FF:751-24B9: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	liver, neonate N10
Species:	Mouse (Mus musculus)
Library ID:	CNhs11115
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	10 days neonate
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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005395

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11115		CAGE		DRX009026		DRR009900

Accession ID Mm9

Library id		BAM		CTSS
CNhs11115		DRZ001325		DRZ002708

Accession ID Mm10

Library id		BAM		CTSS
CNhs11115		DRZ012675		DRZ014058

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

CNhs11115

0	0
1	0
10	0
100	0
1000	0.0235
1001	0.148
1002	-0.0388
1003	-0.00256
1004	0
1005	0.0791
1006	0.021
1007	-0.0614
1008	0
1009	0.0272
101	-0.0232
1010	0
1011	-0.168
1012	0
1013	0.39
1014	0.00534
1015	-0.166
1016	0.0251
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.193
1023	0
1024	0
1025	0.617
1026	0
1027	0
1028	0
1029	0.0278
103	0
1030	0.118
1031	-0.0163
1032	-0.177
1033	0
1034	0.647
1035	0
1036	0.0301
1037	0
1038	-0.0566
1039	0.487
104	0
1040	-0.152
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: CNhs11115

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.134
MA0003.1	MA0003.1	0.364
MA0004.1	MA0004.1	0.942
MA0006.1	MA0006.1	0.197
MA0007.1	MA0007.1	0.489
MA0009.1	MA0009.1	0.552
MA0014.1	MA0014.1	0.55
MA0017.1	MA0017.1	3.28214e-20
MA0018.2	MA0018.2	8.29836e-7
MA0019.1	MA0019.1	0.505
MA0024.1	MA0024.1	0.145
MA0025.1	MA0025.1	0.319
MA0027.1	MA0027.1	0.421
MA0028.1	MA0028.1	0.935
MA0029.1	MA0029.1	0.35
MA0030.1	MA0030.1	0.03
MA0031.1	MA0031.1	0.049
MA0035.2	MA0035.2	0.314
MA0038.1	MA0038.1	0.736
MA0039.2	MA0039.2	0.704
MA0040.1	MA0040.1	0.496
MA0041.1	MA0041.1	0.195
MA0042.1	MA0042.1	0.539
MA0043.1	MA0043.1	0.0337
MA0046.1	MA0046.1	4.63389e-77
MA0047.2	MA0047.2	4.37195e-7
MA0048.1	MA0048.1	0.297
MA0050.1	MA0050.1	0.00242
MA0051.1	MA0051.1	0.00973
MA0052.1	MA0052.1	0.0805
MA0055.1	MA0055.1	0.346
MA0057.1	MA0057.1	0.842
MA0058.1	MA0058.1	0.811
MA0059.1	MA0059.1	0.286
MA0060.1	MA0060.1	0.00381
MA0061.1	MA0061.1	0.332
MA0062.2	MA0062.2	0.735
MA0065.2	MA0065.2	4.75763e-14
MA0066.1	MA0066.1	0.0133
MA0067.1	MA0067.1	0.027
MA0068.1	MA0068.1	0.247
MA0069.1	MA0069.1	0.271
MA0070.1	MA0070.1	0.296
MA0071.1	MA0071.1	6.03811e-4
MA0072.1	MA0072.1	1.29276e-4
MA0073.1	MA0073.1	0.575
MA0074.1	MA0074.1	0.308
MA0076.1	MA0076.1	0.553
MA0077.1	MA0077.1	0.0179
MA0078.1	MA0078.1	0.531
MA0079.2	MA0079.2	0.321
MA0080.2	MA0080.2	0.181
MA0081.1	MA0081.1	0.837
MA0083.1	MA0083.1	0.271
MA0084.1	MA0084.1	0.434
MA0087.1	MA0087.1	0.233
MA0088.1	MA0088.1	0.579
MA0090.1	MA0090.1	0.503
MA0091.1	MA0091.1	0.884
MA0092.1	MA0092.1	0.0518
MA0093.1	MA0093.1	0.932
MA0099.2	MA0099.2	0.198
MA0100.1	MA0100.1	0.274
MA0101.1	MA0101.1	0.784
MA0102.2	MA0102.2	0.326
MA0103.1	MA0103.1	0.31
MA0104.2	MA0104.2	0.559
MA0105.1	MA0105.1	0.0321
MA0106.1	MA0106.1	0.0517
MA0107.1	MA0107.1	0.98
MA0108.2	MA0108.2	0.051
MA0111.1	MA0111.1	0.86
MA0112.2	MA0112.2	1.37527e-6
MA0113.1	MA0113.1	0.531
MA0114.1	MA0114.1	2.4388e-20
MA0115.1	MA0115.1	4.61353e-10
MA0116.1	MA0116.1	0.0841
MA0117.1	MA0117.1	0.918
MA0119.1	MA0119.1	0.00558
MA0122.1	MA0122.1	0.401
MA0124.1	MA0124.1	0.505
MA0125.1	MA0125.1	0.882
MA0131.1	MA0131.1	0.921
MA0135.1	MA0135.1	0.57
MA0136.1	MA0136.1	0.88
MA0137.2	MA0137.2	0.331
MA0138.2	MA0138.2	0.381
MA0139.1	MA0139.1	0.0692
MA0140.1	MA0140.1	0.336
MA0141.1	MA0141.1	1.67293e-5
MA0142.1	MA0142.1	0.211
MA0143.1	MA0143.1	0.127
MA0144.1	MA0144.1	0.549
MA0145.1	MA0145.1	0.13
MA0146.1	MA0146.1	0.201
MA0147.1	MA0147.1	0.674
MA0148.1	MA0148.1	9.56357e-11
MA0149.1	MA0149.1	0.049
MA0150.1	MA0150.1	0.0849
MA0152.1	MA0152.1	0.271
MA0153.1	MA0153.1	3.21055e-51
MA0154.1	MA0154.1	0.0592
MA0155.1	MA0155.1	0.374
MA0156.1	MA0156.1	0.911
MA0157.1	MA0157.1	0.0211
MA0159.1	MA0159.1	2.43601e-4
MA0160.1	MA0160.1	0.00134
MA0162.1	MA0162.1	0.493
MA0163.1	MA0163.1	3.50784e-5
MA0164.1	MA0164.1	0.956
MA0258.1	MA0258.1	0.00436
MA0259.1	MA0259.1	0.368

