FF:11825-124F7: Difference between revisions

Latest revision as of 18:22, 4 June 2020

Name:	Mouse hepatic Stellate Cells (lipocyte), donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs13196
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	NA
sex	male
age	NA
cell type	adipocyte, lipocyte of liver
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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005887

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13196		CAGE		DRX008856		DRR009728

Accession ID Mm9

Library id		BAM		CTSS
CNhs13196		DRZ001153		DRZ002538

Accession ID Mm10

Library id		BAM		CTSS
CNhs13196		DRZ012503		DRZ013888

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

CNhs13196

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.0941
1003	-0.123
1004	0
1005	0
1006	0.00388
1007	-0.144
1008	0
1009	0.0795
101	-0.0954
1010	0
1011	-0.298
1012	0
1013	0.425
1014	-0.0874
1015	-0.316
1016	-0.379
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.179
1022	0.485
1023	0
1024	0.13
1025	0.397
1026	0
1027	0
1028	0
1029	-0.176
103	-0.0787
1030	0
1031	0.0899
1032	-0.227
1033	-0.0665
1034	0.539
1035	0
1036	-0.369
1037	0
1038	0.0498
1039	0.773
104	0
1040	-0.0865
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: CNhs13196

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0803
MA0003.1	MA0003.1	0.205
MA0004.1	MA0004.1	0.865
MA0006.1	MA0006.1	0.168
MA0007.1	MA0007.1	0.412
MA0009.1	MA0009.1	0.873
MA0014.1	MA0014.1	0.195
MA0017.1	MA0017.1	5.7771e-17
MA0018.2	MA0018.2	0.00157
MA0019.1	MA0019.1	0.598
MA0024.1	MA0024.1	1.25216e-4
MA0025.1	MA0025.1	0.09
MA0027.1	MA0027.1	0.795
MA0028.1	MA0028.1	0.889
MA0029.1	MA0029.1	0.59
MA0030.1	MA0030.1	0.0436
MA0031.1	MA0031.1	0.00479
MA0035.2	MA0035.2	0.0353
MA0038.1	MA0038.1	0.654
MA0039.2	MA0039.2	0.311
MA0040.1	MA0040.1	0.196
MA0041.1	MA0041.1	0.24
MA0042.1	MA0042.1	0.552
MA0043.1	MA0043.1	0.26
MA0046.1	MA0046.1	3.97466e-67
MA0047.2	MA0047.2	4.53176e-6
MA0048.1	MA0048.1	0.608
MA0050.1	MA0050.1	4.09488e-4
MA0051.1	MA0051.1	3.75642e-5
MA0052.1	MA0052.1	0.303
MA0055.1	MA0055.1	0.465
MA0057.1	MA0057.1	0.415
MA0058.1	MA0058.1	0.603
MA0059.1	MA0059.1	0.226
MA0060.1	MA0060.1	1.16885e-4
MA0061.1	MA0061.1	0.129
MA0062.2	MA0062.2	0.808
MA0065.2	MA0065.2	5.33758e-13
MA0066.1	MA0066.1	0.157
MA0067.1	MA0067.1	0.325
MA0068.1	MA0068.1	0.417
MA0069.1	MA0069.1	0.465
MA0070.1	MA0070.1	0.411
MA0071.1	MA0071.1	7.92163e-5
MA0072.1	MA0072.1	6.66368e-6
MA0073.1	MA0073.1	0.916
MA0074.1	MA0074.1	0.325
MA0076.1	MA0076.1	0.55
MA0077.1	MA0077.1	0.193
MA0078.1	MA0078.1	0.999
MA0079.2	MA0079.2	0.393
MA0080.2	MA0080.2	0.139
MA0081.1	MA0081.1	0.605
MA0083.1	MA0083.1	0.305
MA0084.1	MA0084.1	0.743
MA0087.1	MA0087.1	0.792
MA0088.1	MA0088.1	0.352
MA0090.1	MA0090.1	0.268
MA0091.1	MA0091.1	0.862
MA0092.1	MA0092.1	0.151
MA0093.1	MA0093.1	0.9
MA0099.2	MA0099.2	0.579
MA0100.1	MA0100.1	0.184
MA0101.1	MA0101.1	0.211
MA0102.2	MA0102.2	0.177
MA0103.1	MA0103.1	0.427
MA0104.2	MA0104.2	0.75
MA0105.1	MA0105.1	0.0185
MA0106.1	MA0106.1	0.274
MA0107.1	MA0107.1	0.251
MA0108.2	MA0108.2	0.656
MA0111.1	MA0111.1	0.615
MA0112.2	MA0112.2	1.40006e-4
MA0113.1	MA0113.1	0.528
MA0114.1	MA0114.1	1.09405e-15
MA0115.1	MA0115.1	9.17531e-8
MA0116.1	MA0116.1	0.191
MA0117.1	MA0117.1	0.648
MA0119.1	MA0119.1	0.021
MA0122.1	MA0122.1	0.811
MA0124.1	MA0124.1	0.725
MA0125.1	MA0125.1	0.195
MA0131.1	MA0131.1	0.594
MA0135.1	MA0135.1	0.276
MA0136.1	MA0136.1	0.259
MA0137.2	MA0137.2	7.45415e-4
MA0138.2	MA0138.2	0.396
MA0139.1	MA0139.1	0.175
MA0140.1	MA0140.1	0.566
MA0141.1	MA0141.1	6.26011e-5
MA0142.1	MA0142.1	0.124
MA0143.1	MA0143.1	0.437
MA0144.1	MA0144.1	0.0138
MA0145.1	MA0145.1	0.0346
MA0146.1	MA0146.1	0.246
MA0147.1	MA0147.1	0.853
MA0148.1	MA0148.1	6.03729e-7
MA0149.1	MA0149.1	0.0153
MA0150.1	MA0150.1	0.00847
MA0152.1	MA0152.1	0.355
MA0153.1	MA0153.1	1.82777e-52
MA0154.1	MA0154.1	0.066
MA0155.1	MA0155.1	0.706
MA0156.1	MA0156.1	0.431
MA0157.1	MA0157.1	0.00106
MA0159.1	MA0159.1	0.00109
MA0160.1	MA0160.1	3.27555e-4
MA0162.1	MA0162.1	0.176
MA0163.1	MA0163.1	5.97778e-4
MA0164.1	MA0164.1	0.515
MA0258.1	MA0258.1	0.0111
MA0259.1	MA0259.1	0.534

