FF:355-15F8: Difference between revisions

Latest revision as of 19:10, 4 June 2020

Name:	liver, embryo E12
Species:	Mouse (Mus musculus)
Library ID:	CNhs10601
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	12 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		SAMD00005264

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10601		CAGE		DRX009015		DRR009889

Accession ID Mm9

Library id		BAM		CTSS
CNhs10601		DRZ001314		DRZ002697

Accession ID Mm10

Library id		BAM		CTSS
CNhs10601		DRZ012664		DRZ014047

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

CNhs10601

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0119
1002	0.0674
1003	-0.152
1004	0
1005	-0.0389
1006	-0.0976
1007	0.0314
1008	0
1009	-0.133
101	0.244
1010	0
1011	-0.0343
1012	0
1013	-0.0943
1014	0.176
1015	0.00886
1016	-0.044
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.176
1022	-0.248
1023	0
1024	-0.0145
1025	0.144
1026	0
1027	0
1028	0
1029	2.64663e-4
103	-0.035
1030	0
1031	0.0165
1032	-0.318
1033	0.125
1034	0
1035	0
1036	0.395
1037	0
1038	-0.267
1039	-0.151
104	0
1040	-0.142
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: CNhs10601

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.195
MA0003.1	MA0003.1	0.97
MA0004.1	MA0004.1	0.0512
MA0006.1	MA0006.1	0.86
MA0007.1	MA0007.1	0.922
MA0009.1	MA0009.1	0.222
MA0014.1	MA0014.1	0.525
MA0017.1	MA0017.1	2.1055e-6
MA0018.2	MA0018.2	0.0389
MA0019.1	MA0019.1	0.407
MA0024.1	MA0024.1	1.04296e-17
MA0025.1	MA0025.1	0.327
MA0027.1	MA0027.1	0.479
MA0028.1	MA0028.1	7.01873e-7
MA0029.1	MA0029.1	0.0146
MA0030.1	MA0030.1	0.962
MA0031.1	MA0031.1	0.237
MA0035.2	MA0035.2	2.15279e-37
MA0038.1	MA0038.1	0.0651
MA0039.2	MA0039.2	0.749
MA0040.1	MA0040.1	0.422
MA0041.1	MA0041.1	0.16
MA0042.1	MA0042.1	0.608
MA0043.1	MA0043.1	0.361
MA0046.1	MA0046.1	3.62489e-17
MA0047.2	MA0047.2	0.327
MA0048.1	MA0048.1	0.00251
MA0050.1	MA0050.1	0.00184
MA0051.1	MA0051.1	0.00176
MA0052.1	MA0052.1	0.0018
MA0055.1	MA0055.1	4.04903e-4
MA0057.1	MA0057.1	0.927
MA0058.1	MA0058.1	0.0317
MA0059.1	MA0059.1	0.00234
MA0060.1	MA0060.1	1.20975e-12
MA0061.1	MA0061.1	0.394
MA0062.2	MA0062.2	1.78831e-8
MA0065.2	MA0065.2	0.00327
MA0066.1	MA0066.1	0.119
MA0067.1	MA0067.1	0.336
MA0068.1	MA0068.1	0.0422
MA0069.1	MA0069.1	0.00727
MA0070.1	MA0070.1	0.973
MA0071.1	MA0071.1	0.54
MA0072.1	MA0072.1	0.377
MA0073.1	MA0073.1	0.805
MA0074.1	MA0074.1	0.722
MA0076.1	MA0076.1	3.56772e-6
MA0077.1	MA0077.1	0.812
MA0078.1	MA0078.1	0.773
MA0079.2	MA0079.2	0.0543
MA0080.2	MA0080.2	0.0279
MA0081.1	MA0081.1	0.281
MA0083.1	MA0083.1	0.958
MA0084.1	MA0084.1	0.288
MA0087.1	MA0087.1	0.0617
MA0088.1	MA0088.1	0.0226
MA0090.1	MA0090.1	0.266
MA0091.1	MA0091.1	0.278
MA0092.1	MA0092.1	0.647
MA0093.1	MA0093.1	0.0599
MA0099.2	MA0099.2	0.665
MA0100.1	MA0100.1	0.00572
MA0101.1	MA0101.1	0.441
MA0102.2	MA0102.2	0.928
MA0103.1	MA0103.1	0.0277
MA0104.2	MA0104.2	0.0163
MA0105.1	MA0105.1	0.00314
MA0106.1	MA0106.1	0.984
MA0107.1	MA0107.1	0.957
MA0108.2	MA0108.2	0.422
MA0111.1	MA0111.1	0.526
MA0112.2	MA0112.2	0.225
MA0113.1	MA0113.1	0.226
MA0114.1	MA0114.1	2.61278e-5
MA0115.1	MA0115.1	8.70248e-4
MA0116.1	MA0116.1	0.00544
MA0117.1	MA0117.1	0.858
MA0119.1	MA0119.1	0.928
MA0122.1	MA0122.1	0.959
MA0124.1	MA0124.1	0.959
MA0125.1	MA0125.1	0.718
MA0131.1	MA0131.1	0.295
MA0135.1	MA0135.1	0.489
MA0136.1	MA0136.1	0.00303
MA0137.2	MA0137.2	0.599
MA0138.2	MA0138.2	6.91924e-4
MA0139.1	MA0139.1	0.517
MA0140.1	MA0140.1	2.3086e-81
MA0141.1	MA0141.1	0.362
MA0142.1	MA0142.1	0.169
MA0143.1	MA0143.1	0.21
MA0144.1	MA0144.1	0.745
MA0145.1	MA0145.1	0.292
MA0146.1	MA0146.1	0.196
MA0147.1	MA0147.1	0.00623
MA0148.1	MA0148.1	0.0651
MA0149.1	MA0149.1	0.298
MA0150.1	MA0150.1	0.017
MA0152.1	MA0152.1	0.535
MA0153.1	MA0153.1	7.66012e-14
MA0154.1	MA0154.1	0.286
MA0155.1	MA0155.1	0.534
MA0156.1	MA0156.1	2.05802e-4
MA0157.1	MA0157.1	0.0412
MA0159.1	MA0159.1	0.0587
MA0160.1	MA0160.1	0.135
MA0162.1	MA0162.1	0.395
MA0163.1	MA0163.1	1.20157e-5
MA0164.1	MA0164.1	0.174
MA0258.1	MA0258.1	0.873
MA0259.1	MA0259.1	0.0904

