FF:684-20A8: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	liver, neonate N06
Species:	Mouse (Mus musculus)
Library ID:	CNhs11101
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	6 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		SAMD00005319

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11101		CAGE		DRX009024		DRR009898

Accession ID Mm9

Library id		BAM		CTSS
CNhs11101		DRZ001323		DRZ002706

Accession ID Mm10

Library id		BAM		CTSS
CNhs11101		DRZ012673		DRZ014056

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

CNhs11101

0	0
1	0
10	0
100	0
1000	0
1001	0.659
1002	0.161
1003	0.3
1004	0
1005	0.348
1006	0.0455
1007	0.13
1008	0
1009	0.197
101	0.0375
1010	0
1011	-0.108
1012	0.49
1013	0.273
1014	0.387
1015	-0.172
1016	-0.0783
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.289
1023	0
1024	0.0799
1025	0.428
1026	0
1027	0
1028	0
1029	0.949
103	0.387
1030	0.588
1031	0.241
1032	-0.246
1033	0
1034	0.739
1035	0
1036	0.0388
1037	0
1038	0.205
1039	0.324
104	0
1040	-0.121
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: CNhs11101

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.645
MA0003.1	MA0003.1	0.406
MA0004.1	MA0004.1	0.953
MA0006.1	MA0006.1	0.373
MA0007.1	MA0007.1	0.362
MA0009.1	MA0009.1	0.336
MA0014.1	MA0014.1	0.575
MA0017.1	MA0017.1	7.18432e-8
MA0018.2	MA0018.2	1.0695e-7
MA0019.1	MA0019.1	0.82
MA0024.1	MA0024.1	0.363
MA0025.1	MA0025.1	0.126
MA0027.1	MA0027.1	0.887
MA0028.1	MA0028.1	0.038
MA0029.1	MA0029.1	0.879
MA0030.1	MA0030.1	0.805
MA0031.1	MA0031.1	0.964
MA0035.2	MA0035.2	0.481
MA0038.1	MA0038.1	0.0173
MA0039.2	MA0039.2	0.00762
MA0040.1	MA0040.1	0.38
MA0041.1	MA0041.1	0.134
MA0042.1	MA0042.1	0.461
MA0043.1	MA0043.1	5.94727e-4
MA0046.1	MA0046.1	2.32812e-12
MA0047.2	MA0047.2	0.127
MA0048.1	MA0048.1	0.0732
MA0050.1	MA0050.1	0.237
MA0051.1	MA0051.1	0.655
MA0052.1	MA0052.1	0.00279
MA0055.1	MA0055.1	0.695
MA0057.1	MA0057.1	0.883
MA0058.1	MA0058.1	0.944
MA0059.1	MA0059.1	0.0724
MA0060.1	MA0060.1	4.25377e-8
MA0061.1	MA0061.1	0.247
MA0062.2	MA0062.2	4.27898e-4
MA0065.2	MA0065.2	3.98505e-5
MA0066.1	MA0066.1	0.0118
MA0067.1	MA0067.1	0.146
MA0068.1	MA0068.1	0.541
MA0069.1	MA0069.1	0.214
MA0070.1	MA0070.1	0.627
MA0071.1	MA0071.1	0.0246
MA0072.1	MA0072.1	0.068
MA0073.1	MA0073.1	0.693
MA0074.1	MA0074.1	0.327
MA0076.1	MA0076.1	0.0064
MA0077.1	MA0077.1	0.0226
MA0078.1	MA0078.1	0.947
MA0079.2	MA0079.2	0.0343
MA0080.2	MA0080.2	0.0126
MA0081.1	MA0081.1	0.212
MA0083.1	MA0083.1	0.132
MA0084.1	MA0084.1	0.485
MA0087.1	MA0087.1	0.164
MA0088.1	MA0088.1	0.471
MA0090.1	MA0090.1	0.947
MA0091.1	MA0091.1	0.262
MA0092.1	MA0092.1	0.102
MA0093.1	MA0093.1	0.972
MA0099.2	MA0099.2	0.0411
MA0100.1	MA0100.1	0.477
MA0101.1	MA0101.1	0.865
MA0102.2	MA0102.2	0.995
MA0103.1	MA0103.1	0.393
MA0104.2	MA0104.2	0.805
MA0105.1	MA0105.1	8.28206e-6
MA0106.1	MA0106.1	0.081
MA0107.1	MA0107.1	0.944
MA0108.2	MA0108.2	4.21709e-7
MA0111.1	MA0111.1	0.497
MA0112.2	MA0112.2	2.179e-6
MA0113.1	MA0113.1	0.372
MA0114.1	MA0114.1	6.7835e-8
MA0115.1	MA0115.1	1.39818e-4
MA0116.1	MA0116.1	0.0157
MA0117.1	MA0117.1	0.968
MA0119.1	MA0119.1	0.022
MA0122.1	MA0122.1	0.0475
MA0124.1	MA0124.1	0.913
MA0125.1	MA0125.1	0.347
MA0131.1	MA0131.1	0.672
MA0135.1	MA0135.1	0.00165
MA0136.1	MA0136.1	4.73062e-6
MA0137.2	MA0137.2	0.227
MA0138.2	MA0138.2	0.908
MA0139.1	MA0139.1	0.46
MA0140.1	MA0140.1	0.0771
MA0141.1	MA0141.1	7.50605e-4
MA0142.1	MA0142.1	0.732
MA0143.1	MA0143.1	0.183
MA0144.1	MA0144.1	0.75
MA0145.1	MA0145.1	0.745
MA0146.1	MA0146.1	0.917
MA0147.1	MA0147.1	0.949
MA0148.1	MA0148.1	0.00679
MA0149.1	MA0149.1	0.0599
MA0150.1	MA0150.1	0.448
MA0152.1	MA0152.1	0.371
MA0153.1	MA0153.1	7.7018e-11
MA0154.1	MA0154.1	0.0061
MA0155.1	MA0155.1	0.722
MA0156.1	MA0156.1	0.00565
MA0157.1	MA0157.1	0.35
MA0159.1	MA0159.1	0.0117
MA0160.1	MA0160.1	0.0677
MA0162.1	MA0162.1	0.457
MA0163.1	MA0163.1	4.6319e-5
MA0164.1	MA0164.1	0.428
MA0258.1	MA0258.1	0.0021
MA0259.1	MA0259.1	0.819

