FF:641-24F4: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	liver, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	CNhs11117
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	0 day 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		SAMD00005838

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11117		CAGE		DRX009022		DRR009896

Accession ID Mm9

Library id		BAM		CTSS
CNhs11117		DRZ001321		DRZ002704

Accession ID Mm10

Library id		BAM		CTSS
CNhs11117		DRZ012671		DRZ014054

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

CNhs11117

0	0
1	0
10	0
100	0
1000	-0.00285
1001	0.0581
1002	0.061
1003	-0.102
1004	0
1005	0.219
1006	-0.143
1007	-0.0684
1008	0
1009	-0.0406
101	0.104
1010	0
1011	-0.165
1012	0.0147
1013	0.0802
1014	0.208
1015	-0.233
1016	-0.261
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0653
1022	0.0653
1023	0
1024	0.122
1025	0.454
1026	0
1027	-0.00994
1028	0
1029	0.185
103	-0.00602
1030	0.172
1031	0.00115
1032	-0.21
1033	-0.00124
1034	0.644
1035	0
1036	0.083
1037	0
1038	-0.126
1039	0.353
104	0
1040	-0.0869
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: CNhs11117

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.156
MA0003.1	MA0003.1	0.702
MA0004.1	MA0004.1	0.547
MA0006.1	MA0006.1	0.26
MA0007.1	MA0007.1	0.18
MA0009.1	MA0009.1	0.189
MA0014.1	MA0014.1	0.883
MA0017.1	MA0017.1	1.02945e-12
MA0018.2	MA0018.2	4.62858e-5
MA0019.1	MA0019.1	0.301
MA0024.1	MA0024.1	0.987
MA0025.1	MA0025.1	0.78
MA0027.1	MA0027.1	0.651
MA0028.1	MA0028.1	0.781
MA0029.1	MA0029.1	0.129
MA0030.1	MA0030.1	0.0296
MA0031.1	MA0031.1	0.04
MA0035.2	MA0035.2	9.49523e-6
MA0038.1	MA0038.1	0.0309
MA0039.2	MA0039.2	0.621
MA0040.1	MA0040.1	0.209
MA0041.1	MA0041.1	0.369
MA0042.1	MA0042.1	0.962
MA0043.1	MA0043.1	0.01
MA0046.1	MA0046.1	1.92565e-27
MA0047.2	MA0047.2	4.44081e-6
MA0048.1	MA0048.1	0.213
MA0050.1	MA0050.1	0.0949
MA0051.1	MA0051.1	0.488
MA0052.1	MA0052.1	3.24587e-5
MA0055.1	MA0055.1	0.55
MA0057.1	MA0057.1	0.829
MA0058.1	MA0058.1	0.579
MA0059.1	MA0059.1	0.125
MA0060.1	MA0060.1	0.00581
MA0061.1	MA0061.1	0.214
MA0062.2	MA0062.2	0.686
MA0065.2	MA0065.2	3.03421e-9
MA0066.1	MA0066.1	0.00572
MA0067.1	MA0067.1	0.231
MA0068.1	MA0068.1	0.973
MA0069.1	MA0069.1	0.193
MA0070.1	MA0070.1	0.777
MA0071.1	MA0071.1	0.00209
MA0072.1	MA0072.1	0.0345
MA0073.1	MA0073.1	0.478
MA0074.1	MA0074.1	0.15
MA0076.1	MA0076.1	0.314
MA0077.1	MA0077.1	0.0335
MA0078.1	MA0078.1	0.455
MA0079.2	MA0079.2	0.103
MA0080.2	MA0080.2	0.00693
MA0081.1	MA0081.1	0.688
MA0083.1	MA0083.1	0.0382
MA0084.1	MA0084.1	0.065
MA0087.1	MA0087.1	0.0186
MA0088.1	MA0088.1	0.596
MA0090.1	MA0090.1	0.51
MA0091.1	MA0091.1	0.316
MA0092.1	MA0092.1	0.11
MA0093.1	MA0093.1	0.618
MA0099.2	MA0099.2	0.585
MA0100.1	MA0100.1	0.995
MA0101.1	MA0101.1	0.677
MA0102.2	MA0102.2	0.144
MA0103.1	MA0103.1	0.261
MA0104.2	MA0104.2	0.956
MA0105.1	MA0105.1	0.00123
MA0106.1	MA0106.1	0.155
MA0107.1	MA0107.1	0.918
MA0108.2	MA0108.2	2.16129e-4
MA0111.1	MA0111.1	0.781
MA0112.2	MA0112.2	2.41757e-6
MA0113.1	MA0113.1	0.129
MA0114.1	MA0114.1	1.8395e-10
MA0115.1	MA0115.1	4.4174e-8
MA0116.1	MA0116.1	0.0125
MA0117.1	MA0117.1	0.996
MA0119.1	MA0119.1	0.0259
MA0122.1	MA0122.1	0.134
MA0124.1	MA0124.1	0.938
MA0125.1	MA0125.1	0.575
MA0131.1	MA0131.1	0.996
MA0135.1	MA0135.1	0.049
MA0136.1	MA0136.1	0.557
MA0137.2	MA0137.2	0.997
MA0138.2	MA0138.2	0.885
MA0139.1	MA0139.1	0.125
MA0140.1	MA0140.1	4.55036e-12
MA0141.1	MA0141.1	3.84837e-5
MA0142.1	MA0142.1	0.351
MA0143.1	MA0143.1	0.227
MA0144.1	MA0144.1	0.61
MA0145.1	MA0145.1	0.487
MA0146.1	MA0146.1	0.195
MA0147.1	MA0147.1	0.738
MA0148.1	MA0148.1	9.44022e-9
MA0149.1	MA0149.1	0.00571
MA0150.1	MA0150.1	0.0828
MA0152.1	MA0152.1	0.283
MA0153.1	MA0153.1	5.88437e-20
MA0154.1	MA0154.1	0.0235
MA0155.1	MA0155.1	0.445
MA0156.1	MA0156.1	0.741
MA0157.1	MA0157.1	0.0222
MA0159.1	MA0159.1	0.00704
MA0160.1	MA0160.1	0.00195
MA0162.1	MA0162.1	0.314
MA0163.1	MA0163.1	1.8764e-6
MA0164.1	MA0164.1	0.431
MA0258.1	MA0258.1	0.00361
MA0259.1	MA0259.1	0.871