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: CNhs13196

Novel motif	Logo	P-value
1	1	0.0986
10	10	0.202
100	100	0.762
101	101	0.664
102	102	0.215
103	103	0.00416
104	104	0.241
105	105	0.404
106	106	0.0213
107	107	0.0296
108	108	0.886
109	109	0.0232
11	11	0.0508
110	110	0.0792
111	111	0.0491
112	112	0.00569
113	113	0.632
114	114	0.0492
115	115	0.345
116	116	0.698
117	117	0.126
118	118	0.702
119	119	0.115
12	12	0.383
120	120	0.98
121	121	0.188
122	122	0.621
123	123	0.418
124	124	0.561
125	125	0.529
126	126	0.453
127	127	0.623
128	128	0.00676
129	129	0.736
13	13	7.90275e-4
130	130	0.979
131	131	0.107
132	132	0.533
133	133	0.745
134	134	0.547
135	135	0.366
136	136	0.46
137	137	0.763
138	138	0.534
139	139	0.716
14	14	0.441
140	140	0.537
141	141	0.131
142	142	0.329
143	143	0.506
144	144	0.95
145	145	0.133
146	146	0.534
147	147	0.52
148	148	0.985
149	149	0.133
15	15	0.177
150	150	0.22
151	151	0.59
152	152	0.0379
153	153	0.297
154	154	0.597
155	155	0.956
156	156	0.00489
157	157	0.872
158	158	0.482
159	159	0.25
160	160	0.253
161	161	0.419
162	162	0.438
163	163	0.255
164	164	0.117
165	165	0.186
166	166	0.159
167	167	0.527
168	168	0.695
169	169	0.00408
17	17	0.0162
18	18	0.828
19	19	0.0283
2	2	0.479
20	20	0.874
21	21	0.726
22	22	0.131
23	23	0.49
24	24	0.106
25	25	0.65
26	26	0.00767
27	27	0.695
28	28	0.542
29	29	0.457
3	3	0.0574
30	30	0.522
31	31	0.272
32	32	0.0969
33	33	0.272
34	34	0.642
35	35	0.711
36	36	0.0273
37	37	0.0302
38	38	0.409
39	39	0.304
4	4	0.934
40	40	0.0642
41	41	0.687
42	42	0.357
43	43	0.0742
44	44	0.0259
45	45	0.626
46	46	0.122
47	47	0.428
48	48	0.182
49	49	0.0817
5	5	0.166
50	50	0.547
51	51	0.357
52	52	0.275
53	53	0.69
54	54	0.383
55	55	0.519
56	56	0.346
57	57	0.818
58	58	0.38
59	59	0.076
6	6	0.853
60	60	0.0827
61	61	0.375
62	62	0.145
63	63	0.0969
64	64	0.518
65	65	0.159
66	66	0.794
67	67	0.879
68	68	0.0712
69	69	0.772
7	7	0.191
70	70	0.0254
71	71	0.0568
72	72	0.58
73	73	0.029
74	74	0.183
75	75	0.0383
76	76	0.887
77	77	0.257
78	78	0.0866
79	79	0.744
8	8	0.00802
80	80	0.49
81	81	0.608
82	82	0.0431
83	83	0.228
84	84	0.09
85	85	0.0385
86	86	0.215
87	87	0.0913
88	88	0.79
89	89	0.0382
9	9	0.954
90	90	0.183
91	91	0.286
92	92	0.0751
93	93	0.082
94	94	0.898
95	95	0.171
96	96	0.931
97	97	0.503
98	98	0.493
99	99	0.16