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: CNhs11101

Novel motif	Logo	P-value
1	1	0.0685
10	10	0.054
100	100	0.686
101	101	0.717
102	102	0.442
103	103	0.00299
104	104	0.801
105	105	0.543
106	106	0.0181
107	107	0.00981
108	108	0.715
109	109	0.321
11	11	0.171
110	110	0.0608
111	111	0.0404
112	112	0.0198
113	113	0.662
114	114	0.0384
115	115	0.398
116	116	0.928
117	117	0.0162
118	118	0.179
119	119	0.162
12	12	0.669
120	120	0.967
121	121	0.276
122	122	0.723
123	123	0.87
124	124	0.0659
125	125	0.909
126	126	0.187
127	127	0.606
128	128	0.00727
129	129	0.325
13	13	0.0106
130	130	0.788
131	131	0.495
132	132	0.735
133	133	0.0565
134	134	0.592
135	135	0.837
136	136	0.423
137	137	0.56
138	138	0.425
139	139	0.247
14	14	0.802
140	140	0.00168
141	141	0.145
142	142	0.0932
143	143	0.29
144	144	0.611
145	145	0.0448
146	146	0.993
147	147	0.676
148	148	0.85
149	149	0.597
15	15	0.228
150	150	0.0933
151	151	0.635
152	152	0.845
153	153	0.0993
154	154	0.147
155	155	0.787
156	156	0.598
157	157	0.973
158	158	0.924
159	159	0.018
160	160	0.0536
161	161	0.694
162	162	0.918
163	163	0.581
164	164	0.0896
165	165	0.95
166	166	0.952
167	167	0.0509
168	168	0.856
169	169	0.0191
17	17	0.0903
18	18	0.244
19	19	0.0503
2	2	0.924
20	20	0.293
21	21	0.951
22	22	0.282
23	23	0.163
24	24	0.96
25	25	0.891
26	26	7.86695e-4
27	27	0.715
28	28	0.618
29	29	0.156
3	3	0.0182
30	30	0.433
31	31	0.31
32	32	0.0479
33	33	0.589
34	34	0.483
35	35	0.125
36	36	0.22
37	37	0.103
38	38	0.577
39	39	0.326
4	4	0.639
40	40	0.86
41	41	0.559
42	42	0.19
43	43	0.0307
44	44	0.0788
45	45	0.643
46	46	0.033
47	47	0.48
48	48	0.34
49	49	0.0456
5	5	0.0848
50	50	0.686
51	51	0.416
52	52	0.656
53	53	0.465
54	54	0.445
55	55	0.957
56	56	0.319
57	57	0.174
58	58	0.698
59	59	0.233
6	6	0.697
60	60	0.155
61	61	0.171
62	62	0.297
63	63	0.236
64	64	0.495
65	65	0.39
66	66	0.298
67	67	0.866
68	68	0.0339
69	69	0.578
7	7	0.25
70	70	0.167
71	71	0.0274
72	72	0.98
73	73	0.443
74	74	0.501
75	75	0.0316
76	76	0.265
77	77	0.396
78	78	0.041
79	79	0.49
8	8	0.0256
80	80	0.789
81	81	0.759
82	82	0.105
83	83	0.88
84	84	0.437
85	85	0.0301
86	86	0.244
87	87	0.0261
88	88	0.593
89	89	0.508
9	9	0.632
90	90	0.0249
91	91	0.0273
92	92	0.0439
93	93	0.94
94	94	0.252
95	95	0.858
96	96	0.154
97	97	0.209
98	98	0.365
99	99	0.266

