FF:409-16E1: Difference between revisions

Latest revision as of 19:15, 4 June 2020

Name:	liver, embryo E14
Species:	Mouse (Mus musculus)
Library ID:	CNhs10594
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	14 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		SAMD00005338

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10594		CAGE		DRX009017		DRR009891

Accession ID Mm9

Library id		BAM		CTSS
CNhs10594		DRZ001316		DRZ002699

Accession ID Mm10

Library id		BAM		CTSS
CNhs10594		DRZ012666		DRZ014049

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

CNhs10594

0	0
1	0
10	0
100	0
1000	-0.0355
1001	0
1002	-0.00274
1003	-0.112
1004	0
1005	0
1006	-0.143
1007	4.236979e-4
1008	0
1009	-0.172
101	0.208
1010	0
1011	-0.108
1012	0
1013	-0.176
1014	0.0683
1015	-0.0558
1016	-0.291
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0881
1022	-0.186
1023	0
1024	-0.00178
1025	0.253
1026	0
1027	-0.048
1028	0
1029	0.0471
103	-0.0595
1030	0
1031	-0.184
1032	-0.333
1033	0.0129
1034	0
1035	0
1036	0.358
1037	0
1038	-0.342
1039	-0.0945
104	0
1040	-0.211
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: CNhs10594

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.042
MA0003.1	MA0003.1	0.999
MA0004.1	MA0004.1	0.234
MA0006.1	MA0006.1	0.634
MA0007.1	MA0007.1	0.408
MA0009.1	MA0009.1	0.084
MA0014.1	MA0014.1	0.891
MA0017.1	MA0017.1	1.57093e-8
MA0018.2	MA0018.2	0.0073
MA0019.1	MA0019.1	0.294
MA0024.1	MA0024.1	1.03426e-8
MA0025.1	MA0025.1	0.344
MA0027.1	MA0027.1	0.839
MA0028.1	MA0028.1	6.06458e-4
MA0029.1	MA0029.1	0.0477
MA0030.1	MA0030.1	0.907
MA0031.1	MA0031.1	0.682
MA0035.2	MA0035.2	1.2573e-25
MA0038.1	MA0038.1	0.169
MA0039.2	MA0039.2	0.351
MA0040.1	MA0040.1	0.431
MA0041.1	MA0041.1	0.367
MA0042.1	MA0042.1	0.547
MA0043.1	MA0043.1	0.0762
MA0046.1	MA0046.1	6.92154e-25
MA0047.2	MA0047.2	0.0406
MA0048.1	MA0048.1	0.0253
MA0050.1	MA0050.1	0.542
MA0051.1	MA0051.1	0.38
MA0052.1	MA0052.1	7.61991e-7
MA0055.1	MA0055.1	0.00887
MA0057.1	MA0057.1	0.666
MA0058.1	MA0058.1	0.176
MA0059.1	MA0059.1	0.00959
MA0060.1	MA0060.1	2.12546e-4
MA0061.1	MA0061.1	0.204
MA0062.2	MA0062.2	4.98778e-5
MA0065.2	MA0065.2	7.48039e-5
MA0066.1	MA0066.1	0.0272
MA0067.1	MA0067.1	0.357
MA0068.1	MA0068.1	0.0203
MA0069.1	MA0069.1	0.0526
MA0070.1	MA0070.1	0.655
MA0071.1	MA0071.1	0.175
MA0072.1	MA0072.1	0.106
MA0073.1	MA0073.1	0.766
MA0074.1	MA0074.1	0.735
MA0076.1	MA0076.1	0.00326
MA0077.1	MA0077.1	0.258
MA0078.1	MA0078.1	0.813
MA0079.2	MA0079.2	0.0558
MA0080.2	MA0080.2	0.002
MA0081.1	MA0081.1	0.572
MA0083.1	MA0083.1	0.0263
MA0084.1	MA0084.1	0.0569
MA0087.1	MA0087.1	0.0333
MA0088.1	MA0088.1	0.0211
MA0090.1	MA0090.1	0.287
MA0091.1	MA0091.1	0.281
MA0092.1	MA0092.1	0.6
MA0093.1	MA0093.1	0.233
MA0099.2	MA0099.2	0.973
MA0100.1	MA0100.1	0.024
MA0101.1	MA0101.1	0.399
MA0102.2	MA0102.2	0.695
MA0103.1	MA0103.1	0.783
MA0104.2	MA0104.2	0.121
MA0105.1	MA0105.1	8.80262e-4
MA0106.1	MA0106.1	0.458
MA0107.1	MA0107.1	0.955
MA0108.2	MA0108.2	0.012
MA0111.1	MA0111.1	0.97
MA0112.2	MA0112.2	0.00734
MA0113.1	MA0113.1	0.161
MA0114.1	MA0114.1	6.22236e-8
MA0115.1	MA0115.1	1.49902e-5
MA0116.1	MA0116.1	6.49299e-4
MA0117.1	MA0117.1	0.861
MA0119.1	MA0119.1	0.165
MA0122.1	MA0122.1	0.241
MA0124.1	MA0124.1	0.875
MA0125.1	MA0125.1	0.676
MA0131.1	MA0131.1	0.43
MA0135.1	MA0135.1	0.395
MA0136.1	MA0136.1	0.00107
MA0137.2	MA0137.2	0.402
MA0138.2	MA0138.2	0.0179
MA0139.1	MA0139.1	0.165
MA0140.1	MA0140.1	3.16649e-59
MA0141.1	MA0141.1	0.0419
MA0142.1	MA0142.1	0.0759
MA0143.1	MA0143.1	0.365
MA0144.1	MA0144.1	0.676
MA0145.1	MA0145.1	0.712
MA0146.1	MA0146.1	0.11
MA0147.1	MA0147.1	0.0711
MA0148.1	MA0148.1	3.27097e-4
MA0149.1	MA0149.1	0.0293
MA0150.1	MA0150.1	0.0011
MA0152.1	MA0152.1	0.747
MA0153.1	MA0153.1	2.77384e-22
MA0154.1	MA0154.1	0.0673
MA0155.1	MA0155.1	0.692
MA0156.1	MA0156.1	0.00128
MA0157.1	MA0157.1	0.442
MA0159.1	MA0159.1	0.0625
MA0160.1	MA0160.1	0.0393
MA0162.1	MA0162.1	0.237
MA0163.1	MA0163.1	1.59989e-6
MA0164.1	MA0164.1	0.218
MA0258.1	MA0258.1	0.219
MA0259.1	MA0259.1	0.274