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: CNhs10601

Novel motif	Logo	P-value
1	1	0.373
10	10	0.0976
100	100	0.133
101	101	0.206
102	102	0.759
103	103	0.247
104	104	0.804
105	105	0.743
106	106	0.61
107	107	0.583
108	108	0.696
109	109	0.0323
11	11	0.226
110	110	0.066
111	111	0.00887
112	112	0.167
113	113	0.443
114	114	0.882
115	115	0.661
116	116	0.942
117	117	0.00193
118	118	0.037
119	119	0.762
12	12	0.84
120	120	0.972
121	121	0.163
122	122	0.708
123	123	0.0127
124	124	0.0608
125	125	0.658
126	126	0.114
127	127	0.0614
128	128	0.99
129	129	0.61
13	13	4.84845e-6
130	130	0.546
131	131	0.81
132	132	0.00609
133	133	0.425
134	134	0.0838
135	135	0.19
136	136	0.371
137	137	0.303
138	138	0.333
139	139	0.464
14	14	0.268
140	140	0.768
141	141	0.0335
142	142	0.185
143	143	0.869
144	144	0.525
145	145	0.00803
146	146	0.939
147	147	0.617
148	148	0.174
149	149	0.174
15	15	0.114
150	150	0.27
151	151	0.72
152	152	0.493
153	153	0.724
154	154	0.44
155	155	0.589
156	156	0.00635
157	157	0.785
158	158	0.0589
159	159	0.854
160	160	0.732
161	161	0.0179
162	162	0.62
163	163	0.74
164	164	0.00155
165	165	0.253
166	166	0.0774
167	167	0.267
168	168	0.809
169	169	0.259
17	17	0.857
18	18	0.506
19	19	0.575
2	2	0.221
20	20	0.00383
21	21	0.493
22	22	0.869
23	23	0.113
24	24	0.638
25	25	0.482
26	26	6.82155e-4
27	27	0.601
28	28	0.806
29	29	0.00157
3	3	0.0782
30	30	0.63
31	31	0.603
32	32	0.996
33	33	0.305
34	34	0.807
35	35	0.665
36	36	0.123
37	37	0.386
38	38	0.957
39	39	0.536
4	4	0.384
40	40	0.264
41	41	0.646
42	42	0.0751
43	43	0.285
44	44	0.853
45	45	0.735
46	46	0.173
47	47	0.26
48	48	0.351
49	49	0.229
5	5	0.247
50	50	0.763
51	51	0.99
52	52	0.526
53	53	0.653
54	54	0.863
55	55	0.575
56	56	0.955
57	57	0.445
58	58	0.932
59	59	0.794
6	6	0.876
60	60	0.92
61	61	0.393
62	62	0.346
63	63	0.898
64	64	0.781
65	65	0.777
66	66	0.115
67	67	0.14
68	68	0.899
69	69	0.609
7	7	0.0331
70	70	0.439
71	71	0.00323
72	72	0.734
73	73	0.552
74	74	0.395
75	75	0.13
76	76	0.321
77	77	0.227
78	78	0.0162
79	79	0.0985
8	8	0.00793
80	80	0.0951
81	81	0.964
82	82	0.453
83	83	0.289
84	84	0.685
85	85	0.485
86	86	0.547
87	87	0.3
88	88	0.175
89	89	0.821
9	9	0.865
90	90	0.234
91	91	0.836
92	92	0.876
93	93	0.344
94	94	0.277
95	95	0.0366
96	96	0.231
97	97	0.229
98	98	0.611
99	99	0.848

