FF:11637-122C8: Difference between revisions

Latest revision as of 18:12, 4 June 2020

Name:	Mouse hepatocyte, donor3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12615
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	CD-1
tissue	liver
dev stage	NA
sex	male
age	NA
cell type	hepatocyte
cell line	NA
company	xenotech
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	M1000.H15
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005998

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12615		CAGE		DRX008858		DRR009730

Accession ID Mm9

Library id		BAM		CTSS
CNhs12615		DRZ001155		DRZ002540

Accession ID Mm10

Library id		BAM		CTSS
CNhs12615		DRZ012505		DRZ013890

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

CNhs12615

0	0
1	0
10	0
100	0
1000	0.115
1001	0.217
1002	-0.116
1003	0.151
1004	0
1005	0
1006	-0.132
1007	-0.282
1008	0
1009	-0.00265
101	-0.116
1010	0
1011	-0.275
1012	0
1013	0.633
1014	-0.0874
1015	-0.342
1016	-0.261
1017	0
1018	0
1019	0
102	0
1020	0.679
1021	0
1022	0.503
1023	0
1024	-0.0899
1025	0
1026	0
1027	0
1028	0
1029	-0.0318
103	-0.0887
1030	0
1031	-0.875
1032	-0.522
1033	-0.0752
1034	0.787
1035	0
1036	-0.603
1037	0
1038	-0.298
1039	0.756
104	0
1040	-0.256
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: CNhs12615

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.103
MA0003.1	MA0003.1	0.753
MA0004.1	MA0004.1	0.361
MA0006.1	MA0006.1	0.425
MA0007.1	MA0007.1	0.127
MA0009.1	MA0009.1	0.947
MA0014.1	MA0014.1	0.125
MA0017.1	MA0017.1	2.18793e-17
MA0018.2	MA0018.2	3.86816e-4
MA0019.1	MA0019.1	0.901
MA0024.1	MA0024.1	3.47234e-4
MA0025.1	MA0025.1	0.436
MA0027.1	MA0027.1	0.927
MA0028.1	MA0028.1	0.561
MA0029.1	MA0029.1	0.563
MA0030.1	MA0030.1	0.0245
MA0031.1	MA0031.1	0.00697
MA0035.2	MA0035.2	0.0793
MA0038.1	MA0038.1	0.0755
MA0039.2	MA0039.2	0.356
MA0040.1	MA0040.1	0.477
MA0041.1	MA0041.1	0.331
MA0042.1	MA0042.1	0.793
MA0043.1	MA0043.1	0.172
MA0046.1	MA0046.1	4.24853e-75
MA0047.2	MA0047.2	3.20429e-6
MA0048.1	MA0048.1	0.276
MA0050.1	MA0050.1	0.662
MA0051.1	MA0051.1	0.811
MA0052.1	MA0052.1	0.00688
MA0055.1	MA0055.1	0.428
MA0057.1	MA0057.1	0.611
MA0058.1	MA0058.1	0.265
MA0059.1	MA0059.1	0.0147
MA0060.1	MA0060.1	1.95194e-5
MA0061.1	MA0061.1	0.664
MA0062.2	MA0062.2	0.824
MA0065.2	MA0065.2	9.38401e-13
MA0066.1	MA0066.1	0.00707
MA0067.1	MA0067.1	0.225
MA0068.1	MA0068.1	0.427
MA0069.1	MA0069.1	0.149
MA0070.1	MA0070.1	0.278
MA0071.1	MA0071.1	1.58017e-5
MA0072.1	MA0072.1	7.403e-5
MA0073.1	MA0073.1	0.85
MA0074.1	MA0074.1	0.155
MA0076.1	MA0076.1	0.984
MA0077.1	MA0077.1	0.0265
MA0078.1	MA0078.1	0.739
MA0079.2	MA0079.2	0.129
MA0080.2	MA0080.2	5.6211e-5
MA0081.1	MA0081.1	0.133
MA0083.1	MA0083.1	0.00448
MA0084.1	MA0084.1	0.678
MA0087.1	MA0087.1	0.256
MA0088.1	MA0088.1	0.2
MA0090.1	MA0090.1	0.551
MA0091.1	MA0091.1	0.883
MA0092.1	MA0092.1	0.306
MA0093.1	MA0093.1	0.395
MA0099.2	MA0099.2	0.838
MA0100.1	MA0100.1	0.681
MA0101.1	MA0101.1	0.835
MA0102.2	MA0102.2	0.547
MA0103.1	MA0103.1	0.0418
MA0104.2	MA0104.2	0.301
MA0105.1	MA0105.1	0.0137
MA0106.1	MA0106.1	0.023
MA0107.1	MA0107.1	0.37
MA0108.2	MA0108.2	3.83941e-5
MA0111.1	MA0111.1	0.861
MA0112.2	MA0112.2	6.06022e-6
MA0113.1	MA0113.1	0.303
MA0114.1	MA0114.1	4.81164e-17
MA0115.1	MA0115.1	8.63658e-12
MA0116.1	MA0116.1	0.0215
MA0117.1	MA0117.1	0.623
MA0119.1	MA0119.1	0.0462
MA0122.1	MA0122.1	0.177
MA0124.1	MA0124.1	0.807
MA0125.1	MA0125.1	0.441
MA0131.1	MA0131.1	0.86
MA0135.1	MA0135.1	0.551
MA0136.1	MA0136.1	4.21035e-4
MA0137.2	MA0137.2	0.118
MA0138.2	MA0138.2	0.533
MA0139.1	MA0139.1	0.0811
MA0140.1	MA0140.1	0.704
MA0141.1	MA0141.1	1.28718e-6
MA0142.1	MA0142.1	0.27
MA0143.1	MA0143.1	0.164
MA0144.1	MA0144.1	0.414
MA0145.1	MA0145.1	0.158
MA0146.1	MA0146.1	0.0782
MA0147.1	MA0147.1	0.21
MA0148.1	MA0148.1	4.99283e-9
MA0149.1	MA0149.1	0.0041
MA0150.1	MA0150.1	0.00385
MA0152.1	MA0152.1	0.779
MA0153.1	MA0153.1	6.88402e-55
MA0154.1	MA0154.1	0.0956
MA0155.1	MA0155.1	0.823
MA0156.1	MA0156.1	0.0345
MA0157.1	MA0157.1	0.00887
MA0159.1	MA0159.1	5.56982e-4
MA0160.1	MA0160.1	4.14715e-5
MA0162.1	MA0162.1	0.414
MA0163.1	MA0163.1	3.12745e-4
MA0164.1	MA0164.1	0.931
MA0258.1	MA0258.1	3.89487e-4
MA0259.1	MA0259.1	0.951

