FF:378-3H6: Difference between revisions

Latest revision as of 19:14, 4 June 2020

Name:	liver, embryo E13
Species:	Mouse (Mus musculus)
Library ID:	CNhs10524
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	liver
dev stage	13 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		SAMD00004746

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10524		CAGE		DRX009016		DRR009890

Accession ID Mm9

Library id		BAM		CTSS
CNhs10524		DRZ001315		DRZ002698

Accession ID Mm10

Library id		BAM		CTSS
CNhs10524		DRZ012665		DRZ014048

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

CNhs10524

0	0
1	0
10	0
100	0
1000	0
1001	-3.848171e-4
1002	0.043
1003	-0.107
1004	0
1005	0
1006	-0.0932
1007	-0.0174
1008	0
1009	-0.19
101	0.235
1010	0
1011	-0.108
1012	0
1013	-0.0359
1014	0.114
1015	-0.0209
1016	-0.108
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0779
1022	0
1023	0
1024	0.00443
1025	0.14
1026	0
1027	-0.048
1028	0
1029	-0.0697
103	-0.0108
1030	0
1031	-0.0914
1032	-0.189
1033	0
1034	0.0779
1035	0
1036	0.314
1037	0
1038	-0.199
1039	-0.155
104	0
1040	-0.138
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: CNhs10524

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.245
MA0003.1	MA0003.1	0.722
MA0004.1	MA0004.1	0.0739
MA0006.1	MA0006.1	0.697
MA0007.1	MA0007.1	0.638
MA0009.1	MA0009.1	0.0747
MA0014.1	MA0014.1	0.851
MA0017.1	MA0017.1	2.54864e-9
MA0018.2	MA0018.2	0.00368
MA0019.1	MA0019.1	0.263
MA0024.1	MA0024.1	1.21152e-13
MA0025.1	MA0025.1	0.206
MA0027.1	MA0027.1	0.711
MA0028.1	MA0028.1	1.38137e-5
MA0029.1	MA0029.1	0.00514
MA0030.1	MA0030.1	0.743
MA0031.1	MA0031.1	0.767
MA0035.2	MA0035.2	1.76882e-36
MA0038.1	MA0038.1	0.197
MA0039.2	MA0039.2	0.158
MA0040.1	MA0040.1	0.195
MA0041.1	MA0041.1	0.107
MA0042.1	MA0042.1	0.58
MA0043.1	MA0043.1	0.0793
MA0046.1	MA0046.1	6.29204e-26
MA0047.2	MA0047.2	0.0322
MA0048.1	MA0048.1	0.0123
MA0050.1	MA0050.1	0.0294
MA0051.1	MA0051.1	0.0136
MA0052.1	MA0052.1	7.48819e-7
MA0055.1	MA0055.1	0.00179
MA0057.1	MA0057.1	0.847
MA0058.1	MA0058.1	0.0345
MA0059.1	MA0059.1	0.00199
MA0060.1	MA0060.1	5.84429e-11
MA0061.1	MA0061.1	0.297
MA0062.2	MA0062.2	1.59903e-6
MA0065.2	MA0065.2	2.76216e-4
MA0066.1	MA0066.1	0.108
MA0067.1	MA0067.1	0.229
MA0068.1	MA0068.1	0.381
MA0069.1	MA0069.1	0.0273
MA0070.1	MA0070.1	0.939
MA0071.1	MA0071.1	0.494
MA0072.1	MA0072.1	0.271
MA0073.1	MA0073.1	0.953
MA0074.1	MA0074.1	0.944
MA0076.1	MA0076.1	1.8574e-4
MA0077.1	MA0077.1	0.662
MA0078.1	MA0078.1	0.676
MA0079.2	MA0079.2	0.0721
MA0080.2	MA0080.2	0.0154
MA0081.1	MA0081.1	0.239
MA0083.1	MA0083.1	0.265
MA0084.1	MA0084.1	0.169
MA0087.1	MA0087.1	0.0301
MA0088.1	MA0088.1	0.017
MA0090.1	MA0090.1	0.191
MA0091.1	MA0091.1	0.176
MA0092.1	MA0092.1	0.893
MA0093.1	MA0093.1	0.0708
MA0099.2	MA0099.2	0.833
MA0100.1	MA0100.1	0.0381
MA0101.1	MA0101.1	0.48
MA0102.2	MA0102.2	0.871
MA0103.1	MA0103.1	0.164
MA0104.2	MA0104.2	0.0316
MA0105.1	MA0105.1	0.00259
MA0106.1	MA0106.1	0.995
MA0107.1	MA0107.1	0.78
MA0108.2	MA0108.2	0.279
MA0111.1	MA0111.1	0.673
MA0112.2	MA0112.2	0.107
MA0113.1	MA0113.1	0.256
MA0114.1	MA0114.1	1.373e-7
MA0115.1	MA0115.1	3.10902e-4
MA0116.1	MA0116.1	0.0017
MA0117.1	MA0117.1	0.966
MA0119.1	MA0119.1	0.225
MA0122.1	MA0122.1	0.822
MA0124.1	MA0124.1	0.772
MA0125.1	MA0125.1	0.569
MA0131.1	MA0131.1	0.213
MA0135.1	MA0135.1	0.43
MA0136.1	MA0136.1	0.00374
MA0137.2	MA0137.2	0.555
MA0138.2	MA0138.2	0.00388
MA0139.1	MA0139.1	0.242
MA0140.1	MA0140.1	2.995e-75
MA0141.1	MA0141.1	0.344
MA0142.1	MA0142.1	0.0668
MA0143.1	MA0143.1	0.3
MA0144.1	MA0144.1	0.682
MA0145.1	MA0145.1	0.555
MA0146.1	MA0146.1	0.0764
MA0147.1	MA0147.1	0.0128
MA0148.1	MA0148.1	0.00278
MA0149.1	MA0149.1	0.0579
MA0150.1	MA0150.1	7.68936e-4
MA0152.1	MA0152.1	0.499
MA0153.1	MA0153.1	1.52462e-20
MA0154.1	MA0154.1	0.141
MA0155.1	MA0155.1	0.675
MA0156.1	MA0156.1	6.49087e-4
MA0157.1	MA0157.1	0.333
MA0159.1	MA0159.1	0.0921
MA0160.1	MA0160.1	0.184
MA0162.1	MA0162.1	0.295
MA0163.1	MA0163.1	1.15471e-6
MA0164.1	MA0164.1	0.237
MA0258.1	MA0258.1	0.892
MA0259.1	MA0259.1	0.213

