FF:389-23F5: Difference between revisions

Latest revision as of 19:14, 4 June 2020

Name:	testis, embryo E13
Species:	Mouse (Mus musculus)
Library ID:	CNhs11031
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	testis
dev stage	13 days embryo
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		SAMD00005814

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11031		CAGE		DRX009102		DRR009976

Accession ID Mm9

Library id		BAM		CTSS
CNhs11031		DRZ001401		DRZ002784

Accession ID Mm10

Library id		BAM		CTSS
CNhs11031		DRZ012751		DRZ014134

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

CNhs11031

0	0
1	0
10	0
100	0
1000	0
1001	-0.0366
1002	0.276
1003	-0.122
1004	0
1005	-0.0389
1006	-0.104
1007	0.133
1008	0
1009	-0.0572
101	0.136
1010	0
1011	-0.0261
1012	0
1013	-0.188
1014	0.114
1015	0.231
1016	0.262
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	-0.0271
1023	0
1024	-0.0899
1025	0
1026	0
1027	0
1028	0
1029	-0.0543
103	0.0354
1030	0
1031	0.244
1032	-0.121
1033	0
1034	0
1035	0.0605
1036	-0.0157
1037	0
1038	0.0143
1039	-0.0649
104	0
1040	0.0401
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: CNhs11031

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0017
MA0003.1	MA0003.1	0.953
MA0004.1	MA0004.1	0.497
MA0006.1	MA0006.1	0.39
MA0007.1	MA0007.1	0.453
MA0009.1	MA0009.1	0.876
MA0014.1	MA0014.1	0.727
MA0017.1	MA0017.1	0.00776
MA0018.2	MA0018.2	0.725
MA0019.1	MA0019.1	0.353
MA0024.1	MA0024.1	7.40215e-7
MA0025.1	MA0025.1	0.582
MA0027.1	MA0027.1	0.239
MA0028.1	MA0028.1	0.0067
MA0029.1	MA0029.1	0.867
MA0030.1	MA0030.1	0.183
MA0031.1	MA0031.1	0.13
MA0035.2	MA0035.2	0.69
MA0038.1	MA0038.1	0.0557
MA0039.2	MA0039.2	0.528
MA0040.1	MA0040.1	0.339
MA0041.1	MA0041.1	0.358
MA0042.1	MA0042.1	0.516
MA0043.1	MA0043.1	0.354
MA0046.1	MA0046.1	5.99726e-25
MA0047.2	MA0047.2	0.0562
MA0048.1	MA0048.1	0.0237
MA0050.1	MA0050.1	8.17823e-4
MA0051.1	MA0051.1	0.00184
MA0052.1	MA0052.1	2.60087e-4
MA0055.1	MA0055.1	0.009
MA0057.1	MA0057.1	0.185
MA0058.1	MA0058.1	0.294
MA0059.1	MA0059.1	0.464
MA0060.1	MA0060.1	5.09244e-13
MA0061.1	MA0061.1	0.104
MA0062.2	MA0062.2	0.0173
MA0065.2	MA0065.2	0.0101
MA0066.1	MA0066.1	0.0481
MA0067.1	MA0067.1	0.69
MA0068.1	MA0068.1	0.0279
MA0069.1	MA0069.1	0.607
MA0070.1	MA0070.1	0.582
MA0071.1	MA0071.1	0.846
MA0072.1	MA0072.1	0.366
MA0073.1	MA0073.1	0.87
MA0074.1	MA0074.1	0.918
MA0076.1	MA0076.1	0.00488
MA0077.1	MA0077.1	0.303
MA0078.1	MA0078.1	0.661
MA0079.2	MA0079.2	0.253
MA0080.2	MA0080.2	1.02789e-5
MA0081.1	MA0081.1	0.99
MA0083.1	MA0083.1	0.223
MA0084.1	MA0084.1	0.898
MA0087.1	MA0087.1	0.584
MA0088.1	MA0088.1	0.999
MA0090.1	MA0090.1	0.79
MA0091.1	MA0091.1	0.718
MA0092.1	MA0092.1	0.38
MA0093.1	MA0093.1	0.434
MA0099.2	MA0099.2	1.03301e-4
MA0100.1	MA0100.1	0.335
MA0101.1	MA0101.1	0.791
MA0102.2	MA0102.2	0.426
MA0103.1	MA0103.1	0.00125
MA0104.2	MA0104.2	0.188
MA0105.1	MA0105.1	2.14407e-4
MA0106.1	MA0106.1	0.339
MA0107.1	MA0107.1	0.341
MA0108.2	MA0108.2	6.38784e-4
MA0111.1	MA0111.1	0.202
MA0112.2	MA0112.2	2.20059e-4
MA0113.1	MA0113.1	0.982
MA0114.1	MA0114.1	0.007
MA0115.1	MA0115.1	0.343
MA0116.1	MA0116.1	0.019
MA0117.1	MA0117.1	0.164
MA0119.1	MA0119.1	0.32
MA0122.1	MA0122.1	0.92
MA0124.1	MA0124.1	0.072
MA0125.1	MA0125.1	0.341
MA0131.1	MA0131.1	0.217
MA0135.1	MA0135.1	0.832
MA0136.1	MA0136.1	0.105
MA0137.2	MA0137.2	0.467
MA0138.2	MA0138.2	4.30425e-4
MA0139.1	MA0139.1	0.356
MA0140.1	MA0140.1	0.576
MA0141.1	MA0141.1	0.229
MA0142.1	MA0142.1	0.242
MA0143.1	MA0143.1	0.0894
MA0144.1	MA0144.1	0.322
MA0145.1	MA0145.1	0.00674
MA0146.1	MA0146.1	0.407
MA0147.1	MA0147.1	0.23
MA0148.1	MA0148.1	0.00632
MA0149.1	MA0149.1	0.099
MA0150.1	MA0150.1	0.00933
MA0152.1	MA0152.1	0.578
MA0153.1	MA0153.1	2.64433e-15
MA0154.1	MA0154.1	0.0109
MA0155.1	MA0155.1	0.629
MA0156.1	MA0156.1	0.908
MA0157.1	MA0157.1	0.147
MA0159.1	MA0159.1	0.00204
MA0160.1	MA0160.1	0.685
MA0162.1	MA0162.1	0.132
MA0163.1	MA0163.1	0.0792
MA0164.1	MA0164.1	0.799
MA0258.1	MA0258.1	0.00126
MA0259.1	MA0259.1	0.24