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: CNhs11117

Novel motif	Logo	P-value
1	1	0.153
10	10	0.0893
100	100	0.499
101	101	0.376
102	102	0.471
103	103	0.00394
104	104	0.917
105	105	0.905
106	106	0.0128
107	107	0.0169
108	108	0.883
109	109	0.0714
11	11	0.098
110	110	0.0784
111	111	0.0297
112	112	0.00167
113	113	0.996
114	114	0.0253
115	115	0.719
116	116	0.828
117	117	0.0157
118	118	0.106
119	119	0.118
12	12	0.509
120	120	0.945
121	121	0.979
122	122	0.658
123	123	0.531
124	124	0.104
125	125	0.464
126	126	0.118
127	127	0.702
128	128	0.00948
129	129	0.471
13	13	0.00207
130	130	0.791
131	131	0.67
132	132	0.759
133	133	0.144
134	134	0.971
135	135	0.985
136	136	0.442
137	137	0.299
138	138	0.303
139	139	0.657
14	14	0.91
140	140	0.00693
141	141	0.498
142	142	0.0538
143	143	0.31
144	144	0.798
145	145	0.0168
146	146	0.486
147	147	0.733
148	148	0.56
149	149	0.71
15	15	0.0678
150	150	0.157
151	151	0.417
152	152	0.186
153	153	0.137
154	154	0.544
155	155	0.796
156	156	0.156
157	157	0.904
158	158	0.851
159	159	0.765
160	160	0.131
161	161	0.603
162	162	0.637
163	163	0.587
164	164	0.0138
165	165	0.353
166	166	0.926
167	167	0.169
168	168	0.955
169	169	0.00294
17	17	0.0334
18	18	0.455
19	19	0.0564
2	2	0.93
20	20	0.231
21	21	0.793
22	22	0.238
23	23	0.463
24	24	0.442
25	25	0.945
26	26	1.08956e-4
27	27	0.722
28	28	0.412
29	29	0.145
3	3	0.0169
30	30	0.805
31	31	0.348
32	32	0.143
33	33	0.23
34	34	0.957
35	35	0.504
36	36	0.0421
37	37	0.0579
38	38	0.616
39	39	0.211
4	4	0.389
40	40	0.274
41	41	0.627
42	42	0.157
43	43	0.0436
44	44	0.104
45	45	0.879
46	46	0.045
47	47	0.459
48	48	0.222
49	49	0.0424
5	5	0.0501
50	50	0.471
51	51	0.339
52	52	0.296
53	53	0.702
54	54	0.36
55	55	0.829
56	56	0.384
57	57	0.435
58	58	0.49
59	59	0.2
6	6	0.827
60	60	0.0788
61	61	0.151
62	62	0.112
63	63	0.115
64	64	0.46
65	65	0.326
66	66	0.706
67	67	0.662
68	68	0.132
69	69	0.348
7	7	0.164
70	70	0.172
71	71	0.0232
72	72	0.57
73	73	0.105
74	74	0.957
75	75	0.0225
76	76	0.539
77	77	0.599
78	78	0.00727
79	79	0.619
8	8	0.0106
80	80	0.246
81	81	0.728
82	82	0.103
83	83	0.454
84	84	0.905
85	85	0.131
86	86	0.185
87	87	0.676
88	88	0.927
89	89	0.566
9	9	0.702
90	90	0.061
91	91	0.184
92	92	0.0906
93	93	0.793
94	94	0.8
95	95	0.0998
96	96	0.0915
97	97	0.683
98	98	0.284
99	99	0.27