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: CNhs12615

Novel motif	Logo	P-value
1	1	0.0562
10	10	0.105
100	100	0.398
101	101	0.868
102	102	0.302
103	103	0.00282
104	104	0.7
105	105	0.796
106	106	0.105
107	107	0.185
108	108	0.973
109	109	0.0767
11	11	0.0586
110	110	0.0549
111	111	0.00141
112	112	0.0135
113	113	0.9
114	114	0.00123
115	115	0.492
116	116	0.989
117	117	0.0755
118	118	0.336
119	119	0.17
12	12	0.483
120	120	0.925
121	121	0.934
122	122	0.739
123	123	0.367
124	124	0.43
125	125	0.908
126	126	0.0865
127	127	0.831
128	128	0.0669
129	129	0.875
13	13	0.00128
130	130	0.434
131	131	0.982
132	132	0.399
133	133	0.714
134	134	0.997
135	135	0.595
136	136	0.755
137	137	0.905
138	138	0.815
139	139	0.212
14	14	0.619
140	140	0.179
141	141	0.44
142	142	0.0509
143	143	0.405
144	144	0.631
145	145	0.15
146	146	0.747
147	147	0.353
148	148	0.482
149	149	0.0671
15	15	0.186
150	150	0.261
151	151	0.474
152	152	0.32
153	153	0.435
154	154	0.939
155	155	0.391
156	156	0.723
157	157	0.804
158	158	0.937
159	159	0.804
160	160	0.283
161	161	0.666
162	162	0.304
163	163	0.592
164	164	0.131
165	165	0.753
166	166	0.532
167	167	0.112
168	168	0.99
169	169	0.00194
17	17	0.0483
18	18	0.633
19	19	0.128
2	2	0.959
20	20	0.41
21	21	0.927
22	22	0.193
23	23	0.294
24	24	0.227
25	25	0.582
26	26	0.00914
27	27	0.75
28	28	0.437
29	29	0.147
3	3	0.0794
30	30	0.9
31	31	0.307
32	32	0.122
33	33	0.446
34	34	0.875
35	35	0.117
36	36	0.0984
37	37	0.0593
38	38	0.407
39	39	0.247
4	4	0.541
40	40	0.275
41	41	0.961
42	42	0.37
43	43	0.0808
44	44	6.67159e-4
45	45	0.879
46	46	0.0891
47	47	0.334
48	48	0.151
49	49	0.0476
5	5	0.122
50	50	0.917
51	51	0.337
52	52	0.755
53	53	0.466
54	54	0.4
55	55	0.478
56	56	0.424
57	57	0.421
58	58	0.37
59	59	0.292
6	6	0.811
60	60	0.211
61	61	0.391
62	62	0.0895
63	63	0.153
64	64	0.447
65	65	0.234
66	66	0.707
67	67	0.72
68	68	0.139
69	69	0.658
7	7	0.245
70	70	0.0104
71	71	0.0221
72	72	0.787
73	73	0.112
74	74	0.465
75	75	0.0111
76	76	0.606
77	77	0.373
78	78	0.0629
79	79	0.622
8	8	0.0063
80	80	0.827
81	81	0.88
82	82	0.0375
83	83	0.379
84	84	0.0813
85	85	0.0259
86	86	0.069
87	87	0.581
88	88	0.73
89	89	0.177
9	9	0.929
90	90	0.0432
91	91	0.371
92	92	0.127
93	93	0.0991
94	94	0.718
95	95	0.254
96	96	0.204
97	97	0.871
98	98	0.394
99	99	0.255

