FF:499-43G4: Difference between revisions

Latest revision as of 19:17, 4 June 2020

Name:	liver, embryo E18
Species:	Mouse (Mus musculus)
Library ID:	CNhs10579
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	18 days embryo
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		SAMD00005697

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10579		CAGE		DRX009021		DRR009895

Accession ID Mm9

Library id		BAM		CTSS
CNhs10579		DRZ001320		DRZ002703

Accession ID Mm10

Library id		BAM		CTSS
CNhs10579		DRZ012670		DRZ014053

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

CNhs10579

0	0
1	0
10	0
100	0
1000	0
1001	-0.0749
1002	-0.116
1003	-0.123
1004	0
1005	0.345
1006	-0.071
1007	-0.126
1008	0
1009	-0.0572
101	0.0025
1010	0
1011	-0.298
1012	0
1013	0.276
1014	0.11
1015	-0.203
1016	-0.2
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.11
1022	0.128
1023	0
1024	-0.0297
1025	0.436
1026	0
1027	0
1028	0
1029	-0.00495
103	-0.0528
1030	0
1031	-0.139
1032	-0.177
1033	0
1034	0.638
1035	0
1036	0.0866
1037	0
1038	-0.101
1039	0.223
104	0
1040	-0.106
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: CNhs10579

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00198
MA0003.1	MA0003.1	0.216
MA0004.1	MA0004.1	0.872
MA0006.1	MA0006.1	0.241
MA0007.1	MA0007.1	0.481
MA0009.1	MA0009.1	0.553
MA0014.1	MA0014.1	0.54
MA0017.1	MA0017.1	1.58421e-14
MA0018.2	MA0018.2	3.86768e-5
MA0019.1	MA0019.1	0.286
MA0024.1	MA0024.1	0.644
MA0025.1	MA0025.1	0.307
MA0027.1	MA0027.1	0.339
MA0028.1	MA0028.1	0.866
MA0029.1	MA0029.1	0.0289
MA0030.1	MA0030.1	0.00244
MA0031.1	MA0031.1	0.00268
MA0035.2	MA0035.2	1.97636e-10
MA0038.1	MA0038.1	0.504
MA0039.2	MA0039.2	0.0151
MA0040.1	MA0040.1	0.0603
MA0041.1	MA0041.1	0.538
MA0042.1	MA0042.1	0.961
MA0043.1	MA0043.1	0.142
MA0046.1	MA0046.1	1.07504e-62
MA0047.2	MA0047.2	3.25368e-10
MA0048.1	MA0048.1	0.278
MA0050.1	MA0050.1	0.00234
MA0051.1	MA0051.1	0.0127
MA0052.1	MA0052.1	9.10054e-4
MA0055.1	MA0055.1	0.326
MA0057.1	MA0057.1	0.486
MA0058.1	MA0058.1	0.755
MA0059.1	MA0059.1	0.315
MA0060.1	MA0060.1	0.314
MA0061.1	MA0061.1	0.147
MA0062.2	MA0062.2	0.922
MA0065.2	MA0065.2	3.181e-8
MA0066.1	MA0066.1	0.0904
MA0067.1	MA0067.1	0.223
MA0068.1	MA0068.1	0.716
MA0069.1	MA0069.1	0.165
MA0070.1	MA0070.1	0.374
MA0071.1	MA0071.1	0.0202
MA0072.1	MA0072.1	0.00583
MA0073.1	MA0073.1	0.732
MA0074.1	MA0074.1	0.383
MA0076.1	MA0076.1	0.454
MA0077.1	MA0077.1	0.0577
MA0078.1	MA0078.1	0.296
MA0079.2	MA0079.2	0.366
MA0080.2	MA0080.2	9.238e-6
MA0081.1	MA0081.1	0.356
MA0083.1	MA0083.1	0.226
MA0084.1	MA0084.1	0.136
MA0087.1	MA0087.1	0.0728
MA0088.1	MA0088.1	0.147
MA0090.1	MA0090.1	0.878
MA0091.1	MA0091.1	0.93
MA0092.1	MA0092.1	0.0985
MA0093.1	MA0093.1	0.901
MA0099.2	MA0099.2	0.777
MA0100.1	MA0100.1	0.781
MA0101.1	MA0101.1	0.566
MA0102.2	MA0102.2	0.00622
MA0103.1	MA0103.1	0.243
MA0104.2	MA0104.2	0.885
MA0105.1	MA0105.1	0.00349
MA0106.1	MA0106.1	0.376
MA0107.1	MA0107.1	0.642
MA0108.2	MA0108.2	0.261
MA0111.1	MA0111.1	0.782
MA0112.2	MA0112.2	1.53651e-4
MA0113.1	MA0113.1	0.184
MA0114.1	MA0114.1	4.65229e-13
MA0115.1	MA0115.1	3.93668e-7
MA0116.1	MA0116.1	0.00902
MA0117.1	MA0117.1	0.996
MA0119.1	MA0119.1	0.00301
MA0122.1	MA0122.1	0.35
MA0124.1	MA0124.1	0.783
MA0125.1	MA0125.1	0.499
MA0131.1	MA0131.1	0.805
MA0135.1	MA0135.1	0.712
MA0136.1	MA0136.1	0.00218
MA0137.2	MA0137.2	0.159
MA0138.2	MA0138.2	0.997
MA0139.1	MA0139.1	0.162
MA0140.1	MA0140.1	1.13367e-25
MA0141.1	MA0141.1	0.0055
MA0142.1	MA0142.1	0.288
MA0143.1	MA0143.1	0.242
MA0144.1	MA0144.1	0.332
MA0145.1	MA0145.1	0.194
MA0146.1	MA0146.1	0.092
MA0147.1	MA0147.1	0.98
MA0148.1	MA0148.1	2.91512e-11
MA0149.1	MA0149.1	0.0381
MA0150.1	MA0150.1	0.00892
MA0152.1	MA0152.1	0.735
MA0153.1	MA0153.1	2.24986e-47
MA0154.1	MA0154.1	0.0171
MA0155.1	MA0155.1	0.659
MA0156.1	MA0156.1	0.0266
MA0157.1	MA0157.1	0.00364
MA0159.1	MA0159.1	0.00695
MA0160.1	MA0160.1	0.00363
MA0162.1	MA0162.1	0.321
MA0163.1	MA0163.1	4.21991e-4
MA0164.1	MA0164.1	0.611
MA0258.1	MA0258.1	0.016
MA0259.1	MA0259.1	0.857