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: CNhs10594

Novel motif	Logo	P-value
1	1	0.103
10	10	0.0411
100	100	0.211
101	101	0.623
102	102	0.858
103	103	0.016
104	104	0.901
105	105	0.813
106	106	0.667
107	107	0.858
108	108	0.372
109	109	0.011
11	11	0.103
110	110	0.0458
111	111	0.00491
112	112	0.0279
113	113	0.628
114	114	0.39
115	115	0.518
116	116	0.878
117	117	0.00153
118	118	0.0291
119	119	0.346
12	12	0.943
120	120	0.995
121	121	0.334
122	122	0.91
123	123	0.0469
124	124	0.268
125	125	0.36
126	126	0.104
127	127	0.204
128	128	0.625
129	129	0.586
13	13	1.03034e-4
130	130	0.563
131	131	0.606
132	132	0.0883
133	133	0.254
134	134	0.249
135	135	0.215
136	136	0.512
137	137	0.277
138	138	0.896
139	139	0.714
14	14	0.839
140	140	0.328
141	141	0.274
142	142	0.128
143	143	0.883
144	144	0.797
145	145	0.00775
146	146	0.581
147	147	0.906
148	148	0.316
149	149	0.634
15	15	0.0364
150	150	0.246
151	151	0.546
152	152	0.885
153	153	0.792
154	154	0.963
155	155	0.196
156	156	3.71578e-7
157	157	0.722
158	158	0.078
159	159	0.315
160	160	0.38
161	161	0.0317
162	162	0.837
163	163	0.937
164	164	0.00155
165	165	0.702
166	166	0.249
167	167	0.0718
168	168	0.602
169	169	0.0287
17	17	0.547
18	18	0.292
19	19	0.291
2	2	0.337
20	20	0.0244
21	21	0.814
22	22	0.525
23	23	0.397
24	24	0.479
25	25	0.389
26	26	7.86077e-4
27	27	0.974
28	28	0.411
29	29	0.0031
3	3	0.025
30	30	0.734
31	31	0.939
32	32	0.812
33	33	0.14
34	34	0.95
35	35	0.944
36	36	0.0222
37	37	0.184
38	38	0.835
39	39	0.682
4	4	0.677
40	40	0.108
41	41	0.665
42	42	0.0565
43	43	0.119
44	44	0.965
45	45	0.783
46	46	0.103
47	47	0.167
48	48	0.169
49	49	0.0663
5	5	0.041
50	50	0.873
51	51	0.591
52	52	0.914
53	53	0.767
54	54	0.746
55	55	0.319
56	56	0.727
57	57	0.345
58	58	0.498
59	59	0.557
6	6	0.88
60	60	0.467
61	61	0.297
62	62	0.127
63	63	0.48
64	64	0.369
65	65	0.818
66	66	0.338
67	67	0.4
68	68	0.724
69	69	0.748
7	7	0.0445
70	70	0.552
71	71	0.00619
72	72	0.439
73	73	0.31
74	74	0.499
75	75	0.0296
76	76	0.36
77	77	0.857
78	78	0.00883
79	79	0.435
8	8	0.00718
80	80	0.0909
81	81	0.874
82	82	0.832
83	83	0.645
84	84	0.971
85	85	0.648
86	86	0.465
87	87	0.59
88	88	0.696
89	89	0.8
9	9	0.992
90	90	0.0678
91	91	0.335
92	92	0.617
93	93	0.679
94	94	0.207
95	95	0.0359
96	96	0.116
97	97	0.567
98	98	0.214
99	99	0.776