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: CNhs12615

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@DRS008748
+|DRA_sample_Accession=CAGE@SAMD00005998
+|accession_numbers=CAGE;DRX008858;DRR009730;DRZ001155;DRZ002540;DRZ012505;DRZ013890
 |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!2.45!321.66!Creb3l3;;chr4:133109285..133109308,+!p1@Nr0b2!2.34!219.66!Nr0b2;;chr2:163372884..163372904,+!p1@Hnf4a!2.23!167.85!Hnf4a;;chr5:135582751..135582788,+!p1@Mlxipl!2.11!490.05!Mlxipl;;chr1:173144144..173144176,+!p1@Nr1i3!1.99!97.69!Nr1i3;;chr9:74709695..74709722,+!p1@Onecut1!1.98!94.45!Onecut1;;chr1:173144100..173144138,+!p2@Nr1i3!1.93!84.19!Nr1i3;;chr10:88969376..88969395,-!p1@Nr1h4!1.91!80.96!Nr1h4;;chr7:19608891..19608895,-!p1@Foxa3!1.86!92.83!Foxa3;;chr16:38294860..38294924,-!p1@Nr1i2!1.79!60.45!Nr1i2;;chr7:35904304..35904320,+!p1@Cebpa!1.72!989.28!Cebpa;;chr15:85566537..85566552,+!p2@Ppara!1.66!44.26!Ppara;;chr2:27531961..27531974,+!p7@Rxra!1.65!43.72!Rxra;;chr15:85566184..85566238,+!p1@Ppara!1.58!55.05!Ppara;;chr11:90249521..90249551,-!p3@Hlf!1.56!35.62!Hlf;;chr19:37509324..37509337,+!p1@Hhex!1.53!222.90!Hhex;;chr6:90415250..90415271,+!p4@Klf15!1.52!32.38!Klf15;;chr11:98636531..98636559,-!p1@Nr1d1!1.47!154.89!Nr1d1;;chr11:98636508..98636524,-!p3@Nr1d1!1.43!31.84!Nr1d1;;chr11:100683839..100683890,-!p2@Stat5b!1.41!56.67!Stat5b;;chr10:88996295..88996335,-!p3@Nr1h4!1.40!28.60!Nr1h4;;chr7:52071956..52071978,-!p1@Atf5!1.38!714.03!Atf5;;chr12:58646974..58647003,-!p1@Foxa1!1.38!30.76!Foxa1;;chr18:64499674..64499696,+!p1@Onecut2!1.36!37.78!Onecut2;;chr10:88996336..88996380,-!p2@Nr1h4!1.36!26.99!Nr1h4;;chr14:76888344..76888348,+!p26@Tsc22d1!1.36!22.13!Tsc22d1;;chr15:75799634..75799645,+!p4@Zfp707!1.35!24.83!Zfp707;;chr2:77357622..77357704,-!p1@Zfp385b!1.33!53.43!Zfp385b;;chr18:64499706..64499721,+!p2@Onecut2!1.33!28.60!Onecut2;;chr2:163372869..163372882,+!p3@Hnf4a!1.33!20.51!Hnf4a;;chr2:91035254..91035271,-!p3@Nr1h3!1.32!24.83!Nr1h3;;chr2:147872790..147872821,-!p2@Foxa2!1.31!19.43!Foxa2;;chr5:115421065..115421088,-!p1@Hnf1a!1.25!16.73!Hnf1a;;chr15:85566241..85566253,+!p6@Ppara!1.22!15.65!Ppara;;chr11:60023912..60023930,-!p1@Srebf1!1.21!358.90!Srebf1;;chr13:31650185..31650201,+!p1@Foxq1!1.19!50.19!Foxq1;;chr6:108610766..108610781,+!p2@Bhlhe40!1.17!24.83!Bhlhe40;;chr2:167514456..167514473,+!p1@Cebpb!1.16!583.42!Cebpb;;chr1:193007123..193007139,-!p1@Atf3!1.16!75.02!Atf3;;chr1:138857076..138857105,-!p1@Nr5a2!1.16!13.49!Nr5a2;;chr10:80555299..80555306,-!p3@Creb3l3!1.16!13.49!Creb3l3;;chr16:43247391..43247422,+!p12@Zbtb20!1.14!12.95!Zbtb20;;chr12:86814833..86814846,+!p1@Fos!1.13!286.58!Fos;;chr6:90412582..90412601,+!p1@Klf15!1.12!57.75!Klf15;;chr16:43363190..43363242,+!p2@Zbtb20!1.12!37.78!Zbtb20;;chr1:138845748..138845766,-!p4@Nr5a2!1.11!15.65!Nr5a2;;chr10:80555285..80555291,-!p4@Creb3l3!1.11!11.87!Creb3l3;;chr1:191994550..191994623,-!p1@Prox1!1.10!79.