FF:839-18H3: Difference between revisions

Latest revision as of 19:21, 4 June 2020

Name:	testis, neonate N20
Species:	Mouse (Mus musculus)
Library ID:	CNhs11110
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	testis
dev stage	20 days neonate
sex	male
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		SAMD00004759

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11110		CAGE		DRX009110		DRR009984

Accession ID Mm9

Library id		BAM		CTSS
CNhs11110		DRZ001409		DRZ002792

Accession ID Mm10

Library id		BAM		CTSS
CNhs11110		DRZ012759		DRZ014142

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

CNhs11110

0	0.505
1	0
10	0
100	0
1000	0.047
1001	0.392
1002	2.087892e-4
1003	0.00324
1004	0
1005	-0.304
1006	-0.0253
1007	0.232
1008	0
1009	0.18
101	0.13
1010	0
1011	0.854
1012	0.094
1013	0.00566
1014	-0.0851
1015	0.472
1016	-0.205
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0
1023	0
1024	-0.14
1025	0
1026	0.968
1027	0.033
1028	0
1029	0.0236
103	0.0275
1030	0
1031	-0.456
1032	-0.418
1033	0.0188
1034	0
1035	0.294
1036	-0.129
1037	0
1038	-0.15
1039	-0.0783
104	0
1040	-0.469
1041	0.237

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: CNhs11110

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.032
MA0003.1	MA0003.1	0.801
MA0004.1	MA0004.1	0.268
MA0006.1	MA0006.1	0.0883
MA0007.1	MA0007.1	0.946
MA0009.1	MA0009.1	0.37
MA0014.1	MA0014.1	0.344
MA0017.1	MA0017.1	0.139
MA0018.2	MA0018.2	0.045
MA0019.1	MA0019.1	0.226
MA0024.1	MA0024.1	0.0692
MA0025.1	MA0025.1	0.776
MA0027.1	MA0027.1	0.768
MA0028.1	MA0028.1	4.81754e-5
MA0029.1	MA0029.1	0.184
MA0030.1	MA0030.1	0.965
MA0031.1	MA0031.1	0.798
MA0035.2	MA0035.2	0.0759
MA0038.1	MA0038.1	0.143
MA0039.2	MA0039.2	0.282
MA0040.1	MA0040.1	0.392
MA0041.1	MA0041.1	0.948
MA0042.1	MA0042.1	0.959
MA0043.1	MA0043.1	0.0289
MA0046.1	MA0046.1	4.39153e-15
MA0047.2	MA0047.2	0.00849
MA0048.1	MA0048.1	0.0542
MA0050.1	MA0050.1	0.00881
MA0051.1	MA0051.1	0.611
MA0052.1	MA0052.1	1.63504e-4
MA0055.1	MA0055.1	8.53065e-4
MA0057.1	MA0057.1	0.398
MA0058.1	MA0058.1	0.139
MA0059.1	MA0059.1	0.0286
MA0060.1	MA0060.1	1.266e-11
MA0061.1	MA0061.1	0.0218
MA0062.2	MA0062.2	1.72785e-7
MA0065.2	MA0065.2	0.704
MA0066.1	MA0066.1	0.0392
MA0067.1	MA0067.1	0.578
MA0068.1	MA0068.1	0.698
MA0069.1	MA0069.1	0.282
MA0070.1	MA0070.1	0.496
MA0071.1	MA0071.1	0.774
MA0072.1	MA0072.1	0.448
MA0073.1	MA0073.1	0.831
MA0074.1	MA0074.1	0.638
MA0076.1	MA0076.1	1.23549e-6
MA0077.1	MA0077.1	0.948
MA0078.1	MA0078.1	0.661
MA0079.2	MA0079.2	0.703
MA0080.2	MA0080.2	1.03555e-4
MA0081.1	MA0081.1	0.329
MA0083.1	MA0083.1	0.0145
MA0084.1	MA0084.1	0.568
MA0087.1	MA0087.1	0.503
MA0088.1	MA0088.1	0.0813
MA0090.1	MA0090.1	0.216
MA0091.1	MA0091.1	0.437
MA0092.1	MA0092.1	0.0967
MA0093.1	MA0093.1	0.225
MA0099.2	MA0099.2	0.00316
MA0100.1	MA0100.1	2.20814e-15
MA0101.1	MA0101.1	0.467
MA0102.2	MA0102.2	0.228
MA0103.1	MA0103.1	0.401
MA0104.2	MA0104.2	6.35214e-4
MA0105.1	MA0105.1	7.89549e-4
MA0106.1	MA0106.1	0.0483
MA0107.1	MA0107.1	0.0823
MA0108.2	MA0108.2	1.09506e-5
MA0111.1	MA0111.1	0.887
MA0112.2	MA0112.2	0.0197
MA0113.1	MA0113.1	0.794
MA0114.1	MA0114.1	0.107
MA0115.1	MA0115.1	0.266
MA0116.1	MA0116.1	0.0195
MA0117.1	MA0117.1	0.846
MA0119.1	MA0119.1	0.0829
MA0122.1	MA0122.1	0.428
MA0124.1	MA0124.1	0.903
MA0125.1	MA0125.1	0.169
MA0131.1	MA0131.1	0.0197
MA0135.1	MA0135.1	0.0508
MA0136.1	MA0136.1	0.719
MA0137.2	MA0137.2	0.612
MA0138.2	MA0138.2	0.0182
MA0139.1	MA0139.1	0.231
MA0140.1	MA0140.1	0.00608
MA0141.1	MA0141.1	0.842
MA0142.1	MA0142.1	0.00503
MA0143.1	MA0143.1	0.456
MA0144.1	MA0144.1	0.317
MA0145.1	MA0145.1	0.0112
MA0146.1	MA0146.1	0.0326
MA0147.1	MA0147.1	0.00182
MA0148.1	MA0148.1	5.50124e-4
MA0149.1	MA0149.1	0.214
MA0150.1	MA0150.1	0.134
MA0152.1	MA0152.1	0.832
MA0153.1	MA0153.1	8.6966e-7
MA0154.1	MA0154.1	0.00484
MA0155.1	MA0155.1	0.101
MA0156.1	MA0156.1	0.0658
MA0157.1	MA0157.1	0.339
MA0159.1	MA0159.1	0.424
MA0160.1	MA0160.1	0.485
MA0162.1	MA0162.1	0.455
MA0163.1	MA0163.1	0.516
MA0164.1	MA0164.1	0.328
MA0258.1	MA0258.1	0.08
MA0259.1	MA0259.1	0.0079