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: CNhs10579

Novel motif	Logo	P-value
1	1	0.159
10	10	0.24
100	100	0.718
101	101	0.813
102	102	0.216
103	103	0.0152
104	104	0.646
105	105	0.442
106	106	0.0306
107	107	0.0261
108	108	0.46
109	109	0.0241
11	11	0.105
110	110	0.0864
111	111	0.102
112	112	0.0106
113	113	0.92
114	114	0.134
115	115	0.938
116	116	0.851
117	117	0.052
118	118	0.141
119	119	0.0934
12	12	0.592
120	120	0.621
121	121	0.735
122	122	0.583
123	123	0.179
124	124	0.299
125	125	0.592
126	126	0.306
127	127	0.328
128	128	0.0341
129	129	0.747
13	13	6.06525e-4
130	130	0.429
131	131	0.0678
132	132	0.895
133	133	0.785
134	134	0.842
135	135	0.981
136	136	0.211
137	137	0.316
138	138	0.446
139	139	0.987
14	14	0.695
140	140	0.154
141	141	0.839
142	142	0.237
143	143	0.204
144	144	0.93
145	145	0.0593
146	146	0.223
147	147	0.936
148	148	0.6
149	149	0.604
15	15	0.0937
150	150	0.149
151	151	0.303
152	152	0.154
153	153	0.36
154	154	0.648
155	155	0.556
156	156	0.0431
157	157	0.86
158	158	0.811
159	159	0.287
160	160	0.0622
161	161	0.3
162	162	0.698
163	163	0.618
164	164	0.014
165	165	0.505
166	166	0.924
167	167	0.698
168	168	0.71
169	169	0.00732
17	17	0.0815
18	18	0.819
19	19	0.0765
2	2	0.639
20	20	0.545
21	21	0.949
22	22	0.137
23	23	0.17
24	24	0.227
25	25	0.734
26	26	3.52945e-4
27	27	0.352
28	28	0.396
29	29	0.0784
3	3	0.025
30	30	0.686
31	31	0.47
32	32	0.348
33	33	0.182
34	34	0.745
35	35	0.804
36	36	0.0667
37	37	0.119
38	38	0.399
39	39	0.457
4	4	0.54
40	40	0.0754
41	41	1
42	42	0.107
43	43	0.0505
44	44	0.182
45	45	0.66
46	46	0.0731
47	47	0.274
48	48	0.187
49	49	0.0627
5	5	0.0958
50	50	0.43
51	51	0.333
52	52	0.218
53	53	0.781
54	54	0.377
55	55	0.347
56	56	0.332
57	57	0.671
58	58	0.539
59	59	0.0691
6	6	0.972
60	60	0.072
61	61	0.292
62	62	0.118
63	63	0.104
64	64	0.408
65	65	0.169
66	66	0.6
67	67	0.929
68	68	0.476
69	69	0.857
7	7	0.0795
70	70	0.403
71	71	0.0335
72	72	0.416
73	73	0.2
74	74	0.608
75	75	0.0398
76	76	0.988
77	77	0.395
78	78	0.0133
79	79	0.812
8	8	0.0422
80	80	0.0201
81	81	0.848
82	82	0.208
83	83	0.363
84	84	0.86
85	85	0.208
86	86	0.255
87	87	0.106
88	88	0.755
89	89	0.37
9	9	0.528
90	90	0.363
91	91	0.148
92	92	0.154
93	93	0.726
94	94	0.728
95	95	0.087
96	96	0.189
97	97	0.854
98	98	0.142
99	99	0.185