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: CNhs13196

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011461 Mouse hepatic Stellate Cells (lipocyte) 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)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0000632 (hepatic stellate cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0002384 (connective tissue)
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)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000077 (hepatic stellate cell sample)
0011461 (Mouse hepatic Stellate Cells (lipocyte) 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)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002107,UBERON:0002100,UBERON:0000483,UBERON:0002530,UBERON:0002384,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0002368,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0003914,UBERON:0007499,UBERON:0002050,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0009569,UBERON:0005291,UBERON:0009854,UBERON:0003929,UBERON:0005177,UBERON:0002365,UBERON:0003104,UBERON:0005057,UBERON:0005172,UBERON:0006925,UBERON:0005256,UBERON:0001048,UBERON:0000925,UBERON:0006598,UBERON:0009497,UBERON:0004185,UBERON:0005173,UBERON:0000015,UBERON:0009856,UBERON:0002532,UBERON:0001555,UBERON:0002417,UBERON:0007026,UBERON:0001041,UBERON:0000949,UBERON:0002330,UBERON:0000916,UBERON:0002405,UBERON:0002423,UBERON:0009142,UBERON:0006235,UBERON:0006595,UBERON:0006603,UBERON:0008835,UBERON:0003894,UBERON:0004161,UBERON:0008836
+|DRA_sample_Accession=CAGE@SAMD00005887
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000055,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000151,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000219,CL:0000499,CL:0000327,CL:0000004,CL:0000134,CL:0000255,CL:0000057,CL:0000632
+|accession_numbers=CAGE;DRX008856;DRR009728;DRZ001153;DRZ002538;DRZ012503;DRZ013888
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,UBERON:0002384,UBERON:0000479,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:0000151,CL:0002320,CL:0002371,CL:0000499,CL:0000327,CL:0000255,CL:0000057,CL:0000632
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000077,FF:0011461
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:80555320..80555378,-!p1@Creb3l3!2.19!176.39!Creb3l3;;chr4:133109285..133109308,+!p1@Nr0b2!2.15!139.39!Nr0b2;;chr5:135582751..135582788,+!p1@Mlxipl!1.97!350.19!Mlxipl;;chr9:74709695..74709722,+!p1@Onecut1!1.84!67.97!Onecut1;;chr10:88969376..88969395,-!p1@Nr1h4!1.80!61.95!Nr1h4;;chr12:86814833..86814846,+!p1@Fos!1.65!958.51!Fos;;chr7:19895354..19895369,-!p1@Fosb!1.60!53.35!Fosb;;chr7:19608891..19608895,-!p1@Foxa3!1.59!49.04!Foxa3;;chr10:88996295..88996335,-!p3@Nr1h4!1.55!40.44!Nr1h4;;chr2:163372884..163372904,+!p1@Hnf4a!1.55!34.42!Hnf4a;;chr1:173144144..173