34!Prox1;;chr11:121380640..121380655,-!p1@Zfp750!1.09!18.89!Zfp750;;chr17:87153519..87153533,+!p5@Epas1!1.09!16.73!Epas1;;chr2:27532754..27532815,+!p1@Rxra!1.07!315.73!Rxra;;chr4:94718861..94718872,-!p2@Jun!1.07!80.42!Jun;;chr6:90415281..90415295,+!p5@Klf15!1.07!10.79!Klf15;;chr2:147871627..147871641,-!p1@Foxa2!1.07!10.79!Foxa2;;chr16:43235969..43235989,+!p20@Zbtb20!1.05!10.25!Zbtb20;;chr2:27532479..27532509,+!p3@Rxra!1.04!20.51!Rxra;;chr14:100683884..100683908,-!p4@Klf12!1.04!18.89!Klf12;;chr3:94176733..94176794,+!p1@Rorc!1.03!75.56!Rorc;;chr6:90412556..90412581,+!p3@Klf15!1.03!21.59!Klf15;;chr15:75799598..75799619,+!p3@Zfp707!1.03!20.51!Zfp707;;chr19:23215509..23215523,+!p4@Klf9!1.03!12.41!Klf9;;chr9:74714303..74714318,+!p2@Onecut1!1.03!9.71!Onecut1;;chr1:138857048..138857071,-!p2@Nr5a2!1.03!9.71!Nr5a2;;chrX:137077716..137077734,-!p1@Tsc22d3!1.01!67.46!Tsc22d3;;chr6:90412608..90412630,+!p2@Klf15!1.01!19.43!Klf15;;chr7:19895354..19895369,-!p1@Fosb!1.01!12.95!Fosb;;chr17:87153505..87153516,+!p6@Epas1!1.01!12.95!Epas1;;chr9:69137716..69137744,+!p1@Rora!1.00!58.29!Rora;;chr9:48644037..48644067,-!p2@Zbtb16!1.00!22.67!Zbtb16;;chr6:72185396..72185413,-!p6@Atoh8!0.98!8.64!Atoh8;;chr2:91035197..91035237,-!p1@Nr1h3!0.97!17.81!Nr1h3;;chr1:138846009..138846038,-!p3@Nr5a2!0.96!9.17!Nr5a2;;chr16:43236037..43236050,+!p35@Zbtb20!0.96!8.10!Zbtb20;;chr14:76887526..76887555,+!p10@Tsc22d1!0.96!8.10!Tsc22d1;;chr8:87502608..87502623,-!p1@Junb!0.95!132.23!Junb;;chr5:77524250..77524300,-!p1@Hopx!0.94!159.75!Hopx;;chr18:35020854..35020869,+!p1@Egr1!0.93!299.00!Egr1;;chr11:60036258..60036276,-!p3@Srebf1!0.93!13.49!Srebf1;;chr2:27532513..27532525,+!p8@Rxra!0.93!8.64!Rxra;;chr10:80555398..80555409,-!p2@Creb3l3!0.93!7.56!Creb3l3;;chr14:18493386..18493464,+!p1@Thrb!0.90!27.52!Thrb;;chr13:53076382..53076393,-!p2@Nfil3!0.90!11.33!Nfil3;;chr8:73905892..73905903,-!p5@Nr2f6!0.89!8.10!Nr2f6;;chr16:43363152..43363186,+!p3@Zbtb20!0.88!15.65!Zbtb20;;chr19:23215673..23215753,+!p1@Klf9!0.87!98.77!Klf9;;chr6:134780234..134780288,+!p1@Crebl2!0.87!21.59!Crebl2;;chr1:191993385..191993405,-!p3@Prox1!0.87!6.48!Prox1;;chr4:94718879..94718898,-!p1@Jun!0.86!483.57!Jun;;chr11:121380611..121380625,-!p3@Zfp750!0.85!7.56!Zfp750;;chr8:125778192..125778217,+!p2@Zfp276!0.84!17.81!Zfp276;;chr6:72185232..72185272,-!p1@Atoh8!0.84!17.81!Atoh8;;chr4:32334732..32334739,+!p7@Bach2!0.84!5.94!Bach2;;chr1:138857112..138857130,-!p7@Nr5a2!0.84!5.94!Nr5a2;;chr1:138846079..138846103,-!p6@Nr5a2!0.84!5.94!Nr5a2;;chr15:85565338..85565355,+!p7@Ppara!0.84!5.94!Ppara;;chr1:13364477..13364492,-!p6@Ncoa2!0.82!7.02!Ncoa2;;chr18:3281034..3281104,-!p1@Crem!0.81!41.56!Crem;;chr9:74714281..74714296,+!p5@Onecut1!0.81!5.40!Onecut1;;chr9:74709682..74709691,+!p3@Onecut1!0.81!5.40!Onecut1;;chr1:169548377..169548430,+!p1@Rxrg!0.81!5.40!Rxrg;;chr6:72185210..72185228,-!p3@Atoh8!0.79!9.17!Atoh8;;chr11:98636400..98636418,-!p4@Nr1d1!0.79!7.02!Nr1d