FF:483-18I2: Difference between revisions

Latest revision as of 19:17, 4 June 2020

Name:	kidney, embryo E17
Species:	Mouse (Mus musculus)
Library ID:	CNhs11028
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	kidney
dev stage	17 days embryo
sex	mixture
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005742

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11028		CAGE		DRX009007		DRR009881

Accession ID Mm9

Library id		BAM		CTSS
CNhs11028		DRZ001306		DRZ002689

Accession ID Mm10

Library id		BAM		CTSS
CNhs11028		DRZ012656		DRZ014039

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

CNhs11028

0	0
1	0
10	0
100	0
1000	0
1001	0.0395
1002	0.504
1003	0.00599
1004	0
1005	-0.0382
1006	0.0366
1007	0.111
1008	0
1009	0.0171
101	0.0824
1010	0
1011	0
1012	0
1013	-0.0296
1014	0.305
1015	0.143
1016	0.206
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.0216
1023	0
1024	0.0805
1025	0.12
1026	0
1027	0
1028	0
1029	0.321
103	0.0907
1030	0
1031	0.353
1032	0.0135
1033	0.014
1034	0
1035	0.0805
1036	0.164
1037	0
1038	0.053
1039	0.0305
104	0
1040	0.195
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression Analyst: Michiel de Hoon link to dataset. data

library id: CNhs11028

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00344
MA0003.1	MA0003.1	0.848
MA0004.1	MA0004.1	0.481
MA0006.1	MA0006.1	0.464
MA0007.1	MA0007.1	0.492
MA0009.1	MA0009.1	0.563
MA0014.1	MA0014.1	0.788
MA0017.1	MA0017.1	0.182
MA0018.2	MA0018.2	5.0839e-6
MA0019.1	MA0019.1	0.812
MA0024.1	MA0024.1	9.40417e-6
MA0025.1	MA0025.1	1.31749e-4
MA0027.1	MA0027.1	0.548
MA0028.1	MA0028.1	0.674
MA0029.1	MA0029.1	0.199
MA0030.1	MA0030.1	0.722
MA0031.1	MA0031.1	0.31
MA0035.2	MA0035.2	2.59498e-5
MA0038.1	MA0038.1	0.484
MA0039.2	MA0039.2	0.172
MA0040.1	MA0040.1	0.409
MA0041.1	MA0041.1	0.177
MA0042.1	MA0042.1	0.437
MA0043.1	MA0043.1	0.00157
MA0046.1	MA0046.1	2.35814e-69
MA0047.2	MA0047.2	0.942
MA0048.1	MA0048.1	1.68431e-4
MA0050.1	MA0050.1	2.98739e-4
MA0051.1	MA0051.1	3.30283e-5
MA0052.1	MA0052.1	0.0028
MA0055.1	MA0055.1	0.00282
MA0057.1	MA0057.1	0.531
MA0058.1	MA0058.1	0.35
MA0059.1	MA0059.1	0.864
MA0060.1	MA0060.1	0.0067
MA0061.1	MA0061.1	0.088
MA0062.2	MA0062.2	2.00038e-4
MA0065.2	MA0065.2	0.639
MA0066.1	MA0066.1	0.968
MA0067.1	MA0067.1	0.0594
MA0068.1	MA0068.1	0.737
MA0069.1	MA0069.1	0.0947
MA0070.1	MA0070.1	0.64
MA0071.1	MA0071.1	0.237
MA0072.1	MA0072.1	0.00466
MA0073.1	MA0073.1	0.789
MA0074.1	MA0074.1	0.737
MA0076.1	MA0076.1	0.187
MA0077.1	MA0077.1	0.436
MA0078.1	MA0078.1	0.0878
MA0079.2	MA0079.2	0.165
MA0080.2	MA0080.2	2.23609e-8
MA0081.1	MA0081.1	0.0789
MA0083.1	MA0083.1	0.215
MA0084.1	MA0084.1	0.883
MA0087.1	MA0087.1	0.847
MA0088.1	MA0088.1	0.987
MA0090.1	MA0090.1	0.0753
MA0091.1	MA0091.1	0.651
MA0092.1	MA0092.1	0.654
MA0093.1	MA0093.1	0.507
MA0099.2	MA0099.2	7.54449e-5
MA0100.1	MA0100.1	0.158
MA0101.1	MA0101.1	0.251
MA0102.2	MA0102.2	0.0138
MA0103.1	MA0103.1	0.359
MA0104.2	MA0104.2	0.273
MA0105.1	MA0105.1	0.771
MA0106.1	MA0106.1	0.89
MA0107.1	MA0107.1	0.124
MA0108.2	MA0108.2	0.36
MA0111.1	MA0111.1	0.369
MA0112.2	MA0112.2	0.394
MA0113.1	MA0113.1	0.744
MA0114.1	MA0114.1	0.0642
MA0115.1	MA0115.1	0.893
MA0116.1	MA0116.1	0.215
MA0117.1	MA0117.1	0.0089
MA0119.1	MA0119.1	0.404
MA0122.1	MA0122.1	0.317
MA0124.1	MA0124.1	0.825
MA0125.1	MA0125.1	0.662
MA0131.1	MA0131.1	0.555
MA0135.1	MA0135.1	0.633
MA0136.1	MA0136.1	1.53564e-11
MA0137.2	MA0137.2	0.0313
MA0138.2	MA0138.2	0.06
MA0139.1	MA0139.1	0.984
MA0140.1	MA0140.1	0.0238
MA0141.1	MA0141.1	0.902
MA0142.1	MA0142.1	0.131
MA0143.1	MA0143.1	0.834
MA0144.1	MA0144.1	0.181
MA0145.1	MA0145.1	0.864
MA0146.1	MA0146.1	0.453
MA0147.1	MA0147.1	0.276
MA0148.1	MA0148.1	0.479
MA0149.1	MA0149.1	0.0924
MA0150.1	MA0150.1	0.00667
MA0152.1	MA0152.1	0.0373
MA0153.1	MA0153.1	6.47626e-31
MA0154.1	MA0154.1	0.291
MA0155.1	MA0155.1	0.0756
MA0156.1	MA0156.1	5.4675e-8
MA0157.1	MA0157.1	0.337
MA0159.1	MA0159.1	0.43
MA0160.1	MA0160.1	0.272
MA0162.1	MA0162.1	0.261
MA0163.1	MA0163.1	0.433
MA0164.1	MA0164.1	0.895
MA0258.1	MA0258.1	0.048
MA0259.1	MA0259.1	0.601