144176,+!p1@Nr1i3!1.53!32.70!Nr1i3;;chr2:133377954..133377973,+!p1@Bmp2!1.46!86.04!Bmp2;;chr16:38294860..38294924,-!p1@Nr1i2!1.46!27.53!Nr1i2;;chr1:193007123..193007139,-!p1@Atf3!1.45!147.99!Atf3;;chr1:173144100..173144138,+!p2@Nr1i3!1.44!26.67!Nr1i3;;chr10:88996336..88996380,-!p2@Nr1h4!1.43!31.84!Nr1h4;;chr8:59799772..59799789,+!p1@Hand2!1.40!67.11!Hand2;;chr19:37509324..37509337,+!p1@Hhex!1.39!160.04!Hhex;;chr14:63864056..63864102,-!p1@Gata4!1.37!38.72!Gata4;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.37!28.39!Zbtb11;;chr9:74714303..74714318,+!p2@Onecut1!1.35!21.51!Onecut1;;chr15:85566184..85566238,+!p1@Ppara!1.34!30.98!Ppara;;chr2:27531961..27531974,+!p7@Rxra!1.34!20.65!Rxra;;chr7:35904304..35904320,+!p1@Cebpa!1.30!374.28!Cebpa;;chr7:19895384..19895399,-!p2@Fosb!1.30!26.67!Fosb;;chr15:85566537..85566552,+!p2@Ppara!1.28!18.07!Ppara;;chr12:58646974..58647003,-!p1@Foxa1!1.23!21.51!Foxa1;;chr11:100683839..100683890,-!p2@Stat5b!1.22!36.14!Stat5b;;chr15:75799634..75799645,+!p4@Zfp707!1.20!17.21!Zfp707;;chr18:35020854..35020869,+!p1@Egr1!1.19!542.93!Egr1;;chr6:90415250..90415271,+!p4@Klf15!1.19!14.63!Klf15;;chr11:90249521..90249551,-!p3@Hlf!1.19!14.63!Hlf;;chr18:64499674..64499696,+!p1@Onecut2!1.18!24.09!Onecut2;;chr4:32334732..32334739,+!p7@Bach2!1.17!13.77!Bach2;;chr11:5420655..5420659,+!p3@Xbp1!1.12!12.05!Xbp1;;chr10:88996274..88996286,-!p4@Nr1h4!1.12!12.05!Nr1h4;;chr6:108610766..108610781,+!p2@Bhlhe40!1.11!21.51!Bhlhe40;;chr10:22539932..22539956,-!p1@Tcf21!1.08!29.25!Tcf21;;chr2:91035197..91035237,-!p1@Nr1h3!1.07!22.37!Nr1h3;;chr3:94176733..94176794,+!p1@Rorc!1.06!82.60!Rorc;;chr9:24578720..24578735,-!p1@Tbx20!1.05!10.33!Tbx20;;chr16:43235969..43235989,+!p20@Zbtb20!1.05!10.33!Zbtb20;;chr6:90412608..90412630,+!p2@Klf15!1.04!20.65!Klf15;;chr2:91034924..91034946,-!p2@Nr1h3!1.03!12.05!Nr1h3;;chr18:75979866..75979890,+!p3@Zbtb7c!1.01!19.79!Zbtb7c;;chr11:60023912..60023930,-!p1@Srebf1!1.00!221.99!Srebf1;;chr6:90412582..90412601,+!p1@Klf15!1.00!43.02!Klf15;;chr4:94718861..94718872,-!p2@Jun!0.99!67.11!Jun;;chr18:64499706..64499721,+!p2@Onecut2!0.98!12.05!Onecut2;;chr3:102768047..102768060,-!p1@Nr1h5!0.98!8.60!Nr1h5;;chr8:87502608..87502623,-!p1@Junb!0.95!134.23!Junb;;chr13:53076382..53076393,-!p2@Nfil3!0.95!12.91!Nfil3;;chr2:77357622..77357704,-!p1@Zfp385b!0.94!21.51!Zfp385b;;chr2:27532479..27532509,+!p3@Rxra!0.94!16.35!Rxra;;chr2:147872790..147872821,-!p2@Foxa2!0.94!7.74!Foxa2;;chr2:163372869..163372882,+!p3@Hnf4a!0.94!7.74!Hnf4a;;chr10:80555299..80555306,-!p3@Creb3l3!0.94!7.74!Creb3l3;;chr16:43363190..43363242,+!p2@Zbtb20!0.93!24.09!Zbtb20;;chr2:91035254..91035271,-!p3@Nr1h3!0.93!9.46!Nr1h3;;chr2:160698288..160698358,-!p3@Zhx3!0.92!23.23!Zhx3;;chr15:85566051..85566080,+!p4@Ppara!0.92!8.60!Ppara;;chr15:75799598..75799619,+!p3@Zfp707!0.91