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: CNhs11101

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011403 mouse liver- neonate N06 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)
0000312 (mouse neonate N6 sample)
0011403 (mouse liver- neonate N06 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@SAMD00005319
+|accession_numbers=CAGE;DRX009024;DRR009898;DRZ001323;DRZ002706;DRZ012673;DRZ014056
 |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=chr18:64499674..64499696,+!p1@Onecut2!2.14!230.03!Onecut2;;chr10:80555320..80555378,-!p1@Creb3l3!1.97!106.39!Creb3l3;;chr7:19608891..19608895,-!p1@Foxa3!1.94!110.70!Foxa3;;chr1:173144144..173144176,+!p1@Nr1i3!1.94!86.26!Nr1i3;;chr18:64499706..64499721,+!p2@Onecut2!1.93!116.45!Onecut2;;chr2:163372884..163372904,+!p1@Hnf4a!1.93!84.82!Hnf4a;;chr1:173144100..173144138,+!p2@Nr1i3!1.86!71.88!Nr1i3;;chr10:88969376..88969395,-!p1@Nr1h4!1.86!71.88!Nr1h4;;chr15:85566184..85566238,+!p1@Ppara!1.82!94.89!Ppara;;chr7:52071956..52071978,-!p1@Atf5!1.80!1867.55!Atf5;;chr10:88996295..88996335,-!p3@Nr1h4!1.79!71.88!Nr1h4;;chr15:85566537..85566552,+!p2@Ppara!1.78!58.94!Ppara;;chr9:74709695..74709722,+!p1@Onecut1!1.77!57.51!Onecut1;;chr10:88996336..88996380,-!p2@Nr1h4!1.76!69.01!Nr1h4;;chr4:108151497..108151514,+!p3@Zcchc11!1.75!107.83!Zcchc11;;chr16:38294860..38294924,-!p1@Nr1i2!1.73!53.19!Nr1i2;;chr1:191994550..191994623,-!p1@Prox1!1.70!320.60!Prox1;;chr11:90249521..90249551,-!p3@Hlf!1.64!43.13!Hlf;;chr4:126700722..126700753,+!p4@Sfpq!1.63!97.76!Sfpq;;chr5:135582751..135582788,+!p1@Mlxipl!1.62!155.27!Mlxipl;;chrX:103070960..103070973,-!p7@Atrx!1.58!48.88!Atrx;;chr19:37509324..37509337,+!p1@Hhex!1.57!242.97!Hhex;;chr4:126703093..126703158,+!p3@Sfpq!1.56!96.32!Sfpq;;chr15:85602655..85602680,+!p5@Ppara!1.55!34.50!Ppara;;chr4:126700650..126700678,+!p5@Sfpq!1.43!50.32!Sfpq;;chr4:126700683..126700704,+!p6@Sfpq!1.43!48.88!Sfpq;;chrX:103070839..103070856,-!p4@Atrx!1.42!38.82!Atrx;;chr1:138846079..138846103,-!p6@Nr5a2!1.41!24.44!Nr5a2;;chr4:133109285..133109308,+!p1@Nr0b2!1.41!24.44!Nr0b2;;chr15:103164702..103164778,-!p3@Zfp385a!1.36!25.88!Zfp385a;;chr2:38206580..38206600,+!p2@Lhx2!1.34!25.88!Lhx2;;chr16:43619057..43619078,+!p8@Zbtb20!1.30!38.82!Zbtb20;;chr10:88145766..88145770,-!p1@Spic!1.30!24.44!Spic;;chr2:27532479..27532509,+!p3@Rxra!1.29!37.38!Rxra;;chr1:138857076..138857105,-!p1@Nr5a2!1.29!18.69!Nr5a2;;chr2:173044380..173044432,-!p1@Zbp1!1.26!40.26!Zbp1;;chr7:122989632..122989668,-!p2@Sox6!1.26!17.25!Sox6;;chr2:169458838..169458859,+!p4@Tshz2!1.25!33.07!Tshz2;;chr1:170362437..170362478,-!p5@Pbx1!1.23!48.88!Pbx1;;chr12:58646974..58647003,-!p1@Foxa1!1.23!21.57!Foxa1;;chr8:87425854..87425891,+!p1@Klf1!1.23!15.81!Klf1;;chr7:52072324..52072336,-!p4@Atf5!1.23!15.81!Atf5;;chr10:22539932..22539956,-!p1@Tcf21!1.21!40.26!Tcf21;;chr4:126700576..126700598,+!p7@Sfpq!1.20!27.32!Sfpq;;chr2:27532513..27532525,+!p8@