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: CNhs11110

Novel motif	Logo	P-value
1	1	0.799
10	10	0.219
100	100	0.254
101	101	0.389
102	102	0.534
103	103	0.554
104	104	0.918
105	105	0.0192
106	106	5.31924e-5
107	107	5.0949e-4
108	108	0.2
109	109	0.703
11	11	0.962
110	110	0.607
111	111	0.18
112	112	0.809
113	113	0.181
114	114	0.925
115	115	0.465
116	116	0.633
117	117	0.0199
118	118	0.449
119	119	0.253
12	12	0.836
120	120	0.894
121	121	0.0858
122	122	0.208
123	123	0.0488
124	124	0.0812
125	125	0.481
126	126	0.443
127	127	0.438
128	128	1.91663e-4
129	129	0.233
13	13	0.519
130	130	0.78
131	131	0.0787
132	132	0.279
133	133	0.251
134	134	0.78
135	135	0.0287
136	136	0.00915
137	137	0.868
138	138	0.973
139	139	0.967
14	14	0.122
140	140	0.205
141	141	0.0055
142	142	0.244
143	143	0.11
144	144	0.399
145	145	0.968
146	146	0.668
147	147	0.27
148	148	0.0966
149	149	0.0198
15	15	0.263
150	150	0.735
151	151	0.105
152	152	0.135
153	153	0.486
154	154	0.994
155	155	0.233
156	156	0.0311
157	157	0.421
158	158	0.618
159	159	0.273
160	160	0.0938
161	161	0.308
162	162	0.329
163	163	0.244
164	164	0.589
165	165	0.143
166	166	0.73
167	167	0.428
168	168	0.0512
169	169	0.364
17	17	0.259
18	18	0.408
19	19	0.439
2	2	0.0171
20	20	0.0213
21	21	0.515
22	22	0.44
23	23	0.12
24	24	0.119
25	25	0.567
26	26	0.665
27	27	0.0314
28	28	0.546
29	29	0.214
3	3	0.493
30	30	0.193
31	31	0.0798
32	32	0.374
33	33	0.64
34	34	0.504
35	35	0.912
36	36	0.363
37	37	0.492
38	38	0.507
39	39	0.501
4	4	0.953
40	40	0.414
41	41	0.998
42	42	0.581
43	43	0.205
44	44	0.323
45	45	0.244
46	46	0.332
47	47	0.833
48	48	0.828
49	49	0.355
5	5	0.252
50	50	0.709
51	51	0.387
52	52	0.0399
53	53	0.254
54	54	0.315
55	55	0.253
56	56	0.0875
57	57	0.657
58	58	0.851
59	59	0.0561
6	6	0.654
60	60	0.111
61	61	0.691
62	62	0.642
63	63	0.262
64	64	0.861
65	65	0.0987
66	66	0.012
67	67	0.137
68	68	0.758
69	69	0.866
7	7	0.967
70	70	0.895
71	71	0.524
72	72	0.711
73	73	0.776
74	74	0.866
75	75	0.815
76	76	0.0641
77	77	0.289
78	78	0.0282
79	79	0.221
8	8	0.776
80	80	0.372
81	81	0.199
82	82	0.346
83	83	0.842
84	84	0.358
85	85	0.302
86	86	0.86
87	87	0.119
88	88	0.282
89	89	0.223
9	9	0.768
90	90	0.7
91	91	0.0793
92	92	0.299
93	93	0.909
94	94	0.349
95	95	0.336
96	96	0.932
97	97	0.603
98	98	0.291
99	99	0.421