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: CNhs11115

Novel motif	Logo	P-value
1	1	0.128
10	10	0.143
100	100	0.66
101	101	0.986
102	102	0.0928
103	103	0.0156
104	104	0.555
105	105	0.827
106	106	0.0403
107	107	0.0387
108	108	0.383
109	109	0.0684
11	11	0.113
110	110	0.0424
111	111	0.0782
112	112	0.00567
113	113	0.899
114	114	0.0371
115	115	0.861
116	116	0.905
117	117	0.0793
118	118	0.188
119	119	0.0979
12	12	0.593
120	120	0.562
121	121	0.767
122	122	0.606
123	123	0.289
124	124	0.409
125	125	0.277
126	126	0.336
127	127	0.55
128	128	0.0286
129	129	0.638
13	13	8.1832e-5
130	130	0.617
131	131	0.157
132	132	0.494
133	133	0.503
134	134	0.816
135	135	0.476
136	136	0.387
137	137	0.976
138	138	0.217
139	139	0.852
14	14	0.409
140	140	0.0187
141	141	0.383
142	142	0.363
143	143	0.843
144	144	0.749
145	145	0.0481
146	146	0.383
147	147	0.449
148	148	0.592
149	149	0.712
15	15	0.177
150	150	0.227
151	151	0.551
152	152	0.142
153	153	0.115
154	154	0.479
155	155	0.988
156	156	0.271
157	157	0.298
158	158	0.343
159	159	0.701
160	160	0.147
161	161	0.868
162	162	0.523
163	163	0.828
164	164	0.17
165	165	0.34
166	166	0.235
167	167	0.226
168	168	0.571
169	169	8.91765e-4
17	17	0.0707
18	18	0.899
19	19	0.014
2	2	0.751
20	20	0.493
21	21	0.477
22	22	0.131
23	23	0.327
24	24	0.254
25	25	0.745
26	26	2.42e-4
27	27	0.725
28	28	0.452
29	29	0.391
3	3	0.0436
30	30	0.911
31	31	0.4
32	32	0.19
33	33	0.298
34	34	0.864
35	35	0.887
36	36	0.0755
37	37	0.0618
38	38	0.269
39	39	0.287
4	4	0.803
40	40	0.197
41	41	0.505
42	42	0.276
43	43	0.0577
44	44	0.249
45	45	0.659
46	46	0.092
47	47	0.384
48	48	0.21
49	49	0.0589
5	5	0.124
50	50	0.531
51	51	0.319
52	52	0.291
53	53	0.726
54	54	0.336
55	55	0.583
56	56	0.435
57	57	0.742
58	58	0.315
59	59	0.214
6	6	0.979
60	60	0.134
61	61	0.193
62	62	0.172
63	63	0.125
64	64	0.593
65	65	0.233
66	66	0.802
67	67	0.87
68	68	0.208
69	69	0.684
7	7	0.142
70	70	0.164
71	71	0.0408
72	72	0.753
73	73	0.148
74	74	0.762
75	75	0.055
76	76	0.995
77	77	0.46
78	78	0.0203
79	79	0.797
8	8	0.0119
80	80	0.637
81	81	0.607
82	82	0.0553
83	83	0.974
84	84	0.961
85	85	0.0589
86	86	0.144
87	87	0.569
88	88	0.663
89	89	0.0304
9	9	0.5
90	90	0.15
91	91	0.222
92	92	0.194
93	93	0.28
94	94	0.934
95	95	0.396
96	96	0.163
97	97	0.812
98	98	0.361
99	99	0.0558