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: CNhs11117

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011395 mouse liver- neonate N00 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)
0000304 (mouse neonate N0 sample)
0011395 (mouse liver- neonate N00 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@SAMD00005838
+|accession_numbers=CAGE;DRX009022;DRR009896;DRZ001321;DRZ002704;DRZ012671;DRZ014054
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000304,FF:0011395
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:80555320..80555378,-!p1@Creb3l3!2.21!183.70!Creb3l3;;chr2:163372884..163372904,+!p1@Hnf4a!1.97!93.07!Hnf4a;;chr16:38294860..38294924,-!p1@Nr1i2!1.85!69.72!Nr1i2;;chr1:173144144..173144176,+!p1@Nr1i3!1.81!63.23!Nr1i3;;chr9:74709695..74709722,+!p1@Onecut1!1.76!57.07!Onecut1;;chr10:88969376..88969395,-!p1@Nr1h4!1.73!52.53!Nr1h4;;chr2:28477452..28477483,-!p1@Gfi1b!1.70!60.80!Gfi1b;;chr7:122989632..122989668,-!p2@Sox6!1.64!42.48!Sox6;;chr7:122989594..122989626,-!p1@Sox6!1.62!40.86!Sox6;;chr7:19608891..19608895,-!p1@Foxa3!1.60!50.59!Foxa3;;chr1:173144100..173144138,+!p2@Nr1i3!1.59!38.26!Nr1i3;;chr8:87425854..87425891,+!p1@Klf1!1.56!35.51!Klf1;;chr9:96159147..96159204,+!p2@Tfdp2!1.53!60.96!Tfdp2;;chr15:103085660..103085681,-!p1@Nfe2!1.53!48.32!Nfe2;;chr15:85602655..85602680,+!p5@Ppara!1.51!31.62!Ppara;;chr15:85566537..85566552,+!p2@Ppara!1.48!29.35!Ppara;;chr15:85566184..85566238,+!p1@Ppara!1.46!41.51!Ppara;;chr10:88996336..88996380,-!p2@Nr1h4!1.46!33.89!Nr1h4;;chr11:90249521..90249551,-!p3@Hlf!1.41!24.81!Hlf;;chr4:133109285..133109308,+!p1@Nr0b2!1.40!23.83!Nr0b2;;chr7:52071956..52071978,-!p1@Atf5!1.35!661.67!Atf5;;chr5:65213356..65213412,+!p6@Klf3!1.35!43.94!Klf3;;chrX:7544943..7545001,-!p1@Gata1!1.33!20.59!Gata1;;chr6:90415250..90415271,+!p4@Klf15!1.31!19.29!Klf15;;chr15:103082088..103082136,-!p2@Nfe2!1.27!17.67!Nfe2;;chr2:163372869..163372882,+!p3@Hnf4a!1.27!17.51!Hnf4a;;chr10:88145766..88145770,-!p1@Spic!1.26!22.70!Spic;;chr4:87452200..87452229,-!p2@Mllt3!1.23!33.56!Mllt3;;chr15:103085690..103085710,-!p3@Nfe2!1.20!16.38!Nfe2;;chr5:138187583..138187602,+!p6@Tsc22d4!1.17!25.46!Tsc22d4;;chr5:135582751..135582788,+!p1@Mlxipl!1.15!52.21!Mlxipl;;chr17:87153519..87153533,+!p5@Epas1!1.15!19.46!Epas1;;chr9:51021788..51021802,+!p1@Pou2af1!1.15!15.56!Pou2af1;;chr15:103085802..103085817,-!p4@Nfe2!1.13!15.56!Nfe2;;chr10:88996295..88996335,-!p3@Nr1h4!1.13!14.92!Nr1h4;;chr11:16908650..16908690,-!p1@Plek!1.11!71.99!Plek;;chr9:96159225..96159249,+!p5@Tfdp2!1.09!12.48!Tfdp2;;chr5:115421065..115421088,-!p1@Hnf1a!1.09!11.35!Hnf1a;;chr4:114732112..114732158,+!p1@Tal1!1.08!24.16