FF:1353-25F3: Difference between revisions

Latest revision as of 19:01, 4 June 2020

Name:	kidney, neonate N25
Species:	Mouse (Mus musculus)
Library ID:	CNhs11122
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	kidney
dev stage	25 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		SAMD00005166

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11122		CAGE		DRX009012		DRR009886

Accession ID Mm9

Library id		BAM		CTSS
CNhs11122		DRZ001311		DRZ002694

Accession ID Mm10

Library id		BAM		CTSS
CNhs11122		DRZ012661		DRZ014044

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

CNhs11122

0	0
1	0
10	0
100	0
1000	0
1001	0.169
1002	0.572
1003	-0.0841
1004	0
1005	0
1006	0
1007	-0.0261
1008	0
1009	0.00611
101	-0.0788
1010	0
1011	0
1012	0.0207
1013	0.392
1014	-0.0218
1015	-0.239
1016	-0.153
1017	0
1018	0.118
1019	0
102	0
1020	0
1021	-0.0487
1022	0.422
1023	0
1024	0.341
1025	0
1026	0
1027	0
1028	0.0633
1029	0.239
103	0
1030	0
1031	-0.0365
1032	0.419
1033	-0.00316
1034	0.478
1035	0.0633
1036	-0.265
1037	0
1038	0.0955
1039	0.526
104	0
1040	0.162
1041	0.119

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: CNhs11122

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.124
MA0003.1	MA0003.1	0.254
MA0004.1	MA0004.1	0.574
MA0006.1	MA0006.1	0.0418
MA0007.1	MA0007.1	0.448
MA0009.1	MA0009.1	0.324
MA0014.1	MA0014.1	0.115
MA0017.1	MA0017.1	4.4864e-22
MA0018.2	MA0018.2	2.6847e-6
MA0019.1	MA0019.1	0.273
MA0024.1	MA0024.1	5.06949e-5
MA0025.1	MA0025.1	0.961
MA0027.1	MA0027.1	0.539
MA0028.1	MA0028.1	0.814
MA0029.1	MA0029.1	0.493
MA0030.1	MA0030.1	0.0303
MA0031.1	MA0031.1	0.00176
MA0035.2	MA0035.2	0.00151
MA0038.1	MA0038.1	0.396
MA0039.2	MA0039.2	0.0216
MA0040.1	MA0040.1	0.523
MA0041.1	MA0041.1	0.336
MA0042.1	MA0042.1	0.591
MA0043.1	MA0043.1	2.88617e-4
MA0046.1	MA0046.1	5.9426e-131
MA0047.2	MA0047.2	0.00229
MA0048.1	MA0048.1	0.362
MA0050.1	MA0050.1	0.0747
MA0051.1	MA0051.1	0.102
MA0052.1	MA0052.1	0.00455
MA0055.1	MA0055.1	0.335
MA0057.1	MA0057.1	0.434
MA0058.1	MA0058.1	0.421
MA0059.1	MA0059.1	0.904
MA0060.1	MA0060.1	0.0134
MA0061.1	MA0061.1	0.68
MA0062.2	MA0062.2	0.0493
MA0065.2	MA0065.2	1.69466e-12
MA0066.1	MA0066.1	0.537
MA0067.1	MA0067.1	0.442
MA0068.1	MA0068.1	0.715
MA0069.1	MA0069.1	0.472
MA0070.1	MA0070.1	0.796
MA0071.1	MA0071.1	0.00482
MA0072.1	MA0072.1	0.366
MA0073.1	MA0073.1	0.875
MA0074.1	MA0074.1	0.4
MA0076.1	MA0076.1	0.486
MA0077.1	MA0077.1	0.0334
MA0078.1	MA0078.1	0.00169
MA0079.2	MA0079.2	0.756
MA0080.2	MA0080.2	0.104
MA0081.1	MA0081.1	0.442
MA0083.1	MA0083.1	0.046
MA0084.1	MA0084.1	0.669
MA0087.1	MA0087.1	0.468
MA0088.1	MA0088.1	0.195
MA0090.1	MA0090.1	0.0012
MA0091.1	MA0091.1	0.35
MA0092.1	MA0092.1	0.0697
MA0093.1	MA0093.1	0.566
MA0099.2	MA0099.2	0.768
MA0100.1	MA0100.1	0.0227
MA0101.1	MA0101.1	0.437
MA0102.2	MA0102.2	0.679
MA0103.1	MA0103.1	0.00151
MA0104.2	MA0104.2	0.0887
MA0105.1	MA0105.1	0.707
MA0106.1	MA0106.1	0.308
MA0107.1	MA0107.1	0.507
MA0108.2	MA0108.2	8.57584e-5
MA0111.1	MA0111.1	0.817
MA0112.2	MA0112.2	5.3993e-4
MA0113.1	MA0113.1	0.415
MA0114.1	MA0114.1	2.54851e-27
MA0115.1	MA0115.1	6.09359e-4
MA0116.1	MA0116.1	0.766
MA0117.1	MA0117.1	0.823
MA0119.1	MA0119.1	0.0176
MA0122.1	MA0122.1	0.322
MA0124.1	MA0124.1	0.619
MA0125.1	MA0125.1	0.472
MA0131.1	MA0131.1	0.338
MA0135.1	MA0135.1	0.839
MA0136.1	MA0136.1	0.00428
MA0137.2	MA0137.2	0.981
MA0138.2	MA0138.2	0.972
MA0139.1	MA0139.1	0.136
MA0140.1	MA0140.1	0.0179
MA0141.1	MA0141.1	1.56514e-9
MA0142.1	MA0142.1	0.00475
MA0143.1	MA0143.1	0.911
MA0144.1	MA0144.1	0.618
MA0145.1	MA0145.1	4.9839e-4
MA0146.1	MA0146.1	0.175
MA0147.1	MA0147.1	0.0627
MA0148.1	MA0148.1	0.00426
MA0149.1	MA0149.1	0.0239
MA0150.1	MA0150.1	0.0656
MA0152.1	MA0152.1	0.05
MA0153.1	MA0153.1	6.46744e-57
MA0154.1	MA0154.1	0.0722
MA0155.1	MA0155.1	0.379
MA0156.1	MA0156.1	0.143
MA0157.1	MA0157.1	0.0286
MA0159.1	MA0159.1	0.0197
MA0160.1	MA0160.1	4.03364e-5
MA0162.1	MA0162.1	0.16
MA0163.1	MA0163.1	0.59
MA0164.1	MA0164.1	0.554
MA0258.1	MA0258.1	0.00554
MA0259.1	MA0259.1	0.137