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: CNhs10524

Novel motif	Logo	P-value
1	1	0.255
10	10	0.0819
100	100	0.147
101	101	0.427
102	102	0.504
103	103	0.0431
104	104	0.712
105	105	0.914
106	106	0.878
107	107	0.919
108	108	0.531
109	109	0.016
11	11	0.222
110	110	0.0985
111	111	0.00649
112	112	0.0466
113	113	0.513
114	114	0.76
115	115	0.91
116	116	0.718
117	117	0.00203
118	118	0.0276
119	119	0.812
12	12	0.947
120	120	0.982
121	121	0.173
122	122	0.573
123	123	0.0226
124	124	0.0742
125	125	0.745
126	126	0.0473
127	127	0.346
128	128	0.588
129	129	0.867
13	13	6.79977e-6
130	130	0.394
131	131	0.332
132	132	0.0268
133	133	0.299
134	134	0.0704
135	135	0.463
136	136	0.23
137	137	0.31
138	138	0.821
139	139	0.678
14	14	0.627
140	140	0.772
141	141	0.0558
142	142	0.0805
143	143	0.829
144	144	0.819
145	145	0.00481
146	146	0.706
147	147	0.749
148	148	0.156
149	149	0.199
15	15	0.0718
150	150	0.222
151	151	0.701
152	152	0.941
153	153	0.855
154	154	0.466
155	155	0.61
156	156	0.0279
157	157	0.974
158	158	0.282
159	159	0.562
160	160	0.506
161	161	0.00566
162	162	0.583
163	163	0.638
164	164	3.34774e-4
165	165	0.5
166	166	0.209
167	167	0.182
168	168	0.603
169	169	0.0833
17	17	0.922
18	18	0.439
19	19	0.343
2	2	0.344
20	20	0.00846
21	21	0.727
22	22	0.705
23	23	0.228
24	24	0.477
25	25	0.436
26	26	6.90933e-4
27	27	0.929
28	28	0.735
29	29	0.00227
3	3	0.0452
30	30	0.893
31	31	0.867
32	32	0.853
33	33	0.143
34	34	0.653
35	35	0.553
36	36	0.017
37	37	0.301
38	38	0.731
39	39	0.909
4	4	0.378
40	40	0.101
41	41	0.665
42	42	0.0499
43	43	0.2
44	44	0.889
45	45	0.822
46	46	0.121
47	47	0.128
48	48	0.18
49	49	0.0988
5	5	0.196
50	50	0.739
51	51	0.917
52	52	0.853
53	53	0.827
54	54	0.948
55	55	0.172
56	56	0.924
57	57	0.467
58	58	0.826
59	59	0.587
6	6	0.897
60	60	0.529
61	61	0.62
62	62	0.214
63	63	0.687
64	64	0.598
65	65	0.862
66	66	0.148
67	67	0.193
68	68	0.761
69	69	0.439
7	7	0.0181
70	70	0.542
71	71	0.00432
72	72	0.632
73	73	0.372
74	74	0.441
75	75	0.0787
76	76	0.381
77	77	0.424
78	78	0.0163
79	79	0.542
8	8	0.00453
80	80	0.108
81	81	0.888
82	82	0.824
83	83	0.539
84	84	0.653
85	85	0.591
86	86	0.379
87	87	0.0369
88	88	0.682
89	89	0.957
9	9	0.74
90	90	0.251
91	91	0.838
92	92	0.983
93	93	0.795
94	94	0.244
95	95	0.0557
96	96	0.219
97	97	0.563
98	98	0.363
99	99	0.915