1;;chr18:36441119..36441158,+!p2@Pura!0.78!12.95!Pura;;chr2:160192793..160192809,-!p1@Mafb!0.77!80.42!Mafb;;chr9:122775033..122775044,-!p2@Zfp445!0.77!9.17!Zfp445;;chr1:138846047..138846074,-!p5@Nr5a2!0.77!5.40!Nr5a2;;chr16:38294929..38294940,-!p2@Nr1i2!0.77!4.86!Nr1i2;;chr1:93309740..93309811,-!p1@Hes6!0.76!105.24!Hes6;;chr16:43619101..43619151,+!p6@Zbtb20!0.76!12.41!Zbtb20;;chr9:48644013..48644027,-!p5@Zbtb16!0.76!5.94!Zbtb16;;chr14:18493480..18493494,+!p2@Thrb!0.76!5.40!Thrb;;chr17:87153462..87153473,+!p3@Epas1!0.75!18.89!Epas1;;chr2:160698288..160698358,-!p3@Zhx3!0.74!15.11!Zhx3;;chr1:194979315..194979359,+!p1@Irf6!0.73!29.68!Irf6;;chr16:43619057..43619078,+!p8@Zbtb20!0.73!9.71!Zbtb20;;chr6:90416275..90416286,+!p9@Klf15!0.73!4.32!Klf15;;chr2:75543161..75543173,-!p5@Nfe2l2!0.73!4.32!Nfe2l2;;chr14:63864056..63864102,-!p1@Gata4!0.71!7.56!Gata4;;chr8:73905806..73905876,-!p1@Nr2f6!0.70!97.15!Nr2f6;;chr3:96002383..96002407,-!p4@Bola1!0.70!5.40!Bola1;;chr11:96690797..96690813,-!p1@Nfe2l1!0.69!86.35!Nfe2l1;;chr11:98821937..98821987,+!p4@Rara!0.68!9.17!Rara;;chr10:67599432..67599444,-!p4@Arid5b!0.68!6.48!Arid5b;;chr1:194979361..194979373,+!p2@Irf6!0.68!5.40!Irf6;;chr10:5734677..5734702,-!p4@Esr1!0.68!3.78!Esr1;;chr14:18493470..18493477,+!p4@Thrb!0.68!3.78!Thrb;;chr12:25780945..25780961,-!p1@Id2!0.67!710.25!Id2;;chr2:27532734..27532749,+!p2@Rxra!0.67!11.87!Rxra;;chr10:5636374..5636421,-!p1@Esr1!0.67!4.86!Esr1;;chr11:98636373..98636387,-!p5@Nr1d1!0.67!4.32!Nr1d1;;chr3:96001503..96001557,-!p1@Bola1!0.66!88.51!Bola1;;chr19:26681226..26681299,+!p7@Smarca2!0.66!9.17!Smarca2;;chr13:53076396..53076452,-!p1@Nfil3!0.65!72.86!Nfil3;;chr1:181733737..181733755,-!p2@Ahctf1!0.65!12.41!Ahctf1;;chr3:54559463..54559493,+!p3@Smad9!0.65!7.02!Smad9;;chr16:43619156..43619171,+!p16@Zbtb20!0.65!4.86!Zbtb20;;chr13:37918684..37918701,+!p12@Rreb1!0.65!4.32!Rreb1;;chr19:10315179..10315241,-!p1@Gm98!0.64!41.02!Gm98;;chr19:26679654..26679675,+!p1@Smarca2!0.64!36.70!Smarca2;;chr19:5637528..5637548,+!p2@Rela!0.64!23.21!Rela;;chr9:122775126..122775133,-!p3@Zfp445!0.64!5.94!Zfp445;;chr7:20408047..20408125,-!p1@Bcl3!0.63!43.72!Bcl3;;chr10:82226613..82226641,-!p4@Nfyb!0.63!10.25!Nfyb;;chr3:89197216..89197258,-!p3@Zbtb7b!0.63!7.56!Zbtb7b;;chr5:120121169..120121171,+!p4@Tbx3!0.63!6.48!Tbx3;;chr6:108610513..108610528,+!p3@Bhlhe40!0.63!5.40!Bhlhe40;;chr11:83664334..83664353,+!p2@Hnf1b!0.63!3.24!Hnf1b;;chr10:88996274..88996286,-!p4@Nr1h4!0.63!3.24!Nr1h4;;chr9:21992581..21992593,+!p1@Zfp872!0.63!3.24!Zfp872;;chr11:5420954..5420969,+!p2@Xbp1!0.62!47.49!Xbp1;;chr18:11052606..11052633,+!p4@Gata6!0.62!9.17!Gata6;;chr16:43363837..43363842,+!p11@Zbtb20!0.62!6.48!Zbtb20;;chr13:37949830..37949861,+!p7@Rreb1!0.62!6.48!Rreb1;;chr11:121380594..121380609,-!p2@Zfp750!0.62!5.94!Zfp750;;chr15:85566051..85566080,+!p4@Ppara!0.62!3.78!Ppara;;chr4:97444471..97444514,+!p1@Nfia!0.61!99.31!Nfia;;chr18:3281750..3281776,-!p2@