FF:434-16F8: Difference between revisions

Latest revision as of 19:16, 4 June 2020

Name:	kidney, embryo E15
Species:	Mouse (Mus musculus)
Library ID:	CNhs10997
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	kidney
dev stage	15 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		SAMD00005060

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10997		CAGE		DRX009005		DRR009879

Accession ID Mm9

Library id		BAM		CTSS
CNhs10997		DRZ001304		DRZ002687

Accession ID Mm10

Library id		BAM		CTSS
CNhs10997		DRZ012654		DRZ014037

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

CNhs10997

0	0
1	0
10	0
100	0.0367
1000	-0.00761
1001	-0.00676
1002	0.266
1003	-0.087
1004	0
1005	-0.0724
1006	-0.0815
1007	0.13
1008	0
1009	-0.0102
101	0.134
1010	0.047
1011	0
1012	0
1013	-0.188
1014	0.196
1015	0.214
1016	0.162
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.047
1022	-0.0655
1023	0
1024	0.0736
1025	0.169
1026	0.0599
1027	0
1028	0.047
1029	0.219
103	0.0982
1030	0
1031	0.335
1032	-0.0645
1033	0
1034	0
1035	0.00898
1036	0.192
1037	0
1038	0.0282
1039	-0.0467
104	0
1040	0.0754
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: CNhs10997

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	3.78415e-4
MA0003.1	MA0003.1	0.146
MA0004.1	MA0004.1	0.72
MA0006.1	MA0006.1	0.661
MA0007.1	MA0007.1	0.511
MA0009.1	MA0009.1	0.553
MA0014.1	MA0014.1	0.546
MA0017.1	MA0017.1	0.0787
MA0018.2	MA0018.2	0.102
MA0019.1	MA0019.1	0.937
MA0024.1	MA0024.1	6.19678e-8
MA0025.1	MA0025.1	1.66802e-4
MA0027.1	MA0027.1	0.0515
MA0028.1	MA0028.1	0.267
MA0029.1	MA0029.1	0.98
MA0030.1	MA0030.1	0.24
MA0031.1	MA0031.1	0.00263
MA0035.2	MA0035.2	0.0727
MA0038.1	MA0038.1	0.0562
MA0039.2	MA0039.2	0.0303
MA0040.1	MA0040.1	0.322
MA0041.1	MA0041.1	0.219
MA0042.1	MA0042.1	0.451
MA0043.1	MA0043.1	0.418
MA0046.1	MA0046.1	4.54147e-22
MA0047.2	MA0047.2	0.111
MA0048.1	MA0048.1	0.0015
MA0050.1	MA0050.1	2.32933e-4
MA0051.1	MA0051.1	3.71033e-5
MA0052.1	MA0052.1	2.67693e-5
MA0055.1	MA0055.1	0.00533
MA0057.1	MA0057.1	0.104
MA0058.1	MA0058.1	0.699
MA0059.1	MA0059.1	0.683
MA0060.1	MA0060.1	1.33753e-9
MA0061.1	MA0061.1	0.0785
MA0062.2	MA0062.2	0.484
MA0065.2	MA0065.2	0.00221
MA0066.1	MA0066.1	0.0997
MA0067.1	MA0067.1	0.232
MA0068.1	MA0068.1	0.912
MA0069.1	MA0069.1	0.23
MA0070.1	MA0070.1	0.676
MA0071.1	MA0071.1	0.057
MA0072.1	MA0072.1	0.0148
MA0073.1	MA0073.1	0.606
MA0074.1	MA0074.1	0.567
MA0076.1	MA0076.1	0.479
MA0077.1	MA0077.1	0.751
MA0078.1	MA0078.1	0.547
MA0079.2	MA0079.2	0.0817
MA0080.2	MA0080.2	2.58903e-10
MA0081.1	MA0081.1	0.121
MA0083.1	MA0083.1	0.805
MA0084.1	MA0084.1	0.258
MA0087.1	MA0087.1	0.168
MA0088.1	MA0088.1	0.945
MA0090.1	MA0090.1	0.703
MA0091.1	MA0091.1	0.95
MA0092.1	MA0092.1	0.501
MA0093.1	MA0093.1	0.758
MA0099.2	MA0099.2	1.32065e-5
MA0100.1	MA0100.1	0.724
MA0101.1	MA0101.1	0.457
MA0102.2	MA0102.2	0.0477
MA0103.1	MA0103.1	0.0112
MA0104.2	MA0104.2	0.976
MA0105.1	MA0105.1	0.149
MA0106.1	MA0106.1	0.591
MA0107.1	MA0107.1	0.145
MA0108.2	MA0108.2	0.236
MA0111.1	MA0111.1	0.588
MA0112.2	MA0112.2	0.00116
MA0113.1	MA0113.1	0.855
MA0114.1	MA0114.1	0.0928
MA0115.1	MA0115.1	0.355
MA0116.1	MA0116.1	0.041
MA0117.1	MA0117.1	0.0565
MA0119.1	MA0119.1	0.0724
MA0122.1	MA0122.1	0.969
MA0124.1	MA0124.1	0.88
MA0125.1	MA0125.1	0.794
MA0131.1	MA0131.1	0.286
MA0135.1	MA0135.1	0.35
MA0136.1	MA0136.1	1.8694e-8
MA0137.2	MA0137.2	0.0949
MA0138.2	MA0138.2	0.00159
MA0139.1	MA0139.1	0.197
MA0140.1	MA0140.1	0.681
MA0141.1	MA0141.1	0.0386
MA0142.1	MA0142.1	0.575
MA0143.1	MA0143.1	0.186
MA0144.1	MA0144.1	0.133
MA0145.1	MA0145.1	0.0406
MA0146.1	MA0146.1	0.055
MA0147.1	MA0147.1	0.975
MA0148.1	MA0148.1	0.13
MA0149.1	MA0149.1	0.0639
MA0150.1	MA0150.1	0.00163
MA0152.1	MA0152.1	0.0465
MA0153.1	MA0153.1	2.16367e-9
MA0154.1	MA0154.1	0.0117
MA0155.1	MA0155.1	0.993
MA0156.1	MA0156.1	0.00159
MA0157.1	MA0157.1	0.0111
MA0159.1	MA0159.1	0.0317
MA0160.1	MA0160.1	0.0164
MA0162.1	MA0162.1	0.981
MA0163.1	MA0163.1	0.231
MA0164.1	MA0164.1	0.517
MA0258.1	MA0258.1	0.00125
MA0259.1	MA0259.1	0.83