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: CNhs10524

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011328 mouse liver- embryo E13 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)
0000293 (mouse embryonic day 13 sample)
0011328 (mouse liver- embryo E13 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@SAMD00004746
+|accession_numbers=CAGE;DRX009016;DRR009890;DRZ001315;DRZ002698;DRZ012665;DRZ014048
 |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=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:87425854..87425891,+!p1@Klf1!2.40!249.63!Klf1;;chr15:103085660..103085681,-!p1@Nfe2!2.18!220.15!Nfe2;;chr2:28477452..28477483,-!p1@Gfi1b!1.96!111.45!Gfi1b;;chrX:7544943..7545001,-!p1@Gata1!1.94!86.09!Gata1;;chr4:114732112..114732158,+!p1@Tal1!1.92!173.56!Tal1;;chr7:122989594..122989626,-!p1@Sox6!1.71!50.32!Sox6;;chr11:11584970..11585030,+!p2@Ikzf1!1.69!68.40!Ikzf1;;chr7:122989632..122989668,-!p2@Sox6!1.69!48.35!Sox6;;chr15:103082088..103082136,-!p2@Nfe2!1.69!47.76!Nfe2;;chr4:87452180..87452196,-!p3@Mllt3!1.66!86.68!Mllt3;;chr15:103085690..103085710,-!p3@Nfe2!1.62!44.03!Nfe2;;chr4:87452200..87452229,-!p2@Mllt3!1.59!79.41!Mllt3;;chr9:96159147..96159204,+!p2@Tfdp2!1.53!60.93!Tfdp2;;chr8:87225670..87225697,+!p2@Lyl1!1.39!67.62!Lyl1;;chr4:135728181..135728203,+!p2@E2f2!1.38!30.27!E2f2;;chr7:19608891..19608895,-!p1@Foxa3!1.35!27.52!Foxa3;;chr9:96159225..96159249,+!p5@Tfdp2!1.34!23.19!Tfdp2;;chr10:79884592..79884621,-!p5@Tcf3!1.34!21.03!Tcf3;;chr4:87452236..87452249,-!p9@Mllt3!1.29!18.67!Mllt3;;chr8:87225702..87225726,+!p3@Lyl1!1.27!35.38!Lyl1;;chr4:114729957..114730012,+!p3@Tal1!1.21!15.33!Tal1;;chr10:80598968..80599012,+!p5@Zbtb7a!1.15!17.10!Zbtb7a;;chr8:59799772..59799789,+!p1@Hand2!1.07!30.86!Hand2;;chr9:96159116..96159130,+!p6@Tfdp2!1.07!13.37!Tfdp2;;chr7:17642177..17642223,-!p3@Hif3a!1.05!10.22!Hif3a;;chr16:92826249..92826325,-!p1@Runx1!1.04!24.96!Runx1;;chr14:63864056..63864102,-!p1@Gata4!1.04!17.49!Gata4;;chr4:114732159..114732166,+!p6@Tal1!1.03!9.63!Tal1;;chr8:124806048..124806094,+!p1@Zfpm1!1.01!85.50!Zfpm1;;chr2:163372884..163372904,+!p1@Hnf4a!1.01!9.24!Hnf4a;;chr5:104183477..104183548,+!p6@Aff1!1.00!18.08!Aff1;;chr10:80555320..80555378,-!p1@Creb3l3!1.00!10.61!Creb3l3;;chr7:122989676..122989687,-!p8@Sox6!0.98!8.45!Sox6;;chr9:96159133..96159145,+!p9@Tfdp2!0.96!8.06!Tfdp2;;chr11:120491440..120491474,-!p3@Mafg!0.94!11.60!Mafg;;chr4:135728473..135728494,+!p5@E2f2!0.94!7.67!E2f2;;chr10:119913278..119913298,-!p2@Hmga