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: CNhs11028

Novel motif	Logo	P-value
1	1	0.0808
10	10	0.765
100	100	0.656
101	101	0.827
102	102	0.612
103	103	0.89
104	104	0.643
105	105	0.944
106	106	0.523
107	107	0.254
108	108	0.503
109	109	0.691
11	11	0.175
110	110	0.999
111	111	0.0553
112	112	0.865
113	113	0.541
114	114	0.00503
115	115	0.787
116	116	0.583
117	117	0.0949
118	118	0.141
119	119	0.319
12	12	0.644
120	120	0.265
121	121	0.379
122	122	0.976
123	123	0.0546
124	124	0.984
125	125	0.204
126	126	0.768
127	127	0.0541
128	128	0.467
129	129	0.281
13	13	0.051
130	130	0.228
131	131	0.113
132	132	0.183
133	133	0.388
134	134	0.624
135	135	0.621
136	136	0.503
137	137	0.287
138	138	0.0159
139	139	0.105
14	14	0.377
140	140	0.54
141	141	0.836
142	142	0.317
143	143	0.481
144	144	0.335
145	145	0.251
146	146	0.376
147	147	0.189
148	148	0.55
149	149	0.273
15	15	0.103
150	150	0.31
151	151	0.0262
152	152	0.819
153	153	0.337
154	154	0.154
155	155	0.794
156	156	0.39
157	157	0.899
158	158	0.783
159	159	0.173
160	160	0.186
161	161	0.579
162	162	0.388
163	163	0.099
164	164	0.396
165	165	0.659
166	166	0.205
167	167	0.739
168	168	0.897
169	169	0.44
17	17	0.458
18	18	0.0445
19	19	0.211
2	2	0.539
20	20	0.805
21	21	0.985
22	22	0.629
23	23	0.334
24	24	0.779
25	25	0.307
26	26	0.593
27	27	0.759
28	28	0.164
29	29	0.594
3	3	0.921
30	30	0.97
31	31	0.41
32	32	0.138
33	33	0.966
34	34	0.988
35	35	0.0768
36	36	0.0543
37	37	0.717
38	38	0.557
39	39	0.455
4	4	0.969
40	40	0.0925
41	41	0.0544
42	42	0.67
43	43	0.257
44	44	0.399
45	45	0.565
46	46	0.576
47	47	0.291
48	48	0.408
49	49	0.193
5	5	0.253
50	50	0.443
51	51	0.647
52	52	0.62
53	53	0.641
54	54	0.303
55	55	0.192
56	56	0.238
57	57	0.934
58	58	0.597
59	59	0.304
6	6	0.93
60	60	0.996
61	61	0.534
62	62	0.0998
63	63	0.258
64	64	0.6
65	65	0.276
66	66	0.713
67	67	0.0807
68	68	0.0618
69	69	0.759
7	7	0.997
70	70	0.00536
71	71	0.749
72	72	0.159
73	73	0.202
74	74	0.913
75	75	0.135
76	76	0.935
77	77	0.935
78	78	0.374
79	79	0.464
8	8	0.349
80	80	0.038
81	81	0.277
82	82	0.164
83	83	0.449
84	84	0.86
85	85	0.165
86	86	0.49
87	87	8.82079e-5
88	88	0.848
89	89	0.397
9	9	0.843
90	90	0.505
91	91	0.872
92	92	0.28
93	93	0.761
94	94	0.555
95	95	0.0937
96	96	0.637
97	97	0.918
98	98	0.2
99	99	0.748