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: CNhs10997

Novel motif	Logo	P-value
1	1	0.11
10	10	0.643
100	100	0.731
101	101	0.497
102	102	0.785
103	103	0.262
104	104	0.723
105	105	0.422
106	106	0.0593
107	107	0.654
108	108	0.597
109	109	0.228
11	11	0.129
110	110	0.762
111	111	0.0132
112	112	0.178
113	113	0.538
114	114	0.00132
115	115	0.572
116	116	0.666
117	117	0.33
118	118	0.265
119	119	0.178
12	12	0.681
120	120	0.23
121	121	0.325
122	122	0.791
123	123	0.0953
124	124	0.578
125	125	0.218
126	126	0.871
127	127	0.0372
128	128	0.0909
129	129	0.26
13	13	0.903
130	130	0.269
131	131	0.408
132	132	0.25
133	133	0.404
134	134	0.448
135	135	0.977
136	136	0.676
137	137	0.898
138	138	0.0569
139	139	0.00977
14	14	0.267
140	140	0.68
141	141	0.487
142	142	0.648
143	143	0.462
144	144	0.655
145	145	0.898
146	146	0.382
147	147	0.437
148	148	0.593
149	149	0.0589
15	15	0.076
150	150	0.894
151	151	0.0371
152	152	0.188
153	153	0.952
154	154	0.406
155	155	0.817
156	156	0.314
157	157	0.611
158	158	0.65
159	159	0.71
160	160	0.727
161	161	0.331
162	162	0.882
163	163	0.0207
164	164	0.504
165	165	0.473
166	166	0.226
167	167	0.996
168	168	0.664
169	169	0.0886
17	17	0.152
18	18	0.229
19	19	0.944
2	2	0.715
20	20	0.633
21	21	0.959
22	22	0.429
23	23	0.0467
24	24	0.445
25	25	0.241
26	26	0.68
27	27	0.473
28	28	0.225
29	29	0.705
3	3	0.39
30	30	0.745
31	31	0.343
32	32	0.0428
33	33	0.839
34	34	0.612
35	35	0.237
36	36	0.272
37	37	0.225
38	38	0.38
39	39	0.723
4	4	0.488
40	40	0.305
41	41	0.0466
42	42	0.534
43	43	0.172
44	44	0.0891
45	45	0.257
46	46	0.303
47	47	0.165
48	48	0.248
49	49	0.135
5	5	0.194
50	50	0.866
51	51	0.527
52	52	0.666
53	53	0.621
54	54	0.33
55	55	0.314
56	56	0.237
57	57	0.874
58	58	0.23
59	59	0.0671
6	6	0.682
60	60	0.255
61	61	0.925
62	62	0.0399
63	63	0.126
64	64	0.54
65	65	0.122
66	66	0.819
67	67	0.254
68	68	0.0696
69	69	0.552
7	7	0.403
70	70	1.68741e-4
71	71	0.519
72	72	0.161
73	73	0.0871
74	74	0.964
75	75	0.0719
76	76	0.768
77	77	0.265
78	78	0.33
79	79	0.342
8	8	0.4
80	80	0.0762
81	81	0.147
82	82	0.0296
83	83	0.427
84	84	0.206
85	85	0.0127
86	86	0.373
87	87	0.0162
88	88	0.935
89	89	0.0779
9	9	0.599
90	90	0.291
91	91	0.822
92	92	0.143
93	93	0.773
94	94	0.976
95	95	0.0848
96	96	0.372
97	97	0.795
98	98	0.157
99	99	0.989

