FF:758-6D5: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	kidney, neonate N10
Species:	Mouse (Mus musculus)
Library ID:	CNhs11206
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	kidney
dev stage	10 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		SAMD00005505

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11206		CAGE		DRX009010		DRR009884

Accession ID Mm9

Library id		BAM		CTSS
CNhs11206		DRZ001309		DRZ002692

Accession ID Mm10

Library id		BAM		CTSS
CNhs11206		DRZ012659		DRZ014042

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

CNhs11206

0	0
1	0
10	0
100	0
1000	-0.00962
1001	0.104
1002	0.691
1003	-0.00321
1004	0
1005	0
1006	-0.0988
1007	0.112
1008	0
1009	0.0897
101	-0.0384
1010	0
1011	-0.0201
1012	0.0266
1013	0.277
1014	0.0263
1015	-0.0369
1016	0.181
1017	0
1018	0.0517
1019	0
102	0
1020	0
1021	0
1022	0.288
1023	0
1024	0.14
1025	0
1026	0
1027	0
1028	0
1029	0.231
103	0.0615
1030	0.0266
1031	0.241
1032	0.193
1033	-0.0235
1034	0.0979
1035	0.0517
1036	-0.0855
1037	0
1038	0.21
1039	0.167
104	0
1040	0.305
1041	0.0266

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: CNhs11206

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.016
MA0003.1	MA0003.1	0.256
MA0004.1	MA0004.1	0.435
MA0006.1	MA0006.1	0.0471
MA0007.1	MA0007.1	0.636
MA0009.1	MA0009.1	0.562
MA0014.1	MA0014.1	0.425
MA0017.1	MA0017.1	2.67397e-9
MA0018.2	MA0018.2	3.08214e-5
MA0019.1	MA0019.1	0.215
MA0024.1	MA0024.1	0.619
MA0025.1	MA0025.1	0.694
MA0027.1	MA0027.1	0.488
MA0028.1	MA0028.1	0.376
MA0029.1	MA0029.1	0.352
MA0030.1	MA0030.1	0.00476
MA0031.1	MA0031.1	0.011
MA0035.2	MA0035.2	7.73336e-4
MA0038.1	MA0038.1	0.575
MA0039.2	MA0039.2	0.0428
MA0040.1	MA0040.1	0.964
MA0041.1	MA0041.1	0.543
MA0042.1	MA0042.1	0.918
MA0043.1	MA0043.1	0.012
MA0046.1	MA0046.1	7.35536e-132
MA0047.2	MA0047.2	0.0135
MA0048.1	MA0048.1	0.368
MA0050.1	MA0050.1	0.84
MA0051.1	MA0051.1	0.683
MA0052.1	MA0052.1	0.00296
MA0055.1	MA0055.1	0.135
MA0057.1	MA0057.1	0.873
MA0058.1	MA0058.1	0.428
MA0059.1	MA0059.1	0.00874
MA0060.1	MA0060.1	0.359
MA0061.1	MA0061.1	0.119
MA0062.2	MA0062.2	0.00931
MA0065.2	MA0065.2	0.0725
MA0066.1	MA0066.1	0.188
MA0067.1	MA0067.1	0.285
MA0068.1	MA0068.1	0.361
MA0069.1	MA0069.1	0.172
MA0070.1	MA0070.1	0.855
MA0071.1	MA0071.1	0.588
MA0072.1	MA0072.1	0.594
MA0073.1	MA0073.1	0.542
MA0074.1	MA0074.1	0.822
MA0076.1	MA0076.1	0.289
MA0077.1	MA0077.1	0.301
MA0078.1	MA0078.1	0.00128
MA0079.2	MA0079.2	0.122
MA0080.2	MA0080.2	0.0754
MA0081.1	MA0081.1	0.361
MA0083.1	MA0083.1	0.203
MA0084.1	MA0084.1	0.869
MA0087.1	MA0087.1	0.383
MA0088.1	MA0088.1	0.648
MA0090.1	MA0090.1	7.35474e-4
MA0091.1	MA0091.1	0.0915
MA0092.1	MA0092.1	0.0859
MA0093.1	MA0093.1	0.459
MA0099.2	MA0099.2	0.0616
MA0100.1	MA0100.1	0.0505
MA0101.1	MA0101.1	0.582
MA0102.2	MA0102.2	0.43
MA0103.1	MA0103.1	0.363
MA0104.2	MA0104.2	0.00135
MA0105.1	MA0105.1	0.00256
MA0106.1	MA0106.1	0.886
MA0107.1	MA0107.1	0.836
MA0108.2	MA0108.2	0.0156
MA0111.1	MA0111.1	0.225
MA0112.2	MA0112.2	0.31
MA0113.1	MA0113.1	0.363
MA0114.1	MA0114.1	2.80232e-10
MA0115.1	MA0115.1	0.238
MA0116.1	MA0116.1	1.95966e-4
MA0117.1	MA0117.1	0.432
MA0119.1	MA0119.1	0.707
MA0122.1	MA0122.1	0.42
MA0124.1	MA0124.1	0.655
MA0125.1	MA0125.1	0.329
MA0131.1	MA0131.1	0.686
MA0135.1	MA0135.1	0.767
MA0136.1	MA0136.1	0.00531
MA0137.2	MA0137.2	0.914
MA0138.2	MA0138.2	0.251
MA0139.1	MA0139.1	0.909
MA0140.1	MA0140.1	0.00624
MA0141.1	MA0141.1	0.0642
MA0142.1	MA0142.1	0.0154
MA0143.1	MA0143.1	0.713
MA0144.1	MA0144.1	0.522
MA0145.1	MA0145.1	1.75271e-4
MA0146.1	MA0146.1	0.518
MA0147.1	MA0147.1	1.02071e-4
MA0148.1	MA0148.1	0.0915
MA0149.1	MA0149.1	0.842
MA0150.1	MA0150.1	0.456
MA0152.1	MA0152.1	0.0209
MA0153.1	MA0153.1	2.04009e-58
MA0154.1	MA0154.1	0.971
MA0155.1	MA0155.1	0.328
MA0156.1	MA0156.1	0.107
MA0157.1	MA0157.1	0.112
MA0159.1	MA0159.1	0.538
MA0160.1	MA0160.1	0.471
MA0162.1	MA0162.1	0.499
MA0163.1	MA0163.1	0.00978
MA0164.1	MA0164.1	0.582
MA0258.1	MA0258.1	0.308
MA0259.1	MA0259.1	0.0503