Crem!0.61!7.02!Crem;;chr5:31262699..31262712,-!p2@Preb!0.61!5.40!Preb;;chr19:26679615..26679646,+!p3@Smarca2!0.60!24.83!Smarca2;;chr3:89197057..89197114,-!p1@Zbtb7b!0.60!11.87!Zbtb7b;;chrX:137135036..137135064,-!p4@Tsc22d3!0.60!6.48!Tsc22d3;;chr9:69137672..69137702,+!p2@Rora!0.59!14.57!Rora;;chr15:57526206..57526241,+!p2@Zhx2!0.59!11.33!Zhx2;;chr16:44173384..44173407,+!p2@Gm608!0.59!8.64!Gm608;;chr1:133904946..133904974,+!p7@Elk4!0.59!4.86!Elk4;;chr8:79423144..79423178,+!p3@Nr3c2!0.59!4.32!Nr3c2;;chr6:144157924..144157955,-!p2@Sox5!0.59!3.78!Sox5;;chr10:80889867..80889924,-!p1@Nfic!0.58!97.15!Nfic;;chr6:29476690..29476724,+!p1@Irf5!0.58!15.65!Irf5;;chr8:107793688..107793736,+!p1@Hsf4!0.57!3.78!Hsf4;;chr1:194982959..194983007,+!p5@Irf6!0.57!2.70!Irf6;;chr14:76887566..76887579,+!p18@Tsc22d1!0.57!2.70!Tsc22d1;;chr15:85602655..85602680,+!p5@Ppara!0.57!2.70!Ppara;;chr16:43236088..43236099,+!p43@Zbtb20!0.57!2.70!Zbtb20;;chr12:81213989..81214006,-!p1@Zfp36l1!0.56!170.55!Zfp36l1;;chr7:97591412..97591431,+!p2@Crebzf!0.56!8.10!Crebzf;;chr10:22451765..22451795,-!p6@Tbpl1!0.56!4.32!Tbpl1;;chr5:34530293..34530318,-!p2@Mxd4!0.55!17.81!Mxd4;;chr7:17200019..17200060,-!p4@Grlf1!0.54!13.49!Grlf1;;chr5:34530277..34530292,-!p3@Mxd4!0.54!7.56!Mxd4;;chr2:91034924..91034946,-!p2@Nr1h3!0.54!3.24!Nr1h3;;chr6:83299445..83299490,+!p1@Bola3!0.53!129.53!Bola3;;chr11:106134241..106134320,-!p2@Smarcd2!0.53!35.08!Smarcd2;;chr8:124806048..124806094,+!p1@Zfpm1!0.53!28.06!Zfpm1;;chr11:53583960..53584007,+!p2@Irf1!0.53!5.94!Irf1;;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141;;chr16:87699206..87699229,+!p3@Bach1!0.06!4.86!Bach1;;chr17:15701286..15701323,-!p1@Prdm9!0.06!3.24!Prdm9;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.06!2.16!Tfcp2l1;;chr1:172797934..172797945,-!p4@Atf6!0.06!2.16!Atf6;;chr12:77471500..77471515,+!p2@Zbtb1!0.06!2.16!Zbtb1;;chr13:23460838..23460880,-!p2@Zfp322a!0.06!2.16!Zfp322a;;chr4:82151148..82151159,-!p5@Nfib!0.06!2.16!Nfib;;chr1:33871319..33871333,-!p3@Zfp451!0.06!1.62!Zfp451;;chr1:95651346..95651383,-!p3@Thap4!0.06!1.62!Thap4;;chr10:26093876..26093894,-!p2@L3mbtl3!0.06!1.62!L3mbtl3;;chr7:74517982..74518012,-!p2@Mef2a!0.06!1.08!Mef2a;;chr17:21145981..21145998,+!p2@Zfp160!0.06!1.08!Zfp160;;chr19:55817629..55817652,+!p14@Tcf7l2!0.06!0.54!Tcf7l2;;chr9:19426719..19426729,+!p4@Zfp317!0.06!0.54!Zfp317;;chr7:30088977..30089002,+!p2@Dpf1!0.06!0.54!Dpf1;;chr8:112229401..112229419,+!p3@Zfp821!0.06!0.54!Zfp821;;chr2:17985518..17985540,+!p6@Mllt10!0.06!0.54!Mllt10;;chr4:149610794..149610876,+!p2@LOC100045967,p2@LOC100503183,p3@Eno1,p3@Gm5506!0.06!0.54!Eno1;;chr10:41996451..41996462,-!p5@Foxo3!0.06!0.54!Foxo3;;chr12:85534690..85534708,-!p9@C130039O16Rik!0.06!0.54!C130039O16Rik;;chr6:108610428..108610440,+!p4@Bhlhe40!0.06!0.54!Bhlhe40;;chr7:17200615..17200625,-!p9@Grlf1!0.06!0.54!Grlf1;;chr4:40216811..40216882,-!p1@Topors!0.05!18.35!Topors;;chr3:87329494..87329