
MA0149.1	MA0149.1	0.00335
MA0150.1	MA0150.1	9.07196e-6
MA0152.1	MA0152.1	0.537
MA0153.1	MA0153.1	1.09216e-44
MA0154.1	MA0154.1	0.16
MA0155.1	MA0155.1	0.984
MA0156.1	MA0156.1	0.0589
MA0157.1	MA0157.1	0.0133
MA0159.1	MA0159.1	3.17121e-4
MA0160.1	MA0160.1	5.06551e-6
MA0162.1	MA0162.1	0.375
MA0163.1	MA0163.1	0.00109
MA0164.1	MA0164.1	0.984
MA0258.1	MA0258.1	6.94323e-4
MA0259.1	MA0259.1	0.418

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 in169 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: CNhs13078

Novel motif	Logo	P-value
1	1	0.0963
10	10	0.261
100	100	0.276
101	101	0.915
102	102	0.789
103	103	0.0214
104	104	0.492
105	105	0.765
106	106	0.0118
107	107	0.0561
108	108	0.664
109	109	0.0853
11	11	0.0871
110	110	0.0639
111	111	0.00253
112	112	0.0203
113	113	0.764
114	114	0.00365
115	115	0.383
116	116	0.915
117	117	0.0453
118	118	0.585
119	119	0.0822
12	12	0.443
120	120	0.827
121	121	0.584
122	122	0.658
123	123	0.443
124	124	0.287
125	125	0.486
126	126	0.221
127	127	0.622
128	128	0.00666
129	129	0.79
13	13	0.0014
130	130	0.0461
131	131	0.905
132	132	0.428
133	133	0.197
134	134	0.691
135	135	0.408
136	136	0.438
137	137	0.793
138	138	0.838
139	139	0.187
14	14	0.837
140	140	0.219
141	141	0.117
142	142	0.426
143	143	0.285
144	144	0.433
145	145	0.15
146	146	0.566
147	147	0.423
148	148	0.842
149	149	0.408
15	15	0.153
150	150	0.247
151	151	0.525
152	152	0.0878
153	153	0.692
154	154	0.89
155	155	0.547
156	156	0.319
157	157	0.806
158	158	0.538
159	159	0.615
160	160	0.396
161	161	0.83
162	162	0.364
163	163	0.255
164	164	0.0802
165	165	0.651
166	166	0.82
167	167	0.413
168	168	0.713
169	169	0.00245
17	17	0.0547
18	18	0.399
19	19	0.189
2	2	0.966
20	20	0.363
21	21	0.792
22	22	0.198
23	23	0.194
24	24	0.319
25	25	0.546
26	26	0.00836
27	27	0.829
28	28	0.334
29	29	0.158
3	3	0.116
30	30	0.986
31	31	0.268
32	32	0.0487
33	33	0.234
34	34	0.804
35	35	0.18
36	36	0.0908
37	37	0.0536
38	38	0.448
39	39	0.314
4	4	0.631
40	40	0.14
41	41	0.525
42	42	0.518
43	43	0.0855
44	44	0.00167
45	45	0.686
46	46	0.0615
47	47	0.507
48	48	0.225
49	49	0.0534
5	5	0.168
50	50	0.868
51	51	0.237
52	52	0.419
53	53	0.507
54	54	0.257
55	55	0.913
56	56	0.48
57	57	0.761
58	58	0.306
59	59	0.184
6	6	0.678
60	60	0.0701
61	61	0.375
62	62	0.0776
63	63	0.133
64	64	0.537
65	65	0.253
66	66	0.554
67	67	0.709
68	68	0.108
69	69	0.921
7	7	0.267
70	70	0.0133
71	71	0.0191
72	72	0.933
73	73	0.0247
74	74	0.839
75	75	0.009
76	76	0.382
77	77	0.255
78	78	0.013
79	79	0.682
8	8	0.0123
80	80	0.813
81	81	0.841
82	82	0.0321
83	83	0.207
84	84	0.049
85	85	0.0678
86	86	0.101
87	87	0.164
88	88	0.954