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: CNhs11206

Novel motif	Logo	P-value
1	1	0.0782
10	10	0.0666
100	100	0.811
101	101	0.614
102	102	0.176
103	103	0.918
104	104	0.642
105	105	0.69
106	106	0.706
107	107	0.11
108	108	0.0294
109	109	0.97
11	11	0.261
110	110	0.721
111	111	0.0726
112	112	0.472
113	113	0.889
114	114	0.0261
115	115	0.511
116	116	0.144
117	117	0.012
118	118	0.0342
119	119	0.771
12	12	0.631
120	120	0.178
121	121	0.813
122	122	0.335
123	123	0.0495
124	124	0.26
125	125	0.101
126	126	0.587
127	127	0.105
128	128	0.637
129	129	0.782
13	13	0.0466
130	130	0.0761
131	131	0.524
132	132	0.755
133	133	0.276
134	134	0.585
135	135	0.94
136	136	0.0847
137	137	0.0356
138	138	0.00705
139	139	0.333
14	14	0.384
140	140	0.971
141	141	0.642
142	142	0.201
143	143	0.237
144	144	0.0854
145	145	0.556
146	146	0.535
147	147	0.522
148	148	0.525
149	149	0.898
15	15	0.676
150	150	0.15
151	151	0.219
152	152	0.0574
153	153	0.685
154	154	0.863
155	155	0.42
156	156	0.347
157	157	0.516
158	158	0.498
159	159	0.288
160	160	0.647
161	161	0.995
162	162	0.282
163	163	0.955
164	164	0.263
165	165	0.151
166	166	0.669
167	167	0.352
168	168	0.932
169	169	0.128
17	17	0.997
18	18	0.00397
19	19	0.0506
2	2	0.154
20	20	0.711
21	21	0.42
22	22	0.244
23	23	0.98
24	24	0.62
25	25	0.465
26	26	0.845
27	27	0.807
28	28	0.844
29	29	0.0729
3	3	0.569
30	30	0.224
31	31	0.658
32	32	0.0158
33	33	0.622
34	34	0.447
35	35	0.0188
36	36	0.0876
37	37	0.918
38	38	0.829
39	39	0.455
4	4	0.926
40	40	0.924
41	41	0.109
42	42	0.361
43	43	0.315
44	44	0.28
45	45	0.339
46	46	0.245
47	47	0.193
48	48	0.665
49	49	0.207
5	5	0.173
50	50	0.737
51	51	0.88
52	52	0.0683
53	53	0.837
54	54	0.477
55	55	0.664
56	56	0.318
57	57	0.438
58	58	0.978
59	59	0.58
6	6	0.781
60	60	0.229
61	61	0.886
62	62	0.253
63	63	0.657
64	64	0.291
65	65	0.585
66	66	0.701
67	67	0.0446
68	68	0.204
69	69	0.583
7	7	0.894
70	70	0.171
71	71	0.0432
72	72	0.288
73	73	0.876
74	74	0.222
75	75	0.115
76	76	0.246
77	77	0.506
78	78	0.961
79	79	0.218
8	8	0.0291
80	80	0.113
81	81	0.207
82	82	0.139
83	83	0.174
84	84	0.607
85	85	0.713
86	86	0.924
87	87	0.256
88	88	0.308
89	89	0.603
9	9	0.972
90	90	0.297
91	91	0.99
92	92	0.243
93	93	0.722
94	94	0.0816
95	95	0.421
96	96	0.462
97	97	0.321
98	98	0.9
99	99	0.736