565,+!p1@Etv3!0.05!14.57!Etv3;;chr2:168780757..168780805,-!p1@LOC100502777,p1@Zfp64!0.05!14.03!Zfp64;;chr11:120494853..120494905,-!p1@Mafg!0.05!9.17!Mafg;;chr2:181100089..181100119,+!p1@Zgpat!0.05!8.64!Zgpat;;chr11:53164378..53164392,+!p2@Aff4!0.05!8.10!Aff4;;chr17:47873985..47874056,+!p1@Tfeb!0.05!7.56!Tfeb;;chr19:6996294..6996324,-!p2@Esrra!0.05!5.94!Esrra;;chr9:21420572..21420591,+!p2@Smarca4!0.05!4.86!Smarca4;;chr8:108583550..108583595,+!p2@Nfatc3!0.05!3.78!Nfatc3;;chr10:5959061..5959104,+!p2@Zbtb2!0.05!3.24!Zbtb2;;chr17:34784073..34784118,+!p2@Atf6b!0.05!3.24!Atf6b;;chr10:126726021..126726053,-!p4@Mbd6!0.05!2.70!Mbd6;;chr2:31428221..31428244,+!p2@Fubp3!0.05!1.62!Fubp3;;chr4:45024965..45025031,-!p3@Zbtb5!0.05!1.62!Zbtb5;;chr4:126700722..126700753,+!p4@Sfpq!0.05!1.62!Sfpq;;chr14:65977427..65977452,+!p4@Zfp395!0.05!1.62!Zfp395;;chr11:23670750..23670789,-!p2@Rel!0.05!1.08!Rel;;chr6:72185553..72185612,-!p2@Atoh8!0.05!1.08!Atoh8;;chr4:126700683..126700704,+!p6@Sfpq!0.05!1.08!Sfpq;;chr18:3337465..3337498,-!p6@Crem!0.05!1.08!Crem;;chr18:3337612..3337644,-!p8@Crem!0.05!1.08!Crem;;chr16:30065394..30065398,+!p3@Hes1!0.05!0.54!Hes1;;chr13:64254572..64254585,-!p6@Zfp367!0.05!0.54!Zfp367;;chr13:37870253..37870272,+!p13@Rreb1!0.05!0.54!Rreb1;;chr14:104867201..104867258,-!p1@Pou4f1!0.05!0.54!Pou4f1;;chr18:36953572..36953591,+!p1@Zmat2!0.04!57.21!Zmat2;;chr2:83484681..83484704,+!p1@Zc3h15!0.04!44.80!Zc3h15;;chr18:74375851..74375891,+!p1@Cxxc1!0.04!38.86!Cxxc1;;chr7:13420322..13420401,+!p1@Zfp110!0.04!19.43!Zfp110;;chr11:4604645..4604705,+!p1@Zmat5!0.04!12.41!Zmat5;;chr2:148506890..148506933,+!p1@Gzf1!0.04!10.25!Gzf1;;chr16:14705961..14705978,+!p2@Snai2!0.04!3.78!Snai2;;chr5:110539087..110539133,+!p1@Zfp605!0.04!2.16!Zfp605;;chr19:9016975..9017004,+!p2@Mta2!0.04!2.16!Mta2;;chr3:95021799..95021840,-!p4@Gabpb2!0.04!2.16!Gabpb2;;chr16:42907554..42907591,+!p5@Zbtb20!0.04!1.62!Zbtb20;;chr11:120494669..120494688,-!p2@Mafg!0.04!1.62!Mafg;;chr13:67433461..67433489,-!p2@Zfp595!0.04!1.62!Zfp595;;chr13:65380103..65380116,+!p3@Zfp369!0.04!1.62!Zfp369;;chr1:74634691..74634719,-!p2@Zfp142!0.04!1.62!Zfp142;;chr5:65194709..65194716,+!p10@Klf3!0.04!1.08!Klf3;;chr7:134169648..134169657,-!p14@Maz!0.04!0.54!Maz;;chr10:127080091..127080100,+!p4@Stat6!0.04!0.54!Stat6;;chr3:9610233..9610247,-!p4@Zfp704!0.04!0.54!Zfp704;;chr1:87546583..87546595,+!p1@Sp100!0.04!0.54!Sp100;;chr15:100058302..100058309,+!p3@Gm1862,p5@Atf1!0.04!0.54!Atf1;;chr6:48395743..48395820,-!p1@Zfp467!0.03!19.97!Zfp467;;chr15:38230448..38230470,-!p1@Klf10!0.03!19.43!Klf10;;chr12:72116953..72117050,+!p1@Arid4a!0.03!10.79!Arid4a;;chr18:80904854..80904919,-!p2@Nfatc1!0.03!10.79!Nfatc1;;chr7:17199897..17199955,-!p1@Grlf1!0.03!10.25!Grlf1;;chr17:21625946..21626024,+!p1@Zfp53!0.03!9.71!Zfp53;;chr2:32218712..32218782,+!p2@Ciz1!0.03!9.17!Ciz1;;chr19:55816770..55816793,+!p2@Tcf7l2!0.03!7.56!Tcf7l2;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