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: CNhs11122

Novel motif	Logo	P-value
1	1	0.42
10	10	0.711
100	100	0.963
101	101	0.933
102	102	0.304
103	103	0.0224
104	104	0.609
105	105	0.62
106	106	0.122
107	107	0.102
108	108	0.0262
109	109	0.0226
11	11	0.263
110	110	0.21
111	111	0.67
112	112	0.0923
113	113	0.691
114	114	0.379
115	115	0.887
116	116	0.463
117	117	0.775
118	118	0.375
119	119	0.0849
12	12	0.847
120	120	0.268
121	121	0.716
122	122	0.299
123	123	0.0464
124	124	0.482
125	125	0.546
126	126	0.381
127	127	0.305
128	128	0.153
129	129	0.929
13	13	6.66475e-6
130	130	0.125
131	131	0.683
132	132	0.823
133	133	0.157
134	134	0.58
135	135	0.419
136	136	0.259
137	137	0.119
138	138	0.0364
139	139	0.341
14	14	0.176
140	140	0.234
141	141	0.701
142	142	0.831
143	143	0.361
144	144	0.148
145	145	0.131
146	146	0.492
147	147	0.57
148	148	0.481
149	149	0.285
15	15	0.184
150	150	0.178
151	151	0.488
152	152	0.0665
153	153	0.652
154	154	0.493
155	155	0.882
156	156	0.174
157	157	0.199
158	158	0.986
159	159	0.129
160	160	0.199
161	161	0.647
162	162	0.375
163	163	0.545
164	164	0.792
165	165	0.0171
166	166	0.804
167	167	0.762
168	168	0.926
169	169	0.00483
17	17	0.0412
18	18	0.0981
19	19	0.00466
2	2	0.204
20	20	0.798
21	21	0.835
22	22	0.0275
23	23	0.336
24	24	0.303
25	25	0.769
26	26	0.205
27	27	0.521
28	28	0.545
29	29	0.948
3	3	0.247
30	30	0.337
31	31	0.618
32	32	0.285
33	33	0.838
34	34	0.655
35	35	0.796
36	36	0.92
37	37	0.0412
38	38	0.329
39	39	0.402
4	4	0.701
40	40	0.356
41	41	0.253
42	42	0.886
43	43	0.287
44	44	0.816
45	45	0.261
46	46	0.694
47	47	0.44
48	48	0.226
49	49	0.177
5	5	0.851
50	50	0.965
51	51	0.61
52	52	0.0651
53	53	0.981
54	54	0.96
55	55	0.886
56	56	0.999
57	57	0.913
58	58	0.221
59	59	0.93
6	6	0.914
60	60	0.0298
61	61	0.489
62	62	0.313
63	63	0.345
64	64	0.982
65	65	0.311
66	66	0.424
67	67	0.103
68	68	0.81
69	69	0.667
7	7	0.0652
70	70	0.19
71	71	0.363
72	72	0.871
73	73	0.111
74	74	0.348
75	75	0.554
76	76	0.536
77	77	0.0814
78	78	0.0772
79	79	0.402
8	8	0.896
80	80	0.367
81	81	0.557
82	82	0.385
83	83	0.599
84	84	0.325
85	85	0.0201
86	86	0.528
87	87	0.254
88	88	0.726
89	89	0.736
9	9	0.756
90	90	0.327
91	91	0.41
92	92	0.607
93	93	0.813
94	94	0.203
95	95	0.575
96	96	0.34
97	97	0.368
98	98	0.33
99	99	0.376