89	89	0.2
9	9	0.927
90	90	0.412
91	91	0.621
92	92	0.0457
93	93	0.44
94	94	0.815
95	95	0.148
96	96	0.369
97	97	0.649
98	98	0.476
99	99	0.393

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: CNhs13078

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000109 mouse hepatocyte 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
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)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000109 (mouse hepatocyte 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
CL:0000134 (mesenchymal cell)
CL:0000223 (endodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008747
+|DRA_sample_Accession=CAGE@SAMD00004776
+|accession_numbers=CAGE;DRX008857;DRR009729;DRZ001154;DRZ002539;DRZ012504;DRZ013889
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0001007,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0002365,UBERON:0005172,UBERON:0006925,UBERON:0002530,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002423
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000181,CL:0000417,CL:0000668,CL:0000412,CL:0000255,CL:0000182
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:80555320..80555378,-!p1@Creb3l3!2.34!248.19!Creb3l3;;chr1:193007123..193007139,-!p1@Atf3!2.11!666.37!Atf3;;chr7:19608891..19608895,-!p1@Foxa3!2.02!131.91!Foxa3;;chr19:5447886..5447905,+!p1@Fosl1!1.88!74.80!Fosl1;;chr2:167514456..167514473,+!p1@Cebpb!1.82!2677.73!Cebpb;;chr10:88969376..88969395,-!p1@Nr1h4!1.79!61.20!Nr1h4;;chr6:108610766..108610781,+!p2@Bhlhe40!1.77!100.64!Bhlhe40;;chr15:79178060..79178074,+!p2@Maff!1.77!75.48!Maff;;chr12:86814833..86814846,+!p1@Fos!1.75!1201.51!Fos;;chr15:61816932..61816952,+!p2@Myc!1.75!434.50!Myc;;chr16:38294860..38294924,-!p1@Nr1i2!1.70!48.96!Nr1i2;;chr6:108610513..108610528,+!p3@Bhlhe40!1.69!72.76!Bhlhe40;;chr7:35904304..35904320,+!p1@Cebpa!1.61!757.49!Cebpa;;chr2:163372884..163372904,+!p1@Hnf4a!1.61!39.44!Hnf4a;;chr1:173144144..173144176,+!p1@Nr1i3!1.59!38.08!Nr1i3;;chr18:11052642..11052659,+!p1@Gata6!1.58!178.83!Gata6;;chr15:79177964..79177986,+!p1@Maff!1.55!114.92!Maff;;chr16:43247391..43247422,+!p12@Zbtb20!1.55!34.68!Zbtb20;;chr13:53076382..53076393,-!p2@Nfil3!1.51!49.64!Nfil3;;chr19:5637528..5637548,+!p2@Rela!1.50!172.03!Rela;;chr18:11052606..11052633,+!p4@Gata6!1.48!71.40!Gata6;;chr1:173144100..173144138,+!p2@Nr1i3!1.46!27.88!Nr1i3;;chr9:119893782..119893802,-!p1@Csrnp1!1.42!25.16!Csrnp1;;chr5:135582751..135582788,+!p1@Mlxipl!1.41!95.88!Mlxipl;;chr12:58646974..58647003,-!p1@Foxa1!1.41!32.64!Foxa1;;chr11:60023912..60023930,-!p1@Srebf1!1.39!543.30!