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: CNhs11206

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011419 mouse kidney- neonate N10 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)
0000305 (mouse neonate N10 sample)
0011419 (mouse kidney- neonate N10 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@DRS008873
+|DRA_sample_Accession=CAGE@SAMD00005505
+|accession_numbers=CAGE;DRX009010;DRR009884;DRZ001309;DRZ002692;DRZ012659;DRZ014042
 |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 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!2.04!280.14!Tcf21;;chr11:83664365..83664383,+!p1@Hnf1b!2.00!99.15!Hnf1b;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.75!152.21!Tfcp2l1;;chr11:34108085..34108092,-!p1@Foxi1!1.71!49.77!Foxi1;;chr15:102828658..102828678,+!p1@Hoxc6!1.65!43.25!Hoxc6;;chr2:24331085..24331100,-!p1@Pax8!1.64!43.13!Pax8;;chr2:163372884..163372904,+!p1@Hnf4a!1.63!41.29!Hnf4a;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.61!49.89!Pou3f3;;chr11:96143666..96143725,+!p1@Hoxb8!1.60!44.58!Hoxb8;;chr6:52190467..52190500,-!p1@Hoxa10!1.59!37.69!Hoxa10;;chr10:102491405..102491416,-!p1@Alx1!1.55!34.72!Alx1;;chr11:96153767..96153822,+!p1@Hoxb6!1.53!50.08!Hoxb6;;chr2:74529970..74529997,+!p1@Hoxd10!1.43!26.12!Hoxd10;;chr10:88969376..88969395,-!p1@Nr1h4!1.41!24.79!Nr1h4;;chr2:74549968..74549996,+!p1@Hoxd3!1.38!28.90!Hoxd3;;chr6:52176164..52176195,-!p1@Hoxa9!1.38!28.14!Hoxa9;;chr19:59533221..59533271,+!p1@Emx2!1.36!26.62!Emx2;;chr1:19202352..19202354,+!p2@Tfap2b!1.34!20.68!Tfap2b;;chr6:52184901..52184959,-!p2@Hoxa10!1.30!19.03!Hoxa10;;chr2:9800207..9800234,-!p1@Gata3!1.21!46.48!Gata3;;chr1:189432881..189432903,+!p2@Esrrg!1.20!14.86!Esrrg;;chr6:52190668..52190682,-!p3@Hoxa10!1.20!14.80!Hoxa10;;chr10:102491237..102491291,-!p2@Alx1!1.19!14.48!Alx1;;chr6:97879817..97879857,+!p2@Mitf!1.18!14.04!Mitf;;chr5:115421065..115421088,-!p1@Hnf1a!1.17!13.91!Hnf1a;;chr6:85137520..85137563,+!p1@Emx1!1.17!13.91!Emx1;;chr11:96147952..96147967,+!p1@Hoxb7!1.16!16.63!Hoxb7;;chr10:30491690..30491727,-!p5@Ncoa7!1.16!13.41!Ncoa7;;chr2:103143336..103143367,-!p1@Ehf!1.15!21.25!Ehf;;chr6:52163319..52163342,-!p1@Hoxa3!1.15!19.03!Hoxa3;;chr1:19199236..19199258,+!p1@Tfap2b!1.14!12.84!Tfap2b;;chr2:104966766..104966786,+!p1@Wt1!1.13!19.73!Wt1;;chr13:72101178..72101203,-!p1@Irx1!1.13!19.48!Irx1;;chr5:135582751..135582788,+!p1@Mlxipl!1.12!49.20!Mlxipl;;chr6:52190840..52190853,-!p5@Hoxa10!1.12!12.20!Hoxa10;;chr6:52195795..52195825,-!p1@Hoxa11!1.10!11.51!Hoxa11;;chr1:19202185..19202187,+!p9@Tfap2b!1.10!11.51!Tfap2b;;chr6:52195763..52195792,-!p2@Hoxa11!1.09!11.32!Hoxa11;;chr6:52190858..52190873,-!p4@Hoxa10!1.09!11.19!Hoxa10;;chr15:97738692..97738747,-!p1@Vdr!1.07!59.70!Vdr;;chr2:74517742..74517758,+!p2@Hoxd11!1.07!10.69!Hoxd11;;chr2:74542918..74542971,+!p1@Hoxd8!1.06!15.94!Hoxd8;;chr2:74529998..74530020,+!p2@Hoxd10!1.05!10.31!Hoxd10;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!1.05!10.24!Sim1;;chr2:74536026..74536039,+!p1@Hoxd9!1.03!9.80!Hoxd9;;chr2:74542680..74542705,+!p6@Hoxd8!1.03!9.61!Hoxd8;;chr2:74517609..74517621,+!p3@Hoxd11!1.02!9.42!Hoxd11;;chr2:74543202..74543213,+!p3@Hoxd8!1.02!9.36!Hoxd8;;chr16:94085471..94085495,+!p1@Sim2!1.02!9.36!Sim2;;chr16:4594740..4594759,+!p1@Glis2!1.01!108.32!Glis2;;chr8:123640063..123640077,+!p1@Foxc2!1.01!16.82!Foxc2;;chr15:102828642..102828653,+!p2@Hoxc6!1.01!9.23!Hoxc6;;chr19:28754692..28754757,-!p1@Glis3!0.99!36.87!Glis3;;chr2:74550015..74550057,+!p2@Hoxd3!0.99!8.73!Hoxd3;;chr12:87762578..87762612,+!p1@Esrrb!0.98!8.60!Esrrb;;chr13:72101161..72101177,-!p2@Irx1!0.96!11.45!Irx1;;chr2:74543397..74543435,+!p2@Hoxd8!0.95!7.97!Hoxd8;;chr1:189432907..189432926,+!p3@Esrrg!0.94!7.71!Esrrg;;chr13:72766279..72766296,+!p2@Irx2!0.91!10.75!Irx2;;chr11:96143843..96143868,+!p3@Hoxb8!0.91!7.08!Hoxb8;;chr2:74543103..74543135,+!p4@Hoxd8!0.89!6.77!Hoxd8;;chr11:85646303..85646329,+!p1@Tbx2!0.88!46.35!Tbx2;;chr4:154010409..154010466,-!p2@Prdm16!0.88!16.13!Prdm16;;chr8:109817400..109817417,+!p1@Nfat5!0.87!142.16!Nfat5;;chr4:120488308..120488366,-!p1@Nfyc!0.87!39.21!Nfyc;;chr2:9809357..9809371,-!p2@Gata3!0.87!6.39!Gata3;;chr1:137155026..137155042,-!p1@Elf3!0.86!38.26!Elf3;;chr1:57029281..57029326,-!p1@Satb2!0.85!9.74!Satb2;;chr13:72766250..72766273,+!p1@Irx2!0.85!9.68!Irx2;;chr2:74560109..74560131,+!p1@Hoxd4!0.85!6.13!Hoxd4;;chr2:74542974..74542986,+!p5@Hoxd8!0.85!6.01!Hoxd8;;chr2:103264213..103264233,+!p1@Elf5!0.85!6.01!Elf5;;chr16:43363968..43364001,+!p7@Zbtb20!0.84!11.32!Zbtb20;;chr3:30408674..30408716,-!p2@Mecom!0.83!9.74!Mecom;;chr6:52167459..52167492,-!p1@Hoxa7!0.83!6.96!Hoxa7;;chr14:98568971..98569025,-!p1@Dach1!0.82!46.61!Dach1;;chr11:96145450..96145517,+!p2@Hoxb7!0.82!8.66!Hoxb7;;chr19:25746898..25746910,+!p1@Dmrt2!0.82!8.54!Dmrt2;;chr2:74520048..74520064,+!p1@Hoxd11!0.82!5.63!Hoxd11;;chr13:99124189..99124205,+!p1@Foxd1!0.81!8.66!Foxd1;;chr14:65994176..65994223,+!p9@Zfp395!0.81!5.50!Zfp395;;chr14:17407878..17407926,-!p1@Rarb!0.80!12.58!Rarb;;chr13:31650185..31650201,+!p1@Foxq1!0.79!19.29!Foxq1;;chr19:28754600..28754612,-!p2@Glis3!0.79!8.66!Glis3;;chr8:94325321..94325366,-!p1@Irx3!0.78!12.90!Irx3;;chr3:30408603..30408668,-!p1@Mecom!0.78!12.27!Mecom;;chr19:59532915..59532940,+!p5@Emx2!0.78!5.06!Emx2;;chr13:96093557..96093561,+!p6@Zbed3!0.78!5.06!Zbed3;;chr11:84339016..84339044,-!p1@Lhx1!0.78!5.06!Lhx1;;chr1:189433521..189433548,+!p5@Esrrg!0.78!5.00!Esrrg;;chr11:85646427..85646451,+!p4@Tbx2!0.77!9.04!Tbx2;;chr8:118231678..118231692,-!p2@Maf!0.76!47.68!Maf;;chr11:85646469..85646488