2!0.93!17.30!Hmga2;;chr4:114730254..114730276,+!p2@Tal1!0.93!9.63!Tal1;;chr8:124806017..124806040,+!p2@Zfpm1!0.92!84.32!Zfpm1;;chr12:3891810..3891829,+!p2@Dnmt3a!0.92!11.60!Dnmt3a;;chr11:16908650..16908690,-!p1@Plek!0.90!44.23!Plek;;chr5:65203599..65203617,+!p8@Klf3!0.90!11.79!Klf3;;chr15:103085802..103085817,-!p4@Nfe2!0.90!8.85!Nfe2;;chr5:135582751..135582788,+!p1@Mlxipl!0.89!28.30!Mlxipl;;chr14:27813679..27813693,+!p2@Hesx1!0.89!6.68!Hesx1;;chr2:162880387..162880413,+!p1@Mybl2!0.88!43.64!Mybl2;;chr11:23980664..23980706,+!p2@Bcl11a!0.87!29.29!Bcl11a;;chr2:166868994..166869023,-!p7@Znfx1!0.87!6.49!Znfx1;;chr4:135728581..135728668,+!p1@E2f2!0.86!31.25!E2f2;;chr10:88145766..88145770,-!p1@Spic!0.86!8.26!Spic;;chr2:38206744..38206766,+!p1@Lhx2!0.86!7.67!Lhx2;;chr6:83301229..83301242,+!p3@Bola3!0.86!6.29!Bola3;;chr10:20880731..20880775,-!p2@Myb!0.85!13.17!Myb;;chr9:96159210..96159221,+!p10@Tfdp2!0.85!6.09!Tfdp2;;chr5:65203575..65203589,+!p11@Klf3!0.84!7.27!Klf3;;chr11:23978353..23978379,+!p10@Bcl11a!0.84!7.08!Bcl11a;;chr3:102768047..102768060,-!p1@Nr1h5!0.84!5.90!Nr1h5;;chr11:90250944..90250982,-!p2@Hlf!0.81!9.43!Hlf;;chr10:119913310..119913366,-!p1@Hmga2!0.80!45.01!Hmga2;;chr10:22539932..22539956,-!p1@Tcf21!0.79!14.74!Tcf21;;chr8:124806111..124806122,+!p3@Zfpm1!0.79!6.49!Zfpm1;;chr9:74709695..74709722,+!p1@Onecut1!0.79!5.11!Onecut1;;chr10:119913546..119913583,-!p3@Hmga2!0.77!10.81!Hmga2;;chr9:24578720..24578735,-!p1@Tbx20!0.77!4.91!Tbx20;;chr14:47896467..47896523,-!p1@Wdhd1!0.76!64.27!Wdhd1;;chr10:12810631..12810649,+!p1@Plagl1!0.75!135.04!Plagl1;;chr2:162880327..162880385,+!p2@Mybl2!0.75!33.81!Mybl2;;chr10:20880629..20880683,-!p1@Myb!0.75!14.55!Myb;;chr18:64499674..64499696,+!p1@Onecut2!0.75!8.45!Onecut2;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.75!7.67!Ncoa4;;chr18:64499706..64499721,+!p2@Onecut2!0.75!6.68!Onecut2;;chr8:107821563..107821642,+!p1@E2f4!0.74!142.51!E2f4;;chr7:56136362..56136400,-!p1@E2f8!0.74!32.24!E2f8;;chr2:91034924..91034946,-!p2@Nr1h3!0.74!5.70!Nr1h3;;chr4:114730015..114730042,+!p7@Tal1!0.74!4.52!Tal1;;chr11:23978078..23978096,+!p4@Bcl11a!0.73!14.55!Bcl11a;;chr10:20880698..20880717,-!p3@Myb!0.73!7.27!Myb;;chr10:119914001..119914078,-!p4@Hmga2!0.73!6.09!Hmga2;;chr11:11585912..11585950,+!p6@Ikzf1!0.73!5.70!Ikzf1;;chr6:83301243..83301258,+!p2@Bola3!0.73!4.32!Bola3;;chr11:23978111..23978134,+!p3@Bcl11a!0.71!9.24!Bcl11a;;chr7:6649134..6649167,-!p1@Zim1!0.70!24.57!Zim1;;chr7:56137011..56137041,-!p2@E2f8!0.70!8.45!E2f8;;