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: CNhs11031

Novel motif	Logo	P-value
1	1	0.107
10	10	0.331
100	100	0.705
101	101	0.404
102	102	0.637
103	103	0.181
104	104	0.841
105	105	0.159
106	106	0.00395
107	107	0.048
108	108	0.675
109	109	0.399
11	11	0.28
110	110	0.649
111	111	0.336
112	112	0.396
113	113	0.436
114	114	0.0973
115	115	0.579
116	116	0.426
117	117	0.943
118	118	0.68
119	119	0.217
12	12	0.642
120	120	0.529
121	121	0.403
122	122	0.655
123	123	0.168
124	124	0.253
125	125	0.0327
126	126	0.805
127	127	0.118
128	128	0.00317
129	129	0.0274
13	13	0.945
130	130	0.377
131	131	0.541
132	132	0.157
133	133	0.823
134	134	0.454
135	135	0.976
136	136	0.101
137	137	0.632
138	138	0.871
139	139	0.0446
14	14	0.145
140	140	0.371
141	141	0.0447
142	142	0.934
143	143	0.077
144	144	0.124
145	145	0.918
146	146	0.561
147	147	0.508
148	148	0.141
149	149	0.165
15	15	0.146
150	150	0.832
151	151	0.0613
152	152	0.343
153	153	0.526
154	154	0.871
155	155	0.599
156	156	2.03758e-4
157	157	0.608
158	158	0.394
159	159	0.027
160	160	0.902
161	161	0.759
162	162	0.623
163	163	0.0915
164	164	0.905
165	165	0.15
166	166	0.891
167	167	0.437
168	168	0.201
169	169	0.286
17	17	0.0964
18	18	0.171
19	19	0.756
2	2	0.515
20	20	0.378
21	21	0.806
22	22	0.674
23	23	0.0452
24	24	0.896
25	25	0.37
26	26	0.735
27	27	0.238
28	28	0.388
29	29	0.873
3	3	0.319
30	30	0.678
31	31	0.136
32	32	0.154
33	33	0.816
34	34	0.833
35	35	0.0972
36	36	0.206
37	37	0.223
38	38	0.629
39	39	0.866
4	4	0.681
40	40	0.494
41	41	0.152
42	42	0.625
43	43	0.209
44	44	0.275
45	45	0.462
46	46	0.17
47	47	0.357
48	48	0.367
49	49	0.128
5	5	0.114
50	50	0.987
51	51	0.754
52	52	0.219
53	53	0.65
54	54	0.389
55	55	0.689
56	56	0.241
57	57	0.649
58	58	0.251
59	59	0.154
6	6	0.827
60	60	0.0742
61	61	0.512
62	62	0.0922
63	63	0.164
64	64	0.708
65	65	0.167
66	66	0.582
67	67	0.679
68	68	2.93841e-4
69	69	0.808
7	7	0.442
70	70	0.00356
71	71	0.254
72	72	0.545
73	73	0.411
74	74	0.494
75	75	0.529
76	76	0.452
77	77	0.309
78	78	0.528
79	79	0.713
8	8	0.258
80	80	0.151
81	81	0.219
82	82	0.528
83	83	0.499
84	84	0.154
85	85	0.0106
86	86	0.315
87	87	0.523
88	88	0.427
89	89	0.0727
9	9	0.844
90	90	0.126
91	91	0.316
92	92	0.105
93	93	0.561
94	94	0.322
95	95	0.757
96	96	0.285
97	97	0.831
98	98	0.0811
99	99	0.818