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: CNhs11028

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011371 mouse kidney- embryo E17 sample

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002113 (kidney)
0002100 (trunk)
0000479 (tissue)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000300 (mouse embryonic day 17 sample)
0011371 (mouse kidney- embryo E17 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@SAMD00005742
+|accession_numbers=CAGE;DRX009007;DRR009881;DRZ001306;DRZ002689;DRZ012656;DRZ014039
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000479,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
 |ancestors_in_cell_lineage_facet=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:22539932..22539956,-!p1@Tcf21!1.91!204.47!Tcf21;;chr11:83664365..83664383,+!p1@Hnf1b!1.82!65.58!Hnf1b;;chr11:96153767..96153822,+!p1@Hoxb6!1.78!90.83!Hoxb6;;chr6:52190467..52190500,-!p1@Hoxa10!1.74!53.36!Hoxa10;;chr15:102828658..102828678,+!p1@Hoxc6!1.69!48.06!Hoxc6;;chr2:74549968..74549996,+!p1@Hoxd3!1.67!56.41!Hoxd3;;chr11:96143666..96143725,+!p1@Hoxb8!1.59!43.79!Hoxb8;;chr2:104966766..104966786,+!p1@Wt1!1.53!51.12!Wt1;;chr2:24331085..24331100,-!p1@Pax8!1.52!31.97!Pax8;;chr19:59533221..59533271,+!p1@Emx2!1.49!36.45!Emx2;;chr11:84339016..84339044,-!p1@Lhx1!1.47!28.51!Lhx1;;chr1:120524520..120524528,+!p1@Tfcp2l1!1.45!75.96!Tfcp2l1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.44!33.60!Pou3f3;;chr6:52176164..52176195,-!p1@Hoxa9!1.38!28.51!Hoxa9;;chr1:19202352..19202354,+!p2@Tfap2b!1.35!21.59!Tfap2b;;chr17:86087592..86087615,-!p1@Six2!1.33!20.57!Six2;;chr6:52184901..52184959,-!p2@Hoxa10!1.29!18.33!Hoxa10;;chr11:34108085..34108092,-!p1@Foxi1!1.29!18.33!Foxi1;;chr5:140019865..140019886,+!p1@Uncx!1.28!18.12!Uncx;;chr13:99124189..99124205,+!p1@Foxd1!1.27!26.68!Foxd1;;chr6:52195795..52195825,-!p1@Hoxa11!1.26!17.31!Hoxa11;;chr2:74517609..74517621,+!p3@Hoxd11!1.25!16.70!Hoxd11;;chr6:52163319..52163342,-!p1@Hoxa3!1.23!23.22!Hoxa3;;chr2:74550015..74550057,+!p2@Hoxd3!1.23!15.88!Hoxd3;;chr2:9800207..9800234,-!p1@Gata3!1.22!46.64!Gata3;;chr6:52195763..52195792,-!p2@Hoxa11!1.21!15.27!Hoxa11;;chr15:102797288..102797302,+!p1@Hoxc10!1.19!14.46!Hoxc10;;chr14:98568971..98569025,-!p1@Dach1!1.18!106.92!Dach1;;chr6:52190668..52190682,-!p3@Hoxa10!1.17!13.85!Hoxa10;;chr5:140019843..140019858,+!p2@Uncx!1.15!13.03!Uncx;;chr11:96147952..96147967,+!p1@Hoxb7!1.14!15.88!Hoxb7;;chr2:74529970..74529997,+!p1@Hoxd10!1.13!12.42!Hoxd10;;chr2:74520048..74520064,+!p1@Hoxd11!1.13!12.42!Hoxd11;;chr2:104966874..104966907,+!p2@Wt1!1.12!12.22!Wt1;;chr8:123640063..123640077,+!p1@Foxc2!1.11!21.59!Foxc2;;chr2:103264213..103264233,+!p1@Elf5!1.09!11.20!Elf5;;chr2:163372884..163372904,+!p1@Hnf4a!1.06!10.59!Hnf4a;;chr10:50614546..50614568,+!p@chr10:50614546..50614568,+!1.06!10.59!Sim1;;chr1:19199236..19199258,+!p1@Tfap2b!1.03!9.78!Tfap2b;;chr2:103123925..103