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!p1@Zfp192!0.25!10.05!Zfp192;;chr11:70577930..70577985,+!p1@Zfp3!0.25!8.85!Zfp3;;chr2:130120884..130120972,+!p1@Ebf4!0.25!8.60!Ebf4;;chr7:5003165..5003203,+!p2@Zfp580!0.25!8.16!Zfp580;;chr18:65741358..65741415,+!p1@Zfp532!0.25!6.20!Zfp532;;chr17:34730333..34730362,+!p2@Pbx2!0.25!5.69!Pbx2;;chr6:48395825..48395846,-!p3@Zfp467!0.25!5.44!Zfp467;;chr17:21520689..21520730,+!p1@Zfp677!0.25!4.93!Zfp677;;chr16:44173384..44173407,+!p2@Gm608!0.25!3.35!Gm608;;chr4:54957886..54957907,+!p3@Zfp462!0.25!1.96!Zfp462;;chr2:115891521..115891532,-!p8@Meis2!0.25!1.52!Meis2;;chr7:122968213..122968266,-!p4@Sox6!0.25!1.08!Sox6;;chr6:52183482..52183486,-!p10@Hoxa10!0.25!0.76!Hoxa10;;chr5:138526401..138526410,+!p3@Zkscan1!0.25!0.76!Zkscan1;;chr16:94085162..94085179,+!p3@Sim2!0.25!0.76!Sim2;;chr12:87762732..87762747,+!p9@Esrrb!0.25!0.76!Esrrb;;chr12:87762625..87762637,+!p7@Esrrb!0.25!0.76!Esrrb;;chr11:69749437..69749467,+!p3@Ybx2!0.25!0.76!Ybx2;;chr12:4484016..4484074,-!p1@Ncoa1!0.24!25.36!Ncoa1;;chr15:81575569..81575599,+!p2@Zc3h7b!0.24!16.63!Zc3h7b;;chr7:30568977..30569047,+!p1@Zfp30!0.24!8.03!Zfp30;;chr9:96620228..96620308,-!p3@Zbtb38!0.24!6.70!Zbtb38;;chrX:45245679..45245702,-!p1@Smarca1!0.24!6.32!Smarca1;;chr13:67274092..67274140,+!p1@Rsl1!0.24!4.93!Rsl1;;chr4:120624269..120624302,-!p1@Zfp69!0.24!4.87!Zfp69;;chr14:22319053..22319105,+!p2@Myst4!0.24!4.49!Myst4;;chr7:87171047..87171078,+!p1@Zfp710!0.24!4.43!Zfp710;;chr2:181100223..181100237,+!p4@Zgpat!0.24!3.54!Zgpat;;chr8:92872242..92872285,-!p1@Tox3!0.24!3.23!Tox3;;chr4:148178529..148178548,+!p3@Casz1!0.24!2.91!Casz1;;chr1:170361730..170361769,-!p7@Pbx1!0.24!2.85!Pbx1;;chr6:108610766..108610781,+!p2@Bhlhe40!0.24!2.02!Bhlhe40;;chr8:24780125..24780143,+!p1@Zmat4!0.24!1.45!Zmat4;;chr8:79423672..79423727,+!p2@Nr3c2!0.24!1.20!Nr3c2;;chr11:44431369..44431389,+!p8@Ebf1!0.24!1.20!Ebf1;;chr10:107769219..107769226,+!p5@Pawr!0.24!1.14!Pawr;;chr11:121380611..121380625,-!p3@Zfp750!0.24!1.08!Zfp750;;chr4:128483422..128483430,-!p6@Zfp362!0.24!1.08!Zfp362;;chr15:50721942..50721987,-!p13@Trps1!0.24!1.01!Trps1;;chr2:77357593..77357606,-!p6@Zfp385b!0.24!0.95!Zfp385b;;chr6:108610610..108610676,+!p1@Bhlhe40!0.23!74.24!Bhlhe40;;chr10:67741461..67741483,-!p1@Arid5b!0.23!41.10!Arid5b;;chr2:165818125..165818167,+!p1@Ncoa3!0.23!40.22!Ncoa3;;chr2:166888107..166888224,-!p1@Znfx1!0.23!21.75!Znfx1;;chr2:169458192..169458247,+!p1@Tshz2!0.23!13.03!Tshz2;;chr8:81552152..81552208,+!p1@Zfp827!0.23!10.43!Zfp827;;chr8:72663347..72663398,+!p2@2310045N01Rik,p2@Mef2b!0.23!7.34!Mef2b;;chr2:92886297..92886329,-!p1@Prdm11!0.23!6.32!Prdm11;;chr13:37918773..37918818,+!p3@Rreb1!0.23!5.75!Rreb1;;chr3:14578741..14578759,+!p3@E2f5!0.23!3.35!E2f5;;chr9:63869751..63869767,-!