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: CNhs10601

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011320 mouse liver- embryo E12 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)
0000295 (mouse embryonic day 12 sample)
0011320 (mouse liver- embryo E12 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:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
+|DRA_sample_Accession=CAGE@SAMD00005264
+|accession_numbers=CAGE;DRX009015;DRR009889;DRZ001314;DRZ002697;DRZ012664;DRZ014047
+|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:0000295,FF:0011320
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:87425854..87425891,+!p1@Klf1!2.30!197.71!Klf1;;chr15:103085660..103085681,-!p1@Nfe2!2.11!188.37!Nfe2;;chr2:28477452..28477483,-!p1@Gfi1b!2.00!120.63!Gfi1b;;chrX:7544943..7545001,-!p1@Gata1!1.92!81.92!Gata1;;chr4:114732112..114732158,+!p1@Tal1!1.84!144.32!Tal1;;chr11:11584970..11585030,+!p2@Ikzf1!1.76!80.42!Ikzf1;;chr7:122989632..122989668,-!p2@Sox6!1.69!47.88!Sox6;;chr4:87452200..87452229,-!p2@Mllt3!1.66!92.10!Mllt3;;chr7:122989594..122989626,-!p1@Sox6!1.63!41.54!Sox6;;chr4:87452180..87452196,-!p3@Mllt3!1.61!76.42!Mllt3;;chr15:103082088..103082136,-!p2@Nfe2!1.59!38.04!Nfe2;;chr15:103085690..103085710,-!p3@Nfe2!1.53!35.54!Nfe2;;chr8:87225670..87225697,+!p2@Lyl1!1.47!80.09!Lyl1;;chr9:96159147..96159204,+!p2@Tfdp2!1.43!47.55!Tfdp2;;chr4:135728181..135728203,+!p2@E2f2!1.43!33.70!E2f2;;chr9:24578720..24578735,-!p1@Tbx20!1.30!19.02!Tbx20;;chr8:87225702..87225726,+!p3@Lyl1!1.28!35.70!Lyl1;;chr4:87452236..87452249,-!p9@Mllt3!1.23!15.85!Mllt3;;chr8:59799772..59799789,+!p1@Hand2!1.21!42.88!Hand2;;chr10:80598968..80599012,+!p5@Zbtb7a!1.20!19.35!Zbtb7a;;chr7:19608891..19608895,-!p1@Foxa3!1.15!17.02!Foxa3;;chr10:79884592..79884621,-!p5@Tcf3!1.14!12.68!Tcf3;;chr7:122989676..122989687,-!p8@Sox6!1.11!11.85!Sox6;;chr8:124806048..124806094,+!p1@Zfpm1!1.09!104.11!Zfpm1;;chr9:96159225..96159249,+!p5@Tfdp2!1.09!12.68!Tfdp2;;chr14:63864056..63864102,-!p1@Gata4!1.06!18.52!Gata4;;chr10:119913278..119913298,-!p2@Hmga2!1.05!23.19!Hmga2;;chr11:16908650..16908690,-!p1@Plek!1.02!58.56!Plek;;chr12:3891810..3891829,+!p2@Dnmt3a!1.00!14.18!Dnmt3a;;chr16:92826249..92826325,-!p1@Runx1!0.99!22.02!Runx1;;chr10:119913546..119913583,-!p3@Hmga2!0.99!18.85!Hmga2;;chr9:96159116..96159130,+!p6@Tfdp2!0.99!11.18!Tfdp2;;chr7:17642177..17642223,-!p3@Hif3a!0.99!8.68!Hif3a;;chr4:114729957..114730012,+!p3@Tal1!0.97!8.34!Tal1;;chr10:119913310..119913366,-!p1@Hmga2!0.95!63.73!Hmga2;;chr11:23980664..23980706,+!p2@Bcl11a!0.95!35.54!Bcl11a;;chr3:102768047..102768060,-!p1@Nr1h5!0.92!7.34!Nr1h5;;chr2:163372884..163372904,+!p1@Hnf4a!0.91!7.17!Hnf4a;;chr5:104183477..104183548,+!p6@Aff1!0.90!14.18!Aff1;;chr4:114730254..114730276,+!p2@Tal1!0.89!8.68!Tal1;;chr2:38206744..38206766,+!p1@Lhx2!0.89!8.34!Lhx2;;chr9:96159133..96159145,+!p9@Tfdp2!0.89!6.84!Tfdp2;;chr9:74709695..74709722,+!p1@Onecut1!0.89!6.67!Onecut1;;chr8:124806017..124806040,+!p2@Zfpm1!0.88!75.75!Zfpm1;;chr4:114732159..114732166,+!p6@Tal1!0.88!6.51!Tal1;;chr14:27813679..27813693,+!p2@Hesx1!0.88!6.51!Hesx1;;chr2:180069370..180069409,-!p1@Gata5!0.87!7.67!Gata5;;chr2:166868994..166869023,-!p7@Znfx1!0.87!6.34!Znfx1;;chr4:135728473..135728494,+!p5@E2f2!0.87!6.34!E2f2;;chr10:20880731..20880775,-!p2@Myb!0.86!13.51!Myb;;chr18:64499674..64499696,+!p1@Onecut2!0.86!11.18!Onecut2;;chr15:103085802..103085817,-!p4@Nfe2!0.84!7.51!Nfe2;;chr11:102178005..102178022,-!p8@Ubtf!0.83!9.84!Ubtf;;chr2:162880387..162880413,+!p1@Mybl2!0.82!38.21!Mybl2;;chr15:103085864..103085876,-!p5@Nfe2!0.81!5.51!Nfe2;;chr10:12810631..12810649,+!p1@Plagl1!0.80!152.66!Plagl1;;chr12:34642510..34642530,+!p1@Twist1!0.80!18.02!Twist1;;chr10:80555320..80555378,-!p1@Creb3l3!0.80!6.34!Creb3l3;;chr7:6649134..6649167,-!p1@Zim1!0.78!29.87!Zim1;;chr11:23978111..23978134,+!p3@Bcl11a!0.77!10.68!Bcl11a;;chr2:38206580..38206600,+!p2@Lhx2!0.77!6.17!Lhx2;;chr2:163332558..163332596,+!p2@Hnf4a!0.77!4.84!Hnf4a;;chr14:47896467..47896523,-!p1@Wdhd1!0.76!64.24!Wdhd1;;chr11:11585912..11585950,+!p6@Ikzf1!0.76!6.17!Ikzf1;;chr7:56136362..56136400,-!p1@E2f8!0.75!32.87!E2f8;;chr5:65203599..65203617,+!p8@Klf3!0.75!8.01!Klf3;;chr11:23978078..23978096,+!p4@Bcl11a!0.74!14.85!Bcl11a;;chr9:96159210..96159221,+!p10@Tfdp2!0.74!4.50!Tfdp2;;chr15:61816932..61816952,+!p2@Myc!0.73!40.54!Myc;;chr2:162880327..162880385,+!p2@Mybl2!0.73!32.70!Mybl2;;chr10:20880629..20880683,-!p1@Myb!0.73!13.68!Myb;;chr4:114730015..114730042,+!p7@Tal1!0.73!4.34!Tal1;;chr5:135582751..135582788,+!p1@Mlxipl!0.71!18.52!Mlxipl;;chr18:64499706..64499721,+!p2@Onecut2!0.71!6.01!Onecut2;;chr11:57645506..57645523,-!p1@Hand1!0.71!4.17!Hand1;;chr4:135728581..135728668,+!p1@E2f2!0.70!21.69!E2f2;;chr7:56137011..56137041,-!p2@E2f8!0.70!8.51!E2f8;;chr1:191993385..191993405,-!p3@Prox1!0.70!4.00!Prox1;;chr8:123608252..123608268,+!p1@Foxf1a!0.69!6.17!Foxf1a;;chr11:120491440..120491474,-!p3@Mafg!0.69!6.01!Mafg;;chr10:119914001..119914078,-!p4@Hmga2!0.69!5.51!Hmga2;;chr11:23978022..23978076,+!p1@Bcl11a!0.67!91.26!Bcl11a;;chr10:20880698..20880717,-!p3@Myb!0.67!6.17!Myb;;chr12:58646974..58647003,-!p1@Foxa1!0.67!5.17!Foxa1;;chr4:87452167..87452178,-!p8@Mllt3!0.67!3.67!Mllt3;;chr6:83301243..83301258,+!p2@Bola3!0.67!3.67!Bola3;;chr19:37509324..37509337,+!p1@Hhex!0.66!28.86!Hhex;;chr11:101413151..101413207,-!p1@Brca1!0.65!38.87!Brca1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.65!6.01!Dnmt3a;;chr11:11585678..11585745,+!p5@Ikzf1!0.65!5.34!Ikzf1;;chr5:65203575..65203589,+!p11@Klf3!0.65!4.34!Klf3;;chr8:107821563..107821642,+!p1@E2f4!0.64!111.12!E2f4;;chr10:22539932..22539956,-!p1@Tcf21!0.64!10.18!Tcf21;;chr13:48758276..48758291,+!p1@Barx1!0.64!3.34!Barx1;;chr17:26978409..26978442,-!p1@Nkx2-5!0.64!3.34!Nkx2-5;;chr7:134170081..134