FF:832-19I1: Difference between revisions

Latest revision as of 19:21, 4 June 2020

Name:	kidney, neonate N20
Species:	Mouse (Mus musculus)
Library ID:	CNhs11113
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	kidney
dev stage	20 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		SAMD00005493

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11113		CAGE		DRX009011		DRR009885

Accession ID Mm9

Library id		BAM		CTSS
CNhs11113		DRZ001310		DRZ002693

Accession ID Mm10

Library id		BAM		CTSS
CNhs11113		DRZ012660		DRZ014043

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

CNhs11113

0	0
1	0
10	0
100	0
1000	0
1001	0.1
1002	0.278
1003	0.0146
1004	0
1005	0
1006	-0.143
1007	-0.0152
1008	0
1009	-0.0572
101	-0.0497
1010	0
1011	0
1012	0
1013	0.376
1014	0
1015	-0.251
1016	-0.138
1017	0
1018	0.0598
1019	0
102	0
1020	0
1021	-0.00939
1022	0.504
1023	0
1024	0.353
1025	0
1026	0
1027	0
1028	0
1029	0.218
103	-0.0424
1030	0
1031	0.00537
1032	0.235
1033	-0.0154
1034	0.281
1035	0
1036	-0.264
1037	0
1038	0.133
1039	0.471
104	0
1040	0.209
1041	0.0598

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: CNhs11113

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.202
MA0003.1	MA0003.1	0.227
MA0004.1	MA0004.1	0.499
MA0006.1	MA0006.1	0.0397
MA0007.1	MA0007.1	0.325
MA0009.1	MA0009.1	0.154
MA0014.1	MA0014.1	0.137
MA0017.1	MA0017.1	1.71076e-20
MA0018.2	MA0018.2	6.36402e-6
MA0019.1	MA0019.1	0.198
MA0024.1	MA0024.1	6.12845e-6
MA0025.1	MA0025.1	0.455
MA0027.1	MA0027.1	0.436
MA0028.1	MA0028.1	0.456
MA0029.1	MA0029.1	0.291
MA0030.1	MA0030.1	0.00357
MA0031.1	MA0031.1	5.74045e-4
MA0035.2	MA0035.2	0.00773
MA0038.1	MA0038.1	0.439
MA0039.2	MA0039.2	0.0145
MA0040.1	MA0040.1	0.366
MA0041.1	MA0041.1	0.488
MA0042.1	MA0042.1	0.85
MA0043.1	MA0043.1	0.00169
MA0046.1	MA0046.1	3.1217e-134
MA0047.2	MA0047.2	3.67272e-4
MA0048.1	MA0048.1	0.4
MA0050.1	MA0050.1	0.135
MA0051.1	MA0051.1	0.277
MA0052.1	MA0052.1	0.00275
MA0055.1	MA0055.1	0.372
MA0057.1	MA0057.1	0.5
MA0058.1	MA0058.1	0.401
MA0059.1	MA0059.1	0.594
MA0060.1	MA0060.1	0.00303
MA0061.1	MA0061.1	0.517
MA0062.2	MA0062.2	0.00853
MA0065.2	MA0065.2	2.36056e-12
MA0066.1	MA0066.1	0.606
MA0067.1	MA0067.1	0.25
MA0068.1	MA0068.1	0.268
MA0069.1	MA0069.1	0.719
MA0070.1	MA0070.1	0.588
MA0071.1	MA0071.1	0.00942
MA0072.1	MA0072.1	0.809
MA0073.1	MA0073.1	0.92
MA0074.1	MA0074.1	0.377
MA0076.1	MA0076.1	0.252
MA0077.1	MA0077.1	0.0748
MA0078.1	MA0078.1	0.00384
MA0079.2	MA0079.2	0.796
MA0080.2	MA0080.2	0.263
MA0081.1	MA0081.1	0.57
MA0083.1	MA0083.1	0.0363
MA0084.1	MA0084.1	0.771
MA0087.1	MA0087.1	0.184
MA0088.1	MA0088.1	0.387
MA0090.1	MA0090.1	0.00147
MA0091.1	MA0091.1	0.291
MA0092.1	MA0092.1	0.0388
MA0093.1	MA0093.1	0.495
MA0099.2	MA0099.2	0.787
MA0100.1	MA0100.1	0.0113
MA0101.1	MA0101.1	0.448
MA0102.2	MA0102.2	0.526
MA0103.1	MA0103.1	8.76532e-4
MA0104.2	MA0104.2	0.0787
MA0105.1	MA0105.1	0.345
MA0106.1	MA0106.1	0.452
MA0107.1	MA0107.1	0.607
MA0108.2	MA0108.2	6.03859e-5
MA0111.1	MA0111.1	0.784
MA0112.2	MA0112.2	0.00699
MA0113.1	MA0113.1	0.144
MA0114.1	MA0114.1	1.31053e-28
MA0115.1	MA0115.1	0.00741
MA0116.1	MA0116.1	0.707
MA0117.1	MA0117.1	0.869
MA0119.1	MA0119.1	0.0478
MA0122.1	MA0122.1	0.265
MA0124.1	MA0124.1	0.444
MA0125.1	MA0125.1	0.326
MA0131.1	MA0131.1	0.269
MA0135.1	MA0135.1	0.554
MA0136.1	MA0136.1	0.0245
MA0137.2	MA0137.2	0.677
MA0138.2	MA0138.2	0.621
MA0139.1	MA0139.1	0.197
MA0140.1	MA0140.1	0.0274
MA0141.1	MA0141.1	1.29342e-8
MA0142.1	MA0142.1	0.0142
MA0143.1	MA0143.1	0.734
MA0144.1	MA0144.1	0.294
MA0145.1	MA0145.1	4.40984e-4
MA0146.1	MA0146.1	0.272
MA0147.1	MA0147.1	0.0466
MA0148.1	MA0148.1	7.65113e-4
MA0149.1	MA0149.1	0.0339
MA0150.1	MA0150.1	0.0906
MA0152.1	MA0152.1	0.0491
MA0153.1	MA0153.1	2.02245e-58
MA0154.1	MA0154.1	0.0509
MA0155.1	MA0155.1	0.399
MA0156.1	MA0156.1	0.219
MA0157.1	MA0157.1	0.0168
MA0159.1	MA0159.1	0.0238
MA0160.1	MA0160.1	8.41754e-5
MA0162.1	MA0162.1	0.2
MA0163.1	MA0163.1	0.888
MA0164.1	MA0164.1	0.559
MA0258.1	MA0258.1	0.0323
MA0259.1	MA0259.1	0.126