!15.49!Zfp707;;chr15:79178060..79178074,+!p2@Maff!0.91!9.46!Maff;;chr15:85602655..85602680,+!p5@Ppara!0.90!6.88!Ppara;;chr15:85566241..85566253,+!p6@Ppara!0.90!6.88!Ppara;;chr10:80555285..80555291,-!p4@Creb3l3!0.90!6.88!Creb3l3;;chr7:148452314..148452329,-!p1@Irf7!0.88!48.18!Irf7;;chr2:173044380..173044432,-!p1@Zbp1!0.88!16.35!Zbp1;;chr14:18493386..18493464,+!p1@Thrb!0.87!25.81!Thrb;;chr17:87153519..87153533,+!p5@Epas1!0.86!9.46!Epas1;;chr2:38206744..38206766,+!p1@Lhx2!0.86!7.74!Lhx2;;chr14:63890491..63890516,-!p2@Gata4!0.85!6.02!Gata4;;chr9:48644429..48644462,-!p3@Zbtb16!0.84!12.05!Zbtb16;;chr18:3281034..3281104,-!p1@Crem!0.83!43.88!Crem;;chr10:88145766..88145770,-!p1@Spic!0.83!7.74!Spic;;chr9:48644037..48644067,-!p2@Zbtb16!0.82!14.63!Zbtb16;;chr2:38206580..38206600,+!p2@Lhx2!0.81!6.88!Lhx2;;chr11:98636508..98636524,-!p3@Nr1d1!0.81!6.88!Nr1d1;;chr2:167514456..167514473,+!p1@Cebpb!0.80!258.13!Cebpb;;chr2:27532754..27532815,+!p1@Rxra!0.80!167.78!Rxra;;chr16:43363152..43363186,+!p3@Zbtb20!0.80!12.91!Zbtb20;;chr11:100683794..100683805,-!p4@Stat5b!0.79!5.16!Stat5b;;chr10:80555398..80555409,-!p2@Creb3l3!0.79!5.16!Creb3l3;;chr5:115421065..115421088,-!p1@Hnf1a!0.79!5.16!Hnf1a;;chr8:123608252..123608268,+!p1@Foxf1a!0.78!7.74!Foxf1a;;chr4:94718879..94718898,-!p1@Jun!0.77!386.33!Jun;;chr11:53583544..53583559,+!p1@Irf1!0.77!90.34!Irf1;;chr19:23215673..23215753,+!p1@Klf9!0.77!78.30!Klf9;;chr18:69681483..69681514,+!p11@Tcf4!0.77!8.60!Tcf4;;chr4:135699731..135699747,+!p1@Id3!0.76!588.53!Id3;;chr4:135700687..135700719,+!p2@Id3!0.76!7.74!Id3;;chr17:87153505..87153516,+!p6@Epas1!0.76!6.88!Epas1;;chr1:93309740..93309811,-!p1@Hes6!0.75!103.25!Hes6;;chr16:44173384..44173407,+!p2@Gm608!0.75!12.91!Gm608;;chr2:173044357..173044377,-!p2@Zbp1!0.75!6.88!Zbp1;;chr1:39250584..39250643,+!p1@Npas2!0.74!24.95!Npas2;;chr8:107793737..107793757,+!p2@Hsf4!0.74!5.16!Hsf4;;chr5:77524250..77524300,-!p1@Hopx!0.73!98.95!Hopx;;chr18:3281750..3281776,-!p2@Crem!0.73!9.46!Crem;;chr11:98636400..98636418,-!p4@Nr1d1!0.73!6.02!Nr1d1;;chr2:27532513..27532525,+!p8@Rxra!0.73!5.16!Rxra;;chr9:69137716..69137744,+!p1@Rora!0.72!30.11!Rora;;chr8:73905892..73905903,-!p5@Nr2f6!0.72!5.16!Nr2f6;;chr14:76887526..76887555,+!p10@Tsc22d1!0.72!4.30!Tsc22d1;;chr16:43247391..43247422,+!p12@Zbtb20!0.72!4.30!Zbtb20;;chr19:5637528..5637548,+!p2@Rela!0.71!27.53!Rela;;chr6:134780234..134780288,+!p1@Crebl2!0.71!14.63!Crebl2;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.71!6.02!Carhsp1;;chr13:31650185..31650201,+!p1@Foxq1!0.70!15.49!Foxq1;;chr17:87153240..87153254,+!p1@Epas1!0.69!87.76!Epas1;;chr1:138846047..138846074,-!p5@Nr5a2!0.69!4.30!Nr5a2;;chr6:134780337..134780355,+!p3@Crebl2!0.68!5.16!Crebl2;;chr8:118230866..118230891,-!p4@Maf!0.67!27.53!Maf;;chr11:98636373..98636387,-!p5@Nr1d1!0.67!4.30!Nr1d1;;chr11