FF:1385-42H1: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	kidney, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11203
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	kidney
dev stage	30 days neonate
sex	mixture
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005811

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11203		CAGE		DRX009013		DRR009887

Accession ID Mm9

Library id		BAM		CTSS
CNhs11203		DRZ001312		DRZ002695

Accession ID Mm10

Library id		BAM		CTSS
CNhs11203		DRZ012662		DRZ014045

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

CNhs11203

0	0
1	0
10	0
100	0
1000	0.0505
1001	0.0849
1002	0.276
1003	-0.0712
1004	0
1005	0.0569
1006	-0.0258
1007	-0.0382
1008	0
1009	0.0796
101	-0.101
1010	0
1011	-0.0212
1012	0
1013	0.44
1014	-0.0851
1015	-0.279
1016	-0.171
1017	0
1018	0.0505
1019	0
102	0
1020	0
1021	0
1022	0.46
1023	0
1024	0.151
1025	0.0347
1026	0
1027	0
1028	0
1029	0.0266
103	-0.0461
1030	0
1031	-0.0667
1032	0.331
1033	-0.016
1034	0.55
1035	0.0505
1036	-0.181
1037	0
1038	0.0634
1039	0.563
104	0
1040	0.0767
1041	0.0958

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: CNhs11203

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.44
MA0003.1	MA0003.1	0.167
MA0004.1	MA0004.1	0.368
MA0006.1	MA0006.1	0.0259
MA0007.1	MA0007.1	0.161
MA0009.1	MA0009.1	0.2
MA0014.1	MA0014.1	0.125
MA0017.1	MA0017.1	2.75044e-24
MA0018.2	MA0018.2	4.3287e-4
MA0019.1	MA0019.1	0.237
MA0024.1	MA0024.1	3.23945e-6
MA0025.1	MA0025.1	0.108
MA0027.1	MA0027.1	0.28
MA0028.1	MA0028.1	0.766
MA0029.1	MA0029.1	0.737
MA0030.1	MA0030.1	0.00707
MA0031.1	MA0031.1	3.96572e-5
MA0035.2	MA0035.2	0.00833
MA0038.1	MA0038.1	0.574
MA0039.2	MA0039.2	0.00208
MA0040.1	MA0040.1	0.183
MA0041.1	MA0041.1	0.484
MA0042.1	MA0042.1	0.491
MA0043.1	MA0043.1	0.0109
MA0046.1	MA0046.1	3.87088e-152
MA0047.2	MA0047.2	2.44663e-4
MA0048.1	MA0048.1	0.775
MA0050.1	MA0050.1	0.341
MA0051.1	MA0051.1	0.163
MA0052.1	MA0052.1	0.0147
MA0055.1	MA0055.1	0.232
MA0057.1	MA0057.1	0.395
MA0058.1	MA0058.1	0.18
MA0059.1	MA0059.1	0.573
MA0060.1	MA0060.1	0.166
MA0061.1	MA0061.1	0.431
MA0062.2	MA0062.2	0.321
MA0065.2	MA0065.2	4.11967e-14
MA0066.1	MA0066.1	0.885
MA0067.1	MA0067.1	0.593
MA0068.1	MA0068.1	0.258
MA0069.1	MA0069.1	0.451
MA0070.1	MA0070.1	0.949
MA0071.1	MA0071.1	7.42148e-4
MA0072.1	MA0072.1	0.0724
MA0073.1	MA0073.1	0.787
MA0074.1	MA0074.1	0.241
MA0076.1	MA0076.1	0.89
MA0077.1	MA0077.1	0.165
MA0078.1	MA0078.1	0.00219
MA0079.2	MA0079.2	0.245
MA0080.2	MA0080.2	0.234
MA0081.1	MA0081.1	0.591
MA0083.1	MA0083.1	0.01
MA0084.1	MA0084.1	0.643
MA0087.1	MA0087.1	0.16
MA0088.1	MA0088.1	0.337
MA0090.1	MA0090.1	0.00279
MA0091.1	MA0091.1	0.0717
MA0092.1	MA0092.1	0.0915
MA0093.1	MA0093.1	0.388
MA0099.2	MA0099.2	0.79
MA0100.1	MA0100.1	0.0189
MA0101.1	MA0101.1	0.558
MA0102.2	MA0102.2	0.805
MA0103.1	MA0103.1	0.00205
MA0104.2	MA0104.2	0.105
MA0105.1	MA0105.1	0.27
MA0106.1	MA0106.1	0.535
MA0107.1	MA0107.1	0.521
MA0108.2	MA0108.2	0.00314
MA0111.1	MA0111.1	0.476
MA0112.2	MA0112.2	0.0101
MA0113.1	MA0113.1	0.11
MA0114.1	MA0114.1	8.99282e-32
MA0115.1	MA0115.1	4.80393e-4
MA0116.1	MA0116.1	0.468
MA0117.1	MA0117.1	0.564
MA0119.1	MA0119.1	0.0679
MA0122.1	MA0122.1	0.442
MA0124.1	MA0124.1	0.43
MA0125.1	MA0125.1	0.913
MA0131.1	MA0131.1	0.583
MA0135.1	MA0135.1	0.0878
MA0136.1	MA0136.1	0.0813
MA0137.2	MA0137.2	0.582
MA0138.2	MA0138.2	0.504
MA0139.1	MA0139.1	0.255
MA0140.1	MA0140.1	0.0111
MA0141.1	MA0141.1	1.70506e-10
MA0142.1	MA0142.1	0.00237
MA0143.1	MA0143.1	0.998
MA0144.1	MA0144.1	0.17
MA0145.1	MA0145.1	3.55991e-4
MA0146.1	MA0146.1	0.0709
MA0147.1	MA0147.1	0.0514
MA0148.1	MA0148.1	5.01966e-4
MA0149.1	MA0149.1	0.0246
MA0150.1	MA0150.1	0.0184
MA0152.1	MA0152.1	0.0949
MA0153.1	MA0153.1	1.77109e-66
MA0154.1	MA0154.1	0.129
MA0155.1	MA0155.1	0.537
MA0156.1	MA0156.1	0.359
MA0157.1	MA0157.1	0.00104
MA0159.1	MA0159.1	0.0108
MA0160.1	MA0160.1	1.5805e-6
MA0162.1	MA0162.1	0.242
MA0163.1	MA0163.1	0.759
MA0164.1	MA0164.1	0.417
MA0258.1	MA0258.1	0.0203
MA0259.1	MA0259.1	0.163