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: CNhs11031

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011332 mouse testis- embryo E13 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)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000293 (mouse embryonic day 13 sample)
0011332 (mouse testis- embryo E13 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@SAMD00005814
+|accession_numbers=CAGE;DRX009102;DRR009976;DRZ001401;DRZ002784;DRZ012751;DRZ014134
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,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:0000999,FF:0000292,FF:0000004,FF:0000293,FF:0011332
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:140739014..140739032,-!p1@Lhx9!2.29!242.67!Lhx9;;chr10:22539932..22539956,-!p1@Tcf21!2.07!298.73!Tcf21;;chrX:90531838..90531861,+!p1@Arx!2.01!127.09!Arx;;chr2:38570011..38570034,-!p1@Nr5a1!1.97!93.30!Nr5a1;;chr7:147129712..147129774,+!p1@Utf1!1.97!92.55!Utf1;;chr14:63864056..63864102,-!p1@Gata4!1.87!122.30!Gata4;;chr15:102828658..102828678,+!p1@Hoxc6!1.72!50.99!Hoxc6;;chr2:104966766..104966786,+!p1@Wt1!1.60!59.66!Wt1;;chr2:74549968..74549996,+!p1@Hoxd3!1.60!48.29!Hoxd3;;chr2:74529970..74529997,+!p1@Hoxd10!1.52!32.45!Hoxd10;;chr2:104966874..104966907,+!p2@Wt1!1.50!30.95!Wt1;;chr10:119913278..119913298,-!p2@Hmga2!1.46!60.40!Hmga2;;chr19:59533221..59533271,+!p1@Emx2!1.45!32.89!Emx2;;chr17:35642997..35643014,+!p1@Pou5f1!1.36!22.13!Pou5f1;;chr2:74536026..74536039,+!p1@Hoxd9!1.33!20.48!Hoxd9;;chr10:119913310..119913366,-!p1@Hmga2!1.32!150.11!Hmga2;;chr10:119913546..119913583,-!p3@Hmga2!1.29!37.98!Hmga2;;chr7:147129777..147129814,+!p2@Utf1!1.26!17.34!Utf1;;chr2:74550015..74550057,+!p2@Hoxd3!1.24!16.45!Hoxd3;;chr2:104966933..104966966,+!p3@Wt1!1.24!16.45!Wt1;;chr11:85646303..85646329,+!p1@Tbx2!1.23!104.96!Tbx2;;chr8:26958093..26958148,-!p2@Ash2l!1.23!16.15!Ash2l;;chr19:25580110..25580163,+!p1@Dmrt1!1.23!15.85!Dmrt1;;chr17:35642973..35642994,+!p2@Pou5f1!1.23!15.85!Pou5f1;;chr3:54985946..54985981,+!p1@Sohlh2!1.16!13.31!Sohlh2;;chr7:147129680..147129693,+!p3@Utf1!1.15!13.16!Utf1;;chr10:126778916..126778974,-!p1@Gli1!1.14!29.01!Gli1;;chr11:85646263..85646278,+!p2@Tbx2!1.13!31.70!Tbx2;;chr10:119914001..119914078,-!p4@Hmga2!1.13!17.19!Hmga2;;chr2:104966465..104966479,+!p6@Wt1!1.11!11.81!Wt1;;chr2:74536050..74536065,+!p2@Hoxd9!1.09!11.36!Hoxd9;;chr14:63864337..63864381,-!p6@Gata4!1.08!10.91!Gata4;;chr14:63890660..63890687,-!p7@Gata4!1.07!10.62!Gata4;;chr15:102828642..102828653,+!p2@Hoxc6!1.05!10.32!Hoxc6;;chr14:63890459..63890484,-!p4@Gata4!1.05!10.32!Gata4;;chrX:83437105..83437121,+!p1@Nr0b1!1.05!10.17!Nr0b1;;chrX:45245679..45245702,-!p1@Smarca1!1.04!45.60!Smarca1;;chr19:59533139..59533152,+!p2@Emx2!1.01!9.12!Emx2;;chr19:59533163..59533185,+!p3@Emx2!1.00!8.97!Emx2;;chr6:122657610..122657626,+!p1@Nanog,p1@Nanogpd!0.98!8.52!Nanog;;chr12:87811