p1@Smad6!0.23!3.23!Smad6;;chr4:118846454..118846506,-!p2@Zfp691!0.23!2.72!Zfp691;;chr1:170361991..170362015,-!p6@Pbx1!0.23!2.66!Pbx1;;chr5:122500142..122500167,-!p2@Cux2!0.23!2.47!Cux2;;chr17:4994491..4994531,+!p6@Arid1b!0.23!2.28!Arid1b;;chr17:37139455..37139469,+!p3@Zfp57!0.23!1.58!Zfp57;;chr10:107769719..107769745,+!p4@Pawr!0.23!1.52!Pawr;;chr11:98605517..98605539,+!p5@Thra!0.23!1.39!Thra;;chr1:173144144..173144176,+!p1@Nr1i3!0.23!0.70!Nr1i3;;chr1:19199221..19199234,+!p6@Tfap2b!0.23!0.70!Tfap2b;;chr2:115890864..115890869,-!p14@Meis2!0.23!0.70!Meis2;;chr15:35225873..35225889,+!p2@Osr2!0.23!0.70!Osr2;;chr16:38294929..38294940,-!p2@Nr1i2!0.23!0.70!Nr1i2;;chr5:77694479..77694574,+!p1@Rest!0.22!31.74!Rest;;chr18:70728080..70728160,+!p2@Mbd2!0.22!29.22!Mbd2;;chr3:152058955..152059023,+!p1@Gm8261,p1@Zzz3!0.22!18.09!Zzz3;;chr9:36954842..36954908,-!p1@Pknox2!0.22!16.69!Pknox2;;chr7:24993112..24993158,-!p1@Zfp111!0.22!14.86!Zfp111;;chr6:140572167..140572236,+!p2@Aebp2!0.22!14.42!Aebp2;;chr19:55816770..55816793,+!p2@Tcf7l2!0.22!12.39!Tcf7l2;;chr4:135840573..135840601,+!p1@Zfp46!0.22!11.13!Zfp46;;chr9:122832168..122832210,+!p1@Zfp105!0.22!10.88!Zfp105;;chr7:13063668..13063721,+!p1@Zfp606!0.22!9.93!Zfp606;;chr1:191994550..191994623,-!p1@Prox1!0.22!9.68!Prox1;;chr17:37139472..37139514,+!p1@Zfp57!0.22!9.36!Zfp57;;chr1:162964925..162964963,-!p1@Zbtb37!0.22!9.23!Zbtb37;;chr8:118230866..118230891,-!p4@Maf!0.22!9.11!Maf;;chr18:24145736..24145783,-!p1@Zscan30!0.22!6.70!Zscan30;;chr5:65194602..65194613,+!p3@Klf3!0.22!5.94!Klf3;;chr16:42875952..42875974,+!p4@Zbtb20!0.22!4.93!Zbtb20;;chr6:92041399..92041417,+!p2@Nr2c2!0.22!4.30!Nr2c2;;chr10:79390075..79390115,+!p2@Arid3a!0.22!4.30!Arid3a;;chr6:134780234..134780288,+!p1@Crebl2!0.22!4.11!Crebl2;;chr18:39649534..39649569,-!p3@Nr3c1!0.22!4.11!Nr3c1;;chr5:130175949..130175975,-!p1@Zfp11!0.22!3.41!Zfp11;;chr15:50721616..50721632,-!p4@Trps1!0.22!3.23!Trps1;;chr11:5761871..5761882,+!p3@Aebp1!0.22!3.16!Aebp1;;chrX:92906980..92907024,+!p2@Zc3h12b!0.22!3.04!Zc3h12b;;chr18:75528166..75528170,+!p3@Smad7!0.22!2.97!Smad7;;chr2:169458352..169458397,+!p3@Tshz2!0.22!2.97!Tshz2;;chr12:75009172..75009223,+!p3@Hif1a!0.22!2.91!Hif1a;;chr11:96690779..96690790,-!p3@Nfe2l1!0.22!2.85!Nfe2l1;;chr14:52639709..52639753,-!p5@Zfp219!0.22!2.53!Zfp219;;chr7:74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@Hoxa6!0.16!0.44!Hoxa6;;chr2:105002682..105002691,+!p10@Wt1!0.16!0.44!Wt1;;chr2:103264277..103264292,+!p3@Elf5!0.16!0.44!Elf5;;chr19:59534008..59534046,+!p7@Emx2!0.16!0.44!Emx2;;chr3:130813586..130813604,+!p7@Lef1!0.16!0.44!Lef1;;chr2:74529942..74529953,+!p4@Hoxd10!0.16!0.44!Hoxd10;;chr11:100553754..100553787,-!p1@Zfp385c!0.16!0.44!Zfp385c;;chr11:96132544..96132553,+!p6@Hoxb9!0.16!0.44!Hoxb9;;chr11:90252