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: CNhs11203

Novel motif	Logo	P-value
1	1	0.904
10	10	0.734
100	100	0.882
101	101	0.689
102	102	0.221
103	103	0.0975
104	104	0.452
105	105	0.66
106	106	0.143
107	107	0.17
108	108	0.0508
109	109	0.00748
11	11	0.238
110	110	0.257
111	111	0.963
112	112	0.118
113	113	0.728
114	114	0.829
115	115	0.937
116	116	0.392
117	117	0.596
118	118	0.275
119	119	0.0786
12	12	0.91
120	120	0.406
121	121	0.856
122	122	0.0785
123	123	0.041
124	124	0.22
125	125	0.159
126	126	0.304
127	127	0.237
128	128	0.178
129	129	0.736
13	13	3.39565e-5
130	130	0.173
131	131	0.687
132	132	0.871
133	133	0.193
134	134	0.552
135	135	0.43
136	136	0.00412
137	137	0.0954
138	138	0.125
139	139	0.729
14	14	0.179
140	140	0.265
141	141	0.81
142	142	0.836
143	143	0.362
144	144	0.0742
145	145	0.178
146	146	0.257
147	147	0.411
148	148	0.883
149	149	0.228
15	15	0.274
150	150	0.198
151	151	0.82
152	152	0.0366
153	153	0.652
154	154	0.835
155	155	0.899
156	156	0.0153
157	157	0.213
158	158	0.596
159	159	0.659
160	160	0.57
161	161	0.437
162	162	0.344
163	163	0.311
164	164	0.997
165	165	0.00852
166	166	0.624
167	167	0.818
168	168	0.799
169	169	0.0137
17	17	0.058
18	18	0.049
19	19	0.0244
2	2	0.109
20	20	0.933
21	21	0.817
22	22	0.0252
23	23	0.633
24	24	0.114
25	25	0.771
26	26	0.515
27	27	0.502
28	28	0.512
29	29	0.715
3	3	0.462
30	30	0.157
31	31	0.598
32	32	0.319
33	33	0.897
34	34	0.508
35	35	0.421
36	36	0.668
37	37	0.0264
38	38	0.444
39	39	0.386
4	4	0.673
40	40	0.215
41	41	0.36
42	42	0.611
43	43	0.506
44	44	0.669
45	45	0.11
46	46	0.826
47	47	0.381
48	48	0.184
49	49	0.433
5	5	0.513
50	50	0.728
51	51	0.798
52	52	0.0396
53	53	0.945
54	54	0.975
55	55	0.995
56	56	0.993
57	57	0.442
58	58	0.291
59	59	0.717
6	6	0.996
60	60	0.0376
61	61	0.92
62	62	0.381
63	63	0.262
64	64	0.951
65	65	0.349
66	66	0.713
67	67	0.0223
68	68	0.947
69	69	0.486
7	7	0.188
70	70	0.28
71	71	0.766
72	72	0.437
73	73	0.0356
74	74	0.232
75	75	0.58
76	76	0.375
77	77	0.0542
78	78	0.0987
79	79	0.37
8	8	0.755
80	80	0.465
81	81	0.366
82	82	0.297
83	83	0.424
84	84	0.0711
85	85	0.061
86	86	0.461
87	87	0.134
88	88	0.58
89	89	0.466
9	9	0.967
90	90	0.612
91	91	0.502
92	92	0.98
93	93	0.548
94	94	0.0652
95	95	0.252
96	96	0.538
97	97	0.384
98	98	0.338
99	99	0.248

