FF:1288-20C7: Difference between revisions

Latest revision as of 18:47, 4 June 2020

Name:	kidney, embryo E18
Species:	Mouse (Mus musculus)
Library ID:	CNhs11001
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	kidney
dev stage	18 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		SAMD00005277

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11001		CAGE		DRX009008		DRR009882

Accession ID Mm9

Library id		BAM		CTSS
CNhs11001		DRZ001307		DRZ002690

Accession ID Mm10

Library id		BAM		CTSS
CNhs11001		DRZ012657		DRZ014040

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

CNhs11001

0	0
1	0
10	0
100	0
1000	0
1001	0.051
1002	0.546
1003	0.00188
1004	0
1005	-0.0389
1006	-0.0464
1007	0.0846
1008	0
1009	0.0615
101	0.0371
1010	0
1011	0.0324
1012	0
1013	0.143
1014	0.156
1015	0.142
1016	0.117
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	0.077
1023	0
1024	0.077
1025	0.142
1026	0
1027	0
1028	0.077
1029	0.351
103	0.111
1030	0
1031	0.29
1032	0.0701
1033	0.133
1034	0
1035	0.077
1036	0.06
1037	0
1038	0.0307
1039	0.0744
104	0
1040	0.173
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: CNhs11001

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00202
MA0003.1	MA0003.1	0.689
MA0004.1	MA0004.1	0.687
MA0006.1	MA0006.1	0.332
MA0007.1	MA0007.1	0.683
MA0009.1	MA0009.1	0.568
MA0014.1	MA0014.1	0.803
MA0017.1	MA0017.1	0.00452
MA0018.2	MA0018.2	2.40895e-5
MA0019.1	MA0019.1	0.328
MA0024.1	MA0024.1	7.92733e-4
MA0025.1	MA0025.1	0.00383
MA0027.1	MA0027.1	0.998
MA0028.1	MA0028.1	0.51
MA0029.1	MA0029.1	0.207
MA0030.1	MA0030.1	0.702
MA0031.1	MA0031.1	0.689
MA0035.2	MA0035.2	8.87645e-6
MA0038.1	MA0038.1	0.388
MA0039.2	MA0039.2	0.553
MA0040.1	MA0040.1	0.545
MA0041.1	MA0041.1	0.25
MA0042.1	MA0042.1	0.638
MA0043.1	MA0043.1	0.0023
MA0046.1	MA0046.1	1.18331e-88
MA0047.2	MA0047.2	0.623
MA0048.1	MA0048.1	3.7845e-4
MA0050.1	MA0050.1	0.124
MA0051.1	MA0051.1	0.0596
MA0052.1	MA0052.1	1.87829e-5
MA0055.1	MA0055.1	4.29493e-4
MA0057.1	MA0057.1	0.645
MA0058.1	MA0058.1	0.566
MA0059.1	MA0059.1	0.819
MA0060.1	MA0060.1	0.00328
MA0061.1	MA0061.1	0.101
MA0062.2	MA0062.2	2.3339e-4
MA0065.2	MA0065.2	0.991
MA0066.1	MA0066.1	0.463
MA0067.1	MA0067.1	0.116
MA0068.1	MA0068.1	0.979
MA0069.1	MA0069.1	0.0653
MA0070.1	MA0070.1	0.739
MA0071.1	MA0071.1	0.475
MA0072.1	MA0072.1	0.0586
MA0073.1	MA0073.1	0.682
MA0074.1	MA0074.1	0.634
MA0076.1	MA0076.1	0.154
MA0077.1	MA0077.1	0.34
MA0078.1	MA0078.1	0.0329
MA0079.2	MA0079.2	0.208
MA0080.2	MA0080.2	3.64623e-5
MA0081.1	MA0081.1	0.0797
MA0083.1	MA0083.1	0.501
MA0084.1	MA0084.1	0.755
MA0087.1	MA0087.1	0.928
MA0088.1	MA0088.1	0.915
MA0090.1	MA0090.1	0.0211
MA0091.1	MA0091.1	0.575
MA0092.1	MA0092.1	0.524
MA0093.1	MA0093.1	0.655
MA0099.2	MA0099.2	9.54234e-4
MA0100.1	MA0100.1	0.0803
MA0101.1	MA0101.1	0.379
MA0102.2	MA0102.2	0.0779
MA0103.1	MA0103.1	0.723
MA0104.2	MA0104.2	0.184
MA0105.1	MA0105.1	0.397
MA0106.1	MA0106.1	0.677
MA0107.1	MA0107.1	0.204
MA0108.2	MA0108.2	0.0148
MA0111.1	MA0111.1	0.774
MA0112.2	MA0112.2	0.492
MA0113.1	MA0113.1	0.566
MA0114.1	MA0114.1	8.50727e-4
MA0115.1	MA0115.1	0.923
MA0116.1	MA0116.1	0.112
MA0117.1	MA0117.1	0.0156
MA0119.1	MA0119.1	0.501
MA0122.1	MA0122.1	0.367
MA0124.1	MA0124.1	0.896
MA0125.1	MA0125.1	0.736
MA0131.1	MA0131.1	0.65
MA0135.1	MA0135.1	0.55
MA0136.1	MA0136.1	1.13604e-7
MA0137.2	MA0137.2	0.318
MA0138.2	MA0138.2	0.00761
MA0139.1	MA0139.1	0.928
MA0140.1	MA0140.1	6.0058e-4
MA0141.1	MA0141.1	0.596
MA0142.1	MA0142.1	0.0932
MA0143.1	MA0143.1	0.512
MA0144.1	MA0144.1	0.429
MA0145.1	MA0145.1	0.302
MA0146.1	MA0146.1	0.415
MA0147.1	MA0147.1	0.155
MA0148.1	MA0148.1	0.56
MA0149.1	MA0149.1	0.317
MA0150.1	MA0150.1	0.0201
MA0152.1	MA0152.1	0.0237
MA0153.1	MA0153.1	1.31386e-38
MA0154.1	MA0154.1	0.699
MA0155.1	MA0155.1	0.286
MA0156.1	MA0156.1	6.48259e-5
MA0157.1	MA0157.1	0.796
MA0159.1	MA0159.1	0.475
MA0160.1	MA0160.1	0.416
MA0162.1	MA0162.1	0.204
MA0163.1	MA0163.1	0.575
MA0164.1	MA0164.1	0.985
MA0258.1	MA0258.1	0.0684
MA0259.1	MA0259.1	0.651