!Tal1;;chr8:59799772..59799789,+!p1@Hand2!1.06!30.16!Hand2;;chr1:38721792..38721845,-!p1@Aff3!1.06!13.13!Aff3;;chr4:135728473..135728494,+!p5@E2f2!1.06!10.38!E2f2;;chr14:63864056..63864102,-!p1@Gata4!1.04!17.51!Gata4;;chr13:31650185..31650201,+!p1@Foxq1!1.03!34.70!Foxq1;;chr18:64499706..64499721,+!p2@Onecut2!1.03!13.62!Onecut2;;chr4:135728581..135728668,+!p1@E2f2!1.02!46.21!E2f2;;chr16:92826249..92826325,-!p1@Runx1!1.02!23.83!Runx1;;chr18:64499674..64499696,+!p1@Onecut2!1.02!16.70!Onecut2;;chr4:87452180..87452196,-!p3@Mllt3!1.01!18.48!Mllt3;;chr5:65213459..65213485,+!p12@Klf3!1.00!11.35!Klf3;;chr11:11584970..11585030,+!p2@Ikzf1!0.99!12.81!Ikzf1;;chr19:37509324..37509337,+!p1@Hhex!0.98!61.45!Hhex;;chr7:6649134..6649167,-!p1@Zim1!0.96!45.24!Zim1;;chr9:96159116..96159130,+!p6@Tfdp2!0.96!10.38!Tfdp2;;chr9:48644037..48644067,-!p2@Zbtb16!0.94!19.62!Zbtb16;;chr17:87153505..87153516,+!p6@Epas1!0.94!10.70!Epas1;;chr15:85566241..85566253,+!p6@Ppara!0.94!7.62!Ppara;;chr10:80555285..80555291,-!p4@Creb3l3!0.94!7.62!Creb3l3;;chr6:90412582..90412601,+!p1@Klf15!0.93!37.13!Klf15;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.93!12.16!Ncoa4;;chr1:138846009..138846038,-!p3@Nr5a2!0.93!8.59!Nr5a2;;chr8:87643578..87643593,-!p1@Zfp791!0.92!15.56!Zfp791;;chr10:80555299..80555306,-!p3@Creb3l3!0.92!7.30!Creb3l3;;chr11:11586218..11586285,+!p1@Ikzf1!0.90!23.35!Ikzf1;;chr13:30841099..30841116,+!p1@Irf4!0.90!11.19!Irf4;;chr6:90415281..90415295,+!p5@Klf15!0.90!6.97!Klf15;;chr4:44723559..44723593,-!p1@Pax5!0.89!6.81!Pax5;;chr16:38294929..38294940,-!p2@Nr1i2!0.89!6.81!Nr1i2;;chr2:38206744..38206766,+!p1@Lhx2!0.88!8.11!Lhx2;;chr9:69137716..69137744,+!p1@Rora!0.87!42.97!Rora;;chr3:54559463..54559493,+!p3@Smad9!0.87!12.16!Smad9;;chr1:135557526..135557551,-!p1@Zbed6!0.87!10.70!Zbed6;;chr4:135728181..135728203,+!p2@E2f2!0.87!8.59!E2f2;;chr2:27532912..27532923,+!p9@Rxra!0.87!6.97!Rxra;;chr11:11585912..11585950,+!p6@Ikzf1!0.85!7.94!Ikzf1;;chr7:134169357..134169366,-!p18@Maz!0.85!7.30!Maz;;chr4:44723520..44723544,-!p2@Pax5!0.85!6.00!Pax5;;chr6:99216488..99216534,-!p2@Foxp1!0.83!17.35!Foxp1;;chr15:85566051..85566080,+!p4@Ppara!0.83!6.81!Ppara;;chr7:122989676..122989687,-!p8@Sox6!0.83!5.84!Sox6;;chr8:87225670..87225697,+!p2@Lyl1!0.82!17.19!Lyl1;;chr9:24578720..24578735,-!p1@Tbx20!0.82!5.67!Tbx20;;chr1:138846079..138846103,-!p6@Nr5a2!0.82!5.67!Nr5a2;;chr6:90412608..90412630,+!p2@Klf15!0.80!11.67!Klf15;;chr10:80555398..80555409,-!p2@Creb3l3!0.80!5.35!Creb3l3;;chr1:138845748..138845766,-!p4@Nr5a2!0.79!6.97!Nr5a2;;chr2:163332558..163332596,+!p2@Hnf4a!0.78!5.03!Hnf4a;;chr9:119893782..119893802,-!p1@Csrnp1!0.78!5.03!Csrnp1;;chr5:65203