Rxra!1.20!17.25!Rxra;;chr2:120365219..120365232,-!p4@Zfp106!1.19!20.13!Zfp106;;chr15:10391745..10391753,-!p3@Dnajc21!1.19!18.69!Dnajc21;;chr13:83643159..83643226,+!p3@Mef2c!1.19!14.38!Mef2c;;chr2:91034924..91034946,-!p2@Nr1h3!1.17!17.25!Nr1h3;;chr6:99470943..99471024,-!p3@Foxp1!1.16!126.52!Foxp1;;chr11:100683839..100683890,-!p2@Stat5b!1.14!30.19!Stat5b;;chr11:83664365..83664383,+!p1@Hnf1b!1.14!12.94!Hnf1b;;chr1:191993385..191993405,-!p3@Prox1!1.14!12.94!Prox1;;chr2:147872074..147872079,-!p4@Foxa2!1.14!12.94!Foxa2;;chr4:44723520..44723544,-!p2@Pax5!1.14!12.94!Pax5;;chr15:85566241..85566253,+!p6@Ppara!1.14!12.94!Ppara;;chr2:77357622..77357704,-!p1@Zfp385b!1.12!33.07!Zfp385b;;chr15:85566051..85566080,+!p4@Ppara!1.12!14.38!Ppara;;chr16:43619101..43619151,+!p6@Zbtb20!1.11!28.75!Zbtb20;;chr9:96159147..96159204,+!p2@Tfdp2!1.10!21.57!Tfdp2;;chr5:115421065..115421088,-!p1@Hnf1a!1.10!11.50!Hnf1a;;chr2:147872790..147872821,-!p2@Foxa2!1.10!11.50!Foxa2;;chr4:97444012..97444045,+!p4@Nfia!1.09!84.82!Nfia;;chrX:103070746..103070764,-!p5@Atrx!1.09!17.25!Atrx;;chr4:32325688..32325777,+!p1@Bach2!1.08!97.76!Bach2;;chr18:11052606..11052633,+!p4@Gata6!1.07!27.32!Gata6;;chr2:148506935..148506954,+!p2@Gzf1!1.07!21.57!Gzf1;;chr1:138857048..138857071,-!p2@Nr5a2!1.04!10.06!Nr5a2;;chr1:191994700..191994711,-!p4@Prox1!1.04!10.06!Prox1;;chr4:32334732..32334739,+!p7@Bach2!1.04!10.06!Bach2;;chr9:24578720..24578735,-!p1@Tbx20!1.04!10.06!Tbx20;;chr15:85565338..85565355,+!p7@Ppara!1.04!10.06!Ppara;;chr19:37511111..37511115,+!p2@Hhex!1.04!10.06!Hhex;;chr7:122989594..122989626,-!p1@Sox6!1.04!10.06!Sox6;;chr13:83643232..83643254,+!p5@Mef2c!1.04!10.06!Mef2c;;chr4:97444471..97444514,+!p1@Nfia!1.03!261.66!Nfia;;chr16:92826249..92826325,-!p1@Runx1!1.03!24.44!Runx1;;chr17:87153240..87153254,+!p1@Epas1!1.01!184.02!Epas1;;chr13:83663600..83663625,+!p6@Mef2c!1.01!14.38!Mef2c;;chr7:35904304..35904320,+!p1@Cebpa!1.00!185.46!Cebpa;;chr14:63864056..63864102,-!p1@Gata4!1.00!15.81!Gata4;;chr4:82151126..82151133,-!p8@Nfib!0.99!11.50!Nfib;;chr1:186556410..186556424,-!p1@Hlx!0.98!27.32!Hlx;;chr1:133914326..133914346,+!p8@Elk4!0.98!15.81!Elk4;;chr15:103085660..103085681,-!p1@Nfe2!0.98!12.94!Nfe2;;chr6:16848347..16848391,-!p1@Tfec!0.98!11.50!Tfec;;chr6:90415250..90415271,+!p4@Klf15!0.98!8.63!Klf15;;chr1:138857112..138857130,-!p7@Nr5a2!0.98!8.63!Nr5a2;;chr9:69137716..69137744,+!p1@Rora!0.97!53.19!Rora;;chr4:97444446..97444470,+!p3@Nfia!0.96!79.07!Nfia;;chr10:20880731..20880775,-!p2@Myb!0.96!17.25!Myb;;chr17:87153519..87153533,+!p5@Epas1!0.94!11.50!Epas1;;chr6:144730427..144730508,-!p1@Sox5!0.93!47.44!Sox5;;chr1:64167851..64167886,-!p3@Klf7!0.93!33.07!Klf7;;chr6:53018700..53018759,-!p2@Jazf1!0.93!28.75!Jazf1;;chr3:5218590..5218614,+!p3@Zfhx4!0.92!12.94!Zfhx4;;chr2:169458519..169458555,+!p2@Tshz2!0.91!30.19!Tshz2;;chr7:87170879..87170914,+!p2@Zfp710!0.91!17.25!Zfp710;;chr5:134741947..134741948,-!p9@Gtf2i!0.91