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: CNhs11113

Novel motif	Logo	P-value
1	1	0.888
10	10	0.748
100	100	0.843
101	101	0.851
102	102	0.26
103	103	0.0359
104	104	0.502
105	105	0.611
106	106	0.0943
107	107	0.0805
108	108	0.0535
109	109	0.0347
11	11	0.352
110	110	0.215
111	111	0.788
112	112	0.0627
113	113	0.822
114	114	0.644
115	115	0.771
116	116	0.385
117	117	0.363
118	118	0.303
119	119	0.0713
12	12	0.951
120	120	0.356
121	121	0.912
122	122	0.281
123	123	0.118
124	124	0.342
125	125	0.635
126	126	0.274
127	127	0.341
128	128	0.115
129	129	0.845
13	13	3.5072e-5
130	130	0.168
131	131	0.595
132	132	0.91
133	133	0.156
134	134	0.386
135	135	0.512
136	136	0.105
137	137	0.0535
138	138	0.0322
139	139	0.458
14	14	0.156
140	140	0.223
141	141	0.954
142	142	0.552
143	143	0.182
144	144	0.0379
145	145	0.106
146	146	0.241
147	147	0.476
148	148	0.545
149	149	0.285
15	15	0.21
150	150	0.105
151	151	0.813
152	152	0.0373
153	153	0.87
154	154	0.632
155	155	0.767
156	156	0.236
157	157	0.216
158	158	0.82
159	159	0.392
160	160	0.236
161	161	0.467
162	162	0.404
163	163	0.822
164	164	0.692
165	165	0.0377
166	166	0.641
167	167	0.812
168	168	0.964
169	169	0.00836
17	17	0.0639
18	18	0.0973
19	19	0.00483
2	2	0.0611
20	20	0.807
21	21	0.911
22	22	0.0313
23	23	0.289
24	24	0.251
25	25	0.788
26	26	0.36
27	27	0.364
28	28	0.493
29	29	0.692
3	3	0.397
30	30	0.185
31	31	0.523
32	32	0.158
33	33	0.75
34	34	0.621
35	35	0.678
36	36	0.637
37	37	0.0404
38	38	0.391
39	39	0.432
4	4	0.621
40	40	0.408
41	41	0.291
42	42	0.776
43	43	0.366
44	44	0.966
45	45	0.141
46	46	0.955
47	47	0.613
48	48	0.196
49	49	0.232
5	5	0.802
50	50	0.963
51	51	0.741
52	52	0.0418
53	53	0.842
54	54	0.89
55	55	0.901
56	56	0.818
57	57	0.931
58	58	0.269
59	59	0.709
6	6	0.647
60	60	0.0222
61	61	0.662
62	62	0.337
63	63	0.372
64	64	0.963
65	65	0.386
66	66	0.418
67	67	0.0496
68	68	0.955
69	69	0.863
7	7	0.134
70	70	0.173
71	71	0.769
72	72	0.752
73	73	0.0951
74	74	0.393
75	75	0.898
76	76	0.376
77	77	0.0624
78	78	0.108
79	79	0.427
8	8	0.673
80	80	0.463
81	81	0.482
82	82	0.398
83	83	0.293
84	84	0.319
85	85	0.0767
86	86	0.436
87	87	0.925
88	88	0.407
89	89	0.374
9	9	0.912
90	90	0.63
91	91	0.49
92	92	0.603
93	93	0.498
94	94	0.181
95	95	0.712
96	96	0.554
97	97	0.397
98	98	0.483
99	99	0.239