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: CNhs11115

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011416 mouse liver- neonate N10 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011416 (mouse liver- neonate N10 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)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005395
+|accession_numbers=CAGE;DRX009026;DRR009900;DRZ001325;DRZ002708;DRZ012675;DRZ014058
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002107,UBERON:0002100,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=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:80555320..80555378,-!p1@Creb3l3!2.15!162.88!Creb3l3;;chr1:173144144..173144176,+!p1@Nr1i3!2.13!135.42!Nr1i3;;chr7:19608891..19608895,-!p1@Foxa3!2.06!144.79!Foxa3;;chr2:163372884..163372904,+!p1@Hnf4a!1.90!77.70!Hnf4a;;chr1:173144100..173144138,+!p2@Nr1i3!1.88!74.58!Nr1i3;;chr9:74709695..74709722,+!p1@Onecut1!1.87!73.02!Onecut1;;chr4:133109285..133109308,+!p1@Nr0b2!1.83!67.09!Nr0b2;;chr5:135582751..135582788,+!p1@Mlxipl!1.75!213.43!Mlxipl;;chr10:88996295..88996335,-!p3@Nr1h4!1.75!65.84!Nr1h4;;chr10:88969376..88969395,-!p1@Nr1h4!1.75!55.54!Nr1h4;;chr15:85566184..85566238,+!p1@Ppara!1.74!78.95!Ppara;;chr16:38294860..38294924,-!p1@Nr1i2!1.73!52.11!Nr1i2;;chr10:88996336..88996380,-!p2@Nr1h4!1.70!60.22!Nr1h4;;chr15:85566537..85566552,+!p2@Ppara!1.58!36.82!Ppara;;chr15:85602655..85602680,+!p5@Ppara!1.56!35.57!Ppara;;chr11:90249521..90249551,-!p3@Hlf!1.56!35.57!Hlf;;chr18:64499674..64499696,+!p1@Onecut2!1.38!39.32!Onecut2;;chr2:147872790..147872821,-!p2@Foxa2!1.33!20.59!Foxa2;;chr4:32334732..32334739,+!p7@Bach2!1.33!20.28!Bach2;;chr13:31650185..31650201,+!p1@Foxq1!1.32!67.71!Foxq1;;chr19:37509324..37509337,+!p1@Hhex!1.30!130.43!Hhex;;chr2:163372869..163372882,+!p3@Hnf4a!1.29!18.41!Hnf4a;;chr18:64499706..64499721,+!p2@Onecut2!1.26!24.03!Onecut2;;chr10:22539932..22539956,-!p1@Tcf21!1.24!43.69!Tcf21;;chr14:63864056..63864102,-!p1@Gata4!1.24!28.40!Gata4;;chr2:77357622..77357704,-!p1@Zfp385b!1.20!39.94!Zfp385b;;chr2:173044380..173044432,-!p1@Zbp1!1.18!33.39!Zbp1;;chr15:85566241..85566253,+!p6@Ppara!1.18!14.04!Ppara;;chr1:191994550..191994623,-!p1@Prox1!1.17!93.92!Prox1;;chr11:121380640..121380655,-!p1@Zfp750!1.13!20.91!Zfp750;;chr11:100683839..100683890,-!p2@Stat5b!1.12!28.71!Stat5b;;chr10:88145766..88145770,-!p1@Spic!1.12!15.91!Spic;;chr11:83664365..83664383,+!p1@Hnf1b!1.12!12.17!Hnf1b;;chr5:115421065..115421088,-!p1@Hnf1a!1.11!11.86!Hnf1a;;chr8:59799772..