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: CNhs11110

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011433 mouse testis- 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)
0000473 (testis)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)

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)
0011433 (mouse testis- 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:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000473,UBERON:0000991,UBERON:0000926,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0000990,UBERON:0002050,UBERON:0005423,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0003135,UBERON:0005291,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0001048,UBERON:0006598,UBERON:0003886,UBERON:0004176,UBERON:0002532,UBERON:0003101,UBERON:0000079,UBERON:0009196,UBERON:0009117,UBERON:0006603,UBERON:0005564
+|DRA_sample_Accession=CAGE@SAMD00004759
+|accession_numbers=CAGE;DRX009110;DRR009984;DRZ001409;DRZ002792;DRZ012759;DRZ014142
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000473,UBERON:0000991,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079
 |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:0011433
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr4:107356135..107356179,-!p1@Dmrtb1!2.88!757.85!Dmrtb1;;chr5:38611867..38611888,+!p2@Lyar!2.80!625.46!Lyar;;chr1:168168856..168168893,-!p1@Mael!2.75!558.30!Mael;;chr6:131338278..131338362,-!p2@Csda!2.51!898.93!Csda;;chr11:69749396..69749433,+!p1@Ybx2!2.41!254.63!Ybx2;;chr2:17985983..17986035,+!p4@Mllt10!2.18!149.06!Mllt10;;chr10:22451680..22451722,-!p3@Tbpl1!2.12!131.18!Tbpl1;;chr4:107356181..107356197,-!p2@Dmrtb1!2.12!129.73!Dmrtb1;;chr1:168168817..168168850,-!p2@Mael!2.00!98.81!Mael;;chr18:50438025..50438057,+!p1@Fam170a!2.00!98.57!Fam170a;;chr2:180377386..180377462,-!p1@Tcfl5!1.96!108.95!Tcfl5;;chr10:22451724..22451752,-!p4@Tbpl1!1.95!88.90!Tbpl1;;chr7:25655099..25655143,+!p1@Dmrtc2!1.90!78.03!Dmrtc2;;chr7:19953851..19953902,+!p4@Ppp1r13l!1.86!72.23!Ppp1r13l;;chr18:3299485..3299513,-!p12@Crem!1.84!68.85!Crem;;chr5:38611831..38611842,+!p3@Lyar!1.82!65.47!Lyar;;chr18:3299535..3299565,-!p10@Crem!1.78!59.67!Crem;;chr11:69749437..69749467,+!p3@Ybx2!1.78!58.70!Ybx2;;chr7:31383850..31383874,-!p1@Zbtb32!1.75!54.84!Zbtb32;;chr7:135020660..135020688,+!p3@Zfp646!1.71!69.33!Zfp646;;chr11:87430678..87430702,+!p1@Hsf5!1.67!45.66!Hsf5;;chr8:26958093..26958148,-!p2@Ash2l!1.65!43.73!Ash2l;;chr7:86937900..86937933,-!p@chr7:86937900..86937933,-!1.65!43.24!Mesp1;;chr6:131338363..131338383,-!p4@Csda!1.64!182.15!Csda;;chrX:83437105..83437121,+!p1@Nr0b1!1.64!43.00!Nr0b1;;chr5:38611816..38611827,+!p4@Lyar!1.61!44.21!Lyar;;chr7:31383882..31383903,-!p2@Zbtb32!1.61!39.38!Zbtb32;;chr10:84300848..84300879,+!p6@Rfx4!1.58!37.45!Rfx4;;chr2:180377307..180377330,-!p2@Tcfl5!1.58!37.20!Tcfl5;;chr4:149610794..149610876,+!p2@LOC100045967,p2@LOC100503183,p3@Eno1,p3@Gm5506!1.57!48.32!Eno1;;chr11:95170996..95171026,-!p3@Myst2!1.56!35.03!Myst2;;chr17:15637