.03!4.86!Zbtb11;;chr9:20297135..20297154,-!p2@Zfp426!0.03!2.70!Zfp426;;chr9:21420610..21420621,+!p5@Smarca4!0.03!2.16!Smarca4;;chr7:134489096..134489123,-!p2@Zfp768!0.03!2.16!Zfp768;;chr1:170362437..170362478,-!p5@Pbx1!0.03!2.16!Pbx1;;chr2:165818108..165818119,+!p2@Ncoa3!0.03!1.62!Ncoa3;;chr7:13063643..13063662,+!p2@Zfp606!0.03!1.62!Zfp606;;chr7:148513574..148513593,-!p5@Deaf1!0.03!1.08!Deaf1;;chr7:74517748..74517757,-!p3@Mef2a!0.03!1.08!Mef2a;;chr8:107694568..107694586,+!p5@Cbfb!0.03!1.08!Cbfb;;chr19:26681721..26681746,+!p9@Smarca2!0.03!1.08!Smarca2;;chr2:37286328..37286341,-!p3@Zbtb6!0.03!1.08!Zbtb6;;chrX:45947787..45947812,-!p3@Zfp280c!0.03!1.08!Zfp280c;;chr4:126700650..126700678,+!p5@Sfpq!0.03!1.08!Sfpq;;chr4:97444563..97444572,+!p12@Nfia!0.03!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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000109
 |is_obsolete=
-|library_ids=CNhs12615
+|library_id=CNhs12615
+|library_id_phase_based=2:CNhs12615
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11637
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11637
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor3.CNhs12615.11637-122C8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor3.CNhs12615.11637-122C8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor3.CNhs12615.11637-122C8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor3.CNhs12615.11637-122C8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatocyte%252c%2520donor3.CNhs12615.11637-122C8.mm9.nobarcode.rdna.fa.gz
 |name=Mouse hepatocyte, donor3
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12615,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0411740900682821,0,0,0,0,0,0.23490537496843,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.00445634086254859,0,0,0,1.02997829108682,0,0,0,0,0,0,0,0,0.932262892080073,-0.0588989077495106,0,0,0,0.187437010020026,0,-0.209322725495826,-0.105152024863223,-0.502991654370686,-0.566057698222585,-0.0824316279903253,0.499523884574521,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.187437010020026,0,0.121991625967888,0,0,0,-0.149507273184257,-0.12321364731936,-0.158091042771083,-0.0365927089968535,0,0,-0.134839636603528,-0.0852915946424746,0,0,-0.0709054426177252,0.035679379972241,1.10403543883334,-0.0788315948399074,0,0,0,0,0,0,0.624609545873197,0.955105018158938,0.572470305367017,0,0,0,0.420258443339529,0
@@ 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=table111:11637-122C8;search_select_hide=table117:11637-122C8
-|DRA_sample_Accession=CAGE@DRS008748
-|accession_numbers=DRX008858;DRR009730;DRZ001155;DRZ002540;CAGE
-|library_id=CNhs12615
 }}

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FF:11637-122C8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:12, 4 June 2020

CNhs12615

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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