!11.50!Gtf2i;;chr10:80555299..80555306,-!p3@Creb3l3!0.91!7.19!Creb3l3;;chr10:88996274..88996286,-!p4@Nr1h4!0.91!7.19!Nr1h4;;chr3:102768047..102768060,-!p1@Nr1h5!0.91!7.19!Nr1h5;;chr4:82151653..82151706,-!p2@Nfib!0.90!204.15!Nfib;;chr4:133276698..133276743,-!p6@Arid1a!0.90!20.13!Arid1a;;chr4:114732112..114732158,+!p1@Tal1!0.90!15.81!Tal1;;chr2:28477452..28477483,-!p1@Gfi1b!0.90!8.63!Gfi1b;;chr1:13364477..13364492,-!p6@Ncoa2!0.90!8.63!Ncoa2;;chr2:91035254..91035271,-!p3@Nr1h3!0.89!8.63!Nr1h3;;chr3:94176733..94176794,+!p1@Rorc!0.88!53.19!Rorc;;chr2:169458352..169458397,+!p3@Tshz2!0.88!17.25!Tshz2;;chr16:55822638..55822669,-!p3@Nfkbiz!0.88!10.06!Nfkbiz;;chr1:138845748..138845766,-!p4@Nr5a2!0.88!8.63!Nr5a2;;chr10:82226649..82226694,-!p2@Nfyb!0.87!43.13!Nfyb;;chr1:138846009..138846038,-!p3@Nr5a2!0.87!7.19!Nr5a2;;chr15:40486566..40486600,+!p1@Zfpm2!0.86!38.82!Zfpm2;;chr8:59799772..59799789,+!p1@Hand2!0.86!18.69!Hand2;;chr13:58501849..58501853,-!p5@Hnrnpk!0.86!11.50!Hnrnpk;;chr19:55817629..55817652,+!p14@Tcf7l2!0.86!8.63!Tcf7l2;;chr19:55816398..55816409,+!p5@Tcf7l2!0.85!30.19!Tcf7l2;;chr12:110031310..110031342,+!p4@Yy1!0.85!25.88!Yy1;;chr8:73905892..73905903,-!p5@Nr2f6!0.85!7.19!Nr2f6;;chr12:110031227..110031254,+!p3@Yy1!0.84!35.94!Yy1;;chr18:11052642..11052659,+!p1@Gata6!0.84!31.63!Gata6;;chrX:45947746..45947762,-!p2@Zfp280c!0.84!12.94!Zfp280c;;chr11:121380640..121380655,-!p1@Zfp750!0.84!10.06!Zfp750;;chr10:5734525..5734569,-!p3@Esr1!0.84!10.06!Esr1;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!0.84!7.19!Ncoa4;;chr16:44173384..44173407,+!p2@Gm608!0.83!15.81!Gm608;;chr7:25917492..25917512,-!p1@Pou2f2!0.83!10.06!Pou2f2;;chr16:38294929..38294940,-!p2@Nr1i2!0.83!5.75!Nr1i2;;chr4:44723559..44723593,-!p1@Pax5!0.83!5.75!Pax5;;chr10:80555285..80555291,-!p4@Creb3l3!0.83!5.75!Creb3l3;;chr2:147871627..147871641,-!p1@Foxa2!0.83!5.75!Foxa2;;chr2:163372869..163372882,+!p3@Hnf4a!0.83!5.75!Hnf4a;;chr1:52176315..52176343,+!p1@Stat1!0.81!84.82!Stat1;;chr14:100684075..100684098,-!p3@Klf12!0.81!14.38!Klf12;;chr17:87153028..87153049,+!p2@Epas1!0.80!117.89!Epas1;;chr2:83499707..83499708,+!p6@Zc3h15!0.80!20.13!Zc3h15;;chr2:91035197..91035237,-!p1@Nr1h3!0.80!11.50!Nr1h3;;chr1:138846047..138846074,-!p5@Nr5a2!0.80!5.75!Nr5a2;;chr14:100683672..100683717,-!p1@Klf12!0.79!25.88!Klf12;;chr3:5218563..5218587,+!p5@Zfhx4!0.79!8.63!Zfhx4;;chr9:96159225..96159249,+!p5@Tfdp2!0.79!5.75!Tfdp2;;chr17:87153505..87153516,+!p6@Epas1!0.78!7.19!Epas1;;chr18:69752598..69752607,+!p26@Tcf4!0.78!5.75!Tcf4;;chr14:18493480..18493494,+!p2@Thrb!0.78!5.75!Thrb;;chr1:87546583..87546595,+!p1@Sp100!0.77!7.19!Sp100;;chr7:51787434..51787448,-!p1@Spib!0.77!7.19!Spib;;chr6:16848395..16848416,-!p2@Tfec!0.77!5.75!Tfec;;chr19:26822880..26822964,+!p2@Smarca2!0.76!44.57!Smarca2;;chr19:55816414..55816425,+!p4@Tcf7l2!0.76!27.32!Tcf7l2;;chr14:100683912..100683947,-!p2@Klf12!0.76!15.81!Klf12;;chr14:17407878..17407926