123959,-!p3@Ehf!1.02!9.57!Ehf;;chr2:9809357..9809371,-!p2@Gata3!1.02!9.57!Gata3;;chr11:96143962..96144035,+!p2@Hoxb8!1.02!9.37!Hoxb8;;chr10:119913546..119913583,-!p3@Hmga2!1.01!19.75!Hmga2;;chr6:52190858..52190873,-!p4@Hoxa10!1.01!9.16!Hoxa10;;chr2:74517742..74517758,+!p2@Hoxd11!1.00!8.96!Hoxd11;;chr2:74520343..74520383,+!p4@Hoxd11!0.98!8.55!Hoxd11;;chr11:96143843..96143868,+!p3@Hoxb8!0.97!8.35!Hoxb8;;chr3:30408603..30408668,-!p1@Mecom!0.96!19.35!Mecom;;chr19:59533139..59533152,+!p2@Emx2!0.96!8.15!Emx2;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.94!7.74!Hoxb2;;chr13:72101178..72101203,-!p1@Irx1!0.93!12.02!Irx1;;chr2:104966465..104966479,+!p6@Wt1!0.93!7.54!Wt1;;chr2:74543202..74543213,+!p3@Hoxd8!0.93!7.54!Hoxd8;;chr19:59532915..59532940,+!p5@Emx2!0.92!7.33!Emx2;;chr14:98568761..98568814,-!p2@Dach1!0.91!50.30!Dach1;;chr15:102828642..102828653,+!p2@Hoxc6!0.91!7.13!Hoxc6;;chr15:102797225..102797243,+!p2@Hoxc10!0.91!7.13!Hoxc10;;chr14:17407878..17407926,-!p1@Rarb!0.90!16.29!Rarb;;chr13:72101161..72101177,-!p2@Irx1!0.90!9.78!Irx1;;chr6:85137520..85137563,+!p1@Emx1!0.90!6.92!Emx1;;chr15:35225845..35225867,+!p1@Osr2!0.89!17.51!Osr2;;chr7:77511403..77511450,-!p3@Nr2f2!0.89!14.87!Nr2f2;;chr1:137155026..137155042,-!p1@Elf3!0.88!40.32!Elf3;;chr2:105003277..105003280,+!p5@Wt1!0.88!6.52!Wt1;;chr11:96160426..96160443,+!p2@Hoxb6!0.86!6.31!Hoxb6;;chr10:102491237..102491291,-!p2@Alx1!0.86!6.31!Alx1;;chr16:94085471..94085495,+!p1@Sim2!0.86!6.31!Sim2;;chr11:96145450..96145517,+!p2@Hoxb7!0.85!9.37!Hoxb7;;chr11:96132637..96132652,+!p1@Hoxb9!0.85!6.11!Hoxb9;;chr19:59533163..59533185,+!p3@Emx2!0.85!6.11!Emx2;;chr7:17647736..17647772,-!p1@Hif3a!0.84!22.40!Hif3a;;chr11:101755669..101755686,-!p1@Meox1!0.84!11.00!Meox1;;chr3:30408674..30408716,-!p2@Mecom!0.84!9.98!Mecom;;chr11:96132767..96132796,+!p2@Hoxb9!0.84!5.91!Hoxb9;;chr2:104966933..104966966,+!p3@Wt1!0.84!5.91!Wt1;;chr7:77505617..77505632,-!p1@Nr2f2!0.83!283.69!Nr2f2;;chr14:98569030..98569059,-!p3@Dach1!0.83!29.73!Dach1;;chr6:52190840..52190853,-!p5@Hoxa10!0.83!5.70!Hoxa10;;chr12:28027561..28027591,-!p1@Sox11!0.82!39.92!Sox11;;chr11:85646303..85646329,+!p1@Tbx2!0.81!39.10!Tbx2;;chr5:140019816..140019825,+!p3@Uncx!0.81!5.50!Uncx;;chr2:74536050..74536065,+!p2@Hoxd9!0.81!5.50!Hoxd9;;chr2:74536026..74536039,+!p1@Hoxd9!0.81!5.50!Hoxd9;;chr10:119913792..119913820,-!p5@Hmga2!0.80!9.57!Hmga2;;chr3:29912058..29912071,-!p6@Mecom!0.80!6.11!Mecom;;chr2:74542680..74542705,+!p6@Hoxd8!0.80!5.29!Hoxd8;;chr11:96160360..96160397,+!p3@Hoxb6!0.80!5.29!Hoxb6;;chr15:102797170..102797182,+!p3@Hoxc10!0.80!5.29!Hoxc10;;chr2:115891534..115891589,-!p1@Meis2!0.79!80.03!Meis2;;chr10:119913310..119913366,-!p1@Hmga2!0.79!43.99!Hmga2;;chr2:115891381..115891392,-!p5@Meis2!0.79!10.59!Meis2;;chr2:115891409..115891425,-!p2@Meis2!0.78!15.68!Meis2;;chr10:126778916..126778974,-!p1@Gli1!0.78!12.02!Gli1;;chr10:88969376..88969395,-!p1@Nr1h4!