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: CNhs10997

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011350 mouse kidney- embryo E15 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)
0002113 (kidney)
0002100 (trunk)
0000479 (tissue)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

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)
0000298 (mouse embryonic day 15 sample)
0011350 (mouse kidney- embryo E15 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:0003104 (mesenchyme)
UBERON:0003918 (kidney mesenchyme)
UBERON:0007687 (kidney field)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
 |DRA_sample_Accession=CAGE@SAMD00005060
-|accession_numbers=CAGE;DRX009005;DRR009879;DRZ001304;DRZ002687
+|accession_numbers=CAGE;DRX009005;DRR009879;DRZ001304;DRZ002687;DRZ012654;DRZ014037
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000479,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
 |ancestors_in_cell_lineage_facet=
@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:22539932..22539956,-!p1@Tcf21!1.79!154.12!Tcf21;;chr11:96153767..96153822,+!p1@Hoxb6!1.67!70.26!Hoxb6;;chr11:83664365..83664383,+!p1@Hnf1b!1.67!45.70!Hnf1b;;chr6:52190467..52190500,-!p1@Hoxa10!1.67!45.47!Hoxa10;;chr11:96143666..96143725,+!p1@Hoxb8!1.63!47.64!Hoxb8;;chr15:102828658..102828678,+!p1@Hoxc6!1.58!36.90!Hoxc6;;chr13:99124189..99124205,+!p1@Foxd1!1.55!51.41!Foxd1;;chr2:74549968..74549996,+!p1@Hoxd3!1.53!40.44!Hoxd3;;chr2:24331085..24331100,-!p1@Pax8!1.51!31.53!Pax8;;chr11:84339016..84339044,-!p1@Lhx1!1.46!27.65!Lhx1;;chr17:86087592..86087615,-!p1@Six2!1.44!26.62!Six2;;chr6:52176164..52176195,-!p1@Hoxa9!1.43!32.22!Hoxa9;;chr19:59533221..59533271,+!p1@Emx2!1.41!29.93!Emx2;;chr2:104966766..104966786,+!p1@Wt1!1.40!37.47!Wt1;;chr5:140019865..140019886,+!p1@Uncx!1.38!23.08!Uncx;;chr6:52184901..52184959,-!p2@Hoxa10!1.38!23.08!Hoxa10;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.35!27.08!Pou3f3;;chr5:140019843..140019858,+!p2@Uncx!1.31!19.42!Uncx;;chr6:52163319..52163342,-!p1@Hoxa3!1.29!26.96!Hoxa3;;chr6:52195795..52195825,-!p1@Hoxa11!1.28!18.17!Hoxa11;;chr15:102797288..102797302,+!p1@Hoxc10!1.27!17.71!Hoxc10;;chr2:74520048..74520064,+!p1@Hoxd11!1.25!16.79!Hoxd11;;chr8:123640063..123640077,+!p1@Foxc2!1.24!29.25!Foxc2;;chr2:74550015..74550057,+!p2@Hoxd3!1.23!16.11!Hoxd3;;chr2:9800207..9800234,-!p1@Gata3!1.21!46.16!Gata3;;chr6:52195763..52195792,-!p2@Hoxa11!1.21!15.31!Hoxa11;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.18!40.33!Tfcp2l1;;chr1:19202352..19202354,+!p2@Tfap2b!1.18!14.28!Tfap2b;;chr6:52190668..52190682,-!p3@Hoxa10!1.17!13.82!Hoxa10;;chr