170122,-!p2@Maz!0.63!71.58!Maz;;chr17:56970481..56970551,-!p2@Rfx2!0.62!11.35!Rfx2;;chr19:10315179..10315241,-!p1@Gm98!0.61!38.54!Gm98;;chr5:138186979..138187025,+!p4@Tsc22d4!0.61!13.18!Tsc22d4;;chr8:124806111..124806122,+!p3@Zfpm1!0.61!4.00!Zfpm1;;chr13:30077847..30077906,-!p1@E2f3!0.60!28.03!E2f3;;chr18:74375772..74375799,+!p2@Cxxc1!0.60!10.01!Cxxc1;;chr11:90250944..90250982,-!p2@Hlf!0.60!5.51!Hlf;;chr1:138857076..138857105,-!p1@Nr5a2!0.60!3.00!Nr5a2;;chr10:88145766..88145770,-!p1@Spic!0.59!4.00!Spic;;chr5:38611720..38611799,+!p1@Lyar!0.58!92.60!Lyar;;chr14:63890491..63890516,-!p2@Gata4!0.58!2.84!Gata4;;chr4:114730288..114730306,+!p8@Tal1!0.58!2.84!Tal1;;chr10:80040030..80040072,-!p1@Klf16!0.57!66.74!Klf16;;chr15:61817095..61817111,+!p1@Myc!0.56!196.21!Myc;;chr2:153067094..153067130,-!p1@Plagl2!0.56!81.25!Plagl2;;chr5:34163023..34163090,+!p2@Whsc1!0.56!20.69!Whsc1;;chr2:153475178..153475196,+!p1@Dnmt3b!0.56!6.51!Dnmt3b;;chr10:119913792..119913820,-!p5@Hmga2!0.56!5.01!Hmga2;;chr10:79957600..79957618,+!p1@Onecut3!0.56!2.67!Onecut3;;chr6:131338435..131338482,-!p1@Csda!0.55!306.16!Csda;;chr11:23977565..23977612,+!p5@Bcl11a!0.55!6.34!Bcl11a;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.55!4.50!Ncoa4;;chr10:88996295..88996335,-!p3@Nr1h4!0.55!3.17!Nr1h4;;chr5:104183579..104183600,+!p9@Aff1!0.55!3.00!Aff1;;chr3:128916868..128916890,+!p1@Pitx2!0.54!3.67!Pitx2;;chr2:104966874..104966907,+!p2@Wt1!0.54!2.50!Wt1;;chr2:91034924..91034946,-!p2@Nr1h3!0.53!3.17!Nr1h3;;chr2:162880418..162880429,+!p4@Mybl2!0.52!3.17!Mybl2;;chr1:140739014..140739032,-!p1@Lhx9!0.52!3.17!Lhx9;;chr16:38294860..38294924,-!p1@Nr1i2!0.52!2.34!Nr1i2;;chr11:23977965..23977974,+!p11@Bcl11a!0.52!2.34!Bcl11a;;chr10:41995430..41995458,-!p3@Foxo3!0.51!7.01!Foxo3;;chr11:23978353..23978379,+!p10@Bcl11a!0.51!2.84!Bcl11a;;chr9:20757282..20757325,-!p2@Dnmt1!0.50!67.24!Dnmt1;;chr1:138857048..138857071,-!p2@Nr5a2!0.50!2.17!Nr5a2;;chrX:7544928..7544938,-!p2@Gata1!0.50!2.17!Gata1;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.49!130.97!Hmga1;;chr2:153067079..153067090,-!p2@Plagl2!0.49!5.34!Plagl2;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.49!2.84!Hmga1;;chr5:111082367..111082441,-!p1@Noc4l!0.48!64.24!Noc4l;;chr3:51144740..51144743,-!p7@Elf2!0.48!3.84!Elf2;;chr10:119913266..119913277,-!p6@Hmga2!0.48!2.00!Hmga2;;chr6:83301229..83301242,+!p3@Bola3!0.48!2.00!Bola3;;chr6:131338363..131338383,-!p4@Csda!0.47!11.18!Csda;;chr2:104966766..104966786,+!p1@Wt1!0.47!3.50!Wt1;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.47!2.67!Hmga1;;chr2:154395581..154395610,-!p1@E2f1!0.46!26.36!E2f1;;chr8:72520225..72520248,-!p9@Gatad2a!0.46!6.51!Gatad2a;;chr13:37949830..37949861,+!p7@Rreb1!0.46!4.17!Rreb1;;chr1:181733959..181733977,-!p4@Ahctf1!0.45!2.50!Ahctf1;;chr13:55932591..55932622,-!p1@Pitx1!0.45!2.34!Pitx1;;chr2:44965593..44965624,-!p3@Zeb2!0.44!13.51!Zeb2;;chr17:56970339..56970428,-!p1@Rfx2!0.44!7.17!Rfx2;;chr6:72849280..72849297,-!p6@Kcmf1!0.44!4.17!Kcmf1;;chr4:102792009..102792021,+!p6@Mier1!0.44!3.50!Mier1;;chr5:138187775..138187845,+!p7@Tsc22d4!0.44!2.67!Tsc22d4;;chr3:95238432..95238455,+!p2@Arnt!0.43!13.68!Arnt;;chr18:11052642..11052659,+!p1@Gata6!0.43!11.85!Gata6;;chr13:64254457..64254497,-!p1@Zfp367!0.43!10.18!Zfp367;;chr2:77357622..77357704,-!p1@Zfp385b!0.43!5.84!Zfp385b;;chr5:65213356..65213412,+!p6@Klf3!0.43!4.50!Klf3;;chr5:38611816..38611827,+!p4@Lyar!0.43!2.00!Lyar;;chr4:135728282..135728310,+!p4@E2f2!0.43!2.00!E2f2;;chr7:122989672..122989673,-!p20@Sox6!0.43!1.67!Sox6;;chr2:28477422..28477433,-!p2@Gfi1b!0.43!1.67!Gfi1b;;chr2:147871627..147871641,-!p1@Foxa2!0.43!1.67!Foxa2;;chr2:163372869..163372882,+!p3@Hnf4a!0.43!1.67!Hnf4a;;chr14:32979060..32979091,+!p4@Gm6768,p4@Ncoa4!0.43!1.67!Ncoa4;;chr10:119913301..119913302,-!p11@Hmga2!0.43!1.67!Hmga2;;chr13:55431084..55431137,-!p1@Mxd3!0.42!18.02!Mxd3;;chr6:131338483..131338494,-!p5@Csda!0.42!12.01!Csda;;chr2:166888058..166888105,-!p2@Znfx1!0.42!7.01!Znfx1;;chr7:17642053..17642066,-!p2@Hif3a!0.42!2.67!Hif3a;;chr7:89137163..89137200,-!p1@Bnc1!0.42!2.17!Bnc1;;chr5:65194752..65194769,+!p1@Klf3!0.41!77.92!Klf3;;chr18:11052456..11052477,+!p3@Gata6!0.41!6.51!Gata6;;chr17:32506357..32506377,-!p3@Wiz!0.41!4.17!Wiz;;chr2:90936978..90937023,+!p3@Sfpi1!0.41!3.67!Sfpi1;;chr7:56136402..56136420,-!p3@E2f8!0.41!3.50!E2f8;;chr1:186556375..186556404,-!p3@Hlx!0.41!3.50!Hlx;;chr15:103164702..103164778,-!p3@Zfp385a!0.41!2.00!Zfp385a;;chr9:96159665..96159680,+!p3@Tfdp2!0.40!9.84!Tfdp2;;chr15:40486883..40486903,+!p4@Zfpm2!0.40!2.34!Zfpm2;;chr9:96159427..96159432,+!p11@Tfdp2!0.40!2.00!Tfdp2;;chr8:87225806..87225809,+!p4@Lyl1!0.40!1.50!Lyl1;;chr2:104966933..104966966,+!p3@Wt1!0.40!1.50!Wt1;;chr5:115421065..115421088,-!p1@Hnf1a!0.40!1.50!Hnf1a;;chr15:103083245..103083260,-!p7@Nfe2!0.40!1.50!Nfe2;;chr14:32978944..32978953,+!p8@Gm6768,p8@Ncoa4!0.40!1.50!Ncoa4;;chr11:23978291..23978323,+!p7@Bcl11a!0.40!1.50!Bcl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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 36: / Line 42: @@
 |has_quality=
 |id=FF:355-15F8
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011320
+|is_a=EFO:0002091;;FF:0011320
+|is_obsolete=
+|library_id=CNhs10601
+|library_id_phase_based=2:CNhs10601
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;355
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;355
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E12.CNhs10601.355-15F8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E12.CNhs10601.355-15F8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E12.CNhs10601.355-15F8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E12.CNhs10601.355-15F8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E12.CNhs10601.355-15F8.mm9.nobarcode.rdna.fa.gz