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: CNhs10579

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011376 mouse liver- embryo E18 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)
0000922 (embryo)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000302 (mouse embryonic day 18 sample)
0011376 (mouse liver- embryo E18 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002107,UBERON:0002100,UBERON:0000483,UBERON:0002530,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@SAMD00005697
+|accession_numbers=CAGE;DRX009021;DRR009895;DRZ001320;DRZ002703;DRZ012670;DRZ014053
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000302,FF:0011376
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr15:103085660..103085681,-!p1@Nfe2!2.06!168.30!Nfe2;;chr9:74709695..74709722,+!p1@Onecut1!2.01!101.84!Onecut1;;chr8:87425854..87425891,+!p1@Klf1!2.01!101.56!Klf1;;chr7:122989594..122989626,-!p1@Sox6!1.86!71.64!Sox6;;chr7:19608891..19608895,-!p1@Foxa3!1.76!73.36!Foxa3;;chr2:28477452..28477483,-!p1@Gfi1b!1.73!65.02!Gfi1b;;chr10:80555320..80555378,-!p1@Creb3l3!1.73!60.42!Creb3l3;;chr4:114732112..114732158,+!p1@Tal1!1.70!103.28!Tal1;;chr7:122989632..122989668,-!p2@Sox6!1.70!48.62!Sox6;;chr9:96159147..96159204,+!p2@Tfdp2!1.64!77.68!Tfdp2;;chr15:103082088..103082136,-!p2@Nfe2!1.55!34.24!Nfe2;;chr15:103085690..103085710,-!p3@Nfe2!1.54!36.54!Nfe2;;chrX:7544943..7545001,-!p1@Gata1!1.53!33.09!Gata1;;chr10:88996336..88996380,-!p2@Nr1h4!1.51!38.84!Nr1h4;;chr2:163372884..163372904,+!p1@Hnf4a!1.51!31.07!Hnf4a;;chr16:38294860..38294924,-!p1@Nr1i2!1.45!27.33!Nr1i2;;chr10:88969376..88969395,-!p1@Nr1h4!1.42!25.03!Nr1h4;;chr15:85602655..85602680,+!p5@Ppara!1.41!24.45!Ppara;;chr9:96159225..96159249,+!p5@Tfdp2!1.37!24.74!Tfdp2;;chr11:11584970..11585030,+!p2@Ikzf1!1.34!29.92!Ikzf1;;chr18:64499674..64499696,+!p1@Onecut2!1.32!33.66!Onecut2;;chr4:87452200..87452229,-!p2@Mllt3!1.28!38.26!Mllt3;;chr1:173144100..173144138,+!p2@Nr1i3!1.28!17.84!Nr1i3;;chr11:90249521..90249551,-!p3@Hlf!1.27!17.55!Hlf;;chr10:88145766..88145770,-!p1@Spic!1.25!21.86!Spic;;chr7:17647736..17647772,-!p1@Hif3a!1.24!57.25!Hif3a;;chr10:88996295..88996335,-!p3@Nr1h4!1.22!18.41!Nr1h4;;chr13:31650185..31650201,+!p1@Foxq1!1.20!52.07!Foxq1;;chr4:135728181..135728203,+!p2@E2f2!1.19!18.99!E2f2;;chr8:87225670..87225697,+!p2@Lyl1!1.18!41.14!Lyl1;;chr7:35904304..35904320,+!p1@Cebpa!1.17!274.75!Cebpa;;chr4:87452180..87452196,-!p3@Mllt3!1.17!26.76!Mllt3;;chr4:135728473..135728494,+!p5@E2f2!1.16!13.52!E2f2;;chr15:85566537..85566552,+!p2@Ppara!1.14!12.66!Ppara;;chr9:96159133..96159