Srebf1;;chr19:5447692..5447711,+!p2@Fosl1!1.39!23.80!Fosl1;;chr19:37509324..37509337,+!p1@Hhex!1.35!145.51!Hhex;;chr17:87153519..87153533,+!p5@Epas1!1.34!30.60!Epas1;;chr11:98636400..98636418,-!p4@Nr1d1!1.32!25.84!Nr1d1;;chr11:98636508..98636524,-!p3@Nr1d1!1.31!23.80!Nr1d1;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.28!51.68!Tfcp2l1;;chr2:77357622..77357704,-!p1@Zfp385b!1.27!46.92!Zfp385b;;chr15:75771423..75771445,+!p2@Zfp623!1.27!26.52!Zfp623;;chr1:193041811..193041838,-!p2@Atf3!1.27!17.68!Atf3;;chr11:98636373..98636387,-!p5@Nr1d1!1.26!19.72!Nr1d1;;chr11:98636531..98636559,-!p1@Nr1d1!1.25!94.52!Nr1d1;;chr15:61817095..61817111,+!p1@Myc!1.23!917.96!Myc;;chr6:108610610..108610676,+!p1@Bhlhe40!1.22!733.01!Bhlhe40;;chr13:31650185..31650201,+!p1@Foxq1!1.22!54.40!Foxq1;;chr16:95923706..95923717,+!p6@Ets2!1.22!15.64!Ets2;;chr13:5860776..5860796,+!p1@Klf6!1.21!360.38!Klf6;;chr13:53076396..53076452,-!p1@Nfil3!1.21!264.51!Nfil3;;chr4:94718861..94718872,-!p2@Jun!1.20!110.84!Jun;;chr7:52071956..52071978,-!p1@Atf5!1.18!451.50!Atf5;;chr16:95923651..95923701,+!p3@Ets2!1.15!21.08!Ets2;;chr10:88996295..88996335,-!p3@Nr1h4!1.15!15.64!Nr1h4;;chr7:20408047..20408125,-!p1@Bcl3!1.14!144.83!Bcl3;;chr15:79178013..79178028,+!p3@Maff!1.14!17.00!Maff;;chr9:74709695..74709722,+!p1@Onecut1!1.14!12.92!Onecut1;;chr16:87699206..87699229,+!p3@Bach1!1.11!63.92!Bach1;;chr17:87153505..87153516,+!p6@Epas1!1.11!16.32!Epas1;;chr11:90249521..90249551,-!p3@Hlf!1.10!11.56!Hlf;;chr16:43363190..43363242,+!p2@Zbtb20!1.09!34.68!Zbtb20;;chr16:95924055..95924077,+!p1@Ets2!1.07!580.70!Ets2;;chr11:112643496..112643562,+!p1@Sox9!1.07!397.78!Sox9;;chr19:23215673..23215753,+!p1@Klf9!1.07!155.71!Klf9;;chr10:80555285..80555291,-!p4@Creb3l3!1.07!10.88!Creb3l3;;chr2:163372869..163372882,+!p3@Hnf4a!1.07!10.88!Hnf4a;;chr5:140267510..140267555,+!p2@Mafk!1.06!25.16!Mafk;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!1.05!25.84!Hmga1;;chr18:64499674..64499696,+!p1@Onecut2!1.05!17.68!Onecut2;;chr10:80555299..80555306,-!p3@Creb3l3!1.05!10.20!Creb3l3;;chr9:69137716..69137744,+!p1@Rora!1.02!59.84!Rora;;chr15:25914114..25914128,+!p2@Zfp622!1.02!39.44!Zfp622;;chr15:61819047..61819076,+!p5@Myc!1.02!11.56!Myc;;chrX:7339938..7339963,+!p1@Tfe3!1.01!47.60!Tfe3;;chr15:79178029..79178044,+!p4@Maff!1.01!11.56!Maff;;chr14:19071466..19071550,-!p1@Nr1d2!0.99!61.88!Nr1d2;;chr11:100683839..100683890,-!p2@Stat5b!0.99!21.08!Stat5b;;chr3:94176733..94176794,+!p1@Rorc!0.97!65.96!Rorc;;chr7:29551464..29551487,-!p2@Nfkbib!0.96!31.96!Nfkbib;;chr5:65213356..65213412,+!p6@Klf3!0.96!17.68!Klf3;;chr