11:96143843..96143868,+!p3@Hoxb8!1.17!13.71!Hoxb8;;chr10:119913546..119913583,-!p3@Hmga2!1.16!28.11!Hmga2;;chr2:104966874..104966907,+!p2@Wt1!1.14!12.91!Wt1;;chr2:74520343..74520383,+!p4@Hoxd11!1.14!12.91!Hoxd11;;chr11:96147952..96147967,+!p1@Hoxb7!1.13!15.65!Hoxb7;;chr2:74517609..74517621,+!p3@Hoxd11!1.11!12.00!Hoxd11;;chr7:108966820..108966835,+!p1@Phox2a!1.08!10.97!Phox2a;;chr8:59799772..59799789,+!p1@Hand2!1.07!31.30!Hand2;;chr2:74529970..74529997,+!p1@Hoxd10!1.07!10.63!Hoxd10;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!1.05!10.17!Sim1;;chr10:119913310..119913366,-!p1@Hmga2!1.03!77.46!Hmga2;;chr14:98568971..98569025,-!p1@Dach1!1.03!75.52!Dach1;;chr5:140019816..140019825,+!p3@Uncx!1.02!9.37!Uncx;;chr2:103123925..103123959,-!p3@Ehf!1.01!9.14!Ehf;;chr10:119913278..119913298,-!p2@Hmga2!0.97!18.97!Hmga2;;chr11:101755669..101755686,-!p1@Meox1!0.95!14.40!Meox1;;chr12:28027561..28027591,-!p1@Sox11!0.94!52.10!Sox11;;chr3:29912058..29912071,-!p6@Mecom!0.94!8.80!Mecom;;chr2:38570011..38570034,-!p1@Nr5a1!0.94!7.77!Nr5a1;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.94!7.77!Hoxb2;;chr2:104966465..104966479,+!p6@Wt1!0.94!7.65!Wt1;;chr2:163372884..163372904,+!p1@Hnf4a!0.94!7.65!Hnf4a;;chr12:3891810..3891829,+!p2@Dnmt3a!0.92!11.65!Dnmt3a;;chr2:104966933..104966966,+!p3@Wt1!0.91!7.20!Wt1;;chr6:52190858..52190873,-!p4@Hoxa10!0.91!7.20!Hoxa10;;chr2:9809357..9809371,-!p2@Gata3!0.91!7.20!Gata3;;chr3:30408603..30408668,-!p1@Mecom!0.90!16.68!Mecom;;chr10:119914001..119914078,-!p4@Hmga2!0.90!9.71!Hmga2;;chr11:57645506..57645523,-!p1@Hand1!0.90!6.85!Hand1;;chr15:35225845..35225867,+!p1@Osr2!0.89!17.59!Osr2;;chr15:102797170..102797182,+!p3@Hoxc10!0.89!6.74!Hoxc10;;chr1:19199236..19199258,+!p1@Tfap2b!0.88!6.63!Tfap2b;;chr11:96143962..96144035,+!p2@Hoxb8!0.88!6.51!Hoxb8;;chr7:77511403..77511450,-!p3@Nr2f2!0.87!14.17!Nr2f2;;chr11:34108085..34108092,-!p1@Foxi1!0.87!6.40!Foxi1;;chr11:96132767..96132796,+!p2@Hoxb9!0.86!6.17!Hoxb9;;chr2:115891534..115891589,-!p1@Meis2!0.85!92.20!Meis2;;chr14:98568761..98568814,-!p2@Dach1!0.85!44.44!Dach1;;chr1:170361730..170361769,-!p7@Pbx1!0.85!14.62!Pbx1;;chr19:59533139..59533152,+!p2@Emx2!0.85!6.06!Emx2;;chr11:96132637..96132652,+!p1@Hoxb9!0.84!5.94!Hoxb9;;chr10:102491405..102491416,-!p1@Alx1!0.84!5.94!Alx1;;chr14:17407878..17407926,-!p1@Rarb!0.83!13.48!Rarb;;chr15:102828642..102828653,+!p2@Hoxc6!0.83!5.83!Hoxc6;;chr2:74536026..74536039,+!p1@Hoxd9!0.83!5.71!Hoxd9;;chr7:77505617..77505632,-!p1@Nr2f2!0.82!280.59!Nr2f2;;chr13:31898729..31898761,+!p1@Foxc1!0.81!14.28!Foxc1;;chr10:119913792..119913820,-!p5@Hmga2!0.81!9.83!Hmga2;;chr6:52190840..52190853