599..65203617,+!p8@Klf3!0.77!8.43!Klf3;;chr17:48015645..48015689,-!p9@Foxp4!0.77!6.49!Foxp4;;chr9:96159133..96159145,+!p9@Tfdp2!0.77!4.86!Tfdp2;;chr15:102301130..102301147,+!p3@Pcbp2!0.76!15.73!Pcbp2;;chr5:134790276..134790294,-!p7@Gtf2i!0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;;chr6:133985709..133985735,+!p5@Etv6!0.11!2.43!Etv6;;chrX:103123886..103123922,-!p3@Atrx!0.11!2.27!Atrx;;chr19:5637475..5637486,+!p6@Rela!0.11!2.11!Rela;;chr16:43619101..43619151,+!p6@Zbtb20!0.11!1.95!Zbtb20;;chr15:103170516..103170531,-!p2@Zfp385a!0.11!1.95!Zfp385a;;chr16:8672256..8672279,-!p1@Carhsp1,p1@Gm9791!0.11!1.78!Carhsp1;;chr6:28211956..28211967,-!p2@Zfp800!0.11!1.62!Zfp800;;chr5:32438894..32438908,+!p2@Fosl2!0.11!1.62!Fosl2;;chr18:69681483..69681514,+!p11@Tcf4!0.11!1.13!Tcf4;;chrX:7339674..7339688,+!p6@Tfe3!0.11!0.97!Tfe3;;chr8:47825166..47825178,+!p2@Irf2!0.11!0.97!Irf2;;chr3:9610033..9610040,-!p3@Zfp704!0.11!0.97!Zfp704;;chr6:115311270..115311298,+!p1@Pparg!0.11!0.81!Pparg;;chr11:102177921..102177960,-!p9@Ubtf!0.11!0.81!Ubtf;;chr10:127080091..127080100,+!p4@Stat6!0.11!0.81!Stat6;;chr10:126723307..126723319,-!p6@Mbd6!0.11!0.65!Mbd6;;chr4:6918396..6918411,-!p4@Tox!0.11!0.65!Tox;;chr2:32219200..32219213,+!p5@Ciz1!0.11!0.65!Ciz1;;chr2:152223852..152223872,-!p7@Sox12!0.11!0.65!Sox12;;chrX:48559029..48559051,-!p7@Mbnl3!0.11!0.65!Mbnl3;;chr4:102787381..102787397,+!p9@Mier1!0.11!0.49!Mier1;;chr2:180069370..180069409,-!p1@Gata5!0.11!0.49!Gata5;;chr6:15135439..15135452,+!p13@Foxp2!0.11!0.49!Foxp2;;chr9:32349174..32349187,-!p6@Fli1!0.11!0.49!Fli1;;chr11:99091744..99091778,-!p1@Smarce1!0.10!48.32!Smarce1;;chr2:72817045..72817123,-!p1@Sp3!0.10!36.64!Sp3;;chr1:13364108..13364150,-!p1@Ncoa2!0.10!24.48!Ncoa2;;chr6:120314112..120314181,+!p1@Kdm5a!0.10!21.08!Kdm5a;;chr2:114027152..114027181,-!p1@Zfp770!0.10!19.29!Zfp770;;chr17:34053127..34053141,+!p1@Zbtb22!0.10!11.67!Zbtb22;;chr8:109620410..109620462,-!p1@Terf2!0.10!10.05!Terf2;;chr15:75771454..75771521,+!p1@Zfp623!0.10!9.73!Zfp623;;chr8:108375881..108375936,-!p1@Cenpt!0.10!9.08!Cenpt;;chr17:48061584..48061601,-!p2@Foxp4!0.10!6.65!Foxp4;;chr5:34163023..34163090,+!p2@Whsc1!0.10!6.65!Whsc1;;chr2:44965593..44965624,-!p3@Zeb2!0.10!5.67!Zeb2;;chr10:79017833..79017871,-!p1@Mier2!0.10!5.67!Mier2;;chr10:80600749..80600766,+!p2@Zbtb7a!0.10!5.19!Zbtb7a;;chr11:102180696..102180760,-!p2@Ubtf!0.10!4.86!Ubtf;;chr4:119406389..119406411,+!p1@Hivep3!0.10!4.86!Hivep3;;chr17:25152743..25152766,-!p2@Cramp1l!0.10!3.89!Cramp1l;;chr3:89197551..89197606,-!p2@Zbtb7b!0.10!3.08!Zbtb7b;;chr1:133904217..133904250,+!p5@Elk4!0.10!2.92!Elk4;;chr13:64253718..64253763,-!p2@Zfp367!0.10!2.11!Zfp367