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: CNhs11113

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011432 mouse kidney- neonate N20 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)
0000308 (mouse neonate N20 sample)
0011432 (mouse kidney- neonate N20 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000926,UBERON:0000479,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0003103,UBERON:0009569,UBERON:0005291,UBERON:0000489,UBERON:0005177,UBERON:0003104,UBERON:0005172,UBERON:0003918,UBERON:0006598,UBERON:0005173,UBERON:0002532,UBERON:0001008,UBERON:0002417,UBERON:0000916,UBERON:0009142,UBERON:0006603,UBERON:0005095,UBERON:0007687
+|DRA_sample_Accession=CAGE@SAMD00005493
+|accession_numbers=CAGE;DRX009011;DRR009885;DRZ001310;DRZ002693;DRZ012660;DRZ014043
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000308,FF:0011432
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:83664365..83664383,+!p1@Hnf1b!2.01!100.97!Hnf1b;;chr2:163372884..163372904,+!p1@Hnf4a!1.99!97.57!Hnf4a;;chr10:88969376..88969395,-!p1@Nr1h4!1.83!66.87!Nr1h4;;chr11:34108085..34108092,-!p1@Foxi1!1.76!55.94!Foxi1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.73!65.54!Pou3f3;;chr2:24331085..24331100,-!p1@Pax8!1.71!50.04!Pax8;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.65!120.60!Tfcp2l1;;chr10:22539932..22539956,-!p1@Tcf21!1.52!84.14!Tcf21;;chr11:96143666..96143725,+!p1@Hoxb8!1.52!36.31!Hoxb8;;chr15:102828658..102828678,+!p1@Hoxc6!1.50!30.85!Hoxc6;;chr10:30491690..30491727,-!p5@Ncoa7!1.49!30.26!Ncoa7;;chr6:52190467..52190500,-!p1@Hoxa10!1.49!29.67!Hoxa10;;chr15:97738692..97738747,-!p1@Vdr!1.44!139.79!Vdr;;chr5:135582751..135582788,+!p1@Mlxipl!1.43!100.08!Mlxipl;;chr6:52176164..52176195,-!p1@Hoxa9!1.42!31.00!Hoxa9;;chr1:19202352..19202354,+!p2@Tfap2b!1.40!24.21!Tfap2b;;chr5:115421065..115421088,-!p1@Hnf1a!1.40!24.06!Hnf1a;;chr12:87762578..87762612,+!p1@Esrrb!1.38!22.88!Esrrb;;chr6:85137520..85137563,+!p1@Emx1!1.34!20.67!Emx1;;chr11:96153767..96153822,+!p1@Hoxb6!1.32!30.41!Hoxb6;;chr1:189432881..189432903,+!p2@Esrrg!1.31!19.63!Esrrg;;chr19:59533221..59533271,+!p1@Emx2!1.29!22.73!Emx2;;chr2:74529970..74529997,+!p1@Hoxd10!1.28!17.86!Hoxd10;;chr6:97879817..97879857,+!p2@Mitf!1.27!17.71!Mitf;;chr2:103143336..103143367,-!p1@Ehf!1.24!26.57!Ehf;;chr1:19199236..19199258,+!p1@Tfap2b!1.20!14.91!Tfap2b;;chr16:43363968..43364001,+!p7@Zbtb20!1.17!25.09!Zbtb20;;chr6:52190840..52190853,-!p5@Hoxa10!1.16!13.43!Hoxa10;;chr11:84339016..84339044,-!p1@Lhx1!1.14!12.84!Lhx1;;chr13:72101178..72101203,-!p1@Irx1!1.13!19.48!Irx1;;chr2:74549968..74549996,+!p1@Hoxd3!1.13!15.79!Hoxd3;;chr1:189432907..189432926,+!p3@Esrrg!1.12!12.25!Esrrg;;chr1:189433521..189433548,+!p5@Esrrg!1.08!10.92!Esrrg;;chr16:4594740..4594759,+!p1@Glis2!1.07!122.07!Glis2;;chr16:94085471..94085495,+!p1@Sim2!1.05!10.33!Sim2;;chr11:96147952..96147967,+!p1@Hoxb7!1.04!12.55!Hoxb7;;chr8:118231678..118231692,-!p2@Maf!1.03!88.71!Maf;;chr15:81633165..81