059..87811072,+!p3@Esrrb!0.96!8.22!Esrrb;;chr2:74529998..74530020,+!p2@Hoxd10!0.96!8.07!Hoxd10;;chr14:63890491..63890516,-!p2@Gata4!0.94!7.63!Gata4;;chr12:3891753..3891801,+!p4@Dnmt3a!0.93!12.41!Dnmt3a;;chr19:59533429..59533470,+!p4@Emx2!0.93!7.48!Emx2;;chr17:25707623..25707639,-!p1@Sox8!0.92!32.45!Sox8;;chr15:40486883..40486903,+!p4@Zfpm2!0.92!9.87!Zfpm2;;chr11:69468531..69468557,+!p1@Sox15!0.92!7.33!Sox15;;chr2:74536071..74536083,+!p4@Hoxd9!0.91!7.18!Hoxd9;;chr7:6649134..6649167,-!p1@Zim1!0.90!39.47!Zim1;;chr1:120879128..120879183,-!p3@Gli2!0.90!13.61!Gli2;;chr1:140739042..140739054,-!p2@Lhx9!0.90!7.03!Lhx9;;chr2:152758901..152758925,-!p1@Foxs1!0.89!31.55!Foxs1;;chr11:85646341..85646352,+!p3@Tbx2!0.89!13.61!Tbx2;;chr3:34548909..34548927,+!p1@Sox2!0.88!11.51!Sox2;;chr2:104966662..104966673,+!p4@Wt1!0.88!6.58!Wt1;;chr2:105003277..105003280,+!p5@Wt1!0.88!6.58!Wt1;;chr14:63890519..63890539,-!p3@Gata4!0.87!6.43!Gata4;;chr12:34642510..34642530,+!p1@Twist1!0.86!20.63!Twist1;;chr15:35225845..35225867,+!p1@Osr2!0.84!15.70!Osr2;;chr12:3891810..3891829,+!p2@Dnmt3a!0.83!9.27!Dnmt3a;;chr2:168592636..168592651,-!p1@Sall4!0.83!5.83!Sall4;;chr2:74535796..74535808,+!p3@Hoxd9!0.82!5.53!Hoxd9;;chr12:28027561..28027591,-!p1@Sox11!0.81!38.58!Sox11;;chr5:31271028..31271040,+!p1@Tcf23!0.80!5.38!Tcf23;;chr9:44249274..44249313,-!p1@Foxr1!0.80!5.38!Foxr1;;chr11:85646469..85646488,+!p5@Tbx2!0.79!7.92!Tbx2;;chr2:74549945..74549965,+!p4@Hoxd3!0.79!5.23!Hoxd3;;chr14:63890691..63890718,-!p8@Gata4!0.79!5.23!Gata4;;chr4:122911086..122911112,+!p1@Heyl!0.78!64.59!Heyl;;chr10:119913266..119913277,-!p6@Hmga2!0.78!5.08!Hmga2;;chr1:168168856..168168893,-!p1@Mael!0.78!5.08!Mael;;chr19:10315179..10315241,-!p1@Gm98!0.77!55.62!Gm98;;chr2:77357622..77357704,-!p1@Zfp385b!0.77!14.20!Zfp385b;;chr1:38684260..38684312,-!p2@Aff3!0.76!36.63!Aff3;;chr13:83712735..83712761,+!p9@Mef2c!0.76!4.78!Mef2c;;chr11:84339016..84339044,-!p1@Lhx1!0.76!4.78!Lhx1;;chr7:52471143..52471186,+!p1@Tead2!0.74!53.68!Tead2;;chr18:11052456..11052477,+!p3@Gata6!0.74!15.10!Gata6;;chr8:90483433..90483457,-!p2@Zfp423!0.74!6.28!Zfp423;;chr4:133109285..133109308,+!p1@Nr0b2!0.74!4.49!Nr0b2;;chr2:181194069..181194144,-!p1@Zbtb46!0.73!27.51!Zbtb46;;chr7:25292076..25292114,+!p4@Zfp428!0.73!13.16!Zfp428;;chr11:121380594..121380609,-!p2@Zfp750!0.73!7.92!Zfp750;;chr2:38567715..38567730,-!p2@Nr5a1!0.73!4.34!Nr5a1;;chr2:104966436..104966455,+!p7@Wt1!0.73!4.34!Wt1;;chr2:104966909..104966920,+!p8@Wt1!0.73!4.34!Wt1;;chr15:102820964..102821006,+!p1@Hoxc8!0.73!4.34!Hoxc8;;chr15:40486854..40486867,+!p7@Zfpm2!0.72!5.23!Zfpm2;;chr7:77505617..77505632,-!p1@Nr2f2!0.71!218.00!Nr2f2;;chr9:36954842..36954908,-!p1@Pknox2!0.71!54.27!Pknox2;;chr10:119913792..119913820,-!p5@Hmga2!0.71!7.48!Hmga2;;chr2:152758938..152758954,-!p2@Foxs1!0.71!5.98!Foxs1;;chr12:87811081..87811100,+!p2@Esrrb!0.71!4.19!Esrrb;;chr15:76701495