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: CNhs11122

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011482 mouse kidney- neonate N25 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)
0000309 (mouse neonate N25 sample)
0011482 (mouse kidney- neonate N25 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@DRS008875
+|DRA_sample_Accession=CAGE@SAMD00005166
-|accession_numbers=CAGE;DRX009012;DRR009886;DRZ001311;DRZ002694
+|accession_numbers=CAGE;DRX009012;DRR009886;DRZ001311;DRZ002694;DRZ012661;DRZ014044
 |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 9: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:83664365..83664383,+!p1@Hnf1b!1.97!92.32!Hnf1b;;chr10:88969376..88969395,-!p1@Nr1h4!1.93!83.84!Nr1h4;;chr2:163372884..163372904,+!p1@Hnf4a!1.85!69.24!Hnf4a;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.74!148.36!Tfcp2l1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.68!59.35!Pou3f3;;chr2:24331085..24331100,-!p1@Pax8!1.67!46.16!Pax8;;chr10:22539932..22539956,-!p1@Tcf21!1.59!97.65!Tcf21;;chr11:96143666..96143725,+!p1@Hoxb8!1.59!43.49!Hoxb8;;chr11:34108085..34108092,-!p1@Foxi1!1.57!36.42!Foxi1;;chr15:102828658..102828678,+!p1@Hoxc6!1.57!36.42!Hoxc6;;chr6:52190467..52190500,-!p1@Hoxa10!1.55!34.38!Hoxa10;;chr10:30491690..30491727,-!p5@Ncoa7!1.49!30.14!Ncoa7;;chr15:97738692..97738747,-!p1@Vdr!1.48!152.92!Vdr;;chr1:19202352..19202354,+!p2@Tfap2b!1.45!27.47!Tfap2b;;chr6:52176164..52176195,-!p1@Hoxa9!1.43!32.18!Hoxa9;;chr11:96153767..96153822,+!p1@Hoxb6!1.40!36.74!Hoxb6;;chr5:135582751..135582788,+!p1@Mlxipl!1.38!88.86!Mlxipl;;chr6:38097380..38097407,-!p6@D630045J12Rik!1.37!22.29!D630045J12Rik;;chr5:115421065..115421088,-!p1@Hnf1a!1.36!21.82!Hnf1a;;chr6:85137520..85137563,+!p1@Emx1!1.33!20.25!Emx1;;chr2:74529970..74529997,+!p1@Hoxd10!1.32!20.10!Hoxd10;;chr1:189432881..189432903,+!p2@Esrrg!1.30!18.84!Esrrg;;chr12:87762578..87762612,+!p1@Esrrb!1.29!18.68!Esrrb;;chr6:97879817..97879857,+!p2@Mitf!1.27!17.43!Mitf;;chr8:118231678..118231692,-!p2@Maf!1.23!141.77!Maf;;chr1:189433521..189433548,+!p5@Esrrg!1.23!15.86!Esrrg;;chr19:59533221..59533271,+!p1@Emx2!1.22!19.00!Emx2;;chr2:74549968..74549996,+!p1@Hoxd3!1.21!19.15!Hoxd3;;chr6:52190840..52190853,-!p5@Hoxa10!1.20!14.91!Hoxa10;;chr1:189432907..189432926,+!p3@Esrrg!1.19!14.60!Esrrg;;chr2:74542680..74542705,+!p6@Hoxd8!1.15!13.19!Hoxd8;;chr2:103143336..103143367,-!p1@Ehf!1.09!18.21!Ehf;;chr11:96147952..96147967,+!p1@Hoxb7!1.09!14.29!Hoxb7;;chr1:19199236..19199258,+!p1@Tfap2b!1.09!11.30!Tfap2b;;chr2:74543397..74543435,+!p2@Hoxd8!1.07!10.83!Hoxd8;;chr11:84339016..84339044,-!p1@Lhx1!1.06!10.52!Lhx1;;chr2:77357622..77357704,-!p1@Zfp385b!1.05!28.10!Zfp385b;;chr3:30408674..30408716,-!p2@Mecom!1.05!16.96!Mecom;;chr13:72101178..72101203,-!p1@Irx1!1.04!15.54!Irx1;;chr6:52163319..52163342,-!p1@Hoxa3!1.03!14.13!Hoxa3;;chr1:19202185..19202187,+!p9@Tfap2b!1.02!9.42!Tfap2b;;chr4:154010409..154010466,-!p2@Prdm16!1.00!21.19!Prdm16;;chr2:74543202..74543