633188,+!p2@Tef!1.02!78.38!Tef;;chr11:90252223..90252240,-!p1@Hlf!1.01!77.79!Hlf;;chr2:74543202..74543213,+!p3@Hoxd8!1.01!9.30!Hoxd8;;chr7:52960555..52960662,+!p1@Dbp!0.99!75.72!Dbp;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!0.99!8.86!Sim1;;chr2:74542680..74542705,+!p6@Hoxd8!0.98!8.56!Hoxd8;;chr1:19202185..19202187,+!p9@Tfap2b!0.98!8.56!Tfap2b;;chr2:9800207..9800234,-!p1@Gata3!0.97!25.83!Gata3;;chr1:57029281..57029326,-!p1@Satb2!0.97!13.28!Satb2;;chr6:52163319..52163342,-!p1@Hoxa3!0.97!12.40!Hoxa3;;chr6:38097380..38097407,-!p6@D630045J12Rik!0.97!8.41!D630045J12Rik;;chr2:74529998..74530020,+!p2@Hoxd10!0.97!8.41!Hoxd10;;chr19:28754692..28754757,-!p1@Glis3!0.95!33.95!Glis3;;chr4:154010409..154010466,-!p2@Prdm16!0.95!18.89!Prdm16;;chr2:163372869..163372882,+!p3@Hnf4a!0.95!7.97!Hnf4a;;chr2:74543397..74543435,+!p2@Hoxd8!0.95!7.82!Hoxd8;;chr4:120488308..120488366,-!p1@Nfyc!0.94!45.91!Nfyc;;chr6:52167459..52167492,-!p1@Hoxa7!0.94!9.45!Hoxa7;;chr11:98636531..98636559,-!p1@Nr1d1!0.93!44.43!Nr1d1;;chr11:90250944..90250982,-!p2@Hlf!0.93!12.69!Hlf;;chr3:30408674..30408716,-!p2@Mecom!0.93!12.69!Mecom;;chr3:3508024..3508069,+!p2@Hnf4g!0.93!7.53!Hnf4g;;chr19:44831390..44831414,+!p1@Pax2!0.93!7.53!Pax2;;chr15:81633203..81633215,+!p3@Tef!0.92!11.66!Tef;;chr2:104966766..104966786,+!p1@Wt1!0.92!11.66!Wt1;;chr13:72101161..72101177,-!p2@Irx1!0.92!10.19!Irx1;;chr2:103123925..103123959,-!p3@Ehf!0.92!7.23!Ehf;;chr1:137155026..137155042,-!p1@Elf3!0.91!43.54!Elf3;;chr8:94325321..94325366,-!p1@Irx3!0.91!17.71!Irx3;;chr15:85566184..85566238,+!p1@Ppara!0.90!10.63!Ppara;;chr2:77357622..77357704,-!p1@Zfp385b!0.88!18.30!Zfp385b;;chr3:30408603..30408668,-!p1@Mecom!0.87!15.35!Mecom;;chr2:74542918..74542971,+!p1@Hoxd8!0.87!10.04!Hoxd8;;chr15:102828642..102828653,+!p2@Hoxc6!0.87!6.35!Hoxc6;;chr13:72766250..72766273,+!p1@Irx2!0.86!10.04!Irx2;;chr12:87702062..87702081,+!p4@Esrrb!0.86!6.20!Esrrb;;chr16:38294860..38294924,-!p1@Nr1i2!0.86!6.20!Nr1i2;;chr2:160698288..160698358,-!p3@Zhx3!0.85!19.93!Zhx3;;chr19:28754600..28754612,-!p2@Glis3!0.85!10.04!Glis3;;chr11:90250894..90250916,-!p5@Hlf!0.85!6.05!Hlf;;chr4:107107224..107107259,+!p2@Glis1!0.84!5.90!Glis1;;chr8:79426176..79426275,+!p1@Nr3c2!0.83!30.85!Nr3c2;;chr16:43363152..43363186,+!p3@Zbtb20!0.83!13.73!Zbtb20;;chr11:96160426..96160443,+!p2@Hoxb6!0.83!5.76!Hoxb6;;chr14:19071466..19071550,-!p1@Nr1d2!0.82!40.74!Nr1d2;;chr6:52184901..52184959,-!p2@Hoxa10!0.82!5.61!Hoxa10;;chr10:102491405..102491416,-!p1@Alx1!0.82!5.61!Alx1;;chr3:94176733..94176794,+!p1@Rorc!0.81!45.91!Rorc;;chr2:74536026..74536039,+!p1@Hoxd9!0.81!5.46!Hoxd9;;chr2:74549945..74549965,+!p4@Hoxd3!0.81!5.46!Hoxd3;;chr11:83666422..83666446,+!p4@Hnf1b!0.81!5.46!Hnf1b;;chr9:106355684..106355744,+!p5@Pcbp4!0.80!8.27!Pcbp4;;chr3:29912058..29912071,-!p6@Mecom!0.80!6.20!Mecom;;chr6:90412582..90412601,+!p1@Klf15!0.79!26.42!Klf15;;chr14:22807216..22807231,-!p3@Zfp503!0.79!9.30!Zfp503;;chr11:96145450..96145517,+!p2@Hoxb7!0.79!8