..76701535,-!p3@Zfp251!0.71!4.19!Zfp251;;chr15:40486566..40486600,+!p1@Zfpm2!0.70!26.46!Zfpm2;;chr16:14705961..14705978,+!p2@Snai2!0.70!21.08!Snai2;;chrX:45245644..45245666,-!p2@Smarca1!0.70!14.35!Smarca1;;chr7:89137163..89137200,-!p1@Bnc1!0.70!4.93!Bnc1;;chr19:25580226..25580261,+!p2@Dmrt1!0.70!4.04!Dmrt1;;chr12:12948633..12948651,-!p1@Mycn!0.69!42.61!Mycn;;chr1:38684383..38684394,-!p4@Aff3!0.69!5.53!Aff3;;chr1:9690398..9690410,-!p2@Mybl1!0.69!4.78!Mybl1;;chr2:169458799..169458832,+!p5@Tshz2!0.68!6.73!Tshz2;;chr10:12810631..12810649,+!p1@Plagl1!0.67!110.94!Plagl1;;chr2:25562346..25562433,+!p1@Bmyc!0.67!77.90!Bmyc;;chr18:11052642..11052659,+!p1@Gata6!0.67!20.93!Gata6;;chr7:17647736..17647772,-!p1@Hif3a!0.67!14.50!Hif3a;;chr8:59799772..59799789,+!p1@Hand2!0.67!11.81!Hand2;;chr18:11052485..11052508,+!p2@Gata6!0.67!11.66!Gata6;;chr19:26822880..26822964,+!p2@Smarca2!0.66!34.84!Smarca2;;chr4:84320893..84320910,-!p1@Bnc2!0.66!8.67!Bnc2;;chr10:80809447..80809515,-!p5@Hmg20b!0.66!4.49!Hmg20b;;chr19:59532915..59532940,+!p5@Emx2!0.66!3.59!Emx2;;chr19:59533595..59533628,+!p6@Emx2!0.66!3.59!Emx2;;chr1:140743964..140743976,-!p3@Lhx9!0.66!3.59!Lhx9;;chr16:14705925..14705951,+!p1@Snai2!0.65!27.96!Snai2;;chr17:48061584..48061601,-!p2@Foxp4!0.65!26.17!Foxp4;;chr2:152223441..152223465,-!p2@Sox12!0.65!16.45!Sox12;;chr7:77511403..77511450,-!p3@Nr2f2!0.65!8.07!Nr2f2;;chr15:40486754..40486771,+!p2@Zfpm2!0.65!6.58!Zfpm2;;chr19:25580272..25580305,+!p3@Dmrt1!0.65!3.44!Dmrt1;;chr2:169458519..169458555,+!p2@Tshz2!0.63!15.40!Tshz2;;chrX:98449898..98449913,+!p2@Foxo4!0.63!11.96!Foxo4;;chr15:76500241..76500250,-!p@chr15:76500241..76500250,-!0.63!3.29!Foxh1;;chr2:74543202..74543213,+!p3@Hoxd8!0.63!3.29!Hoxd8;;chr15:103082088..103082136,-!p2@Nfe2!0.62!3.14!Nfe2;;chr6:52190467..52190500,-!p1@Hoxa10!0.62!3.14!Hoxa10;;chr2:169458192..169458247,+!p1@Tshz2!0.60!32.00!Tshz2;;chr4:128483534..128483613,-!p1@Zfp362!0.60!24.82!Zfp362;;chr4:3865501..3865548,-!p1@Plag1!0.60!18.09!Plag1;;chr17:71202822..71202877,-!p3@Tgif1!0.60!10.17!Tgif1;;chr8:87425854..87425891,+!p1@Klf1!0.60!2.99!Klf1;;chr7:77511234..77511302,-!p2@Nr2f2!0.59!23.03!Nr2f2;;chr13:22036953..22037009,+!p1@Zfp184!0.59!8.82!Zfp184;;chr8:90483459..90483475,-!p1@Zfp423!0.58!8.97!Zfp423;;chr19:59534008..59534046,+!p7@Emx2!0.58!2.84!Emx2;;chr19:25580323..25580335,+!p5@Dmrt1!0.58!2.84!Dmrt1;;chr2:74530022..74530033,+!p3@Hoxd10!0.58!2.84!Hoxd10;;chr2:74549915..74549930,+!p6@Hoxd3!0.58!2.84!Hoxd3;;chr4:84192360..84192376,-!p8@Bnc2!0.58!2.84!Bnc2;;chr2:91864661..91864686,-!p1@Creb3l1!0.57!72.67!Creb3l1;;chr2:91864300..91864379,-!p2@Creb3l1!0.57!9.12!Creb3l1;;chr6:52163319..52163342,-!p1@Hoxa3!0.57!4.34!Hoxa3;;chr15:102865088..102865107,+!p1@Hoxc4!0.57!3.89!Hoxc4;;chr14:63890545..63890560,-!p5@Gata4!0.57!2.69!Gata4;;chr7:147129659..147129668,+!p4@Utf1!0.57!2.69!Utf1;;chr8:26958153..26958170,-!p5@