15:85566184..85566238,+!p1@Ppara!0.96!12.24!Ppara;;chr6:90415250..90415271,+!p4@Klf15!0.96!8.16!Klf15;;chr3:52072329..52072346,+!p1@Foxo1!0.95!125.79!Foxo1;;chr12:36219645..36219730,-!p1@Ahr!0.95!80.24!Ahr;;chr5:144951153..144951203,+!p1@Bhlha15!0.95!11.56!Bhlha15;;chr17:71200529..71200556,-!p1@Tgif1!0.94!128.51!Tgif1;;chr8:107793688..107793736,+!p1@Hsf4!0.94!10.20!Hsf4;;chr18:3281750..3281776,-!p2@Crem!0.93!15.64!Crem;;chr4:133109285..133109308,+!p1@Nr0b2!0.93!7.48!Nr0b2;;chr11:5420655..5420659,+!p3@Xbp1!0.93!7.48!Xbp1;;chr2:27531961..27531974,+!p7@Rxra!0.93!7.48!Rxra;;chr5:140267476..140267493,+!p1@Mafk!0.92!42.84!Mafk;;chr4:94718879..94718898,-!p1@Jun!0.91!542.62!Jun;;chr1:138845748..138845766,-!p4@Nr5a2!0.91!9.52!Nr5a2;;chr10:88996336..88996380,-!p2@Nr1h4!0.91!8.84!Nr1h4;;chr2:126501847..126501876,-!p5@Gabpb1!0.91!8.16!Gabpb1;;chr16:98183746..98183801,-!p1@Zfp295!0.90!80.92!Zfp295;;chr18:74375772..74375799,+!p2@Cxxc1!0.89!20.40!Cxxc1;;chr14:76887526..76887555,+!p10@Tsc22d1!0.89!6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3;;chr11:84339016..84339044,-!p1@Lhx1!0.23!0.68!Lhx1;;chr11:90252108..90252134,-!p6@Hlf!0.23!0.68!Hlf;;chr10:5636354..5636373,-!p2@Esr1!0.23!0.68!Esr1;;chr11:100683822..100683831,-!p8@Stat5b!0.23!0.68!Stat5b;;chr11:83664365..83664383,+!p1@Hnf1b!0.23!0.68!Hnf1b;;chr11:121381087..121381108,-!p4@Zfp750!0.23!0.68!Zfp750;;chr11:98822081..98822092,+!p14@Rara!0.23!0.68!Rara;;chr11:100720767..100720797,+!p4@Stat5a!0.23!0.68!Stat5a;;chr11:100721732..100721742,+!p3@Stat5a!0.23!0.68!Stat5a;;chr11:62271355..62271369,-!p31@Ncor1!0.23!0.68!Ncor1;;chr10:20032169..20032206,+!p8@Bclaf1!0.23!0.68!Bclaf1;;chr7:38557887..38557910,-!p5@Zfp536!0.23!0.68!Zfp536;;chr8:86590283..86590297,+!p5@Rfx1!0.23!0.68!Rfx1;;chr7:52962498..52962512,+!p12@Dbp!0.23!0.68!Dbp;;chr8:94325779..94325791,-!p7@Irx3!0.23!0.68!Irx3;;chr7:31065205..31065207,+!p1@LOC100504904!0.23!0.68!Thap8;;chr9:106355745..106355766,+!p7@Pcbp4!0.23!0.68!Pcbp4;;chr1:179372543..179372557,+!p9@Zfp238!0.23!0.68!Zfp238;;chr1:179372514..179372525,+!p7@Zfp238!0.23!0.68!Zfp238;;chr1:92950128..92950139,+!p4@Lrrfip1!0.23!0.68!Lrrfip1;;chr1:138857112..138857130,-!p7@Nr5a2!0.23!0.68!Nr5a2;;chr2:32229906..32229942,+!p3@Ciz1!0.23!0.68!Ciz1;;chr2:147871948..147871977,-!p3@Foxa2!0.23!0.68!Foxa2;;chr1:191993385..191993405,-!p3@Prox1!0.23!0.68!Prox1;;chr1:57028556..57028583,-!p5@Satb2!0.23!0.68!Satb2;;chr1:194982959..194983007,+!p5@Irf6!0.23!0.68!Irf6;;chr5:138526401..138526410,+!p3@Zkscan1!0.23!0.68!Zkscan1;;chr6:70906450..70906454,+!p1@Foxi3!0.23!0.68!Foxi3;;chr6:72185396..