145,+!p9@Tfdp2!1.13!12.37!Tfdp2;;chr7:52071956..52071978,-!p1@Atf5!1.12!388.68!Atf5;;chr10:22539932..22539956,-!p1@Tcf21!1.12!32.51!Tcf21;;chr18:64499706..64499721,+!p2@Onecut2!1.12!16.97!Onecut2;;chr9:51021788..51021802,+!p1@Pou2af1!1.12!14.38!Pou2af1;;chr5:135582751..135582788,+!p1@Mlxipl!1.11!48.33!Mlxipl;;chr19:37509324..37509337,+!p1@Hhex!1.09!80.84!Hhex;;chr4:135728581..135728668,+!p1@E2f2!1.07!51.79!E2f2;;chr16:43247391..43247422,+!p12@Zbtb20!1.07!10.64!Zbtb20;;chr2:147871627..147871641,-!p1@Foxa2!1.07!10.64!Foxa2;;chr2:163332558..163332596,+!p2@Hnf4a!1.07!10.64!Hnf4a;;chr15:85566184..85566238,+!p1@Ppara!1.06!15.82!Ppara;;chr4:44723559..44723593,-!p1@Pax5!1.06!10.36!Pax5;;chr2:147872790..147872821,-!p2@Foxa2!1.04!10.07!Foxa2;;chr1:38721792..38721845,-!p1@Aff3!1.03!12.08!Aff3;;chr7:17642177..17642223,-!p3@Hif3a!1.03!9.78!Hif3a;;chr8:87643578..87643593,-!p1@Zfp791!1.01!19.28!Zfp791;;chr2:91034924..91034946,-!p2@Nr1h3!0.99!10.93!Nr1h3;;chr1:173144144..173144176,+!p1@Nr1i3!0.98!8.63!Nr1i3;;chr16:92826249..92826325,-!p1@Runx1!0.97!20.71!Runx1;;chr10:79884592..79884621,-!p5@Tcf3!0.97!8.34!Tcf3;;chr5:115421065..115421088,-!p1@Hnf1a!0.97!8.34!Hnf1a;;chr7:148452314..148452329,-!p1@Irf7!0.96!58.40!Irf7;;chr15:103085802..103085817,-!p4@Nfe2!0.96!10.36!Nfe2;;chr4:87452236..87452249,-!p9@Mllt3!0.96!8.06!Mllt3;;chr8:87225702..87225726,+!p3@Lyl1!0.95!16.40!Lyl1;;chr6:90415250..90415271,+!p4@Klf15!0.94!7.77!Klf15;;chr11:11586218..11586285,+!p1@Ikzf1!0.93!24.74!Ikzf1;;chr14:63864056..63864102,-!p1@Gata4!0.92!12.95!Gata4;;chr11:16908650..16908690,-!p1@Plek!0.91!45.17!Plek;;chr2:163372869..163372882,+!p3@Hnf4a!0.91!7.19!Hnf4a;;chr11:120491440..120491474,-!p3@Mafg!0.90!10.36!Mafg;;chr7:122989676..122989687,-!p8@Sox6!0.90!6.90!Sox6;;chr9:96159116..96159130,+!p6@Tfdp2!0.89!8.63!Tfdp2;;chr6:86619104..86619119,-!p1@Mxd1!0.88!56.68!Mxd1;;chr13:30841099..30841116,+!p1@Irf4!0.88!10.64!Irf4;;chr1:191994550..191994623,-!p1@Prox1!0.84!43.15!Prox1;;chr15:103164702..103164778,-!p3@Zfp385a!0.83!6.90!Zfp385a;;chr15:85602581..85602598,+!p8@Ppara!0.83!5.75!Ppara;;chr11:83664365..83664383,+!p1@Hnf1b!0.83!5.75!Hnf1b;;chr4:114729957..114730012,+!p3@Tal1!0.83!5.75!Tal1;;chr11:121380640..121380655,-!p1@Zfp750!0.81!9.49!Zfp750;;chr5:104183477..104183548,+!p6@Aff1!0.80!10.93!Aff1;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.80!8.63!Ncoa4;;chr5:65203575..65203589,+!p11@Klf3!0.80!6.62!Klf3;;chr14:55330976..55330990,-!p1@Cebpe!0.79!5.18!Cebpe;;chr2:77357622..77357704,-!p1@Zfp385b!0.78!14.38!Zfp385b;;chr5:65203599..65203617,+!p8@Klf3!0.78!8.63!Klf3;;chr11