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: CNhs11001

Novel motif	Logo	P-value
1	1	0.0597
10	10	0.963
100	100	0.493
101	101	0.527
102	102	0.494
103	103	0.563
104	104	0.524
105	105	0.913
106	106	0.709
107	107	0.476
108	108	0.281
109	109	0.602
11	11	0.18
110	110	0.852
111	111	0.0688
112	112	0.55
113	113	0.719
114	114	0.00717
115	115	0.831
116	116	0.311
117	117	0.0774
118	118	0.269
119	119	0.963
12	12	0.583
120	120	0.241
121	121	0.505
122	122	0.956
123	123	0.0983
124	124	0.506
125	125	0.147
126	126	0.394
127	127	0.0801
128	128	0.752
129	129	0.583
13	13	0.0468
130	130	0.256
131	131	0.298
132	132	0.636
133	133	0.55
134	134	0.63
135	135	0.847
136	136	0.266
137	137	0.284
138	138	0.0258
139	139	0.226
14	14	0.492
140	140	0.999
141	141	0.998
142	142	0.0917
143	143	0.37
144	144	0.196
145	145	0.386
146	146	0.553
147	147	0.145
148	148	0.711
149	149	0.606
15	15	0.254
150	150	0.229
151	151	0.0163
152	152	0.407
153	153	0.475
154	154	0.359
155	155	0.639
156	156	0.0244
157	157	0.815
158	158	0.517
159	159	0.279
160	160	0.157
161	161	0.769
162	162	0.672
163	163	0.0881
164	164	0.194
165	165	0.21
166	166	0.156
167	167	0.746
168	168	0.656
169	169	0.252
17	17	0.622
18	18	0.0312
19	19	0.0578
2	2	0.461
20	20	0.712
21	21	0.926
22	22	0.599
23	23	0.264
24	24	0.635
25	25	0.198
26	26	0.656
27	27	0.915
28	28	0.276
29	29	0.478
3	3	0.821
30	30	0.666
31	31	0.414
32	32	0.0329
33	33	0.929
34	34	0.807
35	35	0.0861
36	36	0.131
37	37	0.994
38	38	0.608
39	39	0.325
4	4	0.965
40	40	0.412
41	41	0.0482
42	42	0.675
43	43	0.354
44	44	0.291
45	45	0.818
46	46	0.512
47	47	0.218
48	48	0.409
49	49	0.278
5	5	0.264
50	50	0.525
51	51	0.786
52	52	0.408
53	53	0.773
54	54	0.242
55	55	0.303
56	56	0.277
57	57	0.933
58	58	0.763
59	59	0.373
6	6	0.932
60	60	0.86
61	61	0.352
62	62	0.0969
63	63	0.347
64	64	0.571
65	65	0.244
66	66	0.479
67	67	0.0546
68	68	0.054
69	69	0.735
7	7	0.905
70	70	0.0449
71	71	0.73
72	72	0.441
73	73	0.487
74	74	0.927
75	75	0.231
76	76	0.921
77	77	0.888
78	78	0.821
79	79	0.481
8	8	0.224
80	80	0.0351
81	81	0.164
82	82	0.0607
83	83	0.293
84	84	0.59
85	85	0.185
86	86	0.563
87	87	7.63323e-4
88	88	0.502
89	89	0.296
9	9	0.768
90	90	0.426
91	91	0.753
92	92	0.242
93	93	0.75
94	94	0.39
95	95	0.179
96	96	0.65
97	97	0.735
98	98	0.384
99	99	0.515