 |name=liver, embryo E12
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10601,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.055268114492285,0,0,0,0,0.00097314898223809,0.005294522966314,0,0,0,0,0.3682591897408,0,0,0,0,0,0,-0.0668383871863856,0,0.0625274818480945,0,0,0,0,0,0,0,0,0,0,0,-0.0809916677988759,0,0,0,0.222034698029502,0,0.029431594673208,-0.111753818521383,0.230396448656992,0.238074235685108,-0.0936224164153491,0,0,0,0,0,0,0,0,0,0,0,0,0.110240674031562,0,0,0,0,0,0,-0.0425734546532857,0,0,0,-0.0372094494270919,-0.0471979237173458,-0.0910778338529469,-0.0706600546139155,0,0.048677949711965,-0.0940007963519135,-0.120129662648252,0.222034698029502,0,-0.0650997092030214,-0.0834187061139758,-0.227672479221571,-0.0118183859217718,0,0,0,0,0,0,-0.143137776353816,-0.298039870550964,-0.14817328697483,0,0,0,0,0
 |rna_box=15
 |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=GATA6:3.66355968782;STAT5{A,B}:1.88527578944;E2F1..5:1.84127796232;PAX1,9:1.81686713297;NFY{A,B,C}:1.69059481898;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.27271153425;ZNF423:1.20791539503;YY1:1.09411991298;ARID5B:1.061125144;ZNF143:1.02576055503;PBX1:0.892632135566;HOX{A5,B5}:0.878735452205;FOX{F1,F2,J1}:0.875033177417;MYB:0.826274255396;HOXA9_MEIS1:0.752248281894;AIRE:0.736513614325;ELF1,2,4:0.729568585323;NFE2L2:0.725946306791;ELK1,4_GABP{A,B1}:0.677277868184;PAX8:0.668178939419;GFI1:0.64063039218;NRF1:0.637961007359;ONECUT1,2:0.635228245869;bHLH_family:0.568424207519;ZBTB16:0.547761343154;NFE2:0.543383182695;HNF1A:0.538696472509;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.524877196086;NR6A1:0.522426188658;NKX3-2:0.484707583679;FOXA2:0.467876605184;EN1,2:0.462045101476;HES1:0.457574432855;SOX17:0.430010603783;PITX1..3:0.37548467278;STAT1,3:0.364163148317;TFDP1:0.359542748713;POU1F1:0.340303235035;SPIB:0.338762523966;CUX2:0.337190700153;RXR{A,B,G}:0.298639661447;CEBPA,B_DDIT3:0.271912682428;ALX4:0.243210784744;ZNF148:0.228706416518;FOX{I1,J2}:0.225016144397;TOPORS:0.189484597781;PAX6:0.160945445913;SRF:0.155983562953;SOX{8,9,10}:0.128983481184;HNF4A_NR2F1,2:0.118901352339;SPI1:0.108278610157;TBX4,5:0.100286577918;NANOG{mouse}:0.0961022439356;EVI1:0.0899085878436;GZF1:0.0798206807608;RUNX1..3:0.0755735250453;GATA4:0.0650855264372;HMGA1,2:0.0625572341453;NKX3-1:0.0461534311633;ATF4:0.036003058358;RREB1:0.00338149670532;ETS1,2:-0.00516232798452;ATF5_CREB3:-0.0103529371725;HIF1A:-0.0177305299411;FOXD3:-0.023142356939;OCT4_SOX2{dimer}:-0.0419371924978;IKZF2:-0.0529294934207;TBP:-0.0661944101745;BACH2:-0.0924606149849;AHR_ARNT_ARNT2:-0.09894195438;PPARG:-0.11198594708;CRX:-0.126923373656;FOX{D1,D2}:-0.135294191532;PDX1:-0.144534898927;LHX3,4:-0.160823835246;BREu{core}:-0.162689933178;MZF1:-0.163772556703;RORA:-0.164326294989;PAX2:-0.171977081436;ZIC1..3:-0.179199885536;NR1H4:-0.179456653231;HLF:-0.180780767734;PRRX1,2:-0.190167184