:11585912..11585950,+!p6@Ikzf1!0.77!6.33!Ikzf1;;chr2:90936901..90936945,+!p1@Sfpi1!0.76!27.33!Sfpi1;;chr12:58646974..58647003,-!p1@Foxa1!0.76!6.62!Foxa1;;chr8:59799772..59799789,+!p1@Hand2!0.75!14.38!Hand2;;chr5:77543897..77543911,-!p2@Hopx!0.75!9.49!Hopx;;chr3:102768047..102768060,-!p1@Nr1h5!0.75!4.60!Nr1h5;;chr11:85699862..85699920,+!p1@Tbx4!0.75!4.60!Tbx4;;chr1:138857048..138857071,-!p2@Nr5a2!0.75!4.60!Nr5a2;;chr1:138857112..138857130,-!p7@Nr5a2!0.75!4.60!Nr5a2;;chr9:96159210..96159221,+!p10@Tfdp2!0.75!4.60!Tfdp2;;chr8:87225329..87225396,+!p1@Lyl1!0.74!18.41!Lyl1;;chr8:124806017..124806040,+!p2@Zfpm1!0.73!54.09!Zfpm1;;chr8:124806048..124806094,+!p1@Zfpm1!0.73!45.17!Zfpm1;;chr10:20880731..20880775,-!p2@Myb!0.73!9.78!Myb;;chr10:20880698..20880717,-!p3@Myb!0.73!7.19!Myb;;chr9:74709682..74709691,+!p3@Onecut1!0.73!4.32!Onecut1;;chr15:85566051..85566080,+!p4@Ppara!0.71!4.89!Ppara;;chr9:48644037..48644067,-!p2@Zbtb16!0.70!10.93!Zbtb16;;chr14:100683884..100683908,-!p4@Klf12!0.70!8.06!Klf12;;chr10:88996274..88996286,-!p4@Nr1h4!0.70!4.03!Nr1h4;;chr15:79178559..79178584,+!p8@Maff!0.70!4.03!Maff;;chr2:166868994..166869023,-!p7@Znfx1!0.70!4.03!Znfx1;;chr2:90936947..90936977,+!p2@Sfpi1!0.69!8.34!Sfpi1;;chr11:60023912..60023930,-!p1@Srebf1!0.68!105.01!Srebf1;;chr1:191993385..191993405,-!p3@Prox1!0.68!3.74!Prox1;;chr15:103083245..103083260,-!p7@Nfe2!0.68!3.74!Nfe2;;chr6:83301243..83301258,+!p2@Bola3!0.68!3.74!Bola3;;chr6:90415281..90415295,+!p5@Klf15!0.68!3.74!Klf15;;chr16:38294929..38294940,-!p2@Nr1i2!0.68!3.74!Nr1i2;;chr17:48015645..48015689,-!p9@Foxp4!0.67!4.89!Foxp4;;chr2:38206744..38206766,+!p1@Lhx2!0.67!4.60!Lhx2;;chr2:27532479..27532509,+!p3@Rxra!0.66!8.06!Rxra;;chr2:166888058..166888105,-!p2@Znfx1!0.65!12.66!Znfx1;;chr18:76219118..76219155,+!p1@Zbtb7c!0.65!6.62!Zbtb7c;;chr1:138846079..138846103,-!p6@Nr5a2!0.65!3.45!Nr5a2;;chr6:83301229..83301242,+!p3@Bola3!0.65!3.45!Bola3;;chr9:74709664..74709671,+!p6@Onecut1!0.65!3.45!Onecut1;;chr4:114730015..114730042,+!p7@Tal1!0.65!3.45!Tal1;;chr1:52176315..52176343,+!p1@Stat1!0.62!54.95!Stat1;;chr4:63064364..63064384,-!p1@Akna!0.62!10.64!Akna;;chr11:100683839..100683890,-!p2@Stat5b!0.62!8.34!Stat5b;;chr10:80555398..80555409,-!p2@Creb3l3!0.62!3.16!Creb3l3;;chr4:44723520..44723544,-!p2@Pax5!0.62!3.16!Pax5;;chr6:144730427..144730508,-!p1@Sox5!0.61!22.15!Sox5;;chr7:6649134..6649167,-!p1@Zim1!0.61!19.85!Zim1;;chr3:54559496..54559511,+!p1@Smad9!0.61!7.77!Smad9;;chr14:56223010..56223067,+!p1@Irf9!0.60!28.19!Irf9;;chr7:51787434..51787448,-!p1@Spib!0.60!4.60!Spib;;chr6:86619130..86619158,-!p2@Mxd1!0.59