213,+!p3@Hoxd8!1.00!8.95!Hoxd8;;chr2:74536026..74536039,+!p1@Hoxd9!1.00!8.95!Hoxd9;;chr19:44831390..44831414,+!p1@Pax2!1.00!8.95!Pax2;;chr16:43363968..43364001,+!p7@Zbtb20!0.99!16.33!Zbtb20;;chr10:102491405..102491416,-!p1@Alx1!0.99!8.79!Alx1;;chr4:120488308..120488366,-!p1@Nfyc!0.98!50.24!Nfyc;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!0.98!8.63!Sim1;;chr8:118231705..118231722,-!p3@Maf!0.97!68.29!Maf;;chr1:137155026..137155042,-!p1@Elf3!0.97!49.45!Elf3;;chr19:28754692..28754757,-!p1@Glis3!0.97!35.80!Glis3;;chr16:94085471..94085495,+!p1@Sim2!0.97!8.32!Sim2;;chr2:74542918..74542971,+!p1@Hoxd8!0.96!12.56!Hoxd8;;chr2:9800207..9800234,-!p1@Gata3!0.95!24.96!Gata3;;chr2:74529998..74530020,+!p2@Hoxd10!0.95!7.85!Hoxd10;;chr2:103123925..103123959,-!p3@Ehf!0.95!7.85!Ehf;;chr16:43363152..43363186,+!p3@Zbtb20!0.93!17.58!Zbtb20;;chr2:104966766..104966786,+!p1@Wt1!0.91!11.62!Wt1;;chr3:3508024..3508069,+!p2@Hnf4g!0.91!7.22!Hnf4g;;chr11:83666422..83666446,+!p4@Hnf1b!0.91!7.22!Hnf1b;;chr2:163372869..163372882,+!p3@Hnf4a!0.91!7.06!Hnf4a;;chr16:4594740..4594759,+!p1@Glis2!0.89!81.33!Glis2;;chr3:30408603..30408668,-!p1@Mecom!0.88!15.70!Mecom;;chr15:102828642..102828653,+!p2@Hoxc6!0.88!6.59!Hoxc6;;chr13:72101161..72101177,-!p2@Irx1!0.87!9.11!Irx1;;chr12:87702062..87702081,+!p4@Esrrb!0.87!6.44!Esrrb;;chr6:52184901..52184959,-!p2@Hoxa10!0.87!6.44!Hoxa10;;chr10:30491648..30491657,-!p15@Ncoa7!0.87!6.44!Ncoa7;;chr1:57029281..57029326,-!p1@Satb2!0.86!10.05!Satb2;;chr16:43247391..43247422,+!p12@Zbtb20!0.86!6.28!Zbtb20;;chr11:96145450..96145517,+!p2@Hoxb7!0.85!9.42!Hoxb7;;chr6:52167459..52167492,-!p1@Hoxa7!0.85!7.38!Hoxa7;;chr19:59532915..59532940,+!p5@Emx2!0.85!6.12!Emx2;;chr15:85566184..85566238,+!p1@Ppara!0.83!8.95!Ppara;;chr15:85602581..85602598,+!p8@Ppara!0.83!5.81!Ppara;;chr2:74543103..74543135,+!p4@Hoxd8!0.83!5.81!Hoxd8;;chr8:118231723..118231740,-!p1@Maf!0.82!134.70!Maf;;chr4:107107224..107107259,+!p2@Glis1!0.82!5.65!Glis1;;chr6:38097421..38097440,-!p7@D630045J12Rik!0.82!5.65!D630045J12Rik;;chr16:38294860..38294924,-!p1@Nr1i2!0.81!5.49!Nr1i2;;chr2:74542589..74542602,+!p8@Hoxd8!0.81!5.49!Hoxd8;;chr11:83665637..83665671,+!p6@Hnf1b!0.81!5.49!Hnf1b;;chr2:164829847..164829859,-!p5@Ncoa5!0.80!5.34!Ncoa5;;chr8:79426176..79426275,+!p1@Nr3c2!0.79!27.79!Nr3c2;;chr11:96160426..96160443,+!p2@Hoxb6!0.79!5.18!Hoxb6;;chr16:43363190..43363242,+!p2@Zbtb20!0.78!16.48!Zbtb20;;chr3:29912058..29912071,-!p6@Mecom!0.77!5.65!Mecom;;chr2:74549945..74549965,+!p4@Hoxd3!0.77!4.87!Hoxd3;;chr6:52190668..52190682,-!p3@Hoxa10!0.77!4.87!Hoxa10;;chr11:98636531..98636559,-!p1@Nr1d1!0.76!29.83!Nr1d1;;chr6:85137505..85137517,+!p2@Emx1!0.76!4.71!Emx1;;chr6:52195763..52195792,-!p2@Hoxa11!0.76!4.71!Hoxa11;;chr15:35225845..35225867,+!p1@Osr2!0.75!12.40!Osr2;;chr10:30375579..30375616,-!p3@Ncoa7!0.75!11.77!Ncoa7;;chr6:90412582..90412601,+!p1@Klf15!0.74!23.24!Klf15;;chr2:160698288..160698358,-!p3@Zhx3!0.74!15.23!Zhx3;;chr8:94325321..94325366,-!p1@Irx3!0.74!11.77!Irx3;;chr19:28754600..28754612,-!p2@Glis3!0.74!7.54!Glis3;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.74!4.55!Pou3f3;;chr2:9809357..9809371,-!p2@Gata3!0.74!4.55!Gata3;;chr11:96143962..96144035,+!p2@Hoxb8!0.74!4.55!Hoxb8;;chr14:22807107..22807119,-!p2@Zfp503!0.73!20.88!Zfp503;;chr14:17407878..17407926,-!p1@Rarb!0.73!10.68!Rarb;;chr13:72766279..72766296,+!p2@Irx2!0.73!6.75!Irx2;;chr11:98614335..98614349,+!p8@Thra!0.73!4.40!Thra;;chr2:74542882..74542894,+!p10@Hoxd8!0.73!4.40!Hoxd8;;chr2:74535796..74535808,+!p3@Hoxd9!0.73!4.40!Hoxd9;;chr11:90252223..90252240,-!p1@Hlf!0.72!39.56!Hlf;;chr11:85646303..85646329,+!p1@Tbx2!0.72!31.56!Tbx2;;chr11:85646469..85646488,+!p5@Tbx2!0.72!6.59!Tbx2;;chr6:52167513..52167549,-!p2@Hoxa7!0.72!6.28!Hoxa7;;chr16:43236133..43236154,+!p17@Zbtb20!0.72!5.02!Zbtb20;;chr11:83664334..83664353,+!p2@Hnf1b!0.72!4.24!Hnf1b;;chr10:102491237..102491291,-!p2@Alx1!0.72!4.24!Alx1;;chr6:85137491..85137504,+!p3@Emx1!0.71!4.08!Emx1;;chr1:189432857..189432870,+!p7@Esrrg!0.71!4.08!Esrrg;;chr2:103264213..103264233,+!p1@Elf5!0.71!4.08!Elf5;;chr2:74517742..74517758,+!p2@Hoxd11!0.71!4.08!Hoxd11;;chr17:87153240..87153254,+!p1@Epas1!0.70!89.02!Epas1;;chr16:43619101..43619151,+!p6@Zbtb20!0.70!10.52!Zbtb20;;chr8:94325814..94325839,-!p2@Irx3!0.69!8.95!Irx3;;chr10:5734907..5734920,-!p11@Esr1!0.69!3.92!Esr1;;chr2:103252231..103252256,+!p4@Elf5!0.69!3.92!Elf5;;chr11:100800641..100800669,-!p3@Stat3!0.68!7.06!Stat3;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.68!6.91!Hoxb2;;chr14:22807216..22807231,-!p3@Zfp503!0.68!6.91!Zfp503;;chr15:85566051..85566080,+!p4@Ppara!0.68!4.55!Ppara;;chr6:38097369..38097379,-!p11@D630045J12Rik!0.68!3.77!D630045J12Rik;;chr3:98186461..98186476,+!p2@Zfp697!0.68!3.77!Zfp697;;chr11:96143843..96143868,+!p3@Hoxb8!0.68!3.77!Hoxb8;;chr11:90250894..90250916,-!p5@Hlf!0.68!3.77!Hlf;;chr7:77511234..77511302,-!p2@Nr2f2!0.67!28.26!Nr2f2;;chr13:31650185..31650201,+!p1@Foxq1!0.67!14.44!Foxq1;;chr13:72766250..72766273,+!p1@Irx2!0.67!6.12!Irx2;;chr14:22808697..22808715,-!p4@Zfp503!0.67!4.40!Zfp503;;chr11:121380640..121380655,-!p1@Zfp750!0.66!6.28!Zfp750;;chr13:96093557..96093561,+!p6@Zbed3!0.66!3.61!Zbed3;;chr3:3508005..3508021,+!p3@Hnf4g!0.66!3.61!Hnf4g;;chr2:74560109..74560131,+!p1@Hoxd4!0.66!3.61!Hoxd4;;chr16:43619057..43619078,+!p8@Zbtb20!0.65!7.85!Zbtb20;;chr9:106355684..106355744,+!p5@Pcbp4!0.65!5.65!Pcbp4;;chr6:52176144..52176161,-!p2@Hoxa9!0.65!3.45!Hoxa9;;chr1:120524563..120524591,+!p2@Tfcp2l1!0.65!3.45!Tfcp2l1;;chr14:22807083..22807104,-!p1@Zfp503!0.64!69.08!Zfp503;;chr4:148275237..148275311,+!p2@Casz1!0.63!15.70!Casz1;;chr11:90250944..90250982,-!p2@Hlf!0.63!5.97!Hlf;;chr2:91035254..91035271,-!p3@Nr1h3!0.63!4.24!Nr1h3;;chr13:72101141..72101158,-!p3@Irx1!0.63!4.24!Irx1;;chr11:100800621..100800633,-!p5@Stat3!0.63!3.92!Stat3;;chr2:74536050..74536065,+!p2@Hoxd9!0.63!3.30!Hoxd9;;chr4:133109285..133109308,+!p1@Nr0b2!0.63!3.30!Nr0b2;;chr15:81633165..81633188,+!p2@Tef!0.62!30.93!Tef;;chr17:87