108..15637147,+!p3@Tbp!1.55!34.30!Tbp;;chr8:26950937..26950991,-!p3@Ash2l!1.53!38.41!Ash2l;;chr3:95032515..95032553,-!p5@Mllt11!1.52!38.65!Mllt11;;chr13:78164153..78164174,+!p1@Pou5f2!1.52!31.89!Pou5f2;;chr15:100410635..100410667,-!p4@Pou6f1!1.50!30.92!Pou6f1;;chr11:69749367..69749385,+!p4@Ybx2!1.49!29.71!Ybx2;;chr1:39777834..39777860,-!p1@Rfx8!1.48!29.23!Rfx8;;chr8:72356532..72356611,+!p1@Pbx4!1.47!114.99!Pbx4;;chrX:131559846..131559883,-!p3@Zmat1!1.46!28.02!Zmat1;;chr8:107033774..107033794,-!p1@Ccdc79!1.44!31.89!Ccdc79;;chr4:89354729..89354776,+!p1@Dmrta1!1.44!26.57!Dmrta1;;chr5:125342568..125342602,+!p2@Zfp664!1.43!41.55!Zfp664;;chr10:22451660..22451678,-!p7@Tbpl1!1.43!25.85!Tbpl1;;chr3:54985946..54985981,+!p1@Sohlh2!1.41!24.64!Sohlh2;;chr2:38570011..38570034,-!p1@Nr5a1!1.41!24.64!Nr5a1;;chr13:96094769..96094829,+!p4@Zbed3!1.39!33.10!Zbed3;;chr4:118967319..118967330,-!p6@Ybx1!1.39!23.68!Ybx1;;chr10:22451765..22451795,-!p6@Tbpl1!1.37!33.34!Tbpl1;;chr17:68663935..68663949,+!p@chr17:68663935..68663949,+!1.36!21.74!L3mbtl4;;chr18:3337503..3337536,-!p7@Crem!1.35!36.72!Crem;;chr7:86938093..86938119,-!p@chr7:86938093..86938119,-!1.34!20.78!Mesp1;;chr8:72356384..72356434,+!p2@Pbx4!1.33!31.16!Pbx4;;chr11:87430728..87430749,+!p3@Hsf5!1.32!20.05!Hsf5;;chr3:90046414..90046476,-!p1@Creb3l4!1.32!20.05!Creb3l4;;chr14:32979060..32979091,+!p4@Gm6768,p4@Ncoa4!1.32!20.05!Ncoa4;;chrX:133654667..133654672,-!p1@Esx1!1.32!19.81!Esx1;;chr3:95032802..95032830,-!p7@Mllt11!1.32!19.81!Mllt11;;chr11:87430653..87430666,+!p2@Hsf5!1.32!19.81!Hsf5;;chr4:89354785..89354801,+!p2@Dmrta1!1.31!19.33!Dmrta1;;chr11:58717647..58717659,-!p3@Zfp39!1.30!18.84!Zfp39;;chr1:52065054..52065098,+!p4@Stat4!1.30!18.84!Stat4;;chr7:13420092..13420160,+!p2@Zfp110!1.29!34.55!Zfp110;;chr2:17986043..17986056,+!p17@Mllt10!1.29!18.60!Mllt10;;chr11:87430713..87430724,+!p4@Hsf5!1.29!18.60!Hsf5;;chr10:84300905..84300919,+!p7@Rfx4!1.29!18.36!Rfx4;;chr10:102491694..102491714,-!p3@Alx1!1.28!17.88!Alx1;;chr6:83303212..83303243,+!p5@Bola3!1.28!17.88!Bola3;;chr17:56970481..56970551,-!p2@Rfx2!1.27!54.36!Rfx2;;chr16:55966407..55966447,+!p6@Rpl24,p6@Zbtb11!1.27!42.52!Zbtb11;;chr11:69749320..69749345,+!p2@Ybx2!1.27!28.75!Ybx2;;chr15:100058744..100058772,+!p4@Gm1862,p6@Atf1!1.26!17.39!Atf1;;chr1:9690424..9690467,-!p1@Mybl1!1.24!33.82!Mybl1;;chr7:25655066..25655080,+!p2@Dmrtc2!1.24!16.43!Dmrtc2;;chr12:113917774..113917792,+!p5@Zbtb42!1.24!16.19!Zbtb42;;chr3:51144477..51144506,-!p6@Elf2!1.23!24.64!Elf2;;chr10:75384163..75384185,-!p3@Smarcb1!1.23!15.94!Smarcb1;;chr6:72850124..72850210,-!p7@Kcmf1!1.22!20.29!Kcmf1;;chr19:25580272..25580305,+!p3@Dmrt1!1.21!15.22!Dmrt1;;chr12:30525072..30525115,+!p14@Myt1l!1.21!15.22!Myt1l;;chr10:22539932..22539956,-!p1@Tcf21!1.20!38.90!Tcf21;;chr11:69749299..69749319,+!p5@Ybx2!1.20!18.12!Ybx2;;chr11:116196714..116196729,-!p2@Foxj1!1.20!14.74!Foxj1;;chr3:130815433..130815454,+!p15@Lef1!1.19!14.50!Lef1;;chr13:93346120..93346155,-!p1@Spz1!1.18!14.01!Spz1;;chr14:32979026..32979