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: CNhs11001

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011512 mouse kidney- embryo E18 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)
0000302 (mouse embryonic day 18 sample)
0011512 (mouse kidney- embryo E18 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@DRS008871
+|DRA_sample_Accession=CAGE@SAMD00005277
+|accession_numbers=CAGE;DRX009008;DRR009882;DRZ001307;DRZ002690;DRZ012657;DRZ014040
 |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 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:22539932..22539956,-!p1@Tcf21!1.97!234.88!Tcf21;;chr11:83664365..83664383,+!p1@Hnf1b!1.89!76.22!Hnf1b;;chr11:96153767..96153822,+!p1@Hoxb6!1.79!92.90!Hoxb6;;chr15:102828658..102828678,+!p1@Hoxc6!1.71!50.04!Hoxc6;;chr2:74549968..74549996,+!p1@Hoxd3!1.66!55.66!Hoxd3;;chr11:96143666..96143725,+!p1@Hoxb8!1.66!50.62!Hoxb8;;chr6:52190467..52190500,-!p1@Hoxa10!1.60!38.60!Hoxa10;;chr2:24331085..24331100,-!p1@Pax8!1.57!36.46!Pax8;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.54!42.67!Pou3f3;;chr19:59533221..59533271,+!p1@Emx2!1.54!41.51!Emx2;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.49!83.01!Tfcp2l1;;chr2:104966766..104966786,+!p1@Wt1!1.49!46.55!Wt1;;chr6:52176164..52176195,-!p1@Hoxa9!1.43!31.81!Hoxa9;;chr11:34108085..34108092,-!p1@Foxi1!1.41!24.44!Foxi1;;chr11:84339016..84339044,-!p1@Lhx1!1.40!24.24!Lhx1;;chr6:52184901..52184959,-!p2@Hoxa10!1.37!22.69!Hoxa10;;chr1:19202352..19202354,+!p2@Tfap2b!1.35!21.14!Tfap2b;;chr17:86087592..86087615,-!p1@Six2!1.32!19.98!Six2;;chr6:52163319..52163342,-!p1@Hoxa3!1.31!27.93!Hoxa3;;chr2:163372884..163372904,+!p1@Hnf4a!1.29!18.62!Hnf4a;;chr6:52195763..52195792,-!p2@Hoxa11!1.28!18.23!Hoxa11;;chr8:123640063..123640077,+!p1@Foxc2!1.26!31.03!Foxc2;;chr2:74529970..74529997,+!p1@Hoxd10!1.24!16.49!Hoxd10;;chr5:140019865..140019886,+!p1@Uncx!1.23!16.10!Uncx;;chr2:74517609..74517621,+!p3@Hoxd11!1.23!15.90!Hoxd11;;chr2:9800207..9800234,-!p1@Gata3!1.22!46.74!Gata3;;chr2:74550015..74550057,+!p2@Hoxd3!1.21!15.32!Hoxd3;;chr11:96147952..96147967,+!p1@Hoxb7!1.20!18.43!Hoxb7;;chr6:52195795..52195825,-!p1@Hoxa11!1.20!14.93!Hoxa11;;chr13:99124189..99124205,+!p1@Foxd1!1.16!20.37!Foxd1;;chr15:102797288..102797302,+!p1@Hoxc10!1.16!13.38!Hoxc10;;chr2:74520048..74520064,+!p1@Hoxd11!1.14!12.80!Hoxd11;;chr2:103264213..103264233,+!p1@Elf5!1.13!12.41!Elf5;;chr2:104966874..104966907,+!p2@Wt1!1.11!12.03!Wt1;;chr14:98568971..98569025,-!p1@Dach1!1.10!89.22!Dach1;;chr11:96143843..96143868,+!p3@Hoxb8!1.07!10.86!Hoxb8;;chr2:9809357..9809371,-!p2@Gata3!1.07!10.86!Gata3;;chr5:140019843..140019858,+!p2@Uncx!1.07!10.67!Uncx;;chr2:74517742..74517758,+!p2@Hoxd11!1.04!10.09!Hoxd11;;chr6:52190668..52190682,-!p3@Hoxa10!1.03!9.70!Hoxa10;;chr2:74536026..74536039,+!p1@Hoxd9!1.02!9.50!Hoxd9;;chr7:17647736..17647772,-!p1@Hif3a!1.01!33.17!Hif3a;;chr10:88969376..88969395,-!p1@Nr1h4!1.01!9.31!Nr1h4;;chr3:30408603..30408668,-!p1@Mecom!1.00!21.33!Mecom