;;chr1:52176406..52176433,+!p2@Stat1!0.10!1.95!Stat1;;chr6:134780163..134780197,+!p2@Crebl2!0.10!1.78!Crebl2;;chr6:15135456..15135520,+!p3@Foxp2!0.10!1.62!Foxp2;;chr5:143942477..143942493,-!p2@Rbak!0.10!1.46!Rbak;;chr15:61818965..61819046,+!p3@Myc!0.10!1.13!Myc;;chr18:3337503..3337536,-!p7@Crem!0.10!1.13!Crem;;chr1:4486481..4486501,-!p2@Sox17!0.10!0.81!Sox17;;chr15:103170561..103170572,-!p4@Zfp385a!0.10!0.81!Zfp385a;;chr3:30993859..30993870,+!p5@Skil!0.10!0.81!Skil;;chr8:47825203..47825225,+!p3@Irf2!0.10!0.65!Irf2;;chr7:20162663..20162678,+!p1@Zfp296!0.10!0.65!Zfp296;;chr15:40486883..40486903,+!p4@Zfpm2!0.10!0.65!Zfpm2;;chr18:5591389..5591406,+!p3@Zeb1!0.10!0.49!Zeb1;;chr1:87546602..87546617,+!p2@Sp100!0.10!0.49!Sp100;;chr11:11590140..11590187,+!p3@Ikzf1!0.10!0.49!Ikzf1;;chr1:135557922..135557963,-!p1@Zc3h11a!0.09!128.09!Zc3h11a;;chr10:79896360..79896400,-!p1@Tcf3!0.09!44.91!Tcf3;;chr10:80040030..80040072,-!p1@Klf16!0.09!21.56!Klf16;;chr11:96690797..96690813,-!p1@Nfe2l1!0.09!20.92!Nfe2l1;;chr8:108583462..108583523,+!p1@Nfatc3!0.09!19.94!Nfatc3;;chr1:162836503..162836591,+!p1@Rc3h1!0.09!18.97!Rc3h1;;chr9:30837968..30838036,+!p1@Zbtb44!0.09!18.48!Zbtb44;;chr15:76181777..76181802,+!p2@Maf1!0.09!17.51!Maf1;;chr7:120351014..120351109,+!p1@Arntl!0.09!14.59!Arntl;;chr10:80893549..80893590,-!p2@Nfic!0.09!11.84!Nfic;;
+|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 36: / Line 42: @@
 |has_quality=
 |id=FF:641-24F4
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011395
+|is_a=EFO:0002091;;FF:0011395
+|is_obsolete=
+|library_id=CNhs11117
+|library_id_phase_based=2:CNhs11117
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;641
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;641
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N00.CNhs11117.641-24F4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N00.CNhs11117.641-24F4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N00.CNhs11117.641-24F4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N00.CNhs11117.641-24F4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520neonate%2520N00.CNhs11117.641-24F4.mm9.nobarcode.rdna.fa.gz
 |name=liver, neonate N00
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11117,LSID734,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.206523222093841,0.0269475361207726,0.00336677988476126,0,0.0652566657696677,0,0.253430726285608,0,0,0,0,0.210746319794638,0,0,0,0,0,0,0.0659474264060328,0,0,0,0.329387014219756,0,0,0,0,0,0,0,0,0,0.315792746813841,0,0,0,0,0,0.225600123552066,-0.0856060179657283,0.103805167336882,0.469120022469319,-0.147891948609375,0,0,0,0,0,0,0,0,0,0,0.257840777288607,0,