.12!Hoxb7;;chr15:85602581..85602598,+!p8@Ppara!0.79!5.17!Ppara;;chr14:22807107..22807119,-!p2@Zfp503!0.78!23.91!Zfp503;;chr2:103143315..103143328,-!p2@Ehf!0.78!5.02!Ehf;;chr19:59532915..59532940,+!p5@Emx2!0.77!4.87!Emx2;;chr11:100800641..100800669,-!p3@Stat3!0.76!8.71!Stat3;;chr6:52195795..52195825,-!p1@Hoxa11!0.76!4.72!Hoxa11;;chr19:25746898..25746910,+!p1@Dmrt2!0.75!7.23!Dmrt2;;chr6:38097421..38097440,-!p7@D630045J12Rik!0.75!4.58!D630045J12Rik;;chr10:30491648..30491657,-!p15@Ncoa7!0.75!4.58!Ncoa7;;chr15:35225845..35225867,+!p1@Osr2!0.74!12.25!Osr2;;chr13:37918684..37918701,+!p12@Rreb1!0.73!5.31!Rreb1;;chr6:85137505..85137517,+!p2@Emx1!0.73!4.43!Emx1;;chr6:52176144..52176161,-!p2@Hoxa9!0.73!4.43!Hoxa9;;chr13:72766279..72766296,+!p2@Irx2!0.72!6.64!Irx2;;chr13:96093557..96093561,+!p6@Zbed3!0.72!4.28!Zbed3;;chr11:83665637..83665671,+!p6@Hnf1b!0.72!4.28!Hnf1b;;chr2:74517742..74517758,+!p2@Hoxd11!0.72!4.28!Hoxd11;;chr2:9809357..9809371,-!p2@Gata3!0.72!4.28!Gata3;;chr10:30375579..30375616,-!p3@Ncoa7!0.71!10.63!Ncoa7;;chr2:74542589..74542602,+!p8@Hoxd8!0.71!4.13!Hoxd8;;chr15:102797288..102797302,+!p1@Hoxc10!0.71!4.13!Hoxc10;;chr12:75002389..75002406,+!p4@Hif1a!0.71!4.13!Hif1a;;chr1:120524563..120524591,+!p2@Tfcp2l1!0.71!4.13!Tfcp2l1;;chr14:22807083..22807104,-!p1@Zfp503!0.70!79.56!Zfp503;;chr2:103252231..103252256,+!p4@Elf5!0.70!3.99!Elf5;;chr11:83664334..83664353,+!p2@Hnf1b!0.70!3.99!Hnf1b;;chr10:102491237..102491291,-!p2@Alx1!0.70!3.99!Alx1;;chr2:74543103..74543135,+!p4@Hoxd8!0.70!3.99!Hoxd8;;chr8:118231705..118231722,-!p3@Maf!0.69!35.43!Maf;;chr4:148275237..148275311,+!p2@Casz1!0.69!18.01!Casz1;;chr14:17407878..17407926,-!p1@Rarb!0.69!9.59!Rarb;;chr7:77511403..77511450,-!p3@Nr2f2!0.69!9.00!Nr2f2;;chr8:94325814..94325839,-!p2@Irx3!0.69!8.86!Irx3;;chr6:52167513..52167549,-!p2@Hoxa7!0.69!5.76!Hoxa7;;chr11:85646303..85646329,+!p1@Tbx2!0.68!28.34!Tbx2;;chr6:90412608..90412630,+!p2@Klf15!0.68!8.41!Klf15;;chr8:94325486..94325510,-!p4@Irx3!0.68!5.17!Irx3;;chr6:52190858..52190873,-!p4@Hoxa10!0.68!3.84!Hoxa10;;chr7:77511234..77511302,-!p2@Nr2f2!0.67!28.19!Nr2f2;;chr13:31650185..31650201,+!p1@Foxq1!0.67!14.61!Foxq1;;chr10:5734907..5734920,-!p11@Esr1!0.67!3.69!Esr1;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.67!3.69!Pou3f3;;chr17:87153240..87153254,+!p1@Epas1!0.66!81.04!Epas1;;chr14:18493386..18493464,+!p1@Thrb!0.66!15.35!Thrb;;chr2:164829847..164829859,-!p5@Ncoa5!0.66!3.54!Ncoa5;;chr1:189432634..189432643,+!p8@Esrrg!0.66!3.54!Esrrg;;chr2:74536050..74536065,+!p2@Hoxd9!0.66!3.54!Hoxd9;;chr11:96160360..96160397,+!p3@Hoxb6!0.66!3.54!Hoxb6;;chr8:118231723..118231740,-!p1@Maf!0.65!91.67!Maf;;chr16:43363190..43363242,+!p2@Zbtb20!0.65!12.10!Zbtb20;;chr11:121380640..121380655,-!p1@Zfp750!0.65!6.20!Zfp750;;chr11:90251852..90251855,-!p4@Hlf!0.65!4.43!Hlf;;chr1:189432857..189432870,+!p7@Esrrg!0.64!3.40!Esrrg;;chr2:115891409..115891425,-!p2@Meis2!0.63!10.78!Meis2;;chr6:52167434..52167450,-!p3@Hoxa7!0.63!3.25!Hoxa7;