0.78!5.09!Nr1h4;;chr19:44831390..44831414,+!p1@Pax2!0.78!5.09!Pax2;;chr2:104966662..104966673,+!p4@Wt1!0.78!5.09!Wt1;;chr2:115891427..115891441,-!p4@Meis2!0.77!11.00!Meis2;;chr1:189432881..189432903,+!p2@Esrrg!0.77!4.89!Esrrg;;chr2:74513125..74513143,+!p1@Hoxd12!0.77!4.89!Hoxd12;;chr7:77511234..77511302,-!p2@Nr2f2!0.76!34.42!Nr2f2;;chr19:5560600..5560617,-!p1@Ovol1!0.75!5.70!Ovol1;;chr9:24578720..24578735,-!p1@Tbx20!0.75!4.68!Tbx20;;chr2:74549945..74549965,+!p4@Hoxd3!0.75!4.68!Hoxd3;;chr14:22807107..22807119,-!p2@Zfp503!0.74!21.38!Zfp503;;chr13:31898729..31898761,+!p1@Foxc1!0.74!11.81!Foxc1;;chr12:3891810..3891829,+!p2@Dnmt3a!0.74!7.33!Dnmt3a;;chr8:123640090..123640101,+!p2@Foxc2!0.74!5.09!Foxc2;;chr1:19202185..19202187,+!p9@Tfap2b!0.74!4.48!Tfap2b;;chr19:28754692..28754757,-!p1@Glis3!0.73!20.16!Glis3;;chr11:18918434..18918489,-!p3@Meis1!0.73!7.33!Meis1;;chr13:72766250..72766273,+!p1@Irx2!0.73!7.13!Irx2;;chr14:22807083..22807104,-!p1@Zfp503!0.72!84.11!Zfp503;;chr13:40829137..40829205,-!p1@Tfap2a!0.72!4.89!Tfap2a;;chr2:74543397..74543435,+!p2@Hoxd8!0.72!4.28!Hoxd8;;chr2:105002682..105002691,+!p10@Wt1!0.72!4.28!Wt1;;chr4:154010409..154010466,-!p2@Prdm16!0.71!10.39!Prdm16;;chr18:76219118..76219155,+!p1@Zbtb7c!0.71!7.74!Zbtb7c;;chr2:103143336..103143367,-!p1@Ehf!0.71!7.13!Ehf;;chr16:14705961..14705978,+!p2@Snai2!0.70!21.18!Snai2;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.70!7.33!Hoxb2;;chr2:17976799..17976829,+!p5@Mllt10!0.70!5.09!Mllt10;;chr4:62626594..62626651,+!p1@Zfp618!0.69!16.29!Zfp618;;chr10:119913278..119913298,-!p2@Hmga2!0.69!9.57!Hmga2;;chr10:119914001..119914078,-!p4@Hmga2!0.69!5.50!Hmga2;;chrX:110411840..110411860,+!p1@Dach2!0.69!4.89!Dach2;;chr1:170361730..170361769,-!p7@Pbx1!0.68!9.57!Pbx1;;chr13:31898637..31898653,+!p2@Foxc1!0.68!7.33!Foxc1;;chr6:52167459..52167492,-!p1@Hoxa7!0.68!4.68!Hoxa7;;chr6:88148650..88148669,+!p1@Gata2!0.67!35.64!Gata2;;chr13:31650185..31650201,+!p1@Foxq1!0.67!14.46!Foxq1;;chr4:126703093..126703158,+!p3@Sfpq!0.67!11.61!Sfpq;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.67!5.09!Hoxb2;;chr2:180069370..180069409,-!p1@Gata5!0.67!4.48!Gata5;;chr11:96145393..96145407,+!p3@Hoxb7!0.67!3.67!Hoxb7;;chr10:102491405..102491416,-!p1@Alx1!0.67!3.67!Alx1;;chr11:83666422..83666446,+!p4@Hnf1b!0.67!3.67!Hnf1b;;chr2:9809579..9809627,-!p7@Gata3!0.67!3.67!Gata3;;chr2:74543103..74543135,+!p4@Hoxd8!0.67!3.67!Hoxd8;;chr5:115421065..115421088,-!p1@Hnf1a!0.67!3.67!Hnf1a;;chr6:97879817..97879857,+!p2@Mitf!0.67!3.67!Mitf;;chr1:170362273..170362317,-!p1@Pbx1!0.66!118.73!Pbx1;;chr2:74542918..74542971,+!p1@Hoxd8!0.66!5.70!Hoxd8;;chr13:72766279..72766296,+!p2@Irx2!0.66!5.70!Irx2;;chr14:17407549..17407575,-!p3@Rarb!0.66!5.70!Rarb;;chr14:22808697..22808715,-!p4@Zfp503!0.66!4.28!Zfp503;;chr18:65741358..65741415,+!p1@Zfp532!0.65!17.11!Zfp532;;chr11:101646566..101646603,-!p1@Etv4!0.65!12.83!Etv4;;chr8:94325321..94325366,-