!51.21!Mxd1;;chrX:98449898..98449913,+!p2@Foxo4!0.59!10.93!Foxo4;;chr6:99216488..99216534,-!p2@Foxp1!0.59!9.49!Foxp1;;chr2:90936978..90937023,+!p3@Sfpi1!0.59!6.04!Sfpi1;;chr8:123608252..123608268,+!p1@Foxf1a!0.59!4.60!Foxf1a;;chr10:80598968..80599012,+!p5@Zbtb7a!0.59!4.03!Zbtb7a;;chr4:135736690..135736705,+!p6@E2f2!0.59!3.45!E2f2;;chr4:32334732..32334739,+!p7@Bach2!0.59!2.88!Bach2;;chr9:74714303..74714318,+!p2@Onecut1!0.59!2.88!Onecut1;;chr9:119893782..119893802,-!p1@Csrnp1!0.59!2.88!Csrnp1;;chr15:85566241..85566253,+!p6@Ppara!0.59!2.88!Ppara;;chr2:147872074..147872079,-!p4@Foxa2!0.59!2.88!Foxa2;;chr9:69137716..69137744,+!p1@Rora!0.58!21.29!Rora;;chr1:133904946..133904974,+!p7@Elk4!0.57!4.60!Elk4;;chr1:138845748..138845766,-!p4@Nr5a2!0.57!3.74!Nr5a2;;chr11:5420954..5420969,+!p2@Xbp1!0.56!40.57!Xbp1;;chr10:20880629..20880683,-!p1@Myb!0.56!8.92!Myb;;chr3:54559463..54559493,+!p3@Smad9!0.56!5.47!Smad9;;chr2:91035254..91035271,-!p3@Nr1h3!0.56!3.45!Nr1h3;;chr6:15135639..15135655,+!p9@Foxp2!0.56!3.45!Foxp2;;chr7:122989672..122989673,-!p20@Sox6!0.56!2.59!Sox6;;chr4:44723633..44723646,-!p3@Pax5!0.56!2.59!Pax5;;chr9:24578720..24578735,-!p1@Tbx20!0.56!2.59!Tbx20;;chr1:138857076..138857105,-!p1@Nr5a2!0.56!2.59!Nr5a2;;chr12:57636178..57636194,-!p2@Nkx2-1!0.56!2.59!Nkx2-1;;chr14:55330957..55330971,-!p2@Cebpe!0.56!2.59!Cebpe;;chr15:85565338..85565355,+!p7@Ppara!0.56!2.59!Ppara;;chr8:123260252..123260264,+!p1@Irf8!0.55!22.15!Irf8;;chr7:56136362..56136400,-!p1@E2f8!0.55!20.43!E2f8;;chr2:162880387..162880413,+!p1@Mybl2!0.55!19.85!Mybl2;;chr15:79177964..79177986,+!p1@Maff!0.55!10.64!Maff;;chr2:90922554..90922575,+!p4@Sfpi1!0.55!5.18!Sfpi1;;chr5:144951153..144951203,+!p1@Bhlha15!0.55!4.03!Bhlha15;;chr4:114730254..114730276,+!p2@Tal1!0.55!3.45!Tal1;;chr10:79389784..79389833,+!p1@Arid3a!0.54!16.11!Arid3a;;chr4:135728282..135728310,+!p4@E2f2!0.54!2.88!E2f2;;chr1:138846009..138846038,-!p3@Nr5a2!0.54!2.88!Nr5a2;;chr10:30522690..30522752,-!p2@Ncoa7!0.53!18.12!Ncoa7;;chr1:13364477..13364492,-!p6@Ncoa2!0.53!3.16!Ncoa2;;chr6:16848395..16848416,-!p2@Tfec!0.53!2.88!Tfec;;chr3:95238432..95238455,+!p2@Arnt!0.52!16.97!Arnt;;chr10:41995430..41995458,-!p3@Foxo3!0.52!7.19!Foxo3;;chr7:56137011..56137041,-!p2@E2f8!0.52!5.18!E2f8;;chr2:180069370..180069409,-!p1@Gata5!0.52!2.88!Gata5;;chr2:147871948..147871977,-!p3@Foxa2!0.52!2.30!Foxa2;;chr2:103264213..103264233,+!p1@Elf5!0.52!2.30!Elf5;;chr9:74714281..74714296,+!p5@Onecut1!0.52!2.30!Onecut1;;chr4:114732159..114732166,+!p6@Tal1!0.52!2.30!Tal1;;chr15:103085864..103085876,-!p5@Nfe2!0.52!2.30!Nfe2;;chr5:104183219..104