;chr11:96143962..96144035,+!p2@Hoxb8!0.63!3.25!Hoxb8;;chr10:5734677..5734702,-!p4@Esr1!0.63!3.25!Esr1;;chr2:74560109..74560131,+!p1@Hoxd4!0.63!3.25!Hoxd4;;chr2:74550015..74550057,+!p2@Hoxd3!0.63!3.25!Hoxd3;;chr19:23215673..23215753,+!p1@Klf9!0.62!54.62!Klf9;;chr6:88148650..88148669,+!p1@Gata2!0.62!31.29!Gata2;;chr5:104121453..104121479,+!p4@Aff1!0.62!16.98!Aff1;;chr2:115891427..115891441,-!p4@Meis2!0.61!7.38!Meis2;;chr2:74542974..74542986,+!p5@Hoxd8!0.61!3.10!Hoxd8;;chr5:115420882..115420896,-!p3@Hnf1a!0.61!3.10!Hnf1a;;chr15:102797225..102797243,+!p2@Hoxc10!0.61!3.10!Hoxc10;;chr3:128916868..128916890,+!p1@Pitx2!0.60!4.43!Pitx2;;chr2:91035254..91035271,-!p3@Nr1h3!0.60!3.84!Nr1h3;;chr1:19199021..19199048,+!p8@Tfap2b!0.60!2.95!Tfap2b;;chr16:42907676..42907797,+!p1@Zbtb20!0.59!45.61!Zbtb20;;chr13:31898729..31898761,+!p1@Foxc1!0.59!8.12!Foxc1;;chr11:85646427..85646451,+!p4@Tbx2!0.58!5.46!Tbx2;;chr15:85566051..85566080,+!p4@Ppara!0.58!3.40!Ppara;;chr13:40829137..40829205,-!p1@Tfap2a!0.58!3.25!Tfap2a;;chr10:5734717..5734727,-!p12@Esr1!0.58!2.80!Esr1;;chr6:85137491..85137504,+!p3@Emx1!0.58!2.80!Emx1;;chr2:103264213..103264233,+!p1@Elf5!0.58!2.80!Elf5;;chr14:17407970..17408015,-!p2@Rarb!0.57!8.41!Rarb;;chr16:44173384..44173407,+!p2@Gm608!0.57!8.27!Gm608;;chr18:36441119..36441158,+!p2@Pura!0.57!7.68!Pura;;chr8:123640063..123640077,+!p1@Foxc2!0.57!5.46!Foxc2;;chr11:96690797..96690813,-!p1@Nfe2l1!0.56!63.77!Nfe2l1;;chr10:107769168..107769215,+!p1@Pawr!0.56!33.06!Pawr;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.56!9.00!D630045J12Rik;;chr7:52960700..52960719,+!p2@Dbp!0.56!3.40!Dbp;;chr3:3508005..3508021,+!p3@Hnf4g!0.56!2.66!Hnf4g;;chr11:96143843..96143868,+!p3@Hoxb8!0.56!2.66!Hoxb8;;chr12:75002357..75002378,+!p6@Hif1a!0.56!2.66!Hif1a;;chr14:98568971..98569025,-!p1@Dach1!0.55!24.65!Dach1;;chr11:69749320..69749345,+!p2@Ybx2!0.55!4.72!Ybx2;;chr8:94325446..94325459,-!p8@Irx3!0.55!2.80!Irx3;;chr6:52161666..52161711,-!p1@Hoxa6!0.55!2.51!Hoxa6;;chr6:52190668..52190682,-!p3@Hoxa10!0.55!2.51!Hoxa10;;chr1:42752559..42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Ncor2!0.29!5.61!Ncor2;;chr2:115891454..115891471,-!p3@Meis2!0.29!4.58!Meis2;;chr16:42907554..42907591,+!p5@Zbtb20!0.29!3.69!Zbtb20;;chr4:62626682..62626705,+!p2@Zfp618!0.29!3.25!Zfp618;;chr9:96619968..96619983,-!p6@Zbtb38!0.29!2.21!Zbtb38;;chr2:173044357..173044377,-!p2@Zbp1!0.29!1.77!Zbp1;;chr3:9610233..9610247,-!p4@Zfp704!0.29!1.77!Zfp704;;chr6:52154414..52154462,-!p1@Hoxa5!0.29!1.62!Hoxa5;;chr19:5560600..5560617,-!p1@Ovol1!0.29!1.33!Ovol1;;chr11:58136797..58136859,-!p1@Zfp672!0.28!40.45!Zfp672;;chr6:140572167..140572236,+!p2@Aebp2!0.28!16.83!Aebp2;;chr15:50721588..50721610,-!p1@Trps1!0.28!16.68!Trps1;;chr4:97444446..97444470,+!p3@Nfia!0.28!15.79!Nfia;;chr9:122795920..122795977,+!p1@Zfp167!0.28!13.43!Zfp167;;chr3:94641624..94641645,+!p2@Pogz!0.28!11.22!Pogz;;chr19:6996294..6996324,-!p2@Esrra!0.28!10.92!Esrra;;chr7:30568977..30569047,+!p1@Zfp30!0