042,+!p5@Gm6768,p5@Ncoa4!1.17!13.77!Ncoa4;;chr11:69749491..69749502,+!p6@Ybx2!1.17!13.77!Ybx2;;chr5:38611720..38611799,+!p1@Lyar!1.16!354.89!Lyar;;chr8:26950912..26950933,-!p4@Ash2l!1.16!13.53!Ash2l;;chr6:83303284..83303299,+!p6@Bola3!1.15!13.29!Bola3;;chr14:32979005..32979017,+!p7@Gm6768,p7@Ncoa4!1.15!13.29!Ncoa4;;chr2:144157091..144157103,-!p4@Ovol2!1.15!13.29!Ovol2;;chr19:25580110..25580163,+!p1@Dmrt1!1.15!13.05!Dmrt1;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!1.14!42.76!Atf1;;chr16:3872378..3872411,-!p6@Zfp597!1.14!14.50!Zfp597;;chr18:3309876..3309914,-!p9@Crem!1.14!12.80!Crem;;chr10:76424613..76424689,-!p1@Pcbp3!1.13!261.64!Pcbp3;;chr18:52775562..52775650,+!p1@Zfp474!1.13!12.56!Zfp474;;chr19:25580226..25580261,+!p2@Dmrt1!1.13!12.56!Dmrt1;;chr16:11176149..11176163,-!p5@Zc3h7a!1.13!12.56!Zc3h7a;;chrX:35474351..35474366,+!p1@Rhox13!1.13!12.56!Rhox13;;chrX:104863295..104863324,+!p1@Tbx22!1.13!12.56!Tbx22;;chr1:39777805..39777820,-!p2@Rfx8!1.13!12.56!Rfx8;;chr2:144157107..144157128,-!p3@Ovol2!1.13!12.56!Ovol2;;chr17:71202822..71202877,-!p3@Tgif1!1.12!35.27!Tgif1;;chr2:180377331..180377344,-!p3@Tcfl5!1.12!12.32!Tcfl5;;chr16:11176118..11176131,-!p11@Zc3h7a!1.11!11.84!Zc3h7a;;chr12:113917748..113917759,+!p8@Zbtb42!1.11!11.84!Zbtb42;;chr2:104966766..104966786,+!p1@Wt1!1.10!18.36!Wt1;;chr2:104966874..104966907,+!p2@Wt1!1.10!11.60!Wt1;;chrX:137135036..137135064,-!p4@Tsc22d3!1.09!21.98!Tsc22d3;;chr3:51144446..51144456,-!p11@Elf2!1.07!10.87!Elf2;;chrX:7553670..7553688,-!p4@Gata1!1.07!10.87!Gata1;;chrX:58146612..58146615,-!p1@Sox3!1.07!10.87!Sox3;;chr13:78164139..78164148,+!p2@Pou5f2!1.07!10.87!Pou5f2;;chr2:74543397..74543435,+!p2@Hoxd8!1.07!10.63!Hoxd8;;chr4:107356833..107356836,-!p7@Dmrtb1!1.07!10.63!Dmrtb1;;chr3:130815472..130815497,+!p6@Lef1!1.07!10.63!Lef1;;chr15:10400245..10400282,-!p2@Dnajc21!1.06!35.51!Dnajc21;;chr7:86956107..86956152,+!p@chr7:86956107..86956152,+!1.06!16.43!Mesp2;;chr7:135020644..135020659,+!p6@Zfp646!1.06!10.39!Zfp646;;chr2:104966933..104966966,+!p3@Wt1!1.06!10.39!Wt1;;chr11:58717675..58717719,-!p1@Zfp39!1.05!72.96!Zfp39;;chr11:59319921..59319944,-!p5@Zkscan17!1.05!10.15!Zkscan17;;chr9:111020746..111020768,+!p5@Lrrfip2!1.04!9.90!Lrrfip2;;chr17:46520747..46520771,+!p3@Zfp318!1.03!16.91!Zfp318;;chr2:77654815..77654872,-!p2@Zfp385b!1.03!12.32!Zfp385b;;chr7:86937946..86937959,-!p@chr7:86937946..86937959,-!1.03!9.66!Mesp1;;chr5:138202908..138202942,+!p10@Tsc22d4!1.03!9.66!Tsc22d4;;chr18:5334765..5334833,-!p2@Zfp438!1.02!25.61!Zfp438;;chr9:30838314..30838336,+!p4@Zbtb44!1.02!11.35!Zbtb44;;chr8:26958153..26958170,-!p5@Ash2l!1.02!9.42!Ash2l;;chr3:130815455..130815467,+!p10@Lef1!1.02!9.42!Lef1;;chr11:62271076..62271096,-!p19@Ncor1!1.02!9.42!Ncor1;;chr2:17985946..17985957,+!p18@Mllt10!1.01!9.18!Mllt10;;chr6:52663997..52664043,+!p2@Tax1bp1!1.01!9.18!Tax1bp1;;chr18:74375772..74375799,+!p2@Cxxc1!1.00!27.06!Cxxc1;;chr13:21454766..21454791,+!p3@Zscan12!1.00!10.39!Zscan12;;chr7:25655150..25655160,+!p3@Dmrtc2!1.00!8.94!