chr11:101413151..101413207,-!p1@Brca1!0.69!42.46!Brca1;;chr8:123608252..123608268,+!p1@Foxf1a!0.69!6.09!Foxf1a;;chr11:23977965..23977974,+!p11@Bcl11a!0.69!3.93!Bcl11a;;chr11:23978022..23978076,+!p1@Bcl11a!0.68!93.37!Bcl11a;;chr19:37509324..37509337,+!p1@Hhex!0.67!29.68!Hhex;;chr2:180069370..180069409,-!p1@Gata5!0.66!4.32!Gata5;;chr5:104183579..104183600,+!p9@Aff1!0.66!4.13!Aff1;;chr11:90249521..90249551,-!p3@Hlf!0.66!3.54!Hlf;;chr15:61816932..61816952,+!p2@Myc!0.64!33.02!Myc;;chr12:58646974..58647003,-!p1@Foxa1!0.64!4.72!Foxa1;;chr1:191993385..191993405,-!p3@Prox1!0.64!3.34!Prox1;;chr11:23977565..23977612,+!p5@Bcl11a!0.63!7.86!Bcl11a;;chr11:11585678..11585745,+!p5@Ikzf1!0.63!5.11!Ikzf1;;chr2:38206580..38206600,+!p2@Lhx2!0.62!4.13!Lhx2;;chr13:55932591..55932622,-!p1@Pitx1!0.62!3.93!Pitx1;;chr16:38294860..38294924,-!p1@Nr1i2!0.62!3.14!Nr1i2;;chr2:163332558..163332596,+!p2@Hnf4a!0.62!3.14!Hnf4a;;chr11:102178005..102178022,-!p8@Ubtf!0.61!5.50!Ubtf;;chr4:135728282..135728310,+!p4@E2f2!0.61!3.54!E2f2;;chr10:88996295..88996335,-!p3@Nr1h4!0.60!3.73!Nr1h4;;chr4:13678482..13678505,+!p9@Runx1t1!0.60!2.95!Runx1t1;;chr5:38611720..38611799,+!p1@Lyar!0.59!95.72!Lyar;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.58!3.73!Hmga1;;chr1:181733959..181733977,-!p4@Ahctf1!0.58!3.73!Ahctf1;;chr2:166888058..166888105,-!p2@Znfx1!0.57!10.22!Znfx1;;chr1:138857076..138857105,-!p1@Nr5a2!0.57!2.75!Nr5a2;;chr15:103083245..103083260,-!p7@Nfe2!0.57!2.75!Nfe2;;chr10:80040030..80040072,-!p1@Klf16!0.56!66.04!Klf16;;chr2:77357622..77357704,-!p1@Zfp385b!0.56!8.26!Zfp385b;;chr4:135736690..135736705,+!p6@E2f2!0.56!3.14!E2f2;;chr6:86619104..86619119,-!p1@Mxd1!0.55!25.95!Mxd1;;chr13:30077847..30077906,-!p1@E2f3!0.55!24.77!E2f3;;chr17:56970481..56970551,-!p2@Rfx2!0.55!9.43!Rfx2;;chr15:103164702..103164778,-!p3@Zfp385a!0.55!3.14!Zfp385a;;chr18:74375772..74375799,+!p2@Cxxc1!0.54!8.65!Cxxc1;;chr6:28211956..28211967,-!p2@Zfp800!0.54!6.09!Zfp800;;chr15:61817095..61817111,+!p1@Myc!0.53!183.19!Myc;;chr5:65194752..65194769,+!p1@Klf3!0.53!102.41!Klf3;;chr7:134170081..134170122,-!p2@Maz!0.53!55.63!Maz;;chr2:153475178..153475196,+!p1@Dnmt3b!0.53!5.90!Dnmt3b;;chr2:147871627..147871641,-!p1@Foxa2!0.53!2.36!Foxa2;;chr14:32979060..32979091,+!p4@Gm6768,p4@Ncoa4!0.53!2.36!Ncoa4;;chr5:111082367..111082441,-!p1@Noc4l!0.52!69.19!Noc4l;;chr8:72520225..72520248,-!p9@Gatad2a!0.52!7.67!Gatad2a;;chr2:162880418..162880429,+!p4@Mybl2!0.52!3.14!Mybl2;;chr6:131338435..131338482,-!p1@Csda!0.51!281.28!Csda;;chr10:119913792..119913820,-!p5@Hmga2!0.51!4.32!Hmga2;;chr6:131338483..131338494,-!p5@Csda!0.50!14.74!Csda;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.50!2.95!Hmga1;;chr2:104966874..104966907,+!p2@Wt1!0.50!2.16!Wt1;;chr2:163372869..163372882,+!p3@Hnf4a!0.50!2.16!Hnf4a;;chr8:87225806..87225809,+!p4@Lyl1!0.50!2.16!Lyl1;;chr2:153067094..153067130,-!p1@Plagl2!0.49!69.98!Plagl2;;chr5:34163023..34163090,+!p2@Whsc1!0.49!17.69!Whsc1;;chr10:30523091..30523182,-!p4@Ncoa7!0.49!9.04!Ncoa7;;chr11:60036258..60036276,-!p3@Srebf1!0.48!4.13!Srebf1;;chrX:45245679..45245702,-!p1@Smarca1!0.47!11.40!Smarca1;;chr12:34642510..34642530,+!p1@Twist1!0.47!7.86!Twist1;;chr17:32506357..32506377,-!p3@Wiz!0.47!4.91!Wiz;;chr11:3189171..3189197,+!p4@Patz1!0.47!4.52!Patz1;;chr13:37949830..37949861,+!p7@Rreb1!0.47!4.32!Rreb1;;chrX:7544928..7544938,-!p2@Gata1!0.47!1.97!Gata1;;chr1:136186574..136186592,+!p1@Myog!0.47!1.97!Myog;;chr4:87452167..87452178,-!p8@Mllt3!0.47!1.97!Mllt3;;chr2:44965593..44965624,-!p3@Zeb2!0.46!14.35!Zeb2;;chr10:41995430..41995458,-!p3@Foxo3!0.46!6.29!Foxo3;;chr2:153067079..153067090,-!p2@Plagl2!0.46!4.91!Plagl2;;chr13:55431084..55431137,-!p1@Mxd3!0.45!19.46!Mxd3;;chr10:30522690..30522752,-!p2@Ncoa7!0.45!15.14!Ncoa7;;chr13:64254457..64254497,-!p1@Zfp367!0.45!10.81!Zfp367;;chr2:104966766..104966786,+!p1@Wt1!0.45!3.34!Wt1;;chr19:10315179..10315241,-!p1@Gm98!0.44!25.75!Gm98;;chr9:57684520..57684612,-!p1@Arid3b!0.44!21.42!Arid3b;;chr5:138186979..138187025,+!p4@Tsc22d4!0.44!8.65!Tsc22d4;;chr7:56136974..56136989,-!p4@E2f8!0.44!3.34!E2f8;;chr11:102177921..102177960,-!p9@Ubtf!0.44!2.95!Ubtf;;chr1:138857048..138857071,-!p2@Nr5a2!0.44!1.77!Nr5a2;;chr14:32978944..32978953,+!p8@Gm6768,p8@Ncoa4!0.44!1.77!Ncoa4;;chr4:114730288..114730306,+!p8@Tal1!0.44!1.77!Tal1;;chr6:83299445..83299490,+!p1@Bola3!0.43!102.21!Bola3;;chr9:20757282..20757325,-!p2@Dnmt1!0.43!56.61!Dnmt1;;chr12:85534957..85535017,-!p2@C130039O16Rik!0.43!11.79!C130039O16Rik;;chr9:96159665..96159680,+!p3@Tfdp2!0.43!10.61!Tfdp2;;chr3:135271185..135271254,-!p4@Nfkb1!0.43!3.73!Nfkb1;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.42!110.27!Hmga1;;chr5:140267476..140267493,+!p1@Mafk!0.42!12.78!Mafk;;chr16:44173384..44173407,+!p2@Gm608!0.42!5.50!Gm608;;chr4:134708451..134708469,+!p1@Runx3!0.42!3.54!Runx3;;chr17:56970339..56970428,-!p1@Rfx2!0.41!6.68!Rfx2;;chr2:153475210..153475252,+!p2@Dnmt3b!0.41!5.70!Dnmt3b;;chr2:90936947..90936977,+!p2@Sfpi1!0.41!3.93!Sfpi1;;chr7:56136402..56136420,-!p3@E2f8!0.41!