!p1@Irx3!0.65!9.37!Irx3;;chr4:108151497..108151514,+!p3@Zcchc11!0.65!7.54!Zcchc11;;chr2:74560109..74560131,+!p1@Hoxd4!0.65!3.46!Hoxd4;;chr4:114581497..114581519,-!p2@Foxd2!0.65!3.46!Foxd2;;chr2:74535796..74535808,+!p3@Hoxd9!0.65!3.46!Hoxd9;;chr12:12948633..12948651,-!p1@Mycn!0.64!37.88!Mycn;;chr16:14705925..14705951,+!p1@Snai2!0.64!27.49!Snai2;;chr16:4594740..4594759,+!p1@Glis2!0.63!44.19!Glis2;;chr7:6649134..6649167,-!p1@Zim1!0.63!20.77!Zim1;;chr15:102797183..102797205,+!p4@Hoxc10!0.63!3.26!Hoxc10;;chr2:74529998..74530020,+!p2@Hoxd10!0.63!3.26!Hoxd10;;chr4:126700576..126700598,+!p7@Sfpq!0.61!6.31!Sfpq;;chr8:94325486..94325510,-!p4@Irx3!0.61!4.28!Irx3;;chr14:98568683..98568698,-!p6@Dach1!0.61!4.07!Dach1;;chr6:52195747..52195762,-!p3@Hoxa11!0.61!3.05!Hoxa11;;chr1:170362040..170362113,-!p2@Pbx1!0.60!27.90!Pbx1;;chr4:122911086..122911112,+!p1@Heyl!0.59!40.73!Heyl;;chr11:74981654..74981658,-!p1@Hic1!0.59!13.44!Hic1;;chr8:94325814..94325839,-!p2@Irx3!0.59!6.92!Irx3;;chr2:169458838..169458859,+!p4@Tshz2!0.59!6.52!Tshz2;;chr2:115890469..115890485,-!p7@Meis2!0.59!5.09!Meis2;;chr2:115890953..115890974,-!p6@Meis2!0.59!4.68!Meis2;;chr2:24331116..24331125,-!p2@Pax8!0.59!2.85!Pax8;;chr1:189432907..189432926,+!p3@Esrrg!0.59!2.85!Esrrg;;chr2:103264245..103264268,+!p2@Elf5!0.59!2.85!Elf5;;chr2:9809374..9809396,-!p4@Gata3!0.59!2.85!Gata3;;chr3:29911926..29911942,-!p13@Mecom!0.59!2.85!Mecom;;chr11:3189683..3189744,+!p2@Patz1!0.58!6.52!Patz1;;chr19:25746898..25746910,+!p1@Dmrt2!0.58!4.48!Dmrt2;;chr8:109817400..109817417,+!p1@Nfat5!0.57!71.69!Nfat5;;chr7:52471143..52471186,+!p1@Tead2!0.57!35.64!Tead2;;chr4:120488308..120488366,-!p1@Nfyc!0.57!19.14!Nfyc;;chr2:115891454..115891471,-!p3@Meis2!0.57!9.78!Meis2;;chr7:77511311..77511352,-!p4@Nr2f2!0.57!6.31!Nr2f2;;chr4:135699731..135699747,+!p1@Id3!0.56!371.66!Id3;;chr17:35031460..35031518,+!p1@Zbtb12!0.56!16.29!Zbtb12;;chrX:45245679..45245702,-!p1@Smarca1!0.56!14.26!Smarca1;;chr11:101645830..101645881,-!p2@Etv4!0.56!5.50!Etv4;;chr13:31898496..31898519,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chr12:58646974..58647003,-!p1@Foxa1!0.27!1.43!Foxa1;;chrX:103070960..103070973,-!p7@Atrx!0.27!1.43!Atrx;;chr7:119822841..119822887,+!p1@Tead1!0.26!51.73!Tead1;;chr2:44968512..44968530,-!p1@Zeb2!0.26!35.64!Zeb2;;chrX:132420399..132420436,+!p1@Bhlhb9!0.26!9.16!Bhlhb9;;chr6:47785748..47785776,+!p3@Zfp398!0.26!5.50!Zfp398;;chr3:14578741..14578759,+!p3@E2f5!0.26!3.67!E2f5;;chr17:47278081..47278103,+!p1@Trerf1!0.26!3.05!Trerf1;;chr16:43619057..43619078,+!p8@Zbtb20!0.26!2.65!Zbtb20;;chr18:79306603..79306620,-!p4@Setbp1!0.26!1.83!Setbp1;;chr18:65741911..65741929,+!p3@Zfp532!0.26!1.43!Zfp532;;chr5:24107676..24107722,-!p4@Smarcd3!0.26!1.43!Smarcd3;;chr3:133207214..133207228,-!p2@Tet2!0.26!1.22!Tet2;;chr14:52936008..52936019,-!p5@Sall2!0.26!1.22!Sall2;;chr5:38611816..38611827,+!p4@Lyar!0.26!1.02!Lyar;;chr7:119885539..119885574,