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: CNhs10594

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011340 mouse liver- embryo E14 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)
0000296 (mouse embryonic day 14 sample)
0011340 (mouse liver- embryo E14 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@SAMD00005338
+|accession_numbers=CAGE;DRX009017;DRR009891;DRZ001316;DRZ002699;DRZ012666;DRZ014049
+|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:0000296,FF:0011340
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:87425854..87425891,+!p1@Klf1!2.42!261.74!Klf1;;chr15:103085660..103085681,-!p1@Nfe2!2.18!219.02!Nfe2;;chr2:28477452..28477483,-!p1@Gfi1b!2.04!131.77!Gfi1b;;chrX:7544943..7545001,-!p1@Gata1!1.97!92.87!Gata1;;chr7:122989594..122989626,-!p1@Sox6!1.91!80.05!Sox6;;chr4:114732112..114732158,+!p1@Tal1!1.89!162.58!Tal1;;chr7:122989632..122989668,-!p2@Sox6!1.83!66.78!Sox6;;chr15:103082088..103082136,-!p2@Nfe2!1.78!59.14!Nfe2;;chr11:11584970..11585030,+!p2@Ikzf1!1.74!76.00!Ikzf1;;chr9:96159147..96159204,+!p2@Tfdp2!1.66!80.95!Tfdp2;;chr4:87452180..87452196,-!p3@Mllt3!1.63!80.50!Mllt3;;chr15:103085690..103085710,-!p3@Nfe2!1.63!44.97!Nfe2;;chr4:87452200..87452229,-!p2@Mllt3!1.62!84.10!Mllt3;;chr4:135728181..135728203,+!p2@E2f2!1.55!44.97!E2f2;;chr8:87225670..87225697,+!p2@Lyl1!1.47!80.28!Lyl1;;chr9:96159225..96159249,+!p5@Tfdp2!1.42!27.88!Tfdp2;;chr7:19608891..19608895,-!p1@Foxa3!1.36!28.56!Foxa3;;chr4:87452236..87452249,-!p9@Mllt3!1.31!19.56!Mllt3;;chr10:80598968..80599012,+!p5@Zbtb7a!1.26!22.26!Zbtb7a;;chr8:87225702..87225726,+!p3@Lyl1!1.24!32.83!Lyl1;;chr10:79884592..79884621,-!p5@Tcf3!1.21!15.29!Tcf3;;chr7:17642177..17642223,-!p3@Hif3a!1.20!14.84!Hif3a;;chr9:96159133..96159145,+!p9@Tfdp2!1.15!13.27!Tfdp2;;chr16:92826249..92826325,-!p1@Runx1!1.12!29.68!Runx1;;chr9:96159116..96159130,+!p6@Tfdp2!1.12!15.29!Tfdp2;;chr4:114729957..114730012,+!p3@Tal1!1.12!12.14!Tal1;;chr10:88145766..88145770,-!p1@Spic!1.11!15.52!Spic;;chr7:122989676..122989687,-!p8@Sox6!1.05!10.34!Sox6;;chr2:163372884..163372904,+!p1@Hnf4a!1.05!10.34!Hnf4a;;chr8:124806048..124806094,+!p1@Zfpm1!1.04!92.64!Zfpm1;;chr10:80555320..80555378,-!p1@Creb3l3!1.03!11.47!Creb3l3;;chr4:135728473..135728494,+!p5@E2f2!1.03!9.67!E2f2;;chr5:135582751..135582788,+!p1@Mlxipl!1.02!38.90!Mlxipl;;chr9:74709695..74709722,+!p1@Onecut1!1.00!8.99!Onecut1;;chr14:27813679..27813693,+!p2@Hesx1!0.97!8.32!Hesx1;;chr14:63864056..63864102,-!p1@Gata4!0.96!14.39!Gata4;;chr5:65203599..65203617,+!p8@Klf3!0.96!13.72!Klf3;;chr4:135728581..135728668,+!p1@E2f2!0.95!39.35!E2f2;;chr4:114732159..114732166,+!p6@Tal1!0.95!7.87!Tal1;;chr2:162880387..162880413,+!p1@Mybl2!0.94!49.92!Mybl2;;chr5:104183477..104183548,+!p6@Aff1!0.94!15.52!Aff1;;chr2:166868994..166869023,-!p7@Znfx1!0.94!7.65!Znfx1;;chr4:114730254..114730276,+!p2@Tal1!0.92!9.44!Tal1;;chr8:124806017..124806040,+!p2@Zfpm1!0.91!82.30!Zfpm1;;chr11:23980664..23980706,+!p2@Bcl11a!0.91!32.61!Bcl11