:5420954..5420969,+!p2@Xbp1!0.65!50.77!Xbp1;;chr3:135271185..135271254,-!p4@Nfkb1!0.65!6.88!Nfkb1;;chr1:87546583..87546595,+!p1@Sp100!0.65!5.16!Sp100;;chr1:191993385..191993405,-!p3@Prox1!0.65!3.44!Prox1;;chr6:90415281..90415295,+!p5@Klf15!0.65!3.44!Klf15;;chr6:90416275..90416286,+!p9@Klf15!0.65!3.44!Klf15;;chr9:74709664..74709671,+!p6@Onecut1!0.65!3.44!Onecut1;;chr9:74709682..74709691,+!p3@Onecut1!0.65!3.44!Onecut1;;chr16:43236088..43236099,+!p43@Zbtb20!0.65!3.44!Zbtb20;;chr16:38294929..38294940,-!p2@Nr1i2!0.65!3.44!Nr1i2;;chr12:36219283..36219298,-!p2@Ahr!0.65!3.44!Ahr;;chr8:74842952..74842970,+!p1@Klf2!0.64!269.31!Klf2;;chr16:55822241..55822258,-!p1@Nfkbiz!0.64!123.04!Nfkbiz;;chr6:29476690..29476724,+!p1@Irf5!0.64!18.07!Irf5;;chr6:39068163..39068176,-!p2@Parp12!0.64!6.88!Parp12;;chr4:82151500..82151505,-!p11@Nfib!0.64!4.30!Nfib;;chr16:15887371..15887385,+!p1@Cebpd!0.63!133.37!Cebpd;;chr7:52071956..52071978,-!p1@Atf5!0.63!124.76!Atf5;;chr6:72185210..72185228,-!p3@Atoh8!0.63!6.02!Atoh8;;chr6:52154386..52154407,-!p2@Hoxa5!0.63!4.30!Hoxa5;;chr12:56593574..56593592,-!p1@Nfkbia!0.62!195.32!Nfkbia;;chr2:181406327..181406350,-!p1@Sox18!0.62!117.88!Sox18;;chr13:53076396..53076452,-!p1@Nfil3!0.62!67.97!Nfil3;;chr1:191994550..191994623,-!p1@Prox1!0.62!25.81!Prox1;;chr6:90412556..90412581,+!p3@Klf15!0.62!7.74!Klf15;;chr6:72849280..72849297,-!p6@Kcmf1!0.62!6.88!Kcmf1;;chr18:3337503..3337536,-!p7@Crem!0.62!6.02!Crem;;chr8:107793688..107793736,+!p1@Hsf4!0.62!4.30!Hsf4;;chr1:138845748..138845766,-!p4@Nr5a2!0.62!4.30!Nr5a2;;chr16:95680889..95680991,-!p1@Erg!0.61!30.11!Erg;;chr8:123260252..123260264,+!p1@Irf8!0.61!25.81!Irf8;;chr18:75979828..75979864,+!p2@Zbtb7c!0.61!7.74!Zbtb7c;;chr11:5420973..5420992,+!p1@Xbp1!0.60!379.45!Xbp1;;chr9:32503590..32503680,+!p1@Ets1!0.60!132.51!Ets1;;chr12:25780945..25780961,-!p1@Id2!0.59!592.83!Id2;;chr8:118231678..118231692,-!p2@Maf!0.59!31.84!Maf;;chr6:52154414..52154462,-!p1@Hoxa5!0.59!4.30!Hoxa5;;chr6:16848395..16848416,-!p2@Tfec!0.59!3.44!Tfec;;chr6:39068210..39068251,-!p1@Parp12!0.58!15.49!Parp12;;chr1:181733737..181733755,-!p2@Ahctf1!0.58!10.33!Ahctf1;;chr7:97591412..97591431,+!p2@Crebzf!0.58!8.60!Crebzf;;chr11:53583960..53584007,+!p2@Irf1!0.58!6.88!Irf1;;chr7:51787434..51787448,-!p1@Spib!0.58!4.30!Spib;;chr10:127707602..127707633,+!p1@Stat2!0.57!29.25!Stat2;;chr11:70043257..70043263,-!p1@Bcl6b!0.57!5.16!Bcl6b;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.57!5.16!Hoxb2;;chr17:87153462..87153473,+!p3@Epas1!0.56!12.05!Epas1;;chr18:3337339..3337397,-!p5@Crem!0.56!6.02!Crem;;chr2:148506935..148506954,+!p2@Gzf1!0.56!6.02!Gzf1;;chr11:121380594..121380609,-!p2@Zfp750!0.56!5.16!Zfp750;;chr1:4486481..4486501,-!p2@Sox17!0.56!4.30!Sox17;;chr6:144157924..144157955,-!p2@Sox5!0.56!3.44!Sox5;;chr10:92773591..92773623,-!p1@Elk