0.229080012627739,0,0,0,0,0,0,0,0.0652566657696677,0.0652566657696677,0.0163874570776266,0.00608870409889835,0.264109480565217,0.136994517420097,0.234096359875432,0,0.151699202727775,-0.0529746553619055,0.0189839478952266,0.418525387089334,0,0,-0.171248828762397,0.160106359041372,0.0431450945610692,0,0,0,0,0.0326283328848338,0.121976689400977,0.0652566657696677,0.182917273065164,-0.014880032108133,0.0652566657696677,0,0,0,0.0326283328848338
 |rna_box=24
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=liver
 |top_motifs=NKX2-2,8:3.76745366504;FOX{F1,F2,J1}:3.15381156154;FOX{D1,D2}:2.79280630993;CEBPA,B_DDIT3:2.24134533612;FOXM1:2.21955935537;FOXA2:2.04363599697;GATA6:2.00213320209;PITX1..3:1.93821802878;NR6A1:1.92284880213;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.86162802686;HNF1A:1.78647658134;NFIL3:1.66515697461;HNF4A_NR2F1,2:1.48351972541;ARID5B:1.46972573041;HLF:1.41992434144;NR3C1:1.39507484514;ZNF423:1.36040615477;UFEwm:1.32230939094;RXRA_VDR{dimer}:1.30656531505;STAT2,4,6:1.29380263494;EBF1:1.25050982414;ALX4:1.22507070727;HMGA1,2:1.22197961001;AIRE:1.09154544622;ZBTB16:1.07613992604;GZF1:1.02692122493;PAX1,9:0.937813489836;FOXQ1:0.933530035423;POU1F1:0.929980745756;NANOG{mouse}:0.861548048827;STAT5{A,B}:0.853194803341;FOXD3:0.842527866506;BPTF:0.836702730138;FOXP1:0.814463159008;E2F1..5:0.794979042391;NR1H4:0.771151056942;EVI1:0.727871049104;PDX1:0.711798690925;SPIB:0.706921651981;HOXA9_MEIS1:0.656804939785;ONECUT1,2:0.599527462571;bHLH_family:0.487955682622;IRF1,2:0.46800397712;PAX6:0.46008901459;SPI1:0.457889550335;RXR{A,B,G}:0.430166838604;RBPJ:0.404567638142;ESRRA:0.367624994556;PBX1:0.366810769968;TP53:0.361575949726;CUX2:0.314381626524;GCM1,2:0.310743477743;MYB:0.295179228227;HAND1,2:0.295108334879;IKZF1:0.281892583574;PAX4:0.279666299593;DBP:0.277196733874;IRF7:0.264816534127;CDX1,2,4:0.258512491513;EN1,2:0.252226119129;ETS1,2:0.237064169317;FOXO1,3,4:0.188086782328;AR:0.172163170655;NR5A1,2:0.169159551661;NFIX:0.150673623967;ELF1,2,4:0.137502681834;NFY{A,B,C}:0.0833221590505;NKX3-2:0.0650494601598;NFE2:0.0622199709377;SNAI1..3:0.0519110032684;TEF:0.0432081896519;DMAP1_NCOR{1,2}_SMARC:0.0278043781885;MYBL2:-0.0230810272032;MYOD1:-0.0448029019769;ZNF148:-0.0654094045868;RUNX1..3:-0.128368991926;TLX2:-0.1459374587;ZIC1..3:-0.21027537202;ZBTB6:-0.272827465299;NFE2L2:-0.27475773683;TBP:-0.27584665279;IKZF2:-0.312665139787;HIF1A:-0.33622680642;TLX1..3_NFIC{dimer}:-0.359524491444;SREBF1,2:-0.371908501458;MTF1:-0.3761878682;AHR_ARNT_ARNT2:-0.383867763964;PPARG:-0.384512166482;CREB1:-0.398025543755;GFI1B:-0.405793496299;NFE2L1:-0.439745588376;TFAP4:-0.450936077031;