72185413,-!p6@Atoh8!0.23!0.68!Atoh8;;chr5:125523164..125523188,-!p8@Ncor2!0.23!0.68!Ncor2;;chr5:144951136..144951139,+!p2@Bhlha15!0.23!0.68!Bhlha15;;chr6:144157968..144157989,-!p7@Sox5!0.23!0.68!Sox5;;chr5:67490346..67490357,-!p4@Phox2b!0.23!0.68!Phox2b;;chr7:13563626..13563634,+!p6@Zfp446!0.23!0.68!Zfp446;;chr5:31754898..31754907,+!p5@Zfp512!0.23!0.68!Zfp512;;chr7:108966820..108966835,+!p1@Phox2a!0.23!0.68!Phox2a;;chr7:147129777..147129814,+!p2@Utf1!0.23!0.68!Utf1;;chr5:111082367..111082441,-!p1@Noc4l!0.22!34.68!Noc4l;;chr19:26679654..26679675,+!p1@Smarca2!0.22!13.60!Smarca2;;chr5:104183219..104183236,+!p2@Aff1!0.22!9.52!Aff1;;chr4:116480179..116480222,-!p2@Toe1!0.22!7.48!Toe1;;chr11:98636575..98636607,-!p2@Nr1d1!0.22!4.76!Nr1d1;;chr2:128769696..128769712,-!p2@Zc3h8!0.22!4.08!Zc3h8;;chr19:26681226..26681299,+!p7@Smarca2!0.22!2.72!Smarca2;;chr15:25914217..25914232,+!p3@Zfp622!0.22!2.04!Zfp622;;chr6:39068163..39068176,-!p2@Parp12!0.22!2.04!Parp12;;chr5:92391466..92391471,+!p2@Thap6!0.22!1.36!Thap6;;chr13:59924319..59924331,-!p5@Zcchc6!0.22!1.36!Zcchc6;;chr8:118231350..118231385,-!p7@Maf!0.22!1.36!Maf;;chr15:102300965..102300977,+!p1@Pcbp2!0.21!469.18!Pcbp2;;chr7:119822841..119822887,+!p1@Tead1!0.21!46.24!Tead1;;chr7:26035739..26035757,-!p1@Erf!0.21!35.36!Erf;;chr15:100058266..100058287,+!p1@Atf1!0.21!22.44!Atf1;;chr8:72498160..72498214,-!p1@Gatad2a!0.21!18.36!Gatad2a;;chr11:90252223..90252240,-!p1@Hlf!0.21!11.56!Hlf;;chr3:54611674..54611690,-!p2@Rfxap!0.21!10.20!Rfxap;;chr1:191994550..191994623,-!p1@Prox1!0.21!9.52!Prox1;;chr9:113840082..113840105,+!p3@Ubp1!0.21!3.40!Ubp1;;chr3:90097217..90097233,+!p3@Gatad2b!0.21!2.72!Gatad2b;;chr2:181327403..181327432,-!p3@Znf512b!0.21!2.04!Znf512b;;chr5:22940353..22940372,+!p3@Mll5!0.21!2.04!Mll5;;chr5:65194810..65194819,+!p9@Klf3!0.21!2.04!Klf3;;chr12:25336286..25336297,+!p2@Klf11!0.21!1.36!Klf11;;chr17:32501360..32501371,-!p5@Wiz!0.21!1.36!Wiz;;chr19:5423800..5423821,-!p5@Drap1!0.21!1.36!Drap1;;chr2:70313168..70313184,+!p1@Sp5!0.21!1.36!Sp5;;chr2:72817045..72817123,-!p1@Sp3!0.20!45.56!Sp3;;chr8:87324243..87324277,-!p1@Nfix!0.20!34.00!Nfix;;chr3:96001503..96001557,-!p1@Bola1!0.20!29.92!Bola1;;chr10:41996494..41996549,-!p1@Foxo3!0.20!23.80!Foxo3;;chr2:160698721..160698745,-!p1@Zhx3!0.20!19.72!Zhx3;;chr5:145965392..145965443,+!p1@Zkscan5!0.20!12.24!Zkscan5;;chr2:160698681..160698708,-!p2@Zhx3!0.20!10.88!Zhx3;;chr3:95238432..95238455,+!p2@Arnt!0.20!7.48!Arnt;;chr3:89197057..89197114,-!p1@Zbtb7b!0.20!4.08!Zbtb7b;;chr10:127896024..127896045,+!p3@Smarcc2!0.20!2.72!Smarcc2;;chr8:124984566..124