Ash2l!0.57!2.69!Ash2l;;chr14:76904313..76904328,+!p1@Tsc22d1!0.56!636.79!Tsc22d1;;chr6:144730427..144730508,-!p1@Sox5!0.56!20.04!Sox5;;chr9:32443818..32443854,+!p2@Ets1!0.56!14.20!Ets1;;chr1:120949949..120950000,-!p1@Gli2!0.56!13.76!Gli2;;chr4:62626594..62626651,+!p1@Zfp618!0.56!11.81!Zfp618;;chr11:85646427..85646451,+!p4@Tbx2!0.56!5.08!Tbx2;;chr11:96153767..96153822,+!p1@Hoxb6!0.56!4.49!Hoxb6;;chr7:20162663..20162678,+!p1@Zfp296!0.56!3.74!Zfp296;;chr7:6683123..6683142,-!p1@Peg3!0.55!169.70!Peg3;;chr17:37139472..37139514,+!p1@Zfp57!0.55!21.53!Zfp57;;chr14:65977324..65977372,+!p2@Zfp395!0.55!17.64!Zfp395;;chr15:102821007..102821021,+!p2@Hoxc8!0.55!2.54!Hoxc8;;chr14:49282415..49282426,-!p4@Otx2!0.55!2.54!Otx2;;chr14:27813852..27813865,+!p1@Hesx1!0.55!2.54!Hesx1;;chr19:25580353..25580364,+!p4@Dmrt1!0.55!2.54!Dmrt1;;chr2:74543103..74543135,+!p4@Hoxd8!0.55!2.54!Hoxd8;;chr1:9690424..9690467,-!p1@Mybl1!0.54!5.98!Mybl1;;chr2:91864449..91864492,-!p3@Creb3l1!0.54!4.49!Creb3l1;;chr11:112643496..112643562,+!p1@Sox9!0.53!114.83!Sox9;;chr7:25292141..25292158,+!p2@Zfp428!0.53!10.32!Zfp428;;chr15:78994907..78994926,-!p1@Sox10!0.53!7.33!Sox10;;chr4:128483731..128483757,-!p4@Zfp362!0.53!6.43!Zfp362;;chr17:28487603..28487626,-!p2@Tead3!0.53!5.83!Tead3;;chr4:84321317..84321332,-!p4@Bnc2!0.53!2.39!Bnc2;;chr15:102839948..102839975,+!p3@Hoxc6!0.53!2.39!Hoxc6;;chr12:84828663..84828679,-!p1@Dpf3!0.52!23.03!Dpf3;;chr19:7342725..7342784,+!p1@Rcor2!0.52!11.81!Rcor2;;chr16:4594853..4594884,+!p3@Glis2!0.52!4.19!Glis2;;chr5:24107676..24107722,-!p4@Smarcd3!0.52!3.44!Smarcd3;;chr16:4594740..4594759,+!p1@Glis2!0.51!33.04!Glis2;;chr7:30954700..30954715,-!p2@LOC677248,p2@Zfp146!0.51!6.28!Zfp146;;chr1:120950098..120950132,-!p2@Gli2!0.51!6.13!Gli2;;chr4:58956447..58956510,+!p1@Zkscan16!0.51!5.83!Zkscan16;;chr11:3189683..3189744,+!p2@Patz1!0.51!5.38!Patz1;;chr9:63869834..63869849,-!p5@Smad6!0.51!4.34!Smad6;;chr15:102820946..102820961,+!p3@Hoxc8!0.51!2.24!Hoxc8;;chr11:5761889..5761969,+!p1@Aebp1!0.50!119.46!Aebp1;;chr5:138187341..138187406,+!p3@Tsc22d4!0.50!30.35!Tsc22d4;;chr6:483958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+|ffid_belonging_in_development=UBERON:0009117,UBERON:0002532,UBERON:0006603,UBERON:0005564,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011332
 |is_obsolete=
+|library_id=CNhs11031
+|library_id_phase_based=2:CNhs11031
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;389
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;389
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E13.CNhs11031.389-23F5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E13.CNhs11031.389-23F5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E13.CNhs11031.389-23F5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E13.CNhs11031.389-23F5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E13.CNhs11031.389-23F5.mm9.nobarcode.rdna.fa.gz