+!p3@Tead1!0.26!0.81!Tead1;;chr5:120120834..120120845,+!p8@Tbx3!0.26!0.81!Tbx3;;chr6:88148324..88148328,+!p3@Gata2!0.26!0.81!Gata2;;chr6:52190656..52190667,-!p7@Hoxa10!0.26!0.81!Hoxa10;;chr5:31271028..31271040,+!p1@Tcf23!0.26!0.81!Tcf23;;chr16:14705746..14705761,+!p4@Snai2!0.26!0.81!Snai2;;chr17:86087581..86087588,-!p2@Six2!0.26!0.81!Six2;;chr11:96160098..96160112,+!p8@Hoxb6!0.26!0.81!Hoxb6;;chr10:126778639..126778670,-!p3@Gli1!0.26!0.81!Gli1;;chr10:30522660..30522671,-!p10@Ncoa7!0.26!0.81!Ncoa7;;chr11:96160119..96160135,+!p7@Hoxb6!0.26!0.81!Hoxb6;;chr11:96132456..96132467,+!p4@Hoxb9!0.26!0.81!Hoxb9;;chr11:100553754..100553787,-!p1@Zfp385c!0.26!0.81!Zfp385c;;chr12:12947406..12947418,-!p5@Mycn!0.26!0.81!Mycn;;chr12:77278238..77278252,-!p1@Esr2!0.26!0.81!Esr2;;chr14:56443742..56443756,+!p6@Nfatc4!0.26!0.81!Nfatc4;;chr13:96093557..96093561,+!p6@Zbed3!0.26!0.81!Zbed3;;chr12:12947182..12947194,-!p3@Mycn!0.26!0.81!Mycn;;chr12:12947199..12947213,-!p2@Mycn!0.26!0.81!Mycn;;chr1:173144100..173144138,+!p2@Nr1i3!0.26!0.81!Nr1i3;;chr2:104967357..104967379,+!p9@Wt1!0.26!0.81!Wt1;;chr1:136186574..136186592,+!p1@Myog!0.26!0.81!Myog;;chr1:189432857..189432870,+!p7@Esrrg!0.26!0.81!Esrrg;;chr2:74565306..74565327,+!p2@Hoxd4!0.26!0.81!Hoxd4;;chr3:29912249..29912262,-!p26@Mecom!0.26!0.81!Mecom;;chr3:98186461..98186476,+!p2@Zfp697!0.26!0.81!Zfp697;;chr2:74535720..74535731,+!p6@Hoxd9!0.26!0.81!Hoxd9;;chr12:25780945..25780961,-!p1@Id2!0.25!272.08!Id2;;chr16:20141134..20141213,+!p1@Yeats2!0.25!41.34!Yeats2;;chr2:48805082..48805137,+!p1@Mbd5!0.25!32.79!Mbd5;;chr9:22112085..22112138,-!p1@Zfp810!0.25!19.55!Zfp810;;chr3:14578609..14578687,+!p1@E2f5!0.25!14.87!E2f5;;chr16:4559608..4559681,-!p1@Tfap4!0.25!12.63!Tfap4;;chr6:38204109..38204155,-!p1@D630045J12Rik!0.25!7.94!D630045J12Rik;;chr11:62602904..62602945,-!p1@Zfp286!0.25!6.72!Zfp286;;chr18:69504123..69504155,+!p5@Tcf4!0.25!5.09!Tcf4;;chr13:15555496..15555544,+!p1@Gli3!0.25!4.89!Gli3;;chr9:63869850..63869873,-!p2@Smad6!0.25!4.07!Smad6;;chr9:21420744..21420755,+!p3@Smarca4!0.25!3.87!Smarca4;;chr2:27532734..27532749,+!p2@Rxra!0.25!3.87!Rxra;;chr4:148178559..148178603,+!p1@Casz1!0.25!3.87!Casz1;;chr10:114821393..114821431,-!p5@Thap2!0.25!3.67!Thap2;;chrX:98449805..98449834,+!p3@Foxo4!0.25!3.67!Foxo4;;chr16:42907554..42907591,+!p5@Zbtb20!0.25!3.26!Zbtb20;;chr15:50720601..50720630,-!p2@Trps1!0.25!3.05!Trps1;;chr19:55816278..55816287,+!p10@Tcf7l2!0.25!2.44!Tcf7l2;;chr7:119822915..119822936,+!p5@Tead1!0.25!1.83!Tead1;;chr4:122911056..122911065,+!p2@Heyl!0.25!1.63!Heyl;;chr8:109868335..109868338,+!p3@Nfat5!0.25!1.63!Nfat5;;chr17:32525943..32525992,-!p4@Wiz!0.25!1.63!Wiz;;chr4:154010228..154010244,-!p4@Prdm16!0.25!1.43!Prdm16;;chrX:45245621..45245632,-!p3@Smarca1!0.25!1.43!Smarca1;;chr10:62328079..62328093,-!p5@Tet1!0.25!1.43!Tet1;;chr11:120624132..120624143,+!p10@Hmga1,p9@Hmga1-rs1!0.25!1.22!Hmga1;;chr17:27693622..27693635,+!