071..90252093,-!p7@Hlf!0.16!0.44!Hlf;;chr12:99985145..99985256,+!p1@Zc3h14!0.15!42.37!Zc3h14;;chr14:65568675..65568723,-!p1@Hmbox1!0.15!41.17!Hmbox1;;chr7:4947646..4947696,-!p1@Zfp579!0.15!34.21!Zfp579;;chr15:81641878..81641921,+!p1@Tef!0.15!32.69!Tef;;chr1:64167972..64168026,-!p1@Klf7!0.15!29.97!Klf7;;chr9:20297167..20297209,-!p1@Zfp426!0.15!29.22!Zfp426;;chr7:13404186..13404214,-!p1@Zfp329!0.15!24.54!Zfp329;;chr5:46248712..46248750,-!p1@Lcorl!0.15!18.78!Lcorl;;chr6:64992801..64992894,+!p2@Smarcad1!0.15!17.77!Smarcad1;;chr14:52935876..52935928,-!p1@Sall2!0.15!9.86!Sall2;;chr13:67601387..67601448,-!p2@Zfp58!0.15!9.74!Zfp58;;chr5:39075982..39076052,-!p1@Zfp518b!0.15!8.47!Zfp518b;;chr5:24107779..24107825,-!p1@Smarcd3!0.15!7.90!Smarcd3;;chr19:28085676..28085711,-!p2@Rfx3!0.15!7.15!Rfx3;;chr2:84877605..84877687,+!p3@Ssrp1!0.15!6.83!Ssrp1;;chr12:112088483..112088512,+!p1@Zfp839!0.15!6.70!Zfp839;;chr17:28314341..28314394,+!p2@Zfp523!0.15!6.64!Zfp523;;chr2:152223469..152223512,-!p1@Sox12!0.15!6.01!Sox12;;chr3:52072296..52072310,+!p3@Foxo1!0.15!5.63!Foxo1;;chr10:5958538..5958568,+!p1@Zbtb2!0.15!5.00!Zbtb2;;chr3:130813200..130813252,+!p1@Lef1!0.15!4.93!Lef1;;chr2:73730619..73730630,-!p4@Atf2,p4@LOC100047997!0.15!4.62!Atf2;;chr8:72520139..72520157,-!p6@Gatad2a!0.15!4.24!Gatad2a;;chr9:63869850..63869873,-!p2@Smad6!0.15!3.04!Smad6;;chr7:88138532..88138543,+!p3@Zfp592!0.15!2.91!Zfp592;;chr11:49016816..49016846,+!p2@Zfp62!0.15!2.91!Zfp62;;chr18:55152179..55152194,-!p5@Zfp608!0.15!2.85!Zfp608;;chr7:97591412..97591431,+!p2@Crebzf!0.15!2.53!Crebzf;;chr2:91077124..91077146,-!p3@Ddb2!0.15!2.53!Ddb2;;chr13:65380103..65380116,+!p3@Zfp369!0.15!2.40!Zfp369;;chr18:83080255..83080277,+!p4@Zfp516!0.15!2.34!Zfp516;;chr14:65977427..65977452,+!p4@Zfp395!0.15!2.28!Zfp395;;chr14:52935788..52935817,-!p2@Sall2!0.15!1.96!Sall2;;chr10:92773708..92773734,-!p3@Elk3!0.15!1.71!Elk3;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.15!1.58!D630045J12Rik;;chr3:135271185..135271254,-!p4@Nfkb1!0.15!1.52!Nfkb1;;chr18:3337399..3337422,-!p11@Crem!0.15!1.26!Crem;;chr8:72356384..72356434,+!p2@Pbx4!0.15!1.14!Pbx4;;chr11:52096750..52096772,-!p4@Tcf7!0.15!1.14!Tcf7;;chr2:70313168..70313184,+!p1@Sp5!0.15!1.08!Sp5;;chr8:118231350..118231385,-!p7@Maf!0.15!1.01!Maf;;chr9:19426719..19426729,+!p4@Zfp317!0.15!0.89!Zfp317;;chr2:17986337..17986349,+!p8@Mllt10!0.15!0.89!Mllt10;;chr1:69732511..69732540,-!p2@Ikzf2!0.15!0.82!Ikzf2;;chr3:96002383..96002407,-!p4@Bola1!0.15!0.82!Bola1;;chr19:23216166..23216191,+!p6@Klf9!0.15!0.82!Klf9;;chr18:76219161..76219176,+!p4@Zbtb7c!0.15!0.82!Zbtb7c;;chr7:123177377..123177409,-!p7@Sox6!0.15!0.76!Sox6;;chr6:128250380..128250442,-!p2@Tead4!0.15!0.76!Tead4;;chr1:69732682..69732719,-!p4@Ikzf2!0.15!0.70!Ikzf2;;chr4:154597177..154597195