,-!p5@Hoxa10!0.81!5.48!Hoxa10;;chr11:18918434..18918489,-!p3@Meis1!0.80!8.68!Meis1;;chr11:96160360..96160397,+!p3@Hoxb6!0.80!5.37!Hoxb6;;chr2:105003277..105003280,+!p5@Wt1!0.80!5.37!Wt1;;chr2:74517742..74517758,+!p2@Hoxd11!0.80!5.37!Hoxd11;;chr10:102491237..102491291,-!p2@Alx1!0.80!5.26!Alx1;;chr19:59533163..59533185,+!p3@Emx2!0.80!5.26!Emx2;;chr14:98569030..98569059,-!p3@Dach1!0.79!26.85!Dach1;;chr2:115891409..115891425,-!p2@Meis2!0.79!15.99!Meis2;;chr11:85646303..85646329,+!p1@Tbx2!0.78!36.45!Tbx2;;chr12:3891753..3891801,+!p4@Dnmt3a!0.78!8.57!Dnmt3a;;chr11:96145450..96145517,+!p2@Hoxb7!0.78!7.77!Hoxb7;;chr15:102797225..102797243,+!p2@Hoxc10!0.76!4.80!Hoxc10;;chr10:12810631..12810649,+!p1@Plagl1!0.75!133.90!Plagl1;;chr2:115890469..115890485,-!p7@Meis2!0.75!7.65!Meis2;;chr19:59532915..59532940,+!p5@Emx2!0.75!4.57!Emx2;;chr2:74543202..74543213,+!p3@Hoxd8!0.75!4.57!Hoxd8;;chr8:123640090..123640101,+!p2@Foxc2!0.74!5.14!Foxc2;;chr7:52471143..52471186,+!p1@Tead2!0.72!50.38!Tead2;;chr14:22807107..22807119,-!p2@Zfp503!0.72!20.45!Zfp503;;chr1:170361777..170361797,-!p10@Pbx1!0.72!7.88!Pbx1;;chrX:110411840..110411860,+!p1@Dach2!0.72!5.37!Dach2;;chr2:74560109..74560131,+!p1@Hoxd4!0.72!4.23!Hoxd4;;chr6:52195747..52195762,-!p3@Hoxa11!0.71!4.11!Hoxa11;;chr12:12948633..12948651,-!p1@Mycn!0.70!43.30!Mycn;;chr16:14705925..14705951,+!p1@Snai2!0.70!31.76!Snai2;;chr7:17647736..17647772,-!p1@Hif3a!0.70!15.65!Hif3a;;chr11:101646566..101646603,-!p1@Etv4!0.70!14.40!Etv4;;chr2:74520075..74520087,+!p6@Hoxd11!0.70!4.00!Hoxd11;;chr2:103264213..103264233,+!p1@Elf5!0.70!4.00!Elf5;;chr13:72101178..72101203,-!p1@Irx1!0.69!6.40!Irx1;;chr2:17976799..17976829,+!p5@Mllt10!0.69!4.91!Mllt10;;chr2:180069370..180069409,-!p1@Gata5!0.69!4.68!Gata5;;chr7:6649134..6649167,-!p1@Zim1!0.68!23.54!Zim1;;chr16:14705961..14705978,+!p2@Snai2!0.68!20.22!Snai2;;chr10:126778916..126778974,-!p1@Gli1!0.68!9.25!Gli1;;chr2:115891381..115891392,-!p5@Meis2!0.68!8.00!Meis2;;chr13:72101161..72101177,-!p2@Irx1!0.68!5.48!Irx1;;chr6:83020355..83020371,-!p1@Tlx2!0.67!3.66!Tlx2;;chr7:77511234..77511302,-!p2@Nr2f2!0.66!27.53!Nr2f2;;chr2:115891427..115891441,-!p4@Meis2!0.66!8.34!Meis2;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.66!6.63!Hoxb2;;chr6:52176144..52176161,-!p2@Hoxa9!0.66!3.54!Hoxa9;;chr2:74542680..74542705,+!p6@Hoxd8!0.66!3.54!Hoxd8;;chr8:87425854..87425891,+!p1@Klf1!0.66!3.54!Klf1;;chr1:170361678..170361689,-!p13@Pbx1!0.65!4.34!Pbx1;;chr19:59533429..59533470,+!p4@Emx2!0.65!3.43!Emx2;;chr11:96145393..96145407,+!p3@Hoxb7!0.65!3.43!Hoxb7;;chr2:74535796..74535808,+!p3@Hoxd9!0.65!3.43!Hoxd9;;chr14:22807083..22807104,-!p1