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: CNhs11203

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011483 mouse kidney- neonate N30 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011483 (mouse kidney- neonate N30 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@SAMD00005811
+|accession_numbers=CAGE;DRX009013;DRR009887;DRZ001312;DRZ002695;DRZ012662;DRZ014045
 |ancestors_in_anatomy_facet=UBERON:0000468,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 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:88969376..88969395,-!p1@Nr1h4!2.01!101.56!Nr1h4;;chr11:83664365..83664383,+!p1@Hnf1b!1.93!83.17!Hnf1b;;chr2:163372884..163372904,+!p1@Hnf4a!1.87!72.43!Hnf4a;;chr2:24331085..24331100,-!p1@Pax8!1.71!49.85!Pax8;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.67!126.36!Tfcp2l1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.56!44.05!Pou3f3;;chr12:87762578..87762612,+!p1@Esrrb!1.53!33.07!Esrrb;;chr6:52190467..52190500,-!p1@Hoxa10!1.50!30.60!Hoxa10;;chr15:97738692..97738747,-!p1@Vdr!1.49!156.34!Vdr;;chr6:85137520..85137563,+!p1@Emx1!1.49!29.86!Emx1;;chr10:30491690..30491727,-!p5@Ncoa7!1.48!29.37!Ncoa7;;chr6:52176164..52176195,-!p1@Hoxa9!1.45!33.56!Hoxa9;;chr6:38097380..38097407,-!p6@D630045J12Rik!1.45!27.27!D630045J12Rik;;chr11:34108085..34108092,-!p1@Foxi1!1.44!26.41!Foxi1;;chr11:96143666..96143725,+!p1@Hoxb8!1.43!29.49!Hoxb8;;chr5:135582751..135582788,+!p1@Mlxipl!1.42!97.85!Mlxipl;;chr15:102828658..102828678,+!p1@Hoxc6!1.36!21.96!Hoxc6;;chr19:59533221..59533271,+!p1@Emx2!1.35!26.16!Emx2;;chr1:19202352..19202354,+!p2@Tfap2b!1.35!21.59!Tfap2b;;chr5:115421065..115421088,-!p1@Hnf1a!1.30!18.88!Hnf1a;;chr10:22539932..22539956,-!p1@Tcf21!1.29!48.99!Tcf21;;chr2:74529970..74529997,+!p1@Hoxd10!1.28!17.89!Hoxd10;;chr11:96153767..96153822,+!p1@Hoxb6!1.27!27.15!Hoxb6;;chr13:72101178..72101203,-!p1@Irx1!1.17!21.47!Irx1;;chr2:74542680..74542705,+!p6@Hoxd8!1.17!13.82!Hoxd8;;chr8:118231678..118231692,-!p2@Maf!1.15!116.24!Maf;;chr2:74549968..74549996,+!p1@Hoxd3!1.14!15.92!Hoxd3;;chr2:74536026..74536039,+!p1@Hoxd9!1.14!12.71!Hoxd9;;chr2:103143336..103143367,-!p1@Ehf!1.13!20.48!Ehf;;chr1:19199236..19199258,+!p1@Tfap2b!1.13!12.59!Tfap2b;;chr1:189432881..189432903,+!p2@Esrrg!1.13!12.59!Esrrg;;chr6:52190840..52190853,-!p5@Hoxa10!1.11!11.97!Hoxa10;;chr2:103123925..103123959,-!p3@Ehf!1.06!10.61!Ehf;;chr6:97879817..97879857,+!p2@Mitf!1.04!9.87!Mitf;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!1.03!9.75!Sim1;;chr2:74543202..74543213,+!p3@Hoxd8!1.03!9.62!Hoxd8;;chr