,-!p1@Ski!0.14!47.68!Ski;;chr4:149655682..149655742,+!p1@Rere!0.14!38.70!Rere;;chr2:18314363..18314465,-!p1@Dnajc1!0.14!30.16!Dnajc1;;chr15:81575487..81575561,+!p1@Zc3h7b!0.14!26.69!Zc3h7b;;chr8:109817363..109817383,+!p2@Nfat5!0.14!25.36!Nfat5;;chr5:53981912..53981942,+!p1@Rbpj!0.14!23.71!Rbpj;;chr6:116578973..116579022,-!p1@Zfp422!0.14!20.49!Zfp422;;chr15:102034070..102034124,+!p1@Zfp740!0.14!20.36!Zfp740;;chr10:13685899..13685916,+!p1@Hivep2!0.14!12.33!Hivep2;;chr15:96117968..96118035,+!p1@Arid2!0.14!11.07!Arid2;;
@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011419
 |is_obsolete=
-|library_ids=CNhs11206
+|library_id=CNhs11206
+|library_id_phase_based=2:CNhs11206
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;758
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;758
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N10.CNhs11206.758-6D5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N10.CNhs11206.758-6D5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N10.CNhs11206.758-6D5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N10.CNhs11206.758-6D5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N10.CNhs11206.758-6D5.mm9.nobarcode.rdna.fa.gz
 |name=kidney, neonate N10
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11206,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.576923628982111,0.0266298923127834,0.0403060411710864,0,0.0754409701586123,0,0.2697123631979,0.00414094808301782,0.0291743060330738,0,0,0.0553570333617515,0,0,0,0,0,0,0.0686728943482691,0,0,0,0,0.0266298923127834,0.0517208153718376,0,0,0,0,0,0,0,0.139146687700464,0,0.400999993656092,0,0.592052416717414,0.0266298923127834,0.011119551042816,0.0247781738562123,-0.0275124848382131,-0.654151328303554,-0.0742100349908963,0,0,0.471340515218464,0,0,0,0,0,0,0,0,0,0.22370557366274,0.0754409701586123,0,0,0,0,0,0.0391753538423105,0.0266298923127834,0.0266298923127834,0.0517208153718376,0.0413552898587332,0.101122779856079,0.0547263303689997,0.103412563896163,0.0517208153718376,0.000106100283844696,0.0348789488064537,0.126136292620142,0,0,0.0431706925072379,-0.0388613735130523,-0.240898305298586,0.040484578519228,0,0,0,0,0.0133149461563917,0.515412205110751,-0.121051938622268,-0.151604845110282,-0.0342821401282572,0.0266298923127834,0.195658603019455,0,0,0
@@ 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=table111:758-6D5;search_select_hide=table117:758-6D5
-|DRA_sample_Accession=CAGE@DRS008873
-|accession_numbers=DRX009010;DRR009884;DRZ001309;DRZ002692;CAGE
-|library_id=CNhs11206
 }}

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From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs11206

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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