,-!p1@Rarb!0.76!11.50!Rarb;;chr4:133276779..133276796,-!p8@Arid1a!0.76!10.06!Arid1a;;chr13:37918684..37918701,+!p12@Rreb1!0.76!5.75!Rreb1;;chr1:52065508..52065522,+!p2@Stat4!0.76!5.75!Stat4;;chr6:86476158..86476181,-!p1@Pcbp1!0.75!659.90!Pcbp1;;chr2:181327438..181327495,-!p1@Znf512b!0.75!69.01!Znf512b;;chr4:82151148..82151159,-!p5@Nfib!0.75!14.38!Nfib;;chr6:92041489..92041500,+!p4@Nr2c2!0.75!8.63!Nr2c2;;chr11:16908650..16908690,-!p1@Plek!0.74!30.19!Plek;;chr2:168032763..168032802,-!p3@Adnp!0.74!17.25!Adnp;;chr11:11586218..11586285,+!p1@Ikzf1!0.74!15.81!Ikzf1;;chr15:98701606..98701618,-!p1@Mll2!0.74!8.63!Mll2;;chr6:108610766..108610781,+!p2@Bhlhe40!0.74!8.63!Bhlhe40;;chr9:106355684..106355744,+!p5@Pcbp4!0.74!7.19!Pcbp4;;chr9:96159116..96159130,+!p6@Tfdp2!0.74!5.75!Tfdp2;;chr6:15135639..15135655,+!p9@Foxp2!0.74!5.75!Foxp2;;chr1:38721792..38721845,-!p1@Aff3!0.74!5.75!Aff3;;chr1:135557922..135557963,-!p1@Zc3h11a!0.73!560.70!Zc3h11a;;chr4:82151622..82151643,-!p4@Nfib!0.73!20.13!Nfib;;chr2:27532817..27532828,+!p6@Rxra!0.73!7.19!Rxra;;chr6:52154386..52154407,-!p2@Hoxa5!0.73!5.75!Hoxa5;;chr1:138846117..138846129,-!p8@Nr5a2!0.73!4.31!Nr5a2;;chr9:96159133..96159145,+!p9@Tfdp2!0.73!4.31!Tfdp2;;chr10:5734677..5734702,-!p4@Esr1!0.73!4.31!Esr1;;chr10:79884592..79884621,-!p5@Tcf3!0.73!4.31!Tcf3;;chr15:85602581..85602598,+!p8@Ppara!0.73!4.31!Ppara;;chr14:63890491..63890516,-!p2@Gata4!0.73!4.31!Gata4;;chr13:44936077..44936096,+!p9@Jarid2!0.73!4.31!Jarid2;;chrX:7544943..7545001,-!p1@Gata1!0.73!4.31!Gata1;;chr7:31741846..31741930,-!p1@LOC100504922,p1@Usf2!0.72!122.20!Usf2;;chr18:11052485..11052508,+!p2@Gata6!0.72!12.94!Gata6;;chr2:48805065..48805076,+!p4@Mbd5!0.72!11.50!Mbd5;;chr16:43619156..43619171,+!p16@Zbtb20!0.72!5.75!Zbtb20;;chr15:102300965..102300977,+!p1@Pcbp2!0.71!1499.50!Pcbp2;;chr18:36440723..36440805,+!p1@Pura!0.71!74.76!Pura;;chr12:36219645..36219730,-!p1@Ahr!0.71!46.01!Ahr;;chr4:87452180..87452196,-!p3@Mllt3!0.71!8.63!Mllt3;;chr7:56137011..56137041,-!p2@E2f8!0.71!8.63!E2f8;;chr1:193961880..193961929,-!p1@Rcor3!0.70!50.32!Rcor3;;chr1:170362040..170362113,-!p2@Pbx1!0.70!35.94!Pbx1;;chr3:95238432..95238455,+!p2@Arnt!0.70!25.88!Arnt;;chr17:48061692..48061723,-!p5@Foxp4!0.70!21.57!Foxp4;;chr12:110031207..110031224,+!p5@Yy1!0.70!12.94!Yy1;;chr11:90250944..90250982,-!p2@Hlf!0.70!7.19!Hlf;;chr15:85566014..85566045,+!p3@Ppara!0.70!5.75!Ppara;;chr7:87171047..87171078,+!p1@Zfp710!0.69!14.38!Zfp710;;chr14:52640355..52640369,-!p9@Zfp219!0.69!5.75!Zfp219;;chr7:77505617..77505632,-!p1@Nr2f2!0.68!204.15!Nr2f2;;chr8:79426176..79426275,+!p1@Nr3c2!0.68!21.57!Nr3c2;;chr2:48805044..48805063,+!p3@Mbd5!0.68!18.69!Mbd5;;chr16:4214034..4214070,-!p@chr16:4214034..4214070,-!0.68!12.94!Crebbp;;chr2:128793085..128793116,+!p2@Zc3h6!0.68!10.06!Zc3h6;;chr5:65213356..65213412,+!p6@Klf3!0.68!8.63!Klf3;;chr18:39648811..39648818,-!p4@Nr3c1!0.68!7.19!Nr3c1;;chr11:11584970..11585030,+!p2@Ikzf1!0.68!5.75!Ikzf1;;chr9:30838206..30838285,+!p2@Zbtb44!0.67!54.63!Zbtb44;;chr10:70700755..70700772,-!p2@Tfam!0.67!20.13!Tfam;;chr18:11052456..11052477,+!p3@Gata6!0.67!12.94!Gata6;;chr4:97444537..97444555,+!p8@Nfia!0.67!10.06!Nfia;;chr6:99471044..99471066,-!p4@Foxp1!0.67!8.63!Foxp1;;chr5:120121169..120121171,+!p4@Tbx3!0.67!7.19!Tbx3;;chr1:64167972..64168026,-!p1@Klf7!0.66!97.76!Klf7;;chr6:39068210..39068251,-!p1@Parp12!0.66!18.69!Parp12;;chr13:21545538..21545569,-!p2@Zfp187!0.66!18.69!Zfp187;;chr10:67599450..67599456,-!p8@Arid5b!0.66!4.31!Arid5b;;chr7:134170310..134170341,-!p5@Maz!0.65!35.94!Maz;;chr7:52960555..52960662,+!p1@Dbp!0.65!34.50!Dbp;;chr14:19071466..19071550,-!p1@Nr1d2!0.65!27.32!Nr1d2;;chr7:6649134..6649167,-!p1@Zim1!0.65!21.57!Zim1;;chr11:98821937..98821987,+!p4@Rara!0.65!8.63!Rara;;chr5:134790276..134790294,-!p7@Gtf2i!0.65!8.63!Gtf2i;;chr2:90936978..90937023,+!p3@Sfpi1!0.65!7.19!Sfpi1;;chr4:97444120..97444141,+!p13@Nfia!0.65!7.19!Nfia;;chr2:120389480..120389491,-!p6@Zfp106!0.65!4.31!Zfp106;;chr10:67599461..67599470,-!p6@Arid5b!0.65!4.31!Arid5b;;chr11:11590140..11590187,+!p3@Ikzf1!0.65!4.31!Ikzf1;;chr13:59923965..59924003,-!p2@Zcchc6!0.65!4.31!Zcchc6;;chr17:34729193..34729274,+!p1@Pbx2!0.64!186.90!Pbx2;;chr4:133276801..133276891,-!p3@Arid1a!0.64!41.69!Arid1a;;chr1:135557964..135557976,-!p2@Zc3h11a!0.64!34.50!Zc3h11a;;chrX:131543731..131543764,-!p1@Zmat1!0.64!28.75!Zmat1;;chr17:34729160..34729171,+!p3@Pbx2!0.64!7.19!Pbx2;;chr8:87237732..87237745,-!p7@Nfix!0.64!5.75!Nfix;;chr4:82151500..82151505,-!p11@Nfib!0.64!4.31!Nfib;;chr15:50721503..50721514,-!p15@Trps1!0.64!4.31!Trps1;;chr17:57170891..57170961,-!p1@Khsrp!0.63!343.61!Khsrp;;chr11:120494853..120494905,-!p1@Mafg!0.63!37.38!Mafg;;chr19:55816770..55816793,+!p2@Tcf7l2!0.63!33.07!Tcf7l2;;chr3:89197551..89197606,-!p2@Zbtb7b!0.63!12.94!Zbtb7b;;chr3:95021663..95021687,-!p3@Gabpb2!0.63!12.94!Gabpb2;;chr10:82226613..82226641,-!p4@Nfyb!0.63!10.06!Nfyb;;chr5:104183477..104183548,+!p6@Aff1!0.63!7.19!Aff1;;chr4:102787067..102787080,+!p10@Mier1!0.63!4.31!Mier1;;chr18:39649430..39649522,-!p2@Nr3c1!0.62!37.38!Nr3c1;;chr14:65568675..65568723,-!p1@Hmbox1!0.61!120.77!Hmbox1;;chr16:4213951..4213995,-!p@chr16:4213951..4213995,-!0.61!104.95!Crebbp;;chr11:106993428..106993480,-!p1@Bptf!0.61!94.89!Bptf;;chr19:10315179..10315241,-!p1@Gm98!0.61!38.82!Gm98;;chr2:133377954..133377973,+!p1@Bmp2!0.61!11.50!Bmp2;;chr6:134780234..134780288,+!p1@Crebl2!0.61!11.50!Crebl2;;chr8:87643578..87643593,-!p1@Zfp791!0.61!7.19!Zfp791;;chr14:100684036..100684068,-!p5@Klf12!0.61!5.75!Klf12;;chr6:128312772..128312792,+!p2@Foxm1!0.61!5.75!Foxm1;;chr6:134780337..134780355,+!p3@Crebl2!0.61!4.31!Crebl2;;chr8:87237692..87237703,-!p12@Nfix!0.61!4.31!Nfix;;chr17:46520674..46520741,+!p1@Zfp318!0.60!30.19!Zfp318;;chr2:90936901..90936945,+!p1@Sfpi1!0.60!18.69!Sfpi1;;chr14:79881330..79881415,+!p3@Elf1!0.60!11.50!Elf1;;chr1:133904901..133904934