153028..87153049,+!p2@Epas1!0.61!75.52!Epas1;;chr11:85646341..85646352,+!p3@Tbx2!0.61!6.75!Tbx2;;chr19:25746898..25746910,+!p1@Dmrt2!0.61!4.87!Dmrt2;;chr3:30408384..30408431,-!p4@Mecom!0.61!4.08!Mecom;;chr14:18493386..18493464,+!p1@Thrb!0.60!13.34!Thrb;;chr16:43363837..43363842,+!p11@Zbtb20!0.60!6.12!Zbtb20;;chr2:74543235..74543246,+!p7@Hoxd8!0.60!2.98!Hoxd8;;chr7:119885539..119885574,+!p3@Tead1!0.60!2.98!Tead1;;chr6:52190858..52190873,-!p4@Hoxa10!0.60!2.98!Hoxa10;;chr11:96690797..96690813,-!p1@Nfe2l1!0.59!67.98!Nfe2l1;;chr2:152758901..152758925,-!p1@Foxs1!0.59!15.07!Foxs1;;chr16:44173384..44173407,+!p2@Gm608!0.59!8.63!Gm608;;chr7:77511403..77511450,-!p3@Nr2f2!0.59!6.91!Nr2f2;;chr8:123640063..123640077,+!p1@Foxc2!0.59!5.81!Foxc2;;chr1:87546583..87546595,+!p1@Sp100!0.59!4.40!Sp100;;chr10:88996336..88996380,-!p2@Nr1h4!0.59!3.77!Nr1h4;;chr14:98568971..98569025,-!p1@Dach1!0.58!26.06!Dach1;;chr11:70043257..70043263,-!p1@Bcl6b!0.58!5.34!Bcl6b;;chr10:5734717..5734727,-!p12@Esr1!0.58!2.83!Esr1;;chr6:52167434..52167450,-!p3@Hoxa7!0.58!2.83!Hoxa7;;chr15:102797288..102797302,+!p1@Hoxc10!0.58!2.83!Hoxc10;;chr12:75002389..75002406,+!p4@Hif1a!0.58!2.83!Hif1a;;chr1:19199021..19199048,+!p8@Tfap2b!0.58!2.83!Tfap2b;;chr2:103143315..103143328,-!p2@Ehf!0.58!2.83!Ehf;;chr2:74542974..74542986,+!p5@Hoxd8!0.58!2.83!Hoxd8;;chr2:74550015..74550057,+!p2@Hoxd3!0.58!2.83!Hoxd3;;chr15:76709662..76709676,+!p2@Zfp7!0.57!6.44!Zfp7;;chr11:85646427..85646451,+!p4@Tbx2!0.57!5.34!Tbx2;;chr18:24178808..24178865,-!p2@Zfp191!0.56!17.43!Zfp191;;chr13:99124189..99124205,+!p1@Foxd1!0.56!4.40!Foxd1;;chr2:74517609..74517621,+!p3@Hoxd11!0.56!2.67!Hoxd11;;chr10:30522690..30522752,-!p2@Ncoa7!0.55!19.31!Ncoa7;;chr6:38204087..382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Mecom;;chr2:77357593..77357606,-!p6@Zfp385b!0.33!1.41!Zfp385b;;chr17:47873985..47874056,+!p1@Tfeb!0.32!15.07!Tfeb;;chr1:191994550..191994623,-!p1@Prox1!0.32!12.56!Prox1;;chr8:118230866..118230891,-!p4@Maf!0.32!11.77!Maf;;chr6:37392159..37392172,-!p2@Creb3l2!0.32!8.01!Creb3l2;;chr5:125538737..125538781,-!p2@Ncor2!0.32!6.12!Ncor2;;chr17:13897299..13897342,+!p3@Mllt4!0.32!3.61!Mllt4;;chr4:102787521..102787588,+!p4@Mier1!0.32!2.67!Mier1;;chr13:37918661..37918673,+!p17@Rreb1!0.32!1.41!Rreb1;;chr15:35225873..35225889,+!p2@Osr2!0.32!1.10!Osr2;;chr4:53792566..53792578,+!p1@Tal2!0.32!1.10!Tal2;;chr4:84192360..84192376,-!p8@Bnc2!0.32!1.10!Bnc2;;chr2:103264245..103264268,+!p2@Elf5!0.32!1.10!Elf5;;chr1:19199221..19199234,+!p6@Tfap2b!0.32!1.10!Tfap2b;;chr1:19199064..19199075,+!p10@Tfap2b!0.32!1.10!Tfap2b;;chr1:173144100..173144138,+!p2@Nr1i3!0.32!1.10!Nr1i3;;chr19:59534008..59534046,+!p7@Emx2!0.32!1.10!Emx2;;chr18:81183755..81183761,-!p1@Sall3!0.32!1.10!Sall3;;chr19:23215616..23215627,+!p9@Klf9!0.32!1.10!Klf9;;chr16:43235969..43235989,+!p20@Zbtb20!0.32!1.10!Zbtb20;;chr10:30522660..30522671,-!p10@Ncoa7!0.32!1.10!Ncoa7;;chr6:38097441..38097447,-!p13@D630045J12Rik!0.32!1.10!D630045J12Rik;;chr5:115420