.28!9.00!Zfp30;;chr1:133904670..133904731,+!p2@Elk4!0.28!8.27!Elk4;;chr1:172797876..172797887,-!p5@Atf6!0.28!3.10!Atf6;;chr14:76814883..76814898,+!p9@Tsc22d1!0.28!2.66!Tsc22d1;;chr6:115310872..115310899,+!p2@Pparg!0.28!2.21!Pparg;;chr11:53164556..53164567,+!p5@Aff4!0.28!1.92!Aff4;;chr10:107769719..107769745,+!p4@Pawr!0.28!1.77!Pawr;;chr14:98568822..98568837,-!p5@Dach1!0.28!1.77!Dach1;;chr7:31741624..31741643,-!p7@LOC100504922,p7@Usf2!0.28!1.33!Usf2;;chr1:13364477..13364492,-!p6@Ncoa2!0.28!1.33!Ncoa2;;chr15:50721942..50721987,-!p13@Trps1!0.28!1.18!Trps1;;chr15:102797170..102797182,+!p3@Hoxc10!0.28!0.89!Hoxc10;;chr1:191993385..191993405,-!p3@Prox1!0.28!0.89!Prox1;;chr1:19199221..19199234,+!p6@Tfap2b!0.28!0.89!Tfap2b;;chr2:104966933..104966966,+!p3@Wt1!0.28!0.89!Wt1;;chr19:59533206..59533217,+!p9@Emx2!0.28!0.89!Emx2;;chr11:96132544..96132553,+!p6@Hoxb9!0.28!0.89!Hoxb9;;chr11:69749437..69749467,+!p3@Ybx2!0.28!0.89!Ybx2;;chr11:96180069..96180089,+!p3@Hoxb4!0.28!0.89!Hoxb4;;chr5:137042338..137042372,-!p5@Cux1!0.28!0.89!Cux1;;chr6:38097441..38097447,-!p13@D630045J12Rik!0.28!0.89!D630045J12Rik;;chr6:52190760..52190767,-!p9@Hoxa10!0.28!0.89!Hoxa10;;chr5:138526401..138526410,+!p3@Zkscan1!0.28!0.89!Zkscan1;;chr9:59797875..59797929,-!p1@Nr2e3!0.28!0.89!Nr2e3;;chr8:94325779..94325791,-!p7@Irx3!0.28!0.89!Irx3;;chr7:52960663..52960677,+!p6@Dbp!0.28!0.89!Dbp;;chr3:29912169..29912182,-!p12@Mecom!0.28!0.89!Mecom;;chr3:29911926..29911942,-!p13@Mecom!0.28!0.89!Mecom;;chr2:74536071..74536083,+!p4@Hoxd9!0.28!0.89!Hoxd9;;chr2:9800094..9800108,-!p3@Gata3!0.28!0.89!Gata3;;chr2:74535720..74535731,+!p6@Hoxd9!0.28!0.89!Hoxd9;;chr2:9809402..9809422,-!p5@Gata3!0.28!0.89!Gata3;;chr15:85566537..85566552,+!p2@Ppara!0.28!0.89!Ppara;;chr16:14705746..14705761,+!p4@Snai2!0.28!0.89!Snai2;;chr16:43364258..43364270,+!p27@Zbtb20!0.28!0.89!Zbtb20;;chr6:37392095..37392154,-!p1@Creb3l2!0.27!52.84!Creb3l2;;chrX:98449492..98449510,+!p1@Foxo4!0.27!17.27!Foxo4;;chr2:32218712..32218782,+!p2@Ciz1!0.27!16.53!Ciz1;;chr19:55816770..55816793,+!p2@Tcf7l2!0.27!14.02!Tcf7l2;;chr9:96620228..96620308,-!p3@Zbtb38!0.27!7.23!Zbtb38;;chr2:165818108..165818119,+!p2@Ncoa3!0.27!3.54!Ncoa3;;chr4:148178529..148178548,+!p3@Casz1!0.27!3.25!Casz1;;chr4:154010940..154010962,-!p3@Prdm16!0.27!2.95!Prdm16;;chr12:72117645..72117677,+!p3@Arid4a!0.27!2.80!Arid4a;;chrX:103070839..103070856,-!p4@Atrx!0.27!1.77!Atrx;;chr7:51787434..51787448,-!p1@Spib!0.27!1.62!Spib;;chr7:52960730..52960762,+!p3@Dbp!0.27!1.33!Dbp;;chr6:52154386..52154407,-!p2@Hoxa5!0.27!1.33!Hoxa5;;chr7:52960780..52960793,+!p5@Dbp!0.27!1.18!Dbp;;chr4:154010334..154010347,-!p8@Prdm16!0.27!1.18!Prdm16;;chr11:98636568..98636574,-!p9@Nr1d1!0.27!1.18!Nr1d1;;chr13:37918661..37918673,+!p17@Rreb1!0.27!1.18!Rreb1;;chr1:87546602..87546617,+!p2@Sp100!0.27!1.18!Sp100;;chr15:57907747..57907798,-!p1@9130401M01Rik,p1@Zhx1!0.26!42.95!Zhx1;;chr18:39649430..39649522,-!p2@Nr3c1!0.26!15.79!Nr3c1;;chr17:23004085..23004108,-!p1@Zfp945