a;;chr11:16908650..16908690,-!p1@Plek!0.90!44.52!Plek;;chr16:38294860..38294924,-!p1@Nr1i2!0.90!6.97!Nr1i2;;chr5:65203575..65203589,+!p11@Klf3!0.89!8.32!Klf3;;chr5:104183579..104183600,+!p9@Aff1!0.88!7.65!Aff1;;chr6:83301229..83301242,+!p3@Bola3!0.88!6.52!Bola3;;chr9:96159210..96159221,+!p10@Tfdp2!0.88!6.52!Tfdp2;;chr11:120491440..120491474,-!p3@Mafg!0.87!9.67!Mafg;;chr10:20880629..20880683,-!p1@Myb!0.86!18.66!Myb;;chr2:162880327..162880385,+!p2@Mybl2!0.84!41.82!Mybl2;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.84!9.67!Ncoa4;;chr1:191993385..191993405,-!p3@Prox1!0.84!5.85!Prox1;;chr18:64499706..64499721,+!p2@Onecut2!0.82!8.10!Onecut2;;chr7:56136362..56136400,-!p1@E2f8!0.81!38.45!E2f8;;chr11:11585912..11585950,+!p6@Ikzf1!0.81!7.20!Ikzf1;;chr14:47896467..47896523,-!p1@Wdhd1!0.80!70.16!Wdhd1;;chr10:20880731..20880775,-!p2@Myb!0.79!11.47!Myb;;chr2:91034924..91034946,-!p2@Nr1h3!0.79!6.52!Nr1h3;;chr2:163332558..163332596,+!p2@Hnf4a!0.79!5.17!Hnf4a;;chr11:102178005..102178022,-!p8@Ubtf!0.77!8.32!Ubtf;;chr12:3891810..3891829,+!p2@Dnmt3a!0.77!7.87!Dnmt3a;;chr15:103085802..103085817,-!p4@Nfe2!0.77!6.30!Nfe2;;chr15:103085864..103085876,-!p5@Nfe2!0.77!4.95!Nfe2;;chr4:114730015..114730042,+!p7@Tal1!0.77!4.95!Tal1;;chr6:83301243..83301258,+!p2@Bola3!0.76!4.72!Bola3;;chr18:64499674..64499696,+!p1@Onecut2!0.75!8.32!Onecut2;;chr15:103164702..103164778,-!p3@Zfp385a!0.75!5.62!Zfp385a;;chr8:59799772..59799789,+!p1@Hand2!0.73!13.72!Hand2;;chr11:23978111..23978134,+!p3@Bcl11a!0.73!9.67!Bcl11a;;chr4:87452167..87452178,-!p8@Mllt3!0.72!4.27!Mllt3;;chr8:107821563..107821642,+!p1@E2f4!0.71!132.44!E2f4;;chr8:124806111..124806122,+!p3@Zfpm1!0.70!5.17!Zfpm1;;chr11:90249521..90249551,-!p3@Hlf!0.70!4.05!Hlf;;chr10:20880698..20880717,-!p3@Myb!0.68!6.30!Myb;;chr3:102768047..102768060,-!p1@Nr1h5!0.68!3.82!Nr1h5;;chr11:101413151..101413207,-!p1@Brca1!0.67!41.15!Brca1;;chr2:163372869..163372882,+!p3@Hnf4a!0.66!3.60!Hnf4a;;chr11:23978022..23978076,+!p1@Bcl11a!0.65!87.02!Bcl11a;;chr4:135728282..135728310,+!p4@E2f2!0.65!4.05!E2f2;;chr19:37509324..37509337,+!p1@Hhex!0.64!27.66!Hhex;;chr2:162880418..162880429,+!p4@Mybl2!0.64!4.50!Mybl2;;chr1:138857076..138857105,-!p1@Nr5a2!0.64!3.37!Nr5a2;;chr6:86619104..86619119,-!p1@Mxd1!0.63!31.03!Mxd1;;chr11:23978078..23978096,+!p4@Bcl11a!0.63!11.24!Bcl11a;;chr10:88996336..88996380,-!p2@Nr1h4!0.62!4.05!Nr1h4;;chr3:51144740..51144743,-!p7@Elf2!0.61!5.62!Elf2;;chr7:6649134..6649167,-!p1@Zim1!0.59!18.66!Zim1;;chr4:13678514..13678539,+!p14@Runx1t1!0.59!2.92!Runx1t1;;chr10:12810631..12810649,+!p1@Plagl1!0.58!90.39!Plagl1;;chr2:153067094..153067130,-!p1@Plagl2!0.58!86.35!Plagl2;;chr6:131338435..131338482,-!p1@Csda!0.57!319.75!Csda;;chr7:134170081..134170122,-!p2@Maz!0.57!62.06!Maz;;chr8:13339656..13339661,+!p3@Tfdp1!0.57!7.20!Tfdp1;;chr2:147871627..147871641,-!p1@Foxa2!0.57!2.70!Foxa2;;chr11:11586218..11586285,+!p1@Ikzf1!0.56!9.89!Ikzf1;;chr6:124959016..124959061,+!p3@Zfp384!0.56!8.32!Zfp384;;chr10:41995