183236,+!p2@Aff1!0.51!19.85!Aff1;;chr4:62626594..62626651,+!p1@Zfp618!0.51!10.64!Zfp618;;chr13:112476264..112476282,+!p3@Mier3!0.51!3.45!Mier3;;chr10:67599361..67599372,-!p5@Arid5b!0.50!3.74!Arid5b;;chr2:38206580..38206600,+!p2@Lhx2!0.50!2.88!Lhx2;;chr5:104183579..104183600,+!p9@Aff1!0.50!2.59!Aff1;;chr11:11585678..11585745,+!p5@Ikzf1!0.49!3.45!Ikzf1;;chr2:27532754..27532815,+!p1@Rxra!0.48!79.40!Rxra;;chr10:128106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+|ffid_belonging_in_development=UBERON:0001041,UBERON:0002532,UBERON:0006595,UBERON:0003104,UBERON:0004161,UBERON:0009497,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011376
 |is_obsolete=
+|library_id=CNhs10579
+|library_id_phase_based=2:CNhs10579
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;499
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;499
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E18.CNhs10579.499-43G4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E18.CNhs10579.499-43G4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E18.CNhs10579.499-43G4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E18.CNhs10579.499-43G4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E18.CNhs10579.499-43G4.mm9.nobarcode.rdna.fa.gz
 |name=liver, embryo E18
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10579,LSID653,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.220461230627725,0,0,0,0,0,-0.222446257488831,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.00549536064819417,0,0,0,0.270233464711444,0,0,0,0,0,0,0,0,0,0.30664059633713,0,0,0,1.04412270063586,0,0.0829312904358914,-0.0983739808901885,0.424305081124494,0.481085531821133,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0.109813392994768,0,0.131383163967328,0.109813392994768,0,0,0,0.109813392994768,0,-0.0757898689534025,0,0,0,0.021767031598423,0.0219462507152315,0.112142421940361,0.0188187290997574,0,0.031804792242817,-0.0724331379807264,0,0.270233464711444,0,-0.0025748282376927,-0.107551720205319,0.214736039830027,0.0309817981548609,0,0,0,0,0.054906696497384,0,-0.0126560781108049,-0.0796671402108076,0.0466683642985422,0,0,0,0,0
 |rna_box=43
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |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=table111:499-43G4;search_select_hide=table117:499-43G4
 }}

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FF:499-43G4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:17, 4 June 2020

CNhs10579

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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