16:43363968..43364001,+!p7@Zbtb20!1.01!17.03!Zbtb20;;chr6:52167459..52167492,-!p1@Hoxa7!1.01!11.23!Hoxa7;;chr6:38097421..38097440,-!p7@D630045J12Rik!1.01!9.13!D630045J12Rik;;chr2:74542918..74542971,+!p1@Hoxd8!1.00!13.82!Hoxd8;;chr2:74543397..74543435,+!p2@Hoxd8!1.00!9.01!Hoxd8;;chr16:38294860..38294924,-!p1@Nr1i2!1.00!9.01!Nr1i2;;chr1:189432907..189432926,+!p3@Esrrg!0.99!8.88!Esrrg;;chr11:90252223..90252240,-!p1@Hlf!0.98!73.42!Hlf;;chr19:28754692..28754757,-!p1@Glis3!0.98!36.53!Glis3;;chr1:19202185..19202187,+!p9@Tfap2b!0.98!8.51!Tfap2b;;chr6:52163319..52163342,-!p1@Hoxa3!0.97!12.34!Hoxa3;;chr2:163372869..163372882,+!p3@Hnf4a!0.97!8.27!Hnf4a;;chr3:94176733..94176794,+!p1@Rorc!0.95!63.55!Rorc;;chr1:189433521..189433548,+!p5@Esrrg!0.94!7.65!Esrrg;;chr4:154010409..154010466,-!p2@Prdm16!0.93!18.02!Prdm16;;chr11:96147952..96147967,+!p1@Hoxb7!0.91!9.01!Hoxb7;;chr2:74543103..74543135,+!p4@Hoxd8!0.91!7.16!Hoxd8;;chr6:90412582..90412601,+!p1@Klf15!0.90!34.30!Klf15;;chr2:9800207..9800234,-!p1@Gata3!0.90!22.21!Gata3;;chr2:74529998..74530020,+!p2@Hoxd10!0.90!7.03!Hoxd10;;chr11:84339016..84339044,-!p1@Lhx1!0.90!7.03!Lhx1;;chr6:52184901..52184959,-!p2@Hoxa10!0.90!6.91!Hoxa10;;chr8:118231723..118231740,-!p1@Maf!0.89!158.69!Maf;;chr9:106355684..106355744,+!p5@Pcbp4!0.89!10.49!Pcbp4;;chr3:3508024..3508069,+!p2@Hnf4g!0.89!6.79!Hnf4g;;chr2:74535796..74535808,+!p3@Hoxd9!0.88!6.66!Hoxd9;;chr2:74542589..74542602,+!p8@Hoxd8!0.88!6.54!Hoxd8;;chr11:83666422..83666446,+!p4@Hnf1b!0.88!6.54!Hnf1b;;chr14:22807107..22807119,-!p2@Zfp503!0.86!28.50!Zfp503;;chr3:30408674..30408716,-!p2@Mecom!0.86!10.61!Mecom;;chr2:74536050..74536065,+!p2@Hoxd9!0.86!6.29!Hoxd9;;chr6:85137505..85137517,+!p2@Emx1!0.86!6.17!Emx1;;chr8:118231705..118231722,-!p3@Maf!0.85!51.33!Maf;;chr15:85566184..85566238,+!p1@Ppara!0.85!9.38!Ppara;;chr15:35225845..35225867,+!p1@Osr2!0.84!15.67!Osr2;;chr4:120488308..120488366,-!p1@Nfyc!0.83!35.29!Nfyc;;chr8:94325321..94325366,-!p1@Irx3!0.82!14.31!Irx3;;chr11:96145450..96145517,+!p2@Hoxb7!0.82!8.64!Hoxb7;;chr15:85602581..85602598,+!p8@Ppara!0.82!5.68!Ppara;;chr19:44831390..44831414,+!p1@Pax2!0.82!5.68!Pax2;;chr16:94085471..94085495,+!p1@Sim2!0.82!5.68!Sim2;;chr14:22807083..22807104,-!p1@Zfp503!0.80!101.93!Zfp503;;chr2:77357622..77357704,-!p1@Zfp385b!0.79!14.68!Zfp385b;;chr19:25746898..25746910,+!p1@Dmrt2!0.79!8.02!Dmrt2;;chr2:160698288..160698358,-!p3@Zhx3!0.78!16.54!Zhx3;;chr13:72766250..72766273,+!p1@Irx2!0.78!8.14!Irx2;;chr12:87702062..87702081,+!p4@Esrrb!0.78!5.06!Esrrb;;chr6:52167434..52167450,-!p3@Hoxa7!0.78!5.06!Hoxa7;;chr11:85646303..85646329,+!p1@Tbx2!0.77!35.29!Tbx2;;chr19:28754600..28754612,-!p2@Glis3!0.77!8.14!Glis3;;chr11:96160426..96160443,+!p2@Hoxb6!0.77!4.94!Hoxb6;;chr12:75002389..75002406,+!p4@Hif1a!0.77!4.94!Hif1a;;chr1:137155026..137155042,-!p1@Elf3!0.76!30.11!Elf3;;chr11:100800641..100800669,-!p3@Stat3!0.76!8.64!Stat3;;chr2:104966766..104966786,+!p1@Wt1!0.76!7.90!Wt1;;chr4:107107224..107107259,+!p2@Glis1!0.76!4.69!Glis1;;chr14:17407878..17407926,-!p1@Rarb!0.75!11.11!Rarb;;chr11:83664334..83664353,+!p2@Hnf1b!0.75!4.57!Hnf1b;;chr15:102828642..102828653,+!p2@Hoxc6!0.74!4.44!Hoxc6;;chr16:4594740..4594759,+!p1@Glis2!0.73!56.15!Glis2;;chr16:43363190..43363242,+!p2@Zbtb20!0.73!14.81!Zbtb20;;chr3:30408603..30408668,-!p1@Mecom!0.73!10.98!Mecom;;chr16:43363152..43363186,+!p3@Zbtb20!0.73!10.86!Zbtb20;;chr11:85646427..85646451,+!p4@Tbx2!0.73!8.02!Tbx2;;chr1:57029281..57029326,-!p1@Satb2!0.73!7.16!Satb2;;chr3:128916868..128916890,+!p1@Pitx2!0.73!6.29!Pitx2;;chr19:23215509..23215523,+!p4@Klf9!0.73!5.80!Klf9;;chr10:102491405..102491416,-!p1@Alx1!0.73!4.32!Alx1;;chr13:72101161..72101177,-!p2@Irx1!0.72!6.05!Irx1;;chr6:52195763..52195792,-!p2@Hoxa11!0.72!4.20!Hoxa11;;chr15:81633203..81633215,+!p3@Tef!0.71!6.91!Tef;;chr13:72766279..72766296,+!p2@Irx2!0.71!6.42!Irx2;;chr14:22808697..22808715,-!p4@Zfp503!0.71!4.94!Zfp503;;chr11:100800621..100800633,-!p5@Stat3!0.71!4.94!Stat3;;chr11:83665637..83665671,+!p6@Hnf1b!0.71!4.07!Hnf1b;;chr2:103143315..103143328,-!p2@Ehf!0.71!4.07!Ehf;;chr6:52195795..52195825,-!p1@Hoxa11!0.71!4.07!Hoxa11;;chr10:30375579..30375616,-!p3@Ncoa7!0.70!10.37!Ncoa7;;chr19:23215673..23215753,+!p1@Klf9!0.69!65.03!Klf9;;chr8:79426176..79426275,+!p1@Nr3c2!0.69!21.72!Nr3c2;;chr2:74542882..74542894,+!p10@Hoxd8!0.68!3.83!Hoxd8;;chr11:96143843..96143868,+!p3@Hoxb8!0.68!3.83!Hoxb8;;chr6:85137491..85137504,+!p3@Emx1!0.68!3.83!Emx1;;chr14:22807216..22807231,-!p3@Zfp503!0.67!6.66!Zfp503;;chr11:90250944..90250982,-!p2@Hlf!0.67!6.66!Hlf;;chr2:91035254..91035271,-!p3@Nr1h3!0.67!4.69!Nr1h3;;chr2:74549945..74549965,+!p4@Hoxd3!0.67!3.70!Hoxd3;;chr2:9809357..9809371,-!p2@Gata3!0.67!3.70!Gata3;;chr16:43247391..43247422,+!p12@Zbtb20!0.67!3.70!Zbtb20;;chr10:102491237..102491291,-!p2@Alx1!0.67!3.70!Alx1;;chr2:164829847..164829859,-!p5@Ncoa5!0.67!3.70!Ncoa5;;chr4:107107175..107107204,+!p1@Glis1!0.66!4.44!Glis1;;chr2:74542974..74542986,+!p5@Hoxd8!0.66!3.58!Hoxd8;;chr6:52176144..52176161,-!p2@Hoxa9!0.66!3.58!Hoxa9;;chr12:87762625..87762637,+!p7@Esrrb!0.66!3.58!Esrrb;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