;;chr6:52190840..52190853,-!p5@Hoxa10!1.00!8.92!Hoxa10;;chr1:19199236..19199258,+!p1@Tfap2b!0.98!8.53!Tfap2b;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!0.96!8.15!Sim1;;chr11:96143962..96144035,+!p2@Hoxb8!0.96!8.15!Hoxb8;;chr6:85137520..85137563,+!p1@Emx1!0.96!8.15!Emx1;;chr15:102828642..102828653,+!p2@Hoxc6!0.96!8.15!Hoxc6;;chr3:30408674..30408716,-!p2@Mecom!0.95!13.38!Mecom;;chr13:72101178..72101203,-!p1@Irx1!0.95!12.61!Irx1;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.94!7.76!Hoxb2;;chr15:35225845..35225867,+!p1@Osr2!0.93!19.40!Osr2;;chr2:74520343..74520383,+!p4@Hoxd11!0.93!7.56!Hoxd11;;chr11:96145450..96145517,+!p2@Hoxb7!0.91!11.06!Hoxb7;;chr2:104966465..104966479,+!p6@Wt1!0.91!7.18!Wt1;;chr2:103123925..103123959,-!p3@Ehf!0.89!6.79!Ehf;;chr2:74543202..74543213,+!p3@Hoxd8!0.89!6.79!Hoxd8;;chr1:137155026..137155042,-!p1@Elf3!0.88!40.73!Elf3;;chr6:52190858..52190873,-!p4@Hoxa10!0.88!6.59!Hoxa10;;chr5:140019816..140019825,+!p3@Uncx!0.88!6.59!Uncx;;chr3:29912058..29912071,-!p6@Mecom!0.87!7.37!Mecom;;chr2:74542680..74542705,+!p6@Hoxd8!0.87!6.40!Hoxd8;;chr13:31650185..31650201,+!p1@Foxq1!0.86!22.89!Foxq1;;chr13:72101161..72101177,-!p2@Irx1!0.86!8.73!Irx1;;chr11:96132767..96132796,+!p2@Hoxb9!0.86!6.21!Hoxb9;;chr2:74543397..74543435,+!p2@Hoxd8!0.86!6.21!Hoxd8;;chr2:104966933..104966966,+!p3@Wt1!0.86!6.21!Wt1;;chr19:59533139..59533152,+!p2@Emx2!0.86!6.21!Emx2;;chr14:98569030..98569059,-!p3@Dach1!0.85!31.03!Dach1;;chr14:98568761..98568814,-!p2@Dach1!0.83!42.28!Dach1;;chr13:72766250..72766273,+!p1@Irx2!0.83!9.12!Irx2;;chr19:59532915..59532940,+!p5@Emx2!0.83!5.82!Emx2;;chr2:74560109..74560131,+!p1@Hoxd4!0.83!5.82!Hoxd4;;chr2:74529998..74530020,+!p2@Hoxd10!0.83!5.82!Hoxd10;;chr5:115421065..115421088,-!p1@Hnf1a!0.83!5.82!Hnf1a;;chr19:5560600..5560617,-!p1@Ovol1!0.82!6.98!Ovol1;;chr10:102491237..102491291,-!p2@Alx1!0.82!5.62!Alx1;;chr1:189432881..189432903,+!p2@Esrrg!0.82!5.62!Esrrg;;chr11:85646303..85646329,+!p1@Tbx2!0.81!38.79!Tbx2;;chr10:119913546..119913583,-!p3@Hmga2!0.81!12.03!Hmga2;;chr11:96160360..96160397,+!p3@Hoxb6!0.81!5.43!Hoxb6;;chr6:97879817..97879857,+!p2@Mitf!0.81!5.43!Mitf;;chr1:19202185..19202187,+!p9@Tfap2b!0.81!5.43!Tfap2b;;chr2:74536050..74536065,+!p2@Hoxd9!0.81!5.43!Hoxd9;;chr16:94085471..94085495,+!p1@Sim2!0.81!5.43!Sim2;;chr7:77505617..77505632,-!p1@Nr2f2!0.80!268.24!Nr2f2;;chr11:96132637..96132652,+!p1@Hoxb9!0.79!5.24!Hoxb9;;chr10:102491405..102491416,-!p1@Alx1!0.79!5.24!Alx1;;chr2:105003277..105003280,+!p5@Wt1!0.79!5.24!Wt1;;chr19:59533163..59533185,+!p3@Emx2!0.79!5.24!Emx2;;chr2:103143336..103143367,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r8:108160490..108160512,+!p2@Ctcf!0.26!12.99!Ctcf;;chr4:49534086..49534168,+!p1@Zfp189!0.26!11.25!Zfp189;;chr14:65977498..65977528,+!p1@Zfp395!0.26!10.47!Zfp395;;chr5:24107779..24107825,-!p1@Smarcd3!0.26!10.47!Smarcd3;;chr11:99092233..99092273,-!p2@Smarce1!0.26!7.18!Smarce1;;chr9:96159665..96159680,+!p3@Tfdp2!0.26!6.79!Tfdp2;;chr6:97757008..97757061,+!p1@Mitf!0.26!6.40!Mitf;;chr7:105851808..105851822,+!p3@Prkrir!0.26!5.04!Prkrir;;chr9:63869802..63869815,-!p3@Smad6!0.26!2.52!Smad6;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.26!2.13!Zfhx3;;chr5:104183237..104183248,+!p7@Aff1!0.26!1.94!Aff1;;chr4:122911056..122911065,+!p2@Heyl!0.26!1.75!Heyl;;chr12:37835120..37835133,+!p2@Meox2!0.26!1.55!Meox2;;chr18:76219161..76219176,+!p4@Zbtb7c!0.26!1.36!Zbtb7c;;chr16:43619156..43619171,+!p16@Zbtb20!0.26!1.36!Zbtb20;;chr2:127308277..127308313,-!p4@Kcnip3!0.26!1.16!Kcnip3;;chr9:32503590..32503680,+!p1@Ets1!0.25!58.77!Ets1;;chr6:47827642..47827707,+!p1@Zfp282!0.25!16.49!Zfp282;;chr11:50641183..50641244,-!p1@Zfp354c!0.25!12.03!Zfp354c;;chr7:30568977..30569047,+!p1@Zfp30!0.25!8.34!Zfp30;;chr13:56804721..56804792,+!p2@Smad5!0.25!7.56!Smad5;;chr13:44826095..44826185,+!p4@Jarid2!0.25!7.37!Jarid2;;chr10:20032330..20032345,+!p3@Bclaf1!0.25!6.98!Bclaf1;;chr4:120624269..120624302,-!p1@Zfp69!0.25!5.04!Zfp69;;chr3:51081199..51081228,-!p3@Elf2!0.25!5.04!Elf2;;chr15:102034446..102034506,+!p2@Zfp740!0.25!4.85!Zfp740;;chr1:135320962..135320981,-!p2@Sox13!0.25!4.65!Sox13;;chr2:152223881..152223933,-!p3@Sox12!0.25!4.65!Sox12;;chr10:79390075..79390115,+!p2@Arid3a!0.25!4.65!Arid3a;;chr11:98789099..98789124,+!p3@Rara!0.25!4.27!Rara;;chr8:90483459..90483475,-!p1@Zfp423!0.25!3.69!Zfp423;;chr9:63869751..63869767,-!p1@Smad6!0.25!3.49!Smad6;;chr13:15555670..15555771,+!p2@Gli3!0.25!3.30!Gli3;;chr18:14130694..14130697,-!p2@Zfp521!0.25!2.91!Zfp521;;chr7:135019147..135019187,-!p3@Zfp668!0.25!2.72!Zfp668;;chr4:154010940..154010962,-!p3@Prdm16!0.25!2.72!Prdm16;;chr12:25257141..25257173,+!p1@Grhl1!0.25!2.52!Grhl1;;chr4:45024818..45024846,-!p4@Zbtb5!0.25!2.13!Zbtb5;;chr2:152223586..152223604,-!p5@Sox12!0.25!1.55!Sox12;;chr18:65741911..65741929,+!p3@Zfp532!0.25!1.36!Zfp532;;chr6:37391910..37391928,-!p3@Creb3l2!0.25!0.97!Creb3l2;;chr7:119885539..119885574,+!p3@Tead1!0.25!0.78!Tead1;;chr6:52167434..52167450,-!p3@Hoxa7!0.25!0.78!Hoxa7;;chr6:83020355..83020371,-!p1@Tlx2!0.25!0.78!Tlx2;;chr2:104966636..104966641,+!p12@Wt1!0.25!0.78!Wt1;;chr2:104966983..104966990,+!p11@Wt1!0.25!0.78!Wt1;;chr2:33496386..33496410,-!p1@Lmx1b!0.25!0.78!Lmx1b;;chr12:3806003..3806031,+!p11@Dnmt3a!0.25!0.78!Dnmt3a;;chr12:77278238..77278252,-!p1@Esr2!0.25!0.78!Esr2;;chr14:17408022..17408043,-!p6@Rarb!0.25!0.78!Rarb;;chr13:40826100..40826108,-!p10@Tfap2a!0.25!0.78!Tfap2a;;chr15:102821007..102821021,+!p2@Hoxc8!0.25!0.78!Hoxc8;;chr15:102820946..102820961,+!p3@Hoxc8!0.25!0.78!Hoxc8;;chr16:43247391..43247422,+!p12@Zbtb20!0.25!0.78!Zbtb20;;chr17:86087581..86087588,-!p2@Six2!0.25!0.78!Six2;;chr16:25801993..25802014,+!p1@Trp63!0.25!0.78!Trp63;;chr19:44831420..44831432,+!p3@Pax2!0.25!0.78!Pax2;;chr3:29911808..29911833,-!p8@Mecom!0.25!0.78!Mecom;;chr2:74535720..74535731,+!p6@Hoxd9!0.25!0.78!Hoxd9;;chr10:5734660..5734670,-!p7@Esr1!0.25!0.78!Esr1;;chr10:5734582..5734595,-!p10@Esr1!0.25!0.78!Esr1;;chr10:5734473..5734489,-!p