,+!p3@Elk4!0.60!10.06!Elk4;;chr16:42907554..42907591,+!p5@Zbtb20!0.60!8.63!Zbtb20;;chr4:87452200..87452229,-!p2@Mllt3!0.60!7.19!Mllt3;;chr11:121380594..121380609,-!p2@Zfp750!0.60!5.75!Zfp750;;chr8:87324203..87324206,-!p10@Nfix!0.60!4.31!Nfix;;chr6:108610428..108610440,+!p4@Bhlhe40!0.60!4.31!Bhlhe40;;chr6:52154414..52154462,-!p1@Hoxa5!0.60!4.31!Hoxa5;;chr3:90097085..90097175,+!p1@Gatad2b!0.59!140.89!Gatad2b;;chr4:108132605..108132635,+!p1@Zcchc11!0.59!130.83!Zcchc11;;chr5:77694479..77694574,+!p1@Rest!0.59!76.20!Rest;;chr6:29476690..29476724,+!p1@Irf5!0.59!15.81!Irf5;;chr11:59285966..59285990,-!p2@Zfp867!0.59!8.63!Zfp867;;chr13:37918094..37918119,+!p6@Rreb1!0.59!7.19!Rreb1;;chr4:149943593..149943605,+!p5@Rere!0.59!5.75!Rere;;chr7:13421299..13421303,+!p3@Zfp110!0.59!4.31!Zfp110;;chr9:32348906..32348920,-!p3@Fli1!0.59!4.31!Fli1;;chr9:74714303..74714318,+!p2@Onecut1!0.59!2.88!Onecut1;;chr9:96159210..96159221,+!p10@Tfdp2!0.59!2.88!Tfdp2;;chr5: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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 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011403
 |is_obsolete=
+|library_id=CNhs11101
+|library_id_phase_based=2:CNhs11101
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;684
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;684
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N06.CNhs11101.684-20A8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N06.CNhs11101.684-20A8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N06.CNhs11101.684-20A8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N06.CNhs11101.684-20A8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N06.CNhs11101.684-20A8.mm9.nobarcode.rdna.fa.gz
 |name=liver, neonate N06
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11101,LSID733,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.823482050898795,0,0,0,0.386977062110387,0.362671796012724,1.01628633776199,0,0,0,0,0.641004351628906,0,0,0,0,0,0,0.533450241142873,0,0,0,0.725343592025448,0,0,0,0,0,0,0,0,0,1.15185431200459,0,0,0,0.913199597304133,0,0.378989789722664,0,-0.198780715246208,1.51130106821206,-0.269868638010351,0,0,0,0.386977062110387,0,0,0,0,0,0,0,0,0.917444478174681,0,0,0,0,0.386977062110387,0,0.191625835200857,0,0,0.171311708619885,0.435927569366137,0.518699969227049,-0.158091042771083,0.516140370354676,0,0.386977062110387,0,0,0.58831251521849,0,0,0.443271061260878,1.37928402026047,-0.0788315948399074,0,0,0,0,0,0,1.42954010405984,1.94778715495319,1.44987780631386,0,0,0,0,0
 |rna_box=20
 |rna_catalog_number=
@@ Line 60: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:684-20A8;search_select_hide=table117:684-20A8
 }}

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FF:684-20A8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11101

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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