3.54!E2f8;;chr3:51144740..51144743,-!p7@Elf2!0.41!3.14!Elf2;;chr11:102177974..102177992,-!p17@Ubtf!0.41!2.16!Ubtf;;chr6:16848395..16848416,-!p2@Tfec!0.41!1.97!Tfec;;chr7:122989672..122989673,-!p20@Sox6!0.41!1.57!Sox6;;chr11:57645506..57645523,-!p1@Hand1!0.41!1.57!Hand1;;chr3:107398056..107398082,+!p1@Alx3!0.41!1.57!Alx3;;chr2:168032254..168032259,-!p6@Adnp!0.41!1.57!Adnp;;chr7:134169762..134169795,-!p3@Maz!0.40!20.05!Maz;;chr1:191994550..191994623,-!p1@Prox1!0.40!15.14!Prox1;;chr11:11586218..11586285,+!p1@Ikzf1!0.40!6.68!Ikzf1;;chr1:186556323..186556370,-!p2@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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011328
 |is_obsolete=
+|library_id=CNhs10524
+|library_id_phase_based=2:CNhs10524
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;378
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;378
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E13.CNhs10524.378-3H6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E13.CNhs10524.378-3H6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E13.CNhs10524.378-3H6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E13.CNhs10524.378-3H6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E13.CNhs10524.378-3H6.mm9.nobarcode.rdna.fa.gz
 |name=liver, embryo E13
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10524,LSID649,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.006834588088126,0,0,0,0,0,-0.219459130588797,0,0.0389670579605192,0,0,0.116969646354049,0,0,0,0,0,0,-0.113959234961536,0,0.0719939502917345,0,0.0779341159210384,0,0,0,0,0,0,0,0,0,-0.11609498141305,0,0,0,0.338327774086482,0,-0.083353308903066,-0.0996117162591992,0.304630393458024,0.218235634204849,-0.0685597512597606,0,0,0,0,0,0,0,0,0,0,0,0,0.011928568357598,0,0,0,0,-0.0428469550828748,0,-0.058702615159052,0,0,0,0.0181904344572484,0.0276771167470958,-0.158091042771083,-0.028730849363546,0,0,-0.0973736644748266,-0.084844401349818,0.201308886750591,0,-0.0681310518041567,-0.0438189083816729,-0.220084353172321,0.0651563057435618,0,0,0,0,0,0,-0.197219247102159,-0.419041098283968,-0.121164097368705,0,0,0,0,0
@@ Line 83: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:378-3H6;search_select_hide=table117:378-3H6
 }}

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FF:378-3H6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:14, 4 June 2020

CNhs10524

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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