5@Esr1!0.25!0.78!Esr1;;chr11:96143545..96143556,+!p6@Hoxb8!0.25!0.78!Hoxb8;;chr11:96880072..96880079,+!p1@Sp6!0.25!0.78!Sp6;;chr10:119913954..119913972,-!p8@Hmga2!0.25!0.78!Hmga2;;chr17:28314075..28314159,+!p1@Zfp523!0.24!18.23!Zfp523;;chrX:98449492..98449510,+!p1@Foxo4!0.24!15.90!Foxo4;;chr13:30077847..30077906,-!p1@E2f3!0.24!11.44!E2f3;;chr7:11080671..11080750,-!p1@Zik1!0.24!10.28!Zik1;;chr12:112088483..112088512,+!p1@Zfp839!0.24!8.53!Zfp839;;chr10:79389784..79389833,+!p1@Arid3a!0.24!7.76!Arid3a;;chr18:69504195..69504213,+!p4@Tcf4!0.24!6.40!Tcf4;;chr4:133310175..133310212,-!p5@Arid1a!0.24!4.27!Arid1a;;chr7:30875418..30875454,-!p2@Zfp566,p2@Zfp82!0.24!3.69!Zfp566;;chr11:44430788..44430804,+!p3@Ebf1!0.24!3.10!Ebf1;;chr5:77524231..77524245,-!p3@Hopx!0.24!3.10!Hopx;;chr13:44826650..44826661,+!p8@Jarid2!0.24!1.94!Jarid2;;chr18:83079981..83080037,+!p6@Zfp516!0.24!1.94!Zfp516;;chr8:109868335..109868338,+!p3@Nfat5!0.24!1.55!Nfat5;;chr9:21420812..21420815,+!p6@Smarca4!0.24!1.55!Smarca4;;chr7:37483231..37483263,+!p2@Tshz3!0.24!1.55!Tshz3;;chr15:75771423..75771445,+!p2@Zfp623!0.24!1.55!Zfp623;;chr13:37917863..37917872,+!p14@Rreb1!0.24!1.36!Rreb1;;chr5:125538905..125538910,-!p4@Ncor2!0.24!1.16!Ncor2;;chr11:101646480..101646496,-!p4@Etv4!0.24!1.16!Etv4;;chr13:78338288..78338309,-!p7@Nr2f1!0.24!0.97!Nr2f1;;chr12:25780945..25780961,-!p1@Id2!0.23!257.57!Id2;;chr15:99532709..99532743,+!p1@Smarcd1!0.23!39.37!Smarcd1;;chr17:87153240..87153254,+!p1@Epas1!0.23!29.87!Epas1;;chr16:50432467..50432522,-!p1@Bbx!0.23!29.48!Bbx;;chr13:96095213..96095255,+!p1@Zbed3!0.23!22.69!Zbed3;;chr10:79862134..79862173,-!p3@Mbd3!0.23!11.64!Mbd3;;chr17:71199121..71199165,-!p2@Tgif1!0.23!10.28!Tgif1;;chr15: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12834..5912852,-!p2@Dpf2!0.20!2.91!Dpf2;;chr1:52176406..52176433,+!p2@Stat1!0.20!2.72!Stat1;;chr4:128483731..128483757,-!p4@Zfp362!0.20!2.52!Zfp362;;chr15:102087880..102087927,-!p2@Rarg!0.20!2.52!Rarg;;chr17:47278081..47278103,+!p1@Trerf1!0.20!2.52!Trerf1;;chr2:153475381..153475419,+!p3@Dnmt3b!0.20!2.13!Dnmt3b;;chr1:120879128..120879183,-!p3@Gli2!0.20!1.94!Gli2;;chr1:52065454..52065495,+!p1@Stat4!0.20!1.55!Stat4;;chr8:72498017..72498059,-!p13@Gatad2a!0.20!1.55!Gatad2a;;chr15:102087737..102087801,-!p3@Rarg!0.20!1.55!Rarg;;chr7:119822915..119822936,+!p5@Tead1!0.20!1.55!Tead1;;chr2:30700788..30700824,+!p2@Prrx2!0.20!1.36!Prrx2;;chr17:32525943..32525992,-!p4@Wiz!0.20!1.36!Wiz;;chr4:151363123..151363134,-!p2@Thap3!0.20!1.36!Thap3;;chr14:65568651..65568657,-!p4@Hmbox1!0.20!1.36!Hmbox1;;chr3:130813736..130813752,+!p3@Lef1!0.20!1.16!Lef1;;chr4:154010228..154010244,-!p4@Prdm16!0.20!1.16!Prdm16;;chr9:32348906..32348920,-!p3@Fli1!0.20!1.16!Fli1;;chr6:52154386..52154407,-!p2@Hoxa5!0.20!0.97!Hoxa5;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.20!0.97!Hmga1;;chr4:87678639..87678653,-!p11@Mllt3!0.20!0.97!Mllt3;;chr2:77357593..77357606,-!p6@Zfp385b!0.20!0.78!Zfp385b;;chr3:130813557..130813582,+!p5@Lef1!0.20