Dmrtc2;;chr10:20032169..20032206,+!p8@Bclaf1!1.00!8.94!Bclaf1;;chr6:92042363..92042413,+!p3@Nr2c2!0.99!21.50!Nr2c2;;chr13:78164176..78164185,+!p3@Pou5f2!0.99!8.70!Pou5f2;;chr11:45793757..45793775,+!p2@Sox30!0.99!8.70!Sox30;;chr11:69749347..69749356,+!p8@Ybx2!0.99!8.70!Ybx2;;chr10:84224957..84224991,+!p3@Rfx4!0.99!8.70!Rfx4;;chrX:90531838..90531861,+!p1@Arx!0.98!10.87!Arx;;chr7:52252978..52252989,+!p5@Irf3!0.98!8.46!Irf3;;chr8:72356661..72356680,+!p3@Pbx4!0.98!8.46!Pbx4;;chr11:116196698..116196713,-!p3@Foxj1!0.98!8.46!Foxj1;;chr17:25707623..25707639,-!p1@Sox8!0.97!36.24!Sox8;;chr10:80809447..80809515,-!p5@Hmg20b!0.96!9.90!Hmg20b;;chr15:96117679..96117696,+!p6@Arid2!0.96!8.21!Arid2;;chr2:180377022..180377040,-!p4@Tcfl5!0.96!8.21!Tcfl5;;chr10:84300888..84300898,+!p8@Rfx4!0.95!7.97!Rfx4;;chr10:102491677..102491687,-!p5@Alx1!0.95!7.97!Alx1;;chr16:50331135..50331178,-!p5@Bbx!0.94!7.73!Bbx;;chr6:143895612..143895631,-!p3@Sox5!0.94!7.73!Sox5;;chr2:77654650..77654685,-!p3@Zfp385b!0.93!9.66!Zfp385b;;chr2:17985967..17985975,+!p22@Mllt10!0.93!7.49!Mllt10;;chr11:95171032..95171046,-!p4@Myst2!0.93!7.49!Myst2;;chr7:31383918..31383931,-!p4@Zbtb32!0.93!7.49!Zbtb32;;chr5:135582751..135582788,+!p1@Mlxipl!0.92!30.44!Mlxipl;;chr7:17200198..17200209,-!p8@Grlf1!0.92!9.90!Grlf1;;chr3:51144465..51144476,-!p12@Elf2!0.92!7.25!Elf2;;chr11:58717660..58717670,-!p4@Zfp39!0.92!7.25!Zfp39;;chr11:62271059..62271073,-!p21@Ncor1!0.92!7.25!Ncor1;;chr15:75447162..75447217,+!p2@Zfp41!0.91!21.98!Zfp41;;chr6:28211956..28211967,-!p2@Zfp800!0.90!15.22!Zfp800;;chr5:108698309..108698321,+!p8@Dr1!0.90!7.01!Dr1;;chr18:3299515..3299521,-!p26@Crem!0.90!7.01!Crem;;chrX:7544943..7545001,-!p1@Gata1!0.90!7.01!Gata1;;chr19:47125313..47125405,-!p1@Pcgf6!0.89!153.89!Pcgf6;;chr13:112476433..112476448,+!p2@Mier3!0.89!13.05!Mier3;;chr3:103772552..103772584,+!p2@Phtf1!0.89!10.63!Phtf1;;chr6:98978189..98978198,-!p10@Foxp1!0.89!8.70!Foxp1;;chr14:63890491..63890516,-!p2@Gata4!0.89!6.76!Gata4;;chr7:31383838..31383845,-!p5@Zbtb32!0.89!6.76!Zbtb32;;chr7:29552143..29552173,-!p4@Nfkbib!0.89!6.76!Nfkbib;;chr17:46520674..46520741,+!p1@Zfp318!0.88!58.46!Zfp318;;chr1:9690398..9690410,-!p2@Mybl1!0.88!7.97!Mybl1;;chr5:3648013..3648038,-!p5@Gatad1!0.88!7.73!Gatad1;;chr19:25580353..25580364,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1!Arnt2;;chr7:20162663..20162678,+!p1@Zfp296!0.18!0.97!Zfp296;;chr16:43619156..43619171,+!p16@Zbtb20!0.18!0.97!Zbtb20;;chr19:7342786..7342803,+!p2@Rcor2!0.18!0.97!Rcor2;;chr4:150513630..150513686,-!p4@Camta1!0.18!0.72!Camta1;;chr15:75799634..75799645,+!p4@Zfp707!0.18!0.72!Zfp707;;chr7:52253119..52253130,+!p4@Irf3!0.18!0.72!Irf3;;chr18:76401314..76401395,+!p2@Smad2!0.17!8.70!Smad2;;chr2:156665817..156665877,+!p1@Tgif2!0.17!7.73!Tgif2;;chr5:92391901..92391936,+!p1@Thap6!0.17!5.80!Thap6;;chr2:83484738..83484749,+!p5@Zc3h15!0.17!4.59!Zc3h15;;chr14:19071567..19071612,-!p2@Nr1d2!0.17!4.35!Nr1d2;;chr8:114167325..114167350,+!p2@Zfp1!0.17!4.11!Zfp1;;chr9:71959562..71959624,-!p3@