430..41995458,-!p3@Foxo3!0.56!8.10!Foxo3;;chr7:56137011..56137041,-!p2@E2f8!0.56!5.85!E2f8;;chr11:90250944..90250982,-!p2@Hlf!0.56!4.95!Hlf;;chr10:80040030..80040072,-!p1@Klf16!0.55!64.31!Klf16;;chr2:44965593..44965624,-!p3@Zeb2!0.55!17.76!Zeb2;;chr17:56970339..56970428,-!p1@Rfx2!0.55!9.67!Rfx2;;chr6:16848347..16848391,-!p1@Tfec!0.55!3.60!Tfec;;chr11:23977742..23977794,+!p6@Bcl11a!0.55!3.37!Bcl11a;;chr10:88996295..88996335,-!p3@Nr1h4!0.55!3.15!Nr1h4;;chr5:65194752..65194769,+!p1@Klf3!0.54!104.79!Klf3;;chr5:138186979..138187025,+!p4@Tsc22d4!0.54!11.02!Tsc22d4;;chr10:30523091..30523182,-!p4@Ncoa7!0.54!10.34!Ncoa7;;chr7:56136349..56136360,-!p5@E2f8!0.54!3.37!E2f8;;chr9:96159427..96159432,+!p11@Tfdp2!0.54!3.15!Tfdp2;;chr11:23977965..23977974,+!p11@Bcl11a!0.54!2.47!Bcl11a;;chrX:7544928..7544938,-!p2@Gata1!0.54!2.47!Gata1;;chr5:38611720..38611799,+!p1@Lyar!0.53!82.52!Lyar;;chr3:95238432..95238455,+!p2@Arnt!0.53!17.09!Arnt;;chr2:166888058..166888105,-!p2@Znfx1!0.53!9.22!Znfx1;;chr2:77357622..77357704,-!p1@Zfp385b!0.53!7.65!Zfp385b;;chr13:37949830..37949861,+!p7@Rreb1!0.53!5.17!Rreb1;;chr13:55431084..55431137,-!p1@Mxd3!0.52!23.16!Mxd3;;chr5:104183219..104183236,+!p2@Aff1!0.52!20.24!Aff1;;chr13:30077847..30077906,-!p1@E2f3!0.51!22.49!E2f3;;chr3:95021663..95021687,-!p3@Gabpb2!0.51!9.44!Gabpb2;;chr17:56970481..56970551,-!p2@Rfx2!0.51!8.54!Rfx2;;chr11:102177974..102177992,-!p17@Ubtf!0.51!2.92!Ubtf;;chr5:115421065..115421088,-!p1@Hnf1a!0.51!2.25!Hnf1a;;chr9:24578720..24578735,-!p1@Tbx20!0.51!2.25!Tbx20;;chr15:103083245..103083260,-!p7@Nfe2!0.51!2.25!Nfe2;;chr10:119913310..119913366,-!p1@Hmga2!0.50!21.81!Hmga2;;chr10:30522690..30522752,-!p2@Ncoa7!0.50!17.09!Ncoa7;;chr5:140267476..140267493,+!p1@Mafk!0.50!15.52!Mafk;;chr2:153067079..153067090,-!p2@Plagl2!0.50!5.40!Plagl2;;chr12:58646974..58647003,-!p1@Foxa1!0.50!3.15!Foxa1;;chr11:23978353..23978379,+!p10@Bcl11a!0.50!2.70!Bcl11a;;chr9:20757282..20757325,-!p2@Dnmt1!0.49!64.99!Dnmt1;;chr6:86619130..86619158,-!p2@Mxd1!0.49!40.48!Mxd1;;chr8:72520225..72520248,-!p9@Gatad2a!0.49!6.97!Gatad2a;;chr2:162880306..162880319,+!p3@Mybl2!0.49!3.37!Mybl2;;chr11:11585678..11585745,+!p5@Ikzf1!0.49!3.37!Ikzf1;;chr18:74375754..74375763,+!p4@Cxxc1!0.49!2.70!Cxxc1;;chr5:111082367..111082441,-!p1@Noc4l!0.48!62.96!Noc4l;;chr2:154395581..154395610,-!p1@E2f1!0.48!27.66!E2f1;;chr5:34163023..34163090,+!p2@Whsc1!0.48!17.09!Whsc1;;chr15:103085821..103085828,-!p6@Nfe2!0.48!2.02!Nfe2;;chr14:32979060..32979091,+!p4@Gm6768,p4@Ncoa4!0.48!2.02!Ncoa4;;chr4:135736707..135736724,+!p8@E2f2!0.48!2.02!E2f2;;chr4:13678482..13678505,+!p9@Runx1t1!0.48!2.02!Runx1t1;;chr2:147872790..147872821,-!p2@Foxa2!0.48!2.02!Foxa2;;chr11:23977565..23977612,+!p5@Bcl11a!0.47!5.17!Bcl11a;;chr5:65213356..65213412,+!p6@Klf3!0.47!4.95!Klf3;;chr1:181733959..181733977,-!p4@Ahctf1!0.47!2.70!Ahctf1;;chr6:131338363..131338383,-!p4@Csda!0.46!11.02!Csda;;chr6:28211956..28211967,-!p2@Zfp800!0.46!4.95!Zfp800;;chr2:90936947..90936977,+!p2@Sfpi1!0.46!4.50!Sfpi1;;chr3:135271185..135271254,-!p4@Nfkb1!0.46!4.05!Nfkb1;;chr8:123608252..123608268,+!p1@Foxf1a!0.46!3.15!Foxf1a;;chr2:38206744..38206766,+!p1@Lhx2!0.46!2.47!Lhx2;;chr15:61817095..61817111,+!p1@Myc!0.45!153.81!Myc;;chr6:131338483..131338494,-!p5@Csda!0.45!12.82!Csda;;chr12:85534957..85535017,-!p2@C130039O16Rik!0.45!12.37!C130039O16Rik;;chr13:112476264..112476282,+!p3@Mier3!0.45!2.92!Mier3;;chr4:135736690..135736705,+!p6@E2f2!0.45!2.25!E2f2;;chr1:138846047..138846074,-!p5@Nr5a2!0.45!2.02!Nr5a2;;chr1:138857112..138857130,-!p7@Nr5a2!0.45!1.80!Nr5a2;;chr11:83664365..83664383,+!p1@Hnf1b!0.45!1.80!Hnf1b;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.44!114.90!Hmga1;;chr16:55966451..55966484,+!p3@Rpl24,p3@Zbtb11!0.44!14.17!Zbtb11;;chr14:100683884..100683908,-!p4@Klf12!0.44!4.05!Klf12;;chr6:83299445..83299490,+!p1@Bola3!0.43!103.89!Bola3;;chr15:61816932..61816952,+!p2@Myc!0.43!19.56!Myc;;chr11:58717675..58717719,-!p1@Zfp39!0.43!16.86!Zfp39;;chr2:90936901..90936945,+!p1@Sfpi1!0.43!12.37!Sfpi1;;chr4:134708451..134708469,+!p1@Runx3!0.43!3.60!Runx3;;chr1:138846009..138846038,-!p3@Nr5a2!0.43!2.02!Nr5a2;;chr13:64254457..64254497,-!p1@Zfp367!0.42!10.12!Zfp367;;chr10:119913278..119913298,-!p2@Hmga2!0.42!4.72!Hmga2;;chr7:56136402..56136420,-!p3@E2f8!0.42!3.60!E2f8;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.42!2.25!Hmga1;;chr6:16848395..16848416,-!p2@Tfec!0.42!2.02!Tfec;;chr19:10315179..10315241,-!p1@Gm98!0.41!23.84!Gm98;;chr11:102180696..102180760,-!p2@Ubtf!0.41!11.02!Ubtf;;chr6:72849280..72849297,-!p6@Kcmf1!0.41!3.82!Kcmf1;;chr11:60036258..60036276,-!p3@Srebf1!0.41!3.37!Srebf1;;chr11:120624132..120624143,+!p10@Hmga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0.22!Csrnp1;;chr7:35841438..35841447,-!p4@Cebpg!0.09!0.22!Cebpg;;chr7:52962498..52962512,+!p12@Dbp!0.09!0.22!Dbp;;chr7:53631837..53631850,+!p1@Myod1!0.09!0.22!Myod1;;chr8:26958093..26958148,-!p2@Ash2l!0.09!0.22!Ash2l;;chr8:77540128..77540145,+!p2@Hmgxb4!0.09!0.22!Hmgxb4;;chr7:52071279..52071296,-!p9@Atf5!0.09!0.22!Atf5;;chr9:87626109..87626120,-!p3@Tbx18!0.09!0.22!Tbx18;;chr8:86590283..86590297,+!p5@Rfx1!0.09!0.22!Rfx1;;chr8:72676653..72676668,+!p4@2310045N01Rik,p4@Mef2b!0.09!0.22!Mef2b;;chr11:23978291..23978323,+!p7@Bcl11a!0.09!0.22!Bcl11a;;chr11:121121426..121121435,+!p3@Foxk2!0.09!0.22!Foxk2;;chr11:90249836..90249849,-!p15@Hlf!0.09!0.22!Hlf;;chr11:23978206..23978219,+!p12@Bcl11a!0.09!0.22!Bcl11a;;chr10:61595830..61595846,+!p1@Neurog3!0.09!0.22!Neurog3;;chr11:100721492..100721499,+!p5@Stat5a!0.09!0.22!Stat5a;;chr11:116196698..116196713,-!p3@Foxj1!0.09!0.22!Foxj1;;chr10:84218800..84218829,+!p2@Rfx4!0.09!0.22!Rfx4;;chr11:59319947..59319958,-!p9@Zkscan17!0.09!0.22!Zkscan17;;chr11:100721584..100721587,+!p8@Stat5a!0.09!0.22!Stat5a;;chr11:57645506..57645523,-!p1@Hand1!0.09!0.22!Hand1;;chr11:50641158..50641165,-!p3@Zfp354c!0.09!0.22!Zfp354c;;chr10:80555299..80555306,-!p3@Creb3l3!0.09!0.22!Creb3l3;;chr11:44431115..44431132,+!p9@Ebf1!0.09!0.22!Ebf1;;chr11:11590205..11590216,+!p9@Ikzf1!0.09!0.22!Ikzf1;;chr10:5734473..5734489,-!p5@Esr1!0.09!0.22!Esr1;;chr11:96685444..96685473,-!p5@Nfe2l1!0.09!0.22!Nfe2l1;;chr10:20881210..20881226,-!p8@Myb!0.09!0.22!Myb;;chr10:20872753..20872775,-!p11@Myb!0.09!0.22!Myb;;chr10:20881239..20881254,-!p5@Myb!0.09!0.22!Myb;;chr10:119913766..119913779,-!p10@Hmga2!0.09!0.22!Hmga2;;chr10:30375530..30375535,-!p12@Ncoa7!0.09!0.22!Ncoa7;;chr10:20881160..20881175,-!p4@Myb!0.09!0.22!Myb;;chr11:98826178..98826197,+!p7@Rara!0.09!0.22!Rara;;chr10:30522660..30522671,-!p10@Ncoa7!0.09!0.22!Ncoa7;;chr10:51397572..51397595,+!p1@Rfx6!0.09!0.22!Rfx6;;chr15:85602581..85602598,+!p8@Ppara!0.09!0.22!Ppara;;chr17:44873235..44873245,-!p17@Runx2!0.09!0.22!Runx2;;chr18:11052516..11052525,+!p5@Gata6!0.09!0.22!Gata6;;chr17:27865882..27865901,-!p1@Spdef!0.09!0.22!Spdef;;chr17:28408632..28408682,+!p1@1810013A23Rik,p4@Ppard!0.09!0.22!Ppard;;chr17:47906140..47906150,+!p6@Tfeb!0.09!0.22!Tfeb;;chr19:46380399..46380417,+!p4@Nfkb2!0.09!0.22!Nfkb2;;chr18:3309750..3309787,-!p21@Crem!0.09!0.22!Crem;;chr19:28085572..28085579,-!p9@Rfx3!0.09!0.22!Rfx3;;chr16:43364258..43364270,+!p27@Zbtb20!0.09!0.22!Zbtb20;;chr17:86087592..86087615,-!p1@Six2!0.09!0.22!Six2;;chr16:14705746..14705761,+!p4@Snai2!0.09!0.22!Snai2;;chr16:92826180..92826191,-!p5@Runx1!0.09!0.22!Runx1;;chr16:92826232..92826245,-!p4@Runx1!0.09!0.22!Runx1;;chrX:7541292..7541317,-!p3@Gata1!0.09!0.22!Gata1;;chr6:144157869..144157876,-!p26@Sox5!0.09!0.22!Sox5;;chr5:38611867..38611888,+!p2@Lyar!0.09!0.22!Lyar;;chr6:99216360..99216372,-!p8@Foxp1!0.09!0.22!Foxp1;;chr5:125523164..125523188,-!p8@Ncor2!0.09!0.22!Ncor2;;chr6:52167434..52167450,-!p3@Hoxa7!0.09!0.22!Hoxa7;;chr5:148081722..148081744,+!p2@Pdx1!0.09!0.22!Pdx1;;chr6:88143570..88143590,+!p4@Gata2!0.09!0.22!Gata2;;chr6:90416275..90416286,+!p9@Klf15!0.09!0.22!Klf15;;chr6:28348078..28348109,-!p5@Zfp800!0.09!0.22!Zfp800;;chr5:115421126..115421137,-!p4@Hnf1a!0.09!0.22!Hnf1a;;chr5:115420882..115420896,-!p3@Hnf1a!0.09!0.22!Hnf1a;;chr5:108698309..108698321,+!p8@Dr1!0.09!0.22!Dr1;;chr7:108966820..108966835,+!p1@Phox2a!0.09!0.22!Phox2a;;chr6:144157991..144158007,-!p9@Sox5!0.09!0.22!Sox5;;chr5:38611831..38611842,+!p3@Lyar!0.09!0.22!Lyar;;chr12:87762578..87762612,+!p1@Esrrb!0.09!0.22!Esrrb;;chr13:48758276..48758291,+!p1@Barx1!0.09!0.22!Barx1;;chr15:102828642..102828653,+!p2@Hoxc6!0.09!0.22!Hoxc6;;chr14:63890459..63890484,-!p4@Gata4!0.09!0.22!Gata4;;chr14:63890691..63890718,-!p8@Gata4!0.09!0.22!Gata4;;chr12:86939997..86940040,+!p4@Jdp2!0.09!0.22!Jdp2;;chr15:102839948..102839975,+!p3@Hoxc6!0.09!0.22!Hoxc6;;chr12:12947199..12947213,-!p2@Mycn!0.09!0.22!Mycn;;chr15:102820964..102821006,+!p1@Hoxc8!0.09!0.22!Hoxc8;;chr14:63890660..63890687,-!p7@Gata4!0.09!0.22!Gata4;;chr13:48758328..48758335,+!p4@Barx1!0.09!0.22!Barx1;;chr15:37163124..37163153,+!p3@Grhl2!0.09!0.22!Grhl2;;chr12:25257265..25257294,+!p2@Grhl1!0.09!0.22!Grhl1;;chr12:3806003..3806031,+!p11@Dnmt3a