 |name=testis, embryo E13
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11031,LSID732,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0159982154761825,0,0,0,0,0,-0.154448502768632,0,0,0,0,0.158098503922483,0,0,0,0,0,0,0.0505443934364495,0,0,0,0,0,0,0,0,0,0,0,0,0,0.266459549009751,0,0.113620214605082,0,0,0,0.0687673328601242,0,-0.122812810615636,0.128437989924987,0.00822142034559903,0,0,0,0,0,0,0,0,0,0,0.0605152268483434,0.0605152268483434,0.0476146670416413,0.203594761728394,0,0,0,-0.0428469550828748,0,0,0,0,0,0.0258607790015079,0.0310078556300524,0.00284233919702115,0.0171238978890727,0,0.163970701477458,0.0168785086801104,0,0.242437744319024,0,0.00502920439515496,-0.0260888351153183,-0.392320119012175,0.0821017871281962,0,0,0,0,0,0,-0.166054332644373,-0.290268253956248,-0.212992894928859,0,0,0,0,0
 |rna_box=23
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
 |top_motifs=ZNF143:1.65695412506;NANOG{mouse}:1.44581631445;NFY{A,B,C}:1.44381900466;ZNF238:1.24380950503;NR6A1:1.24241490988;RBPJ:1.23508571005;NRF1:1.2284449455;E2F1..5:1.22372290769;YY1:1.08369291334;MYBL2:1.0811779458;RXR{A,B,G}:1.07619077441;EP300:1.05200776713;FOXD3:1.02971622267;PATZ1:0.986586585947;ZNF384:0.983526001311;FOXP1:0.95183386547;HIF1A:0.938896930434;NKX6-1,2:0.925033152647;HBP1_HMGB_SSRP1_UBTF:0.918001677371;GFI1B:0.911067789345;GFI1:0.90670288887;TFAP2{A,C}:0.890222293133;ZBTB16:0.875309954857;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.846287565906;NR5A1,2:0.843258021079;SOX17:0.83972036232;GATA4:0.836465221172;CRX:0.80194099717;PITX1..3:0.775712172422;ELK1,4_GABP{A,B1}:0.750872391915;ZNF423:0.70232183024;STAT1,3:0.697252802609;TEF:0.675862559324;HOX{A5,B5}:0.673890956651;SP1:0.641822307823;MZF1:0.630326579792;SOX{8,9,10}:0.577890814757;TFDP1:0.558626955009;NFIX:0.554829263319;EGR1..3:0.522209737088;XCPE1{core}:0.517428019006;IKZF1:0.460717881965;SOX2:0.43709470408;MAZ:0.432673853781;TLX1..3_NFIC{dimer}:0.432570241993;SOX5:0.431268784446;MTE{core}:0.423658891355;TEAD1:0.411404445836;TOPORS:0.405901231513;CDC5L:0.402105847927;LEF1_TCF7_TCF7L1,2:0.387089591381;STAT5{A,B}:0.386485897496;bHLH_family:0.360343141519;GTF2I:0.356307989319;HSF1,2:0.350119376439;RREB1:0.34773178081;GLI1..3:0.344373725529;BREu{core}:0.309894905561;ADNP_IRX_SIX_ZHX:0.295193157014;ALX1:0.269661903514;NKX2-2,8:0.269417484901;MYB:0.267204055417;ESRRA:0.259378063666;IKZF2:0.247481440611;MED-1{core}:0.246419659057;AIRE:0.230225087657;POU6F1:0.207009724882;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.206559361613;FOXP3:0.200363079296;PAX4:0.189156915874;EVI1:0.187821849529;GATA6:0.177769979403;RORA:0.169919669876;ZIC1..3:0.158104664611;AHR_ARNT_ARNT2:0.158039297849;PBX1:0.14205399988;CREB1:0.126381267665;GCM1,2:0.115533479138;ELF1,2,4:0.113586680686;ZFP161:0.11220055252;NR1H4:0.110249719254;PRRX1,2:0.101007598465;HOXA9_MEIS1:0.0976424423398;PAX1,9:0.0951266984597;NKX3-1:0.0414999404758;CUX2:0.0325976830356;VSX1,2:0.0269563205598;PAX6:0.0264118018885;EN1,2:0.0251996494145;T:0.00927752448293;NKX2-1,4:-0.010297204259;HIC1:-0.0313328665894;KLF4:-0.0465345381268;NANOG:-0.0667505143123;PDX1:-0.0743586310306;HMX1:-0.0811264791881;UFEwm:-0.085210154821;TFAP4:-0.0977665555244;POU2F1..3:-0.104066229988;POU1F1:-0.110556346439;LHX3,4:-0.121376214729;TFAP2B:-0.123700651161;NFATC1..3:-0.14324987243;SPIB:-0.152335761971;BPTF:-0.159834983942;GTF2A1,2:-0.161917197316;RFX1:-0.162039197842;HAND1,2:-0.165631852394;FOX{D1,D2}:-0.17743647307;TAL1_TCF{3,4,12}:-0.18929849867;TBX4,5:-0.198948995578;FOXN1:-0.212037934588;ATF4:-0.212770150028;HES1:-0.21322949331;HMGA1,2:-0.222328135926;RUNX1..3:-0.223152386314;MEF2{A,B,C,D}:-0.228618152866;PAX5:-0.232007665834;OCT4_SOX2{dimer}:-0.243135193178;REST:-0.246194444099;GZF1:-0.251639189823;ETS1,2:-0.26352438206;SPZ1:-0.265205829045;PAX8:-0.267731954226;FOXL1:-0.305889261018;RFX2..5_RFXANK_RFXAP:-0.316331583534;DBP:-0.317388122329;ESR1:-0.322628631955;TFCP2:-0.3371733968;ONECUT1,2:-0.359769305498;CDX1,2,4:-0.3617609634;FOXM1:-0.393842542211;SRF:-0.413187668532;ZNF148:-0.414260850585;MYFfamily:-0.415383180917;SPI1:-0.417838162843;HNF4A_NR2F1,2:-0.45034730651;TP53:-0.458831944681;POU5F1:-0.46845434922;NFKB1_REL_RELA:-0.471403778983;HOX{A4,D4}:-0.493784605818;FOXQ1:-0.495827138575;ZBTB6:-0.50188429667;ATF2:-0.558893111519;POU3F1..4:-0.558919832216;SREBF1,2:-0.588315585114;ALX4:-0.604654711677;HLF:-0.614014663272;FOXA2:-0.61603123978;MTF1:-0.61974611519;SMAD1..7,9:-0.627793818873;BACH2:-0.645888613143;PRDM1:-0.651581650826;NKX2-3_NKX2-5:-0.658090805752;HNF1A:-0.665988049051;ARID5B:-0.668808320881;DMAP1_NCOR{1,2}_SMARC:-0.677151888868;TBP:-0.704647912564;FOXO1,3,4:-0.727583031668;NHLH1,2:-0.752330210423;RXRA_VDR{dimer}:-0.78261762167;MAFB:-0.804377159555;NFIL3:-0.812173104376;NFE2:-0.822600252475;AR:-0.837567757289;ATF6:-0.882831312823;TGIF1:-0.885952072957;IRF1,2:-0.901615017379;FOS_FOS{B,L1}_JUN{B,D}:-0.902377964705;CEBPA,B_DDIT3:-0.93177893638;JUN:-0.941606246121;NR3C1:-0.970058755146;SNAI1..3:-1.02944767799;PAX2:-1.05200792932;FOSL2:-1.05239369245;IRF7:-1.06129396646;NKX3-2:-1.06708560418;EBF1:-1.06795572201;NFE2L1:-1.11444818171;NFE2L2:-1.11623919489;FOX{F1,F2,J1}:-1.13966637748;ATF5_CREB3:-1.1427580264;MYOD1:-1.16387926957;LMO2:-1.24293126388;ZEB1:-1.25507480988;PPARG:-1.26290114387;STAT2,4,6:-1.32555385649;TLX2:-1.33699504142;FOX{I1,J2}:-1.51756596666
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:389-23F5;search_select_hide=table117:389-23F5
 }}

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FF:389-23F5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:14, 4 June 2020

CNhs11031

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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