@Zfp503!0.64!69.01!Zfp503;;chr1:137155026..137155042,-!p1@Elf3!0.64!22.74!Elf3;;chr11:3189683..3189744,+!p2@Patz1!0.64!7.65!Patz1;;chr12:37835120..37835133,+!p2@Meox2!0.64!5.14!Meox2;;chr9:71743854..71743909,-!p1@Tcf12!0.63!30.50!Tcf12;;chr1:170362040..170362113,-!p2@Pbx1!0.63!30.28!Pbx1;;chr11:18918406..18918431,-!p6@Meis1!0.63!4.68!Meis1;;chr19:59533595..59533628,+!p6@Emx2!0.63!3.31!Emx2;;chr2:74536050..74536065,+!p2@Hoxd9!0.63!3.31!Hoxd9;;chr2:74549945..74549965,+!p4@Hoxd3!0.63!3.31!Hoxd3;;chr2:9809374..9809396,-!p4@Gata3!0.63!3.31!Gata3;;chr6:88148650..88148669,+!p1@Gata2!0.62!31.53!Gata2;;chr17:35031460..35031518,+!p1@Zbtb12!0.62!18.62!Zbtb12;;chr12:34642510..34642530,+!p1@Twist1!0.62!11.65!Twist1;;chr11:85646263..85646278,+!p2@Tbx2!0.62!9.14!Tbx2;;chr2:115890953..115890974,-!p6@Meis2!0.62!5.14!Meis2;;chr8:90483433..90483457,-!p2@Zfp423!0.62!4.57!Zfp423;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.62!4.46!Hoxb2;;chr1:170361695..170361722,-!p12@Pbx1!0.62!4.23!Pbx1;;chr1:136186574..136186592,+!p1@Myog!0.62!3.20!Myog;;chr4:114581497..114581519,-!p2@Foxd2!0.62!3.20!Foxd2;;chr2:74513125..74513143,+!p1@Hoxd12!0.62!3.20!Hoxd12;;chr1:170362273..170362317,-!p1@Pbx1!0.61!107.05!Pbx1;;chr15:61816932..61816952,+!p2@Myc!0.60!29.70!Myc;;chr7:77511311..77511352,-!p4@Nr2f2!0.60!6.74!Nr2f2;;chr15:103085660..103085681,-!p1@Nfe2!0.60!4.80!Nfe2;;chr6:52167459..52167492,-!p1@Hoxa7!0.60!3.77!Hoxa7;;chr1:19202185..19202187,+!p9@Tfap2b!0.60!2.97!Tfap2b;;chr4:122911086..122911112,+!p1@Heyl!0.59!41.47!Heyl;;chrX:45245679..45245702,-!p1@Smarca1!0.59!15.54!Smarca1;;chr18:76219118..76219155,+!p1@Zbtb7c!0.59!5.71!Zbtb7c;;chr4:154335024..154335039,+!p1@Hes5!0.59!3.66!Hes5;;chr18:65741935..65741964,+!p2@Zfp532!0.58!9.03!Zfp532;;chr13:31898637..31898653,+!p2@Foxc1!0.58!5.60!Foxc1;;chr13:31898496..31898519,+!p3@Foxc1!0.58!5.03!Foxc1;;chr3:30408674..30408716,-!p2@Mecom!0.58!5.03!Mecom;;chr4:114581524..114581551,-!p1@Foxd2!0.58!4.46!Foxd2;;chr18:65741358..65741415,+!p1@Zfp532!0.57!14.28!Zfp532;;chr13:31650185..31650201,+!p1@Foxq1!0.57!11.42!Foxq1;;chr5:115421065..115421088,-!p1@Hnf1a!0.57!2.74!Hnf1a;;chr11:96160426..96160443,+!p2@Hoxb6!0.57!2.74!Hoxb6;;chr4:135699731..135699747,+!p1@Id3!0.56!373.25!Id3;;chr13:30077847..30077906,-!p1@E2f3!0.56!25.02!E2f3;;chr12:37835141..37835194,+!p1@Meox2!0.56!9.71!Meox2;;chr11:101645830..101645881,-!p2@Etv4!0.56!5.48!Etv4;;chr10:119913839..119913869,-!p7@Hmga2!0.56!3.54!Hmga2;;chr14:98568683..98568698,-!p6@Dach1!0.56!3.54!Dach1;;chr6:85137520..85137563,+!p1@Emx1!0.56!2.63!Emx1;;chr8:91568074..91568094,-!p1@Sall1!0.56!2.63!Sall1;;chr1:4483679..4483695,-!p1@Sox17!0.55!14.74!Sox17;;chr14:17407549..17407575,-!p3@Rarb!0.55!4.23!Rarb;;chr11:101646480..101646496,-!p4@Etv4!0.55!3.43!Etv4;;chr2:74543397..74543435,+!p2@Hoxd8!0.55!2.51!Hoxd8;;chr2:9809402..9809422,-!p5@Gata3!0.55!2.51!Gata3;;chr1:189432881..189432903,+!p2@Esrrg!0.55!2.51!Esrrg;;chr2:24331116..24331125,-!p2@Pax8!0.55!2.51!Pax8;;chr14:17407970..17408015,-!p2@Rarb!0.54!7.88!Rarb;;chr1:170361991..170362015,-!p6@Pbx1!0.54!6.40!Pbx1;;chr14:52935860..52935874,-!p3@Sall2!0.54!3.88!Sall2;;chr9:106356211..106356242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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs10997
-|library_id_phase_based=1:CNhs10997
+|library_id_phase_based=2:CNhs10997
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;434
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;434
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E15.CNhs10997.434-16F8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E15.CNhs10997.434-16F8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E15.CNhs10997.434-16F8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E15.CNhs10997.434-16F8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E15.CNhs10997.434-16F8.mm9.nobarcode.rdna.fa.gz
 |name=kidney, embryo E15
 |namespace=FANTOM5
@@ Line 51: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10997,LSID730,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.26150158801413,0.0232131743944767,0.0234910315133595,0,0,0.0641499434652318,0.280105989400145,0,0.144253244734027,0,0,0.594197431080698,0,0,0,0,0,0,0.394267642692462,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0763774955158204,0,0.046982063026719,0,0.0893741091821246,0.0335406025720573,0.132876333549331,0.0271660716228538,-0.011263283153196,0.369761937700081,0.125498065490159,0,0,0,0,0,0,0,0,0,0,0.127993717815825,0,0.308922737071086,0,0,0,0,0.0850217567645435,0,-0.00309173055466413,0.046982063026719,0.127993717815825,0.046982063026719,0.20180485458727,0.0847160461611239,0.149027575512398,0.149111038094678,0,0.0490386458677781,0.0399317718732868,0.00148697397223374,0.046982063026719,0,0.046982063026719,-0.0176068233299043,-0.14443913031503,0.11741164027124,0,0,0,0,0,0,0,0.174358677786095,0.0203003777050728,0.0241620524620674,0,0,0,0
@@ Line 88: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:434-16F8;search_select_hide=table117:434-16F8
 }}

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FF:434-16F8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:16, 4 June 2020

CNhs10997

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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