!0.09!0.22!Dnmt3a;;chr12:58647114..58647128,-!p2@Foxa1!0.09!0.22!Foxa1;;chr14:17407671..17407684,-!p7@Rarb!0.09!0.22!Rarb;;chr14:55331167..55331204,-!p3@Cebpe!0.09!0.22!Cebpe;;chr13:53568081..53568094,-!p3@Msx2!0.09!0.22!Msx2;;chr14:56443742..56443756,+!p6@Nfatc4!0.09!0.22!Nfatc4;;chr12:77470660..77470671,-!p8@Zbtb25!0.09!0.22!Zbtb25;;chr14:52640336..52640341,-!p20@Zfp219!0.09!0.22!Zfp219;;chr13:83712735..83712761,+!p9@Mef2c!0.09!0.22!Mef2c;;chr1:186556307..186556318,-!p7@Hlx!0.09!0.22!Hlx;;chr2:104966465..104966479,+!p6@Wt1!0.09!0.22!Wt1;;chr2:156665551..156665562,+!p6@Tgif2!0.09!0.22!Tgif2;;chr1:92950128..92950139,+!p4@Lrrfip1!0.09!0.22!Lrrfip1;;chr1:92949751..92949769,+!p5@Lrrfip1!0.09!0.22!Lrrfip1;;chr2:104966874..104966907,+!p2@Wt1!0.09!0.22!Wt1;;chr1:138846117..138846129,-!p8@Nr5a2!0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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 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011340
 |is_obsolete=
+|library_id=CNhs10594
+|library_id_phase_based=2:CNhs10594
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;409
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;409
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E14.CNhs10594.409-16E1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E14.CNhs10594.409-16E1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E14.CNhs10594.409-16E1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E14.CNhs10594.409-16E1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E14.CNhs10594.409-16E1.mm9.nobarcode.rdna.fa.gz
 |name=liver, embryo E14
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10594,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0737519957455875,0,0,0,0.0880872011895838,0.00281459198754034,-0.123861511718838,0,0,0,0,0.242878767997128,0,0,0,0,0,0,-0.103806149692991,0,0.0440436005947919,0,0.0880872011895838,0,0,0,0,0,0,0,0,0,0.215872697736754,0,0,0,0.278627511428843,-0.00302342667277758,0.0349289766972893,-0.12277105942502,0.298237209725528,0.57573535589941,-0.108583242017791,0,0,0,0,0,0,0,0,0,0,0,0,0.0952798484291203,0,0,0,0,-0.0428469550828748,0,0,0.0880872011895838,0.37091494046575,0,-0.0733462023135343,0.0602642831263637,-0.0700038415814987,0.207309937898573,0,0.100939699936862,-0.121354825755431,-0.110816368280424,0.410614411864076,0,-0.0733001047639908,-0.105401417857191,-0.317287369311727,0.0092556063496764,0,0,0,0,0,0,-0.188798140967711,-0.372967106898722,-0.189160304235119,0,0,0,0,0
 |rna_box=16
 |rna_catalog_number=
@@ Line 56: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=16E1
+|rna_tube_id=1.60E+02
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:409-16E1;search_select_hide=table117:409-16E1
 }}

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FF:409-16E1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:15, 4 June 2020

CNhs10594

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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