59799789,+!p1@Hand2!1.10!33.70!Hand2;;chr6:90415250..90415271,+!p4@Klf15!1.09!11.23!Klf15;;chr1:191993385..191993405,-!p3@Prox1!1.09!11.23!Prox1;;chr15:103164702..103164778,-!p3@Zfp385a!1.08!13.11!Zfp385a;;chr3:94176733..94176794,+!p1@Rorc!1.05!79.88!Rorc;;chr1:138857048..138857071,-!p2@Nr5a2!1.05!10.30!Nr5a2;;chr1:138857076..138857105,-!p1@Nr5a2!1.05!10.30!Nr5a2;;chr11:60023912..60023930,-!p1@Srebf1!1.04!242.45!Srebf1;;chr7:52071956..52071978,-!p1@Atf5!1.03!316.09!Atf5;;chr7:35904304..35904320,+!p1@Cebpa!1.03!200.33!Cebpa;;chr14:100683884..100683908,-!p4@Klf12!1.03!18.41!Klf12;;chr10:5734677..5734702,-!p4@Esr1!1.03!9.67!Esr1;;chr2:91034924..91034946,-!p2@Nr1h3!1.02!11.86!Nr1h3;;chr9:24578720..24578735,-!p1@Tbx20!1.02!9.36!Tbx20;;chr15:85566051..85566080,+!p4@Ppara!1.00!10.61!Ppara;;chr2:147871627..147871641,-!p1@Foxa2!0.99!8.74!Foxa2;;chr10:88996274..88996286,-!p4@Nr1h4!0.97!8.43!Nr1h4;;chr2:91035254..91035271,-!p3@Nr1h3!0.96!10.30!Nr1h3;;chr1:138857112..138857130,-!p7@Nr5a2!0.96!8.11!Nr5a2;;chr17:87153519..87153533,+!p5@Epas1!0.95!11.86!Epas1;;chr10:80555299..80555306,-!p3@Creb3l3!0.94!7.80!Creb3l3;;chr10:5734660..5734670,-!p7@Esr1!0.94!7.80!Esr1;;chr3:102768047..102768060,-!p1@Nr1h5!0.93!7.49!Nr1h5;;chr16:38294929..38294940,-!p2@Nr1i2!0.93!7.49!Nr1i2;;chr2:173044357..173044377,-!p2@Zbp1!0.91!10.30!Zbp1;;chr2:148506935..148506954,+!p2@Gzf1!0.90!14.35!Gzf1;;chr9:69137716..69137744,+!p1@Rora!0.89!44.31!Rora;;chr2:27532479..27532509,+!p3@Rxra!0.87!13.73!Rxra;;chr15:85602581..85602598,+!p8@Ppara!0.86!6.24!Ppara;;chr10:80555398..80555409,-!p2@Creb3l3!0.86!6.24!Creb3l3;;chr10:80555285..80555291,-!p4@Creb3l3!0.84!5.93!Creb3l3;;chr4:44723559..44723593,-!p1@Pax5!0.84!5.93!Pax5;;chr1:13364477..13364492,-!p6@Ncoa2!0.83!7.18!Ncoa2;;chr2:27531961..27531974,+!p7@Rxra!0.82!5.62!Rxra;;chr2:160698288..160698358,-!p3@Zhx3!0.81!17.79!Zhx3;;chr1:138845748..138845766,-!p4@Nr5a2!0.81!7.18!Nr5a2;;chr9:51021788..51021802,+!p1@Pou2af1!0.81!6.55!Pou2af1;;chr14:100683912..100683947,-!p2@Klf12!0.80!17.47!Klf12;;chr8:87643578..87643593,-!p1@Zfp791!0.80!11.55!Zfp791;;chr7:51787434..51787448,-!p1@Spib!0.80!7.80!Spib;;chr9:74709682..74709691,+!p3@Onecut1!0.80!5.30!Onecut1;;chr2:91035197..91035237,-!p1@Nr1h3!0.79!11.23!Nr1h3;;chr12:58646974..58647003,-!p1@Foxa1!0.78!6.86!Foxa1;;chr6:15135639..15135655,+!p9@Foxp2!0.78!6.24!Foxp2;;chr8:73905892..73905903,-!p5@Nr2f6!0.78!5.93!Nr2f6;;chr10:5734907..5734920,-!p11@Esr1!0.78!4.99!Esr1;;chr12:36219645..36219730,-!p1@Ahr!0.77!52.42!Ahr;;chr10:82226649..82226694,-!p2@Nfyb!0.76!33.08!Nfyb;;chr2:38206744..38206766,+!p1@Lhx2!0.76!5.93!Lhx2;;chr11:121380594..121380609,-!p2@Zfp750!0.75!8.43!Zfp750;;chr2:38206580..38206600,+!p2@Lhx2!0.75!5.93!Lhx2;;chr19:37511111..37511115,+!p2@Hhex!0.75!4.68!Hhex;;chr10:5734525..5734569,-!p3@Esr1!0.74!7.80!Esr1;;chr17:87153505..87153516,+!p6@Epas1!0.73!6.24!Epas1;;chr6:16848347..16848391,-!p1@Tfec!0.73!5.93!Tfec;;chr15:85565338..85565355,+!p7@Ppara!0.73!4.37!Ppara;;chr3:3508024..3508069,+!p2@Hnf4g!0.73!4.37!Hnf4g;;chr6:144730427..144730508,-!p1@Sox5!0.71!28.71!Sox5;;chr14:100683672..100683717,-!p1@Klf12!0.71!21.53!Klf12;;chr6:134780337..134780355,+!p3@Crebl2!0.71!5.62!Crebl2;;chr19:10315179..10315241,-!p1@Gm98!0.70!47.12!Gm98;;chr11:121380611..121380625,-!p3@Zfp750!0.70!4.99!Zfp750;;chr13:83643159..83643226,+!p3@Mef2c!0.70!4.06!Mef2c;;chr1:38721792..38721845,-!p1@Aff3!0.69!4.99!Aff3;;chr17:87153028..87153049,+!p2@Epas1!0.68!89.87!Epas1;;chr7:148452314..148452329,-!p1@Irf7!0.68!29.96!Irf7;;chr13:30841099..30841116,+!p1@Irf4!0.68!6.24!Irf4;;chr6:90415281..90415295,+!p5@Klf15!0.68!3.74!Klf15;;chr10:5734717..5734727,-!p12@Esr1!0.68!3.74!Esr1;;chr10:82226613..82226641,-!p4@Nfyb!0.67!11.23!Nfyb;;chr2:27532754..27532815,+!p1@Rxra!0.66!121.38!Rxra;;chr1:191994700..191994711,-!p4@Prox1!0.65!3.43!Prox1;;chr4:44723520..44723544,-!p2@Pax5!0.65!3.43!Pax5;;chr11:100720767..100720797,+!p4@Stat5a!0.65!3.43!Stat5a;;chr8:79426176..79426275,+!p1@Nr3c2!0.64!19.66!Nr3c2;;chr6:108610766..108610781,+!p2@Bhlhe40!0.64!6.55!Bhlhe40;;chr6:90412582..90412601,+!p1@Klf15!0.63!17.79!Klf15;;chr17:87153240..87153254,+!p1@Epas1!0.62!74.89!Epas1;;chr14:17407970..17408015,-!p2@Rarb!0.62!9.67!Rarb;;chr8:123608252..123608268,+!p1@Foxf1a!0.62!4.99!Foxf1a;;chr2:27532513..27532525,+!p8@Rxra!0.62!3.74!Rxra;;chr2:133377954..133377973,+!p1@Bmp2!0.61!11.55!Bmp2;;chr6:144157924..144157955,-!p2@Sox5!0.61!4.06!Sox5;;chr14:18493386..18493464,+!p1@Thrb!0.60!13.42!Thrb;;chr4:6917921..6917970,-!p2@Tox!0.60!9.67!Tox;;chr11:53583960..53584007,+!p2@Irf1!0.60!7.18!Irf1;;chr9:96159147..96159204,+!p2@Tfdp2!0.60!6.24!Tfdp2;;chr4:97444471..97444514,+!p1@Nfia!0.59!92.99!Nfia;;chr10:127707602..127707633,+!p1@Stat2!0.59!30.89!Stat2;;chr11:11586218..11586285,+!p1@Ikzf1!0.59!10.92!Ikzf1;;chr18:36441119..36441158,+!p2@Pura!0.59!8.11!Pura;;chr6:115310872..115310899,+!p2@Pparg!0.59!5.62!Pparg;;chr2:153475178..153475196,+!p1@Dnmt3b!0.58!6.86!Dnmt3b;;chr1:194979361..194979373,+!p2@Irf6!0.58!4.06!Irf6;;chr2:147871948..147871977