Tcf12!0.17!3.87!Tcf12;;chr9:21420610..21420621,+!p5@Smarca4!0.17!3.38!Smarca4;;chr4:151401710..151401733,-!p2@Zbtb48!0.17!3.38!Zbtb48;;chr4:6917921..6917970,-!p2@Tox!0.17!2.90!Tox;;chr2:91077124..91077146,-!p3@Ddb2!0.17!2.66!Ddb2;;chr10:80812991..80813004,-!p3@Hmg20b!0.17!1.93!Hmg20b;;chr5:138199361..138199441,+!p2@Tsc22d4!0.17!1.69!Tsc22d4;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!0.17!1.69!Zbtb38;;chr6:128312772..128312792,+!p2@Foxm1!0.17!1.45!Foxm1;;chr12:9581317..9581333,+!p3@Osr1!0.17!1.21!Osr1;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!0.17!0.72!Ncoa4;;chr9:72122748..72122757,+!p4@Zfp280d!0.17!0.72!Zfp280d;;chr8:73905967..73905978,-!p4@Nr2f6!0.17!0.72!Nr2f6;;chr9:18282826..18282845,+!p2@Mbd3l1!0.17!0.48!Mbd3l1;;chr9:63514630..63514652,-!p8@Smad3!0.17!0.48!Smad3;;chr7:30088957..30088966,+!p6@Dpf1!0.17!0.48!Dpf1;;chr9:18282704..18282748,-!p3@Zfp558!0.17!0.48!Zfp558;;chr7:31377960..31377973,-!p3@Zbtb32!0.17!0.48!Zbtb32;;chr7:88007115..88007129,+!p2@Zscan2!0.17!0.48!Zscan2;;chr10:79393164..79393173,+!p12@Arid3a!0.17!0.48!Arid3a;;chr11:96143962..96144035,+!p2@Hoxb8!0.17!0.48!Hoxb8;;chr10:5734582..5734595,-!p10@Esr1!0.17!0.48!Esr1;;chr10:5734677..5734702,-!p4@Esr1!0.17!0.48!Esr1;;chr11:52096305..52096328,-!p11@Tcf7!0.17!0.48!Tcf7;;chr10:61595830..61595846,+!p1@Neurog3!0.17!0.48!Neurog3;;chr11:21901608..21901634,-!p1@Otx1!0.17!0.48!Otx1;;chr10:126778639..126778670,-!p3@Gli1!0.17!0.48!Gli1;;chr12:100009260..100009274,+!p3@Zc3h14!0.17!0.48!Zc3h14;;chr11:96685444..96685473,-!p5@Nfe2l1!0.17!0.48!Nfe2l1;;chr2:38567715..38567730,-!p2@Nr5a1!0.17!0.48!Nr5a1;;chr2:168592636..168592651,-!p1@Sall4!0.17!0.48!Sall4;;chr2:24331085..24331100,-!p1@Pax8!0.17!0.48!Pax8;;chrY:1426341..1426344,-!p1@Zfy2!0.17!0.48!Zfy2;;chrX:83437070..83437078,+!p2@Nr0b1!0.17!0.48!Nr0b1;;chr16:18588291..18588301,-!p2@Tbx1!0.17!0.48!Tbx1;;chr17:14011485..14011507,+!p2@Mllt4!0.17!0.48!Mllt4;;chr13:83643159..83643226,+!p3@Mef2c!0.17!0.48!Mef2c;;chr15:76352740..76352781,-!p5@Scrt1!0.17!0.48!Scrt1;;chr15:76352832..76352900,-!p1@Scrt1!0.17!0.48!Scrt1;;chr15:102821007..102821021,+!p2@Hoxc8!0.17!0.48!Hoxc8;;chr14:32978944..32978953,+!p8@Gm6768,p8@Ncoa4!0.17!0.48!Ncoa4;;chr13:56804798..56804806,+!p7@Smad5!0.17!0.48!Smad5;;chr5:31271010..31271019,+!p2@Tcf23!0.17!0.48!Tcf23;;chr7:138553839..138553860,-!p2@Ikzf5!0.17!0.48!Ikzf5;;chr5:38611199..38611209,+!p6@Lyar!0.17!0.48!Lyar;;chr6:85967211..85967223,+!p1@Figla!0.17!0.48!Figla;;chr5:24104751..24104773,-!p5@Smarcd3!0.17!0.48!Smarcd3;;chr7:150155143..150155156,-!p1@Ascl2!0.17!0.48!Ascl2;;chr7:116093986..116093999,+!p4@Tub!0.17!0.48!Tub;;chr7:147129777..147129814,+!p2@Utf1!0.17!0.48!Utf1;;chr5:77524043..77524064,-!p9@Hopx!0.17!0.48!Hopx;;chr5:138202904..138202907,+!p24@Tsc22d4!0.17!0.48!Tsc22d4;;chr5:137042338..137042372,-!p5@Cux1!0.17!0.48!Cux1;;chr4:115612528..115612533,-!p1@Dmbx1!0.17!0.48!Dmbx1;;chr2:74536050..74536065,+!p2@Hoxd9!0.17!0.48!Hoxd9;;chr2:77655725..77655739,-!p15@Zfp385b!0.17!0.48!Zfp385b;;chr2:74