882..115420896,-!p3@Hnf1a!0.32!1.10!Hnf1a;;chr2:75542527..75542590,-!p1@Nfe2l2!0.31!166.42!Nfe2l2;;chr3:152059628..152059666,+!p2@Gm8261,p2@Zzz3!0.31!15.54!Zzz3;;chr17:71199121..71199165,-!p2@Tgif1!0.31!12.56!Tgif1;;chr6:38204109..38204155,-!p1@D630045J12Rik!0.31!9.26!D630045J12Rik;;chr16:44173352..44173383,+!p1@Gm608!0.31!8.63!Gm608;;chr17:15701286..15701323,-!p1@Prdm9!0.31!6.59!Prdm9;;chr7:91558392..91558434,-!p1@Arnt2!0.31!4.40!Arnt2;;chr15:57526316..57526332,+!p4@Zhx2!0.31!3.61!Zhx2;;chr4:62626682..62626705,+!p2@Zfp618!0.31!3.45!Zfp618;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!0.31!2.67!Zbtb38;;chr18:76219118..76219155,+!p1@Zbtb7c!0.31!2.51!Zbtb7c;;chr2:165818125..165818167,+!p1@Ncoa3!0.30!47.26!Ncoa3;;chr2:160698721..160698745,-!p1@Zhx3!0.30!25.59!Zhx3;;chr5:104183173..104183207,+!p1@Aff1!0.30!23.55!Aff1;;chr4:62626594..62626651,+!p1@Zfp618!0.30!6.12!Zfp618;;chr14:79881330..79881415,+!p3@Elf1!0.30!5.34!Elf1;;chr15:10400245..10400282,-!p2@Dnajc21!0.30!5.34!Dnajc21;;chr18:75979866..75979890,+!p3@Zbtb7c!0.30!2.98!Zbtb7c;;chr1:133914326..133914346,+!p8@Elk4!0.30!2.51!Elk4;;chr4:45024818..45024846,-!p4@Zbtb5!0.30!2.51!Zbtb5;;chr15:50721211..50721234,-!p6@Trps1!0.30!2.20!Trps1;;chr7:52963269..52963305,+!p4@Dbp!0.30!1.73!Dbp;;chr19:5560600..5560617,-!p1@Ovol1!0.30!1.41!Ovol1;;chr6:52663725..52663794,+!p1@Tax1bp1!0.29!263.29!Tax1bp1;;chr2:166888107..166888224,-!p1@Znfx1!0.29!25.28!Znfx1;;chr7:120351014..120351109,+!p1@Arntl!0.29!23.86!Arntl;;chr13:44826694..44826710,+!p3@Jarid2!0.29!18.84!Jarid2;;chr17:34730333..34730362,+!p2@Pbx2!0.29!6.28!Pbx2;;chr7:134169741..134169760,-!p10@Maz!0.29!4.55!Maz;;chr2:115891454..115891471,-!p3@Meis2!0.29!4.55!Meis2;;chr2:165818108..165818119,+!p2@Ncoa3!0.29!3.77!Ncoa3;;chr1:52176406..52176433,+!p2@Stat1!0.29!3.61!Stat1;;chr4:97439519..97439539,+!p11@Nfia!0.29!2.98!Nfia;;chr8:94881733..94881790,+!p1@Irx5!0.29!2.67!Irx5;;chr7:25917492..25917512,-!p1@Pou2f2!0.29!2.20!Pou2f2;;chr9:69137709..69137714,+!p7@Rora!0.29!1.41!Rora;;chr8:94325273..94325288,-!p5@Irx3!0.29!1.41!Irx3;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.29!1.41!Hoxb2;;chr2:180069370..180069409,-!p1@Gata5!0.29!1.26!Gata5;;chr2:105003277..105003280,+!p5@Wt1!0.29!0.94!Wt1;;chr2:74536003..74536008,+!p7@Hoxd9!0.29!0.94!Hoxd9;;chr14:17408022..17408043,-!p6@Rarb!0.29!0.94!Rarb;;chr12:87762617..87762622,+!p13@Esrrb!0.29!0.94!Esrrb;;chr13:40825465..40825469,-!p2@Tfap2a!0.29!0.94!Tfap2a;;chr12:75002335..75002352,+!p7@Hif1a!0.29!0.94!Hif1a;;chr15:85602655..85602680,+!p5@Ppara!0.29!0.94!Ppara;;chr11:96164821..96164865,+!p1@Hoxb5!0.29!0.94!Hoxb5;;chr6:38097449..38097457,-!p16@D630045J12Rik!0.29!0.94!D630045J12Rik;;chr5:120130377..120130432,+!p10@Tbx3!0.29!0.94!Tbx3;;chr7:25917459..25917474,-!p2@Pou2f2!0.29!0.94!Pou2f2;;chr7:77511928..77511937,-!p12@Nr2f2!0.29!0.94!Nr2f2;;chr1:181476358..181476391,-!p1@Tfb2m!0.28!26.38!Tfb2m;;chr5:134790548..134790591,-!p3@Gtf2i!0.28!18.84!Gtf2i;;chr14:55482892..55482988,-!p1@Homez