!0.78!Lef1;;chr5:120121262..120121282,+!p6@Tbx3!0.20!0.78!Tbx3;;chr6:47998855..47998863,-!p5@Zfp777!0.20!0.78!Zfp777;;chr6:85137505..85137517,+!p2@Emx1!0.20!0.58!Emx1;;chr5:120130377..120130432,+!p10@Tbx3!0.20!0.58!Tbx3;;chr5:120120834..120120845,+!p8@Tbx3!0.20!0.58!Tbx3;;chr2:9811653..9811662,-!p8@Gata3!0.20!0.58!Gata3;;chr4:154010882..154010889,-!p10@Prdm16!0.20!0.58!Prdm16;;chr3:32264814..32264835,-!p5@Zmat3!0.20!0.58!Zmat3;;chr3:30039329..30039355,-!p5@Mecom!0.20!0.58!Mecom;;chr3:130813586..130813604,+!p7@Lef1!0.20!0.58!Lef1;;chr2:74565306..74565327,+!p2@Hoxd4!0.20!0.58!Hoxd4;;chr16:30064437..30064449,+!p11@Hes1!0.20!0.58!Hes1;;chr1:57028125..57028149,-!p2@Satb2!0.20!0.58!Satb2;;chr1:189432634..189432643,+!p8@Esrrg!0.20!0.58!Esrrg;;chr1:186556307..186556318,-!p7@Hlx!0.20!0.58!Hlx;;chr1:92949751..92949769,+!p5@Lrrfip1!0.20!0.58!Lrrfip1;;chr1:19199221..19199234,+!p6@Tfap2b!0.20!0.58!Tfap2b;;chr8:94881686..94881700,+!p4@Irx5!0.20!0.58!Irx5;;chr9:63869510..63869530,-!p10@Smad6!0.20!0.58!Smad6;;chr7:38554684..38554696,-!p10@Zfp536!0.20!0.58!Zfp536;;chr9:77899745..77899755,+!p1@Gcm1!0.20!0.58!Gcm1;;chr7:77511928..77511937,-!p12@Nr2f2!0.20!0.58!Nr2f2;;chr10:5734717..5734727,-!p12@Esr1!0.20!0.58!Esr1;;chr11:95170996..95171026,-!p3@Myst2!0.20!0.58!Myst2;;chr11:44431053..44431060,+!p14@Ebf1!0.20!0.58!Ebf1;;chr10:119913974..119913992,-!p9@Hmga2!0.20!0.58!Hmga2;;chr11:96145537..96145556,+!p6@Hoxb7!0.20!0.58!Hoxb7;;chr11:69749396..69749433,+!p1@Ybx2!0.20!0.58!Ybx2;;chr11:101755710..101755715,-!p2@Meox1!0.20!0.58!Meox1;;chr11:96160098..96160112,+!p8@Hoxb6!0.20!0.58!Hoxb6;;chr10:30522660..30522671,-!p10@Ncoa7!0.20!0.58!Ncoa7;;chr12:12947406..12947418,-!p5@Mycn!0.20!0.58!Mycn;;chr12:87702062..87702081,+!p4@Esrrb!0.20!0.58!Esrrb;;chr13:72766234..72766243,+!p3@Irx2!0.20!0.58!Irx2;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!0.20!0.58!Insm2;;chr15:37163065..37163092,+!p4@Grhl2!0.20!0.58!Grhl2;;chr13:40826236..40826248,-!p8@Tfap2a!0.20!0.58!Tfap2a;;chr15:102839948..102839975,+!p3@Hoxc6!0.20!0.58!Hoxc6;;chr15:102839912..102839938,+!p5@Hoxc6!0.20!0.58!Hoxc6;;chr13:40824310..40824314,-!p6@Tfap2a!0.20!0.58!Tfap2a;;chr15:37163041..37163061,+!p5@Grhl2!0.20!0.58!Grhl2;;chr6:86475924..86475935,-!p2@Pcbp1!0.19!22.89!Pcbp1;;chr12:3807017..3807063,+!p1@Dnmt3a!0.19!22.69!Dnmt3a;;chr13:44826722..44826742,+!p1@Jarid2!0.19!21.92!Jarid2;;chr5:46248712..46248750,-!p1@Lcorl!0.19!20.95!Lcorl;;chr11:3189883..3189925,+!p1@Patz1!0.19!18.62!Patz1;;chr16:4559608..4559681,-!p1@Tfap4!0.19!10.86!Tfap4;;chr4:128483534..128483613,-!p1@Zfp362!0.19!9.12!Zfp362;;chr7:5003165..5003203,+!p2@Zfp580!0.19!6.98!Zfp580;;chr11:50872733..50872809,+!p1@Zfp354a!0.19!5.62!Zfp354a;;chr13:30076168..30076222,-!p2@E2f3!0.19!5.62!E2f3;;chr5:104121453..104121479,+!p4@Aff1!0.19!5.62!Aff1;;chr13:37918773..37918818,+!p3@Rreb1!0.19!5.24!Rreb1;;chr18:69504123..69504155,+!p5@Tcf4!0.19!4.27!Tcf4;;chr16:84835315..84835342,+!p3@Gabpa!0.19!4.27!Gabpa;;chr7:28764153..28764173,-!