.65!6.42!Hoxb2;;chr5:67698263..67698272,+!p3@Slc30a9!0.65!5.68!Slc30a9;;chr7:119885539..119885574,+!p3@Tead1!0.65!3.46!Tead1;;chr11:98614335..98614349,+!p8@Thra!0.65!3.46!Thra;;chr13:72101141..72101158,-!p3@Irx1!0.64!4.32!Irx1;;chr6:52190858..52190873,-!p4@Hoxa10!0.64!3.33!Hoxa10;;chr11:85646341..85646352,+!p3@Tbx2!0.63!7.16!Tbx2;;chr19:28754655..28754673,-!p3@Glis3!0.63!5.31!Glis3;;chr11:96690797..96690813,-!p1@Nfe2l1!0.62!73.30!Nfe2l1;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.62!10.49!D630045J12Rik;;chr18:36441119..36441158,+!p2@Pura!0.62!8.64!Pura;;chr1:120524563..120524591,+!p2@Tfcp2l1!0.62!3.21!Tfcp2l1;;chr15:102797170..102797182,+!p3@Hoxc10!0.62!3.21!Hoxc10;;chr13:99124189..99124205,+!p1@Foxd1!0.61!5.06!Foxd1;;chr8:94325486..94325510,-!p4@Irx3!0.61!4.32!Irx3;;chr15:102797225..102797243,+!p2@Hoxc10!0.61!3.08!Hoxc10;;chr15:85565338..85565355,+!p7@Ppara!0.61!3.08!Ppara;;chr2:74517742..74517758,+!p2@Hoxd11!0.61!3.08!Hoxd11;;chr11:85646469..85646488,+!p5@Tbx2!0.60!4.81!Tbx2;;chr6:52167513..52167549,-!p2@Hoxa7!0.60!4.57!Hoxa7;;chr11:90251852..90251855,-!p4@Hlf!0.60!3.83!Hlf;;chr19:44831420..44831432,+!p3@Pax2!0.60!2.96!Pax2;;chr2:74535720..74535731,+!p6@Hoxd9!0.60!2.96!Hoxd9;;chr1:39250584..39250643,+!p1@Npas2!0.59!17.65!Npas2;;chr13:31898637..31898653,+!p2@Foxc1!0.59!5.68!Foxc1;;chr15:85566051..85566080,+!p4@Ppara!0.59!3.46!Ppara;;chr15:81633165..81633188,+!p2@Tef!0.58!28.01!Tef;;chr4:148275237..148275311,+!p2@Casz1!0.58!13.70!Casz1;;chr14:18493386..18493464,+!p1@Thrb!0.58!12.71!Thrb;;chr6:38097369..38097379,-!p11@D630045J12Rik!0.58!2.84!D630045J12Rik;;chr16:43364012..43364030,+!p22@Zbtb20!0.58!2.84!Zbtb20;;chr19:6996243..6996293,-!p1@Esrra!0.57!37.27!Esrra;;chr16:44173384..44173407,+!p2@Gm608!0.57!8.27!Gm608;;chr3:29912058..29912071,-!p6@Mecom!0.57!3.21!Mecom;;chr2:74550015..74550057,+!p2@Hoxd3!0.57!2.71!Hoxd3;;chr5:134750916..134750921,-!p24@Gtf2i!0.57!2.71!Gtf2i;;chr14:69808725..69808748,+!p1@Nkx3-1!0.57!2.71!Nkx3-1;;chr8:94325814..94325839,-!p2@Irx3!0.56!6.29!Irx3;;chr13:40829137..40829205,-!p1@Tfap2a!0.56!3.08!Tfap2a;;chr15:102797288..102797302,+!p1@Hoxc10!0.56!2.59!Hoxc10;;chr2:103264213..103264233,+!p1@Elf5!0.56!2.59!Elf5;;chr4:133109285..133109308,+!p1@Nr0b2!0.56!2.59!Nr0b2;;chr3:3508005..3508021,+!p3@Hnf4g!0.56!2.59!Hnf4g;;chr17:87153240..87153254,+!p1@Epas1!0.55!62.44!Epas1;;chr13:31650185..31650201,+!p1@Foxq1!0.55!10.86!Foxq1;;chr2:91035197..91035237,-!p1@Nr1h3!0.55!6.05!Nr1h3;;chr17:87153028..87153049,+!p2@Epas1!0.53!63.80!Epas1;;chr13:64253