p11@Hmga1-rs1,p12@Hmga1!0.25!1.22!Hmga1;;chr5:125538905..125538910,-!p4@Ncor2!0.25!1.22!Ncor2;;chr15:102865048..102865073,+!p3@Hoxc4!0.25!1.22!Hoxc4;;chr15:102865131..102865151,+!p2@Hoxc4!0.25!1.02!Hoxc4;;chr19:28754622..28754633,-!p4@Glis3!0.25!1.02!Glis3;;chr2:77357593..77357606,-!p6@Zfp385b!0.25!1.02!Zfp385b;;chr2:152223762..152223777,-!p8@Sox12!0.25!1.02!Sox12;;chr2:119722948..119723028,+!p1@Mga!0.24!45.01!Mga;;chr15:99532709..99532743,+!p1@Smarcd1!0.24!40.73!Smarcd1;;chr6:116578973..116579022,-!p1@Zfp422!0.24!26.07!Zfp422;;chr17:71199121..71199165,-!p2@Tgif1!0.24!10.59!Tgif1;;chr7:88005795..88005858,+!p1@Zscan2!0.24!10.59!Zscan2;;chr14:65977498..65977528,+!p1@Zfp395!0.24!9.78!Zfp395;;chr19:28085676..28085711,-!p2@Rfx3!0.24!8.96!Rfx3;;chr8:79426176..79426275,+!p1@Nr3c2!0.24!7.13!Nr3c2;;chr19:28086045..28086080,-!p4@Rfx3!0.24!6.72!Rfx3;;chr6:133986088..133986122,+!p4@Etv6!0.24!5.91!Etv6;;chr4:120624269..120624302,-!p1@Zfp69!0.24!4.89!Zfp69;;chr6:38204087..38204108,-!p2@D630045J12Rik!0.24!3.87!D630045J12Rik;;chr7:19679964..19679982,+!p1@Six5!0.24!3.67!Six5;;chr3:8666997..8667012,-!p2@Hey1!0.24!2.85!Hey1;;chr17:34729160..34729171,+!p3@Pbx2!0.24!2.24!Pbx2;;chr7:38554763..38554780,-!p1@Zfp536!0.24!2.04!Zfp536;;chr15:102076652..102076679,-!p4@Rarg!0.24!2.04!Rarg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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011371
 |is_obsolete=
+|library_id=CNhs11028
+|library_id_phase_based=2:CNhs11028
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;483
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;483
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm9.nobarcode.rdna.fa.gz
 |name=kidney, embryo E17
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11028,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.455993551097255,0,0,0,0,0.0126394207418371,0.463098808682689,0,0.0805006992779881,0,0,0.452700690735272,0,0,0,0,0,0,0.345146580249239,0,0,0,0,0,0,0,0,0,0,0,0,0,0.180383855744233,0,0.0805006992779881,0,0.346726066206739,0.0108687479710982,0.192995911547083,0,-0.149802832180563,0.130247099005091,0.0351077517960241,0,0,0,0,0,0,0,0,0,0,0.0805006992779881,0,0.192776630167171,0,0,0,0,0,0,0,0,0,0.0371197045808488,0.164641238328144,-0.00567426753301087,-0.0775903434930944,0.03760104461084,0,0.129074534340238,0.000836995395048695,0,0,0,0.00695621948533348,-0.0369793328058527,-0.1436894694923,0.00166910443808069,0,0,0,0,0,0.20708313509219,-0.0531600503965874,0.127648436268061,-0.166261434685304,0.0141859117653472,0,0,0,0
 |rna_box=18
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:483-18I2;search_select_hide=table117:483-18I2
 }}

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FF:483-18I2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:17, 4 June 2020

CNhs11028

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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