p2@Zfp780b!0.19!4.07!Zfp780b;;chr2:44966659..44966675,-!p7@Zeb2!0.19!3.30!Zeb2;;chr10:114821393..114821431,-!p5@Thap2!0.19!3.10!Thap2;;chrX:34443339..34443348,-!p2@Nkrf!0.19!2.91!Nkrf;;chr18:75528166..75528170,+!p3@Smad7!0.19!2.72!Smad7;;chr10:93610727..93610754,+!p2@Nr2c1!0.19!2.72!Nr2c1;;chr3:152058408..152058453,+!p5@Gm8261,p5@Zzz3!0.19!2.33!Zzz3;;chr5:104182963..104182982,+!p5@Aff1!0.19!2.13!Aff1;;chr4:54960387..54960415,+!p4@Zfp462!0.19!2.13!Zfp462;;chrX:103124736..103124747,-!p6@Atrx!0.19!1.75!Atrx;;chr7:25862363..25862382,+!p2@Zfp574!0.19!1.75!Zfp574;;chr7:46773162..46773172,+!p2@Zfp619!0.19!1.55!Zfp619;;chr7:4946900..4946921,-!p5@Zfp579!0.19!1.55!Zfp579;;chr7:134376558..134376587,+!p2@Zfp553!0.19!1.55!Zfp553;;chr9:110034493..110034502,+!p2@Smarcc1!0.19!1.36!Smarcc1;;chr11:99092280..99092302,-!p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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011512
 |is_obsolete=
-|library_ids=CNhs11001
+|library_id=CNhs11001
+|library_id_phase_based=2:CNhs11001
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1288
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1288
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E18.CNhs11001.1288-20C7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E18.CNhs11001.1288-20C7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E18.CNhs11001.1288-20C7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E18.CNhs11001.1288-20C7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E18.CNhs11001.1288-20C7.mm9.nobarcode.rdna.fa.gz
 |name=kidney, embryo E18
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11001,LSID730,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.416615448070281,0.0202932774506214,0.00190081328948414,0,0.142359732304287,0,0.346088656301301,0,0.138077195978515,0,0,0.38393789876236,0,0,0,0,0,0,0.143306689507046,0,0,0,0,0,0,0,0,0,0,0,0,0,0.163136792229981,0,0.294413851021516,0,0.294413851021516,0.00268270257914661,0.105484220209742,0,-0.239820866777957,0.0754820668860733,-0.0204721532908767,0,0,0,0,0,0,0,0,0,0,0,0,0.402271591595461,0,0,0,0,0.00065503170907194,0,-0.0238390353011091,0.0769870445726752,0.0769870445726752,0.0525058311074236,0.145371667633311,0.0618318829811866,-0.158091042771083,0.0920162588451266,0,0.0769870445726752,0,0,0,0,0.0220382462043781,-0.0932325290255124,-0.189098900653073,0.06352813746438,0,0,0,0,0,0.294413851021516,-0.0864205139534754,0.0152480046836425,-0.0990394623870784,0.0583957403865942,0,0,0,0.0384935222863376
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1288-20C7;search_select_hide=table117:1288-20C7
-|DRA_sample_Accession=CAGE@DRS008871
-|accession_numbers=DRX009008;DRR009882;DRZ001307;DRZ002690;CAGE
-|library_id=CNhs11001
 }}

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From FANTOM5_SSTAR

Latest revision as of 18:47, 4 June 2020

CNhs11001

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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