!0.26!15.79!Zfp945;;chr1:133904183..133904211,+!p1@Elk4!0.26!13.58!Elk4;;chr7:148452314..148452329,-!p1@Irf7!0.26!10.92!Irf7;;chr7:25039763..25039831,+!p1@Zfp108!0.26!7.23!Zfp108;;chr17:23004125..23004157,-!p3@Zfp945!0.26!4.43!Zfp945;;chr16:42907656..42907675,+!p10@Zbtb20!0.26!2.80!Zbtb20;;chr4:54957886..54957907,+!p3@Zfp462!0.26!2.07!Zfp462;;chr6:134780337..134780355,+!p3@Crebl2!0.26!1.33!Crebl2;;chr11:44431369..44431389,+!p8@Ebf1!0.26!1.33!Ebf1;;chr10:80809447..80809515,-!p5@Hmg20b!0.26!1.18!Hmg20b;;chr11:58136641..58136663,-!p3@Zfp672!0.26!1.18!Zfp672;;chr2:169459017..169459029,+!p9@Tshz2!0.26!1.18!Tshz2;;chr9:48644013..48644027,-!p5@Zbtb16!0.26!1.18!Zbtb16;;chr13:31898529..31898542,+!p5@Foxc1!0.26!1.18!Foxc1;;chr10:127080031..127080090,+!p1@Stat6!0.25!34.10!Stat6;;chr7:148513456..148513506,-!p1@Deaf1!0.25!24.80!Deaf1;;chr10:30522881..30522960,-!p1@Ncoa7!0.25!18.89!Ncoa7;;chr7:148513409..148513455,-!p2@Deaf1!0.25!6.79!Deaf1;;chr5:65194602..65194613,+!p3@Klf3!0.25!6.35!Klf3;;chr13:67274092..67274140,+!p1@Rsl1!0.25!5.02!Rsl1;;chr17:21520689..21520730,+!p1@Zfp677!0.25!4.87!Zfp677;;chr3:89197551..89197606,-!p2@Zbtb7b!0.25!4.72!Zbtb7b;;chr15:57526206..57526241,+!p2@Zhx2!0.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+|ffid_belonging_in_development=UBERON:0003104,UBERON:0003918,UBERON:0007687,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011432
 |is_obsolete=
+|library_id=CNhs11113
+|library_id_phase_based=2:CNhs11113
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;832
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;832
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm9.nobarcode.rdna.fa.gz
 |name=kidney, neonate N20
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11113,LSID734,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.571017592008611,0,0,0,0,0,0.408526496512155,0,0.056171820572638,0,0,-0.0843392403965415,0,0,0,0,0,0,0.175181274658109,0,0,0,0,0,0.112343641145276,0.0597943799295356,0,0,0,0,0,0,0.231605743953826,0,0.874762743246502,0,0.883232984490065,0,-0.0786668098071278,-0.00974409868912951,-0.163237089726713,-0.782693915029966,-0.11065334058863,0,0,0.0597943799295356,0,0,0,0,0,0,0,0,0,0.327762892143406,0,0,0,0,0.0597943799295356,0,0.183537312770341,0,0,0.031619777046085,0.0492399399570154,-0.00245538321119221,0.150104231357112,0.0159362511806082,0,0.0597943799295356,0,0.147343800664484,0.0597943799295356,0,0,-0.0809844055049926,-0.05068541024364,0.122685856607953,0,0,0,0,0.10075872572393,0.20151745144786,-0.0856562580541553,-0.254746367958675,-0.0858081752025345,0,0.746316112557849,0,0,0
 |rna_box=19
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:832-19I1;search_select_hide=table117:832-19I1
 }}

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FF:832-19I1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:21, 4 June 2020

CNhs11113

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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