3!0.55!72.28!Elk3;;chr6:39068181..39068206,-!p3@Parp12!0.55!6.02!Parp12;;chr1:186556375..186556404,-!p3@Hlx!0.55!5.16!Hlx;;chr10:127176667..127176679,+!p2@Zbtb39!0.55!4.30!Zbtb39;;chr11:83664365..83664383,+!p1@Hnf1b!0.55!2.58!Hnf1b;;chr14:76887566..76887579,+!p18@Tsc22d1!0.55!2.58!Tsc22d1;;chr1:138846079..138846103,-!p6@Nr5a2!0.55!2.58!Nr5a2;;chr2:147871627..147871641,-!p1@Foxa2!0.55!2.58!Foxa2;;chr9:74714281..74714296,+!p5@Onecut1!0.55!2.58!Onecut1;;chr16:43236037..43236050,+!p35@Zbtb20!0.55!2.58!Zbtb20;;chr7:120351014..120351109,+!p1@Arntl!0.54!43.02!Arntl;;chr1:52176315..52176343,+!p1@Stat1!0.53!43.88!Stat1;;chr16:42907676..42907797,+!p1@Zbtb20!0.53!39.58!Zbtb20;;chr10:92773736..92773761,-!p4@Elk3!0.53!4.30!Elk3;;chr5:107003725..107003746,-!p5@Zfp644!0.53!3.44!Zfp644;;chr1:194979361..194979373,+!p2@Irf6!0.53!3.44!Irf6;;chr6:83299445..83299490,+!p1@Bola3!0.52!125.62!Bola3;;chr7:20408047..20408125,-!p1@Bcl3!0.52!33.56!Bcl3;;chr14:56223010..56223067,+!p1@Irf9!0.52!23.23!Irf9;;chr13:99954640..99954681,+!p1@Zfp366!0.52!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+|ffid_belonging_in_development=CL:0000134
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011461
 |is_obsolete=
+|library_id=CNhs13196
+|library_id_phase_based=2:CNhs13196
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11825
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11825
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520hepatic%2520Stellate%2520Cells%2520%2528lipocyte%2529%252c%2520donor1.CNhs13196.11825-124F7.mm9.nobarcode.rdna.fa.gz
 |name=Mouse hepatic Stellate Cells (lipocyte), donor1
 |namespace=
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13196,LSID1004,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0170103560001075,0,0,0,0,0,-0.060712958466895,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,1.21715822720348,0,0,0,0,0,0,0,0,0.134805952340487,0.0891259906681807,0,0,0,0,0,0.060289179185148,-0.0661618130246221,-0.392470759882259,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,0.203606357117534,0,0,0,0,0.226764949598099,0,0.00410938688970023,0,0.269611904680974,0,0.0107385330867252,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.108827423911227,0,0,0,-0.00288560825292755,-0.132310320660092,1.00308423924918,-0.0788315948399074,0,0,0,0,0,0,0.586720340194693,0.537004697431422,1.11231577838063,0,0,0,0,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=1.12
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11825-124F7;search_select_hide=table117:11825-124F7
 }}

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FF:11825-124F7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:22, 4 June 2020

CNhs13196

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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