718..64253763,-!p2@Zfp367!0.53!7.40!Zfp367;;chr16:43236133..43236154,+!p17@Zbtb20!0.53!2.84!Zbtb20;;chr4:154010918..154010931,-!p1@Prdm16!0.52!8.14!Prdm16;;chr8:94325273..94325288,-!p5@Irx3!0.52!3.08!Irx3;;chr14:22806778..22806795,-!p5@Zfp503!0.52!2.59!Zfp503;;chr13:40825465..40825469,-!p2@Tfap2a!0.52!2.34!Tfap2a;;chr2:74543143..74543158,+!p9@Hoxd8!0.52!2.34!Hoxd8;;chr2:74543235..74543246,+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+|ffid_belonging_in_development=UBERON:0003104,UBERON:0003918,UBERON:0007687,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011483
 |is_obsolete=
+|library_id=CNhs11203
+|library_id_phase_based=2:CNhs11203
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1385
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1385
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N30.CNhs11203.1385-42H1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N30.CNhs11203.1385-42H1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N30.CNhs11203.1385-42H1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N30.CNhs11203.1385-42H1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N30.CNhs11203.1385-42H1.mm9.nobarcode.rdna.fa.gz
 |name=kidney, neonate N30
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11203,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.429668675415135,0,0,0,0,0,0.203793889486499,0,0.0400572276334659,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.0176623445430252,0,0,0,0,0,0.0505333231410966,0,0,0,0,0,0,0,0.136069145870758,0,0.884424149790413,0,0.92447725002438,0,-0.0123070065985004,-0.0264362361082547,-0.1927275903155,-0.888416548644461,-0.133087371579876,0.0505333231410966,0,0.174231006339549,0,0,0,0,0,0,0,0.372427531883206,0,0.174639280794999,0,0,0,0,0.0325263057443339,0,0.112382164740323,0,0,0,-0.104116407566851,0.162742089469784,-0.0622962249377175,-0.00359337162908763,0.0505333231410966,0,-0.0230164866067692,0.136781266430475,0,0,0,-0.124397439170921,-0.104868264605285,-0.0788315948399074,0.00884870742802735,0,0,0,0.135197340709779,0.136781266430475,-0.00441938025834554,0.174903004497894,-0.0032495557749879,0,0.095794817833365,0,0,0
 |rna_box=42
 |rna_catalog_number=
@@ Line 60: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1385-42H1;search_select_hide=table117:1385-42H1
 }}

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FF:1385-42H1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11203

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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