021;UFEwm:-0.207257139162;HSF1,2:-0.228499487649;POU2F1..3:-0.230366431269;MEF2{A,B,C,D}:-0.241336783665;FOXM1:-0.245319321238;NFIL3:-0.252197561754;KLF4:-0.271798568119;XCPE1{core}:-0.273077799138;CDX1,2,4:-0.274647172841;NR5A1,2:-0.290820792292;NFE2L1:-0.29387556222;TEAD1:-0.302250557916;ESRRA:-0.305244454992;TEF:-0.306994991162;TLX2:-0.325304401317;FOXL1:-0.345746954646;FOXP3:-0.353238469776;GCM1,2:-0.359964579713;CREB1:-0.367325833666;PATZ1:-0.377135814947;EGR1..3:-0.38626687064;SOX2:-0.394269816124;ALX1:-0.410040633757;EBF1:-0.424220016994;MAZ:-0.437329084343;HOX{A4,D4}:-0.437654841321;TGIF1:-0.438959631371;MYBL2:-0.45551610687;NFKB1_REL_RELA:-0.463989211269;DMAP1_NCOR{1,2}_SMARC:-0.480411786547;NKX2-1,4:-0.486323645687;AR:-0.493800375463;GLI1..3:-0.501800872476;STAT2,4,6:-0.502999586029;RFX1:-0.505584850914;RXRA_VDR{dimer}:-0.513226583329;VSX1,2:-0.516457130007;PRDM1:-0.535173194046;NKX2-2,8:-0.541332591759;RFX2..5_RFXANK_RFXAP:-0.546029126421;ADNP_IRX_SIX_ZHX:-0.546111614696;ATF2:-0.552784556024;MAFB:-0.554420731794;FOXP1:-0.577668148578;ZFP161:-0.587053595949;RBPJ:-0.59020422273;MTF1:-0.596038534646;DBP:-0.603152177627;POU3F1..4:-0.609022584359;IKZF1:-0.62644614028;MED-1{core}:-0.640610873728;NANOG:-0.648900459123;ZNF384:-0.652335184149;IRF1,2:-0.655873644215;MYOD1:-0.662679450162;GTF2I:-0.663149855404;TP53:-0.681515859222;REST:-0.685479304062;T:-0.687847403898;LMO2:-0.68966668493;EP300:-0.689937981003;LEF1_TCF7_TCF7L1,2:-0.705715689512;FOXN1:-0.71235228389;FOS_FOS{B,L1}_JUN{B,D}:-0.715785490793;SNAI1..3:-0.717889648604;TFAP2{A,C}:-0.718465208111;TFAP4:-0.719541953679;GFI1B:-0.722720841159;HAND1,2:-0.731707338163;PAX4:-0.737778930101;HMX1:-0.738441145981;SREBF1,2:-0.754105105673;TFCP2:-0.759515701152;JUN:-0.766099778329;SPZ1:-0.77490292699;NR3C1:-0.780745285555;MYFfamily:-0.824791025624;TAL1_TCF{3,4,12}:-0.832542037894;TLX1..3_NFIC{dimer}:-0.834985735389;HIC1:-0.835205111489;IRF7:-0.837951125567;FOXQ1:-0.838672808532;NFIX:-0.842908373956;POU6F1:-0.888856113887;FOXO1,3,4:-0.898008208761;NHLH1,2:-0.90672642505;MTE{core}:-0.91031029417;FOSL2:-0.926543961847;SMAD1..7,9:-0.941160268339;ZBTB6:-0.950421050801;NKX2-3_NKX2-5:-0.957067239157;ZEB1:-0.998445678132;TFAP2B:-1.00253186057;POU5F1:-1.02182868845;ZNF238:-1.02739031819;NFATC1..3:-1.09446632375;SP1:-1.10505693256;SOX5:-1.1519675402;CDC5L:-1.23646705445;NKX6-1,2:-1.2637791195;ESR1:-1.31597078609;GTF2A1,2:-1.3160329979;BPTF:-1.40848151769;HBP1_HMGB_SSRP1_UBTF:-1.41237731009;PAX5:-1.43254325502;ATF6:-1.74427440173
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:355-15F8;search_select_hide=table117:355-15F8
 }}

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FF:355-15F8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:10, 4 June 2020

CNhs10601

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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