,-!p3@Foxa2!0.58!2.81!Foxa2;;chr8:91568074..91568094,-!p1@Sall1!0.58!2.81!Sall1;;chr11:60036258..60036276,-!p3@Srebf1!0.57!5.30!Srebf1;;chr1:194979315..194979359,+!p1@Irf6!0.56!19.66!Irf6;;chr3:95238432..95238455,+!p2@Arnt!0.56!18.41!Arnt;;chr1:186556375..186556404,-!p3@Hlx!0.56!5.30!Hlx;;chr18:11052606..11052633,+!p4@Gata6!0.55!7.49!Gata6;;chr1:138846047..138846074,-!p5@Nr5a2!0.55!2.81!Nr5a2;;chr18:3281034..3281104,-!p1@Crem!0.54!21.84!Crem;;chr2:90936901..90936945,+!p1@Sfpi1!0.54!16.23!Sfpi1;;chr10:57206224..57206260,+!p2@Hsf2!0.54!6.86!Hsf2;;chr16:55822638..55822669,-!p3@Nfkbiz!0.54!4.06!Nfkbiz;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!0.54!3.12!Ncoa4;;chr13:37918684..37918701,+!p12@Rreb1!0.54!3.12!Rreb1;;chr8:124984566..124984595,-!p1@Snai3!0.53!4.06!Snai3;;chr1:133904946..133904974,+!p7@Elk4!0.53!4.06!Elk4;;chr1:52176315..52176343,+!p1@Stat1!0.52!42.75!Stat1;;chr2:90936947..90936977,+!p2@Sfpi1!0.52!5.30!Sfpi1;;chr11:90250944..90250982,-!p2@Hlf!0.52!4.37!Hlf;;chr16:43363190..43363242,+!p2@Zbtb20!0.51!8.43!Zbtb20;;chr16:42907676..42907797,+!p1@Zbtb20!0.50!36.82!Zbtb20;;chr9:32443818..32443854,+!p2@Ets1!0.50!12.17!Ets1;;chr17:87153462..87153473,+!p3@Epas1!0.50!10.30!Epas1;;chr13:37949830..37949861,+!p7@Rreb1!0.50!4.68!Rreb1;;chr2:160698668..160698679,-!p4@Zhx3!0.50!4.68!Zhx3;;chr1:138846009..138846038,-!p3@Nr5a2!0.50!2.50!Nr5a2;;chr1:169548377..169548430,+!p1@Rxrg!0.50!2.18!Rxrg;;chr5:115421126..115421137,-!p4@Hnf1a!0.50!2.18!Hnf1a;;chr5:115420882..115420896,-!p3@Hnf1a!0.50!2.18!Hnf1a;;chr14:76887526..76887555,+!p10@Tsc22d1!0.50!2.18!Tsc22d1;;chr12:36219283..36219298,-!p2@Ahr!0.50!2.18!Ahr;;chr11:83664334..83664353,+!p2@Hnf1b!0.50!2.18!Hnf1b;;chr15:81633165..81633188,+!p2@Tef!0.49!22.78!Tef;;chr14:52640373..52640412,-!p1@Zfp219!0.49!15.91!Zfp219;;chr9:96619823..96619898,-!p2@Zbtb38!0.49!11.86!Zbtb38;;chr6:134780234..134780288,+!p1@Crebl2!0.49!8.43!Crebl2;;chr7:87170879..87170914,+!p2@Zfp710!0.49!5.93!Zfp710;;chr14:17407878..17407926,-!p1@Rarb!0.49!5.62!Rarb;;chr15:85566014..85566045,+!p3@Ppara!0.49!3.12!Ppara;;chr2:103143336..103143367,-!p1@Ehf!0.48!3.74!Ehf;;chr15:103085660..103085681,-!p1@Nfe2!0.48!3.43!Nfe2;;chr19:55816398..55816409,+!p5@Tcf7l2!0.47!12.17!Tcf7l2;;chr6:39068210..39068251,-!p1@Parp12!0.47!11.86!Parp12;;chr10:26093876..26093894,-!p2@L3mbtl3!0.47!5.62!L3mbtl3;;chr18:39648811..39648818,-!p4@Nr3c1!0.47!4.06!Nr3c1;;chr6:115311030..115311065,+!p4@Pparg!0.47!3.12!Pparg;;chr10:80889867..80889924,-!p1@Nfic!0.46!73.33!Nfic;;chr7:120351014..120351109,+!p1@Arntl!0.46!35.88!Arntl;;chrX:132420525..132420558,+!p3@Bhlhb9!0.46!10.61!Bhlhb9;;chr1:170362437..170362478,-!p5@Pbx1!0.46!7.49!Pbx1;;chr18:69681483..69681514,+!p11@Tcf4!0.46!3.74!Tcf4;;chrX:103070960..103070973,-!p7@Atrx!0.46!2.81!Atrx;;chr7:25917459..25917474,-!p2@Pou2f2!0.46!1.87!Pou2f2;;chr8:87425854..87425891,+!p1@Klf1!0.46!1.87!Klf1;;chr9:74714281..74714296,+!p5@Onecut1!0.46!1.87!Onecut1;;chr1:120524563..120524591,+!p2@Tfcp2l1!0.46!1.87!Tfcp2l1;;chr2:164228702..164228719,+!p1@Rbpjl!0.46!1.87!Rbpjl;;chr4:44723633..44723646,-!p3@Pax5!0.46!1.87!Pax5;;chrX:7544943..7545001,-!p1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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011416
 |is_obsolete=
+|library_id=CNhs11115
+|library_id_phase_based=2:CNhs11115
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;751
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;751
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N10.CNhs11115.751-24B9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N10.CNhs11115.751-24B9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N10.CNhs11115.751-24B9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N10.CNhs11115.751-24B9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N10.CNhs11115.751-24B9.mm9.nobarcode.rdna.fa.gz
 |name=liver, neonate N10
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11115,LSID734,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.309621626674781,0,0,0,0,0.117946305307076,0.327498749012386,0,0.0082716889057459,0,0,0.202591464974938,0,0,0,0,0,0,0.0187128228479983,0,0,0,0.351825418422672,0,0,0,0,0,0,0,0,0,0.443704052396548,0,0,0,0.799660323566278,0,-0.03341001628449,-0.0642983270704141,-0.0233371678777377,0.460383601989688,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,0.22092515780804,0,0,0,0,-0.0237583952881394,0,0.0717419398884913,0,0,0,0.192527445792385,-0.0237199519679062,0.0525151309594904,0.0983435310688386,0,0.032918362238592,-0.0149871250073208,0,0,0,0,-0.228850584369725,0.348614269677482,0.0391147104671686,0,0,0,0,0,0,0.212971178032784,0.356494034113171,0.0171277031400809,0,0,0,0,0
 |rna_box=24
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:751-24B9;search_select_hide=table117:751-24B9
 }}

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FF:751-24B9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs11115

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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