!0.28!11.15!Homez;;chr19:26679596..26679607,+!p8@Smarca2!0.28!2.83!Smarca2;;chr5:147760297..147760304,+!p4@Gtf3a!0.28!2.35!Gtf3a;;chr5:92391948..92391968,+!p3@Thap6!0.28!1.88!Thap6;;chr10:127176667..127176679,+!p2@Zbtb39!0.28!1.88!Zbtb39;;chr1:4486530..4486557,-!p4@Sox17!0.28!1.41!Sox17;;chr6:52664406..52664434,+!p3@Tax1bp1!0.28!1.26!Tax1bp1;;chr6:37392095..37392154,-!p1@Creb3l2!0.27!52.44!Creb3l2;;chr15:36937137..36937157,-!p2@Gm10193,p2@Zfp706!0.27!50.87!Zfp706;;chr5:67698180..67698216,+!p1@Slc30a9!0.27!43.80!Slc30a9;;chr5:137043177..137043190,-!p2@Cux1!0.27!13.34!Cux1;;chr3:95021612..95021650,-!p2@Gabpb2!0.27!7.85!Gabpb2;;chr5:9160908..9160912,-!p2@Dmtf1!0.27!6.28!Dmtf1;;chr2:44968721..44968734,-!p6@Zeb2!0.27!5.65!Zeb2;;chr11:96690779..96690790,-!p3@Nfe2l1!0.27!3.30!Nfe2l1;;chr6:39068181..39068206,-!p3@Parp12!0.2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@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11122
+|library_id_phase_based=2:CNhs11122
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1353
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1353
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N25.CNhs11122.1353-25F3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N25.CNhs11122.1353-25F3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N25.CNhs11122.1353-25F3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N25.CNhs11122.1353-25F3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N25.CNhs11122.1353-25F3.mm9.nobarcode.rdna.fa.gz
 |name=kidney, neonate N25
 |namespace=FANTOM5
@@ Line 49: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11122,LSID734,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.699719205139173,0.0311096316228697,0.0247766929008436,0,0,0.0633328814307688,0.55612632832998,0,0.0316664407153844,0,0,-0.0843392403965415,0,0,0,0,0,0,0.312982689859057,0,0,0,0,0.0422092184599547,0.0633328814307688,0,0,0,0,0,0,0,0.209990376633196,0,0.914974381383991,0,1.09554965935881,0,0.0423139473544717,-0.022916821438831,-0.132822085117989,-0.816599820518864,-0.0582155949321922,0,0,0.167611545958962,0,0,0,0,0,0,0,0.118594524292246,0,0.256005048499426,0,0,0,0,0.118594524292246,0,0.204965486776856,0,0.0633328814307688,0.0472191249198448,0.0059140107525925,0.194225383402246,0.22446421845182,0.0866443079427335,0.0633328814307688,0.110559707099912,-0.00895929169740983,0.118594524292246,0.118594524292246,0,0,-0.10181810960796,-0.0910388399989378,0.132821448238252,0,0,0,0,0.059297262146123,0.409930973553713,-0.0940408059574807,-0.117616467284638,-0.0249919312204851,0,0.969459366449707,0,0,0.0316664407153844
@@ Line 86: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1353-25F3;search_select_hide=table117:1353-25F3
 }}

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FF:1353-25F3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:01, 4 June 2020

CNhs11122

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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