529942..74529953,+!p4@Hoxd10!0.17!0.48!Hoxd10;;chr2:77654737..77654748,-!p17@Zfp385b!0.17!0.48!Zfp385b;;chr4:107353455..107353476,-!p8@Dmrtb1!0.17!0.48!Dmrtb1;;chr2:74543202..74543213,+!p3@Hoxd8!0.17!0.48!Hoxd8;;chr17:57074836..57074927,-!p1@Mllt1!0.16!35.03!Mllt1;;chr13:14156043..14156089,+!p1@Arid4b!0.16!31.41!Arid4b;;chr8:13869673..13869740,+!p1@Zfp828!0.16!30.92!Zfp828;;chr5:67698217..67698253,+!p2@Slc30a9!0.16!25.61!Slc30a9;;chr11:106134020..106134128,-!p1@Smarcd2!0.16!25.12!Smarcd2;;chr6:29997979..29998049,+!p1@Nrf1!0.16!23.19!Nrf1;;chr9:31193772..31193820,+!p1@Nfrkb!0.16!20.05!Nfrkb;;chr10:85379647..85379751,-!p1@Prdm4!0.16!13.77!Prdm4;;chr3:94758041..94758142,+!p1@Rfx5!0.16!11.35!Rfx5;;chr17:47873985..47874056,+!p1@Tfeb!0.16!10.15!Tfeb;;chr16:3847206..3847307,+!p1@Zfp174!0.16!5.56!Zfp174;;
+|ffid_belonging_in_development=UBERON:0009117,UBERON:0002532,UBERON:0006603,UBERON:0005564,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011433
 |is_obsolete=
+|library_id=CNhs11110
+|library_id_phase_based=2:CNhs11110
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;839
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;839
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N20.CNhs11110.839-18H3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N20.CNhs11110.839-18H3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N20.CNhs11110.839-18H3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N20.CNhs11110.839-18H3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N20.CNhs11110.839-18H3.mm9.nobarcode.rdna.fa.gz
 |name=testis, neonate N20
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11110,LSID734,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.09716842173435,0,0.0469880747817416,0,0,0,0.188589933157333,0,0.0852565313929955,0,0,0.417302857552358,0,0,0,0,0.343556862337715,0,0.275370284987064,0,0,0,0,0,0,0,0,0.293657837167637,0,0,0.049110609127556,0,0.0832671913299474,0,0.236726748493521,0.997325756787597,0,0,0.0912365013624241,-0.140007411481081,-0.334682572012978,-0.342521382823847,0.0237891991572862,0,0,0,0,0,0,0,0.916323568242477,0,0,0.171190417567041,0.343983452296214,0.027970602000043,0.0939761495634833,0,0,0,-0.0428469550828748,0,0.0169292753551805,0,0.0939761495634833,0,0.160222558019096,0.156612978530252,-0.0641148932075992,0.0782921176625562,0,0.13610707822213,-0.0664163131862825,0,0,0,0,0.0601699177342352,-0.16598684459111,0.265151857456307,0,0.236726748493521,0,0.0939761495634833,0,0,-0.0752205997629372,-0.0933870569610522,-0.00461070940082,0.0417874454540353,0,0.0939761495634833,0,0.118419915860757
 |rna_box=18
 |rna_catalog_number=
@@ Line 59: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:839-18H3;search_select_hide=table117:839-18H3
 }}

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FF:839-18H3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:21, 4 June 2020

CNhs11110

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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