984595,-!p1@Snai3!0.20!1.36!Snai3;;chr18:24113207..24113218,+!p3@Zfp397!0.20!1.36!Zfp397;;chr6:37392095..37392154,-!p1@Creb3l2!0.19!44.20!Creb3l2;;chr17:25152711..25152736,-!p1@Cramp1l!0.19!13.60!Cramp1l;;chr7:105851601..105851647,+!p2@Prkrir!0.19!12.24!Prkrir;;chr11:98821749..98821799,+!p2@Rara!0.19!8.16!Rara;;chr11:74644716..74644780,+!p2@Mnt!0.19!3.40!Mnt;;chr12:85534778..85534812,-!p3@C130039O16Rik!0.19!3.40!C130039O16Rik;;chr3:135354452..135354475,-!p5@Nfkb1!0.19!2.72!Nfkb1;;chrX:91368504..91368516,-!p3@Zfx!0.19!2.04!Zfx;;chr10:67599361..67599372,-!p5@Arid5b!0.19!1.36!Arid5b;;chr15:80085678..80085693,+!p2@Atf4!0.19!1.36!Atf4;;chr15:81633203..81633215,+!p3@Tef!0.19!1.36!Tef;;chr8:87237732..87237745,-!p7@Nfix!0.19!1.36!Nfix;;chr1:138846047..138846074,-!p5@Nr5a2!0.19!0.68!Nr5a2;;chr19:53403997..53404008,+!p7@Mxi1!0.19!0.68!Mxi1;;chr10:70700783..70700832,-!p1@Tfam!0.18!51.68!Tfam;;chr7:31741846..317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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000109
 |is_obsolete=
-|library_ids=CNhs13078
+|library_id=CNhs13078
+|library_id_phase_based=2:CNhs13078
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11714
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11714
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor1.CNhs13078.11714-123C4.mm9.nobarcode.rdna.fa.gz
 |name=Mouse hepatocyte, donor1
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13078,LSID1000,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.0051446607508875,0,0,0,0,0,-0.306283960472796,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0.852464256481948,0,0,0,0,0,0,0,0,0.372901452322848,-0.558422792324031,0,0,0,0,-0.0148545648523418,0.144758858910228,-0.0580694366219585,-0.017894939798506,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0835971705837681,0,0.223385018955267,0,0,-0.0354470656487682,-0.130574842604779,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0973736644748266,-0.200745418790066,0,0,-0.0712348665943568,-0.0658904525838042,0.748066708889265,-0.0788315948399074,0,0,0,0,0,0,0.51960640036207,0.450342711659795,0.337181038750703,0,0,0,0.348898797568663,0
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11714-123C4;search_select_hide=table117:11714-123C4
-|DRA_sample_Accession=CAGE@DRS008747
-|accession_numbers=DRX008857;DRR009729;DRZ001154;DRZ002539;CAGE
-|library_id=CNhs13078
 }}

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FF:11714-123C4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs13078

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0