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.470195500938;YY1:-0.48256233099;MYFfamily:-0.492069606491;NKX6-1,2:-0.501175619371;PAX2:-0.524516374454;ATF5_CREB3:-0.526110396586;BACH2:-0.534615414015;SRF:-0.5399592388;POU3F1..4:-0.563531624557;ATF4:-0.564485534824;NKX2-1,4:-0.567067571761;KLF4:-0.577068178468;ZEB1:-0.596438533674;TOPORS:-0.598471869226;FOXL1:-0.60704924755;NFKB1_REL_RELA:-0.612724167366;RREB1:-0.628200289093;RORA:-0.661108741714;XCPE1{core}:-0.667585134236;TEAD1:-0.669694173145;FOX{I1,J2}:-0.700673685299;GATA4:-0.715206804274;EGR1..3:-0.728245295601;TFCP2:-0.729606911693;GFI1:-0.736410769281;PAX5:-0.740467054475;SP1:-0.768163654092;MEF2{A,B,C,D}:-0.786602704735;NHLH1,2:-0.787397720039;FOXN1:-0.791345439717;MAZ:-0.802992919625;HMX1:-0.812893959233;REST:-0.819848439206;LMO2:-0.883621254178;GTF2I:-0.904264900163;HOX{A4,D4}:-0.924620752349;FOXP3:-0.927948426495;SOX{8,9,10}:-0.939481721965;ELK1,4_GABP{A,B1}:-0.941654422012;TAL1_TCF{3,4,12}:-0.945657634057;BREu{core}:-0.955483801969;PRDM1:-1.00633634463;ATF6:-1.01209502384;SOX17:-1.02197134855;PATZ1:-1.02320734895;MZF1:-1.03432728903;TGIF1:-1.03771241984;SOX5:-1.0438199065;TFAP2{A,C}:-1.0491749309;OCT4_SOX2{dimer}:-1.05104299307;FOS_FOS{B,L1}_JUN{B,D}:-1.06102570719;PAX8:-1.06841321773;ZFP161:-1.09665772178;POU2F1..3:-1.09678540112;MAFB:-1.10985820514;T:-1.11095486053;TFAP2B:-1.11243503381;MTE{core}:-1.12490348036;TFDP1:-1.13167370309;CDC5L:-1.13550886699;ESR1:-1.13937395021;NKX3-1:-1.14871478578;HSF1,2:-1.16379692849;LEF1_TCF7_TCF7L1,2:-1.1919456512;HIC1:-1.19309147635;POU5F1:-1.20886702904;CRX:-1.21475751881;MED-1{core}:-1.21622549464;TBX4,5:-1.24757918498;ZNF143:-1.25163462675;RFX1:-1.29798951109;GLI1..3:-1.32279049829;LHX3,4:-1.39119979362;SOX2:-1.42287046986;RFX2..5_RFXANK_RFXAP:-1.42560802919;ZNF238:-1.42676776385;ADNP_IRX_SIX_ZHX:-1.42764908062;POU6F1:-1.44398453209;VSX1,2:-1.4444248884;ZNF384:-1.47076087695;SMAD1..7,9:-1.49186042945;PRRX1,2:-1.51541015139;ALX1:-1.51960223638;NRF1:-1.54954965761;HES1:-1.61334866127;ATF2:-1.61726320296;HOX{A5,B5}:-1.63240940738;STAT1,3:-1.63407905162;GTF2A1,2:-1.63522843061;JUN:-1.66766309524;NFATC1..3:-1.71465838017;FOSL2:-1.72723395837;EP300:-1.87374808956;NKX2-3_NKX2-5:-1.91192464901;SPZ1:-1.94555731761;NANOG:-2.16211224175;HBP1_HMGB_SSRP1_UBTF:-3.28130585394
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:641-24F4;search_select_hide=table117:641-24F4
 }}

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FF:641-24F4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11117

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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