FF:470-26G5: Difference between revisions

Latest revision as of 19:17, 4 June 2020

Name:	testis, embryo E16
Species:	Mouse (Mus musculus)
Library ID:	CNhs11033
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	testis
dev stage	16 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		SAMD00005676

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11033		CAGE		DRX009104		DRR009978

Accession ID Mm9

Library id		BAM		CTSS
CNhs11033		DRZ001403		DRZ002786

Accession ID Mm10

Library id		BAM		CTSS
CNhs11033		DRZ012753		DRZ014136

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

CNhs11033

0	0
1	0
10	0
100	0
1000	0
1001	-2.109203e-4
1002	0.645
1003	0.0233
1004	0
1005	-0.0389
1006	0.0538
1007	0.16
1008	0
1009	0.18
101	0.0674
1010	0
1011	0.0703
1012	0
1013	-0.156
1014	0.143
1015	0.152
1016	0.335
1017	0
1018	0.0772
1019	0
102	0
1020	0
1021	-0.0487
1022	0.0723
1023	0
1024	-0.0624
1025	0
1026	0.0477
1027	0
1028	0
1029	-0.0196
103	0.248
1030	0
1031	0.437
1032	7.252914e-4
1033	0
1034	0
1035	0
1036	0.0663
1037	0
1038	-0.0304
1039	-0.0195
104	0
1040	0.105
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: CNhs11033

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00447
MA0003.1	MA0003.1	0.812
MA0004.1	MA0004.1	0.329
MA0006.1	MA0006.1	0.123
MA0007.1	MA0007.1	0.421
MA0009.1	MA0009.1	0.749
MA0014.1	MA0014.1	0.76
MA0017.1	MA0017.1	0.00218
MA0018.2	MA0018.2	0.708
MA0019.1	MA0019.1	0.379
MA0024.1	MA0024.1	8.08751e-6
MA0025.1	MA0025.1	0.857
MA0027.1	MA0027.1	0.664
MA0028.1	MA0028.1	0.146
MA0029.1	MA0029.1	0.799
MA0030.1	MA0030.1	0.135
MA0031.1	MA0031.1	0.34
MA0035.2	MA0035.2	0.846
MA0038.1	MA0038.1	0.00902
MA0039.2	MA0039.2	0.0346
MA0040.1	MA0040.1	0.305
MA0041.1	MA0041.1	0.424
MA0042.1	MA0042.1	0.559
MA0043.1	MA0043.1	0.154
MA0046.1	MA0046.1	4.47548e-25
MA0047.2	MA0047.2	0.0469
MA0048.1	MA0048.1	0.197
MA0050.1	MA0050.1	0.00181
MA0051.1	MA0051.1	0.00497
MA0052.1	MA0052.1	0.00689
MA0055.1	MA0055.1	0.0182
MA0057.1	MA0057.1	0.446
MA0058.1	MA0058.1	0.108
MA0059.1	MA0059.1	0.456
MA0060.1	MA0060.1	2.18761e-18
MA0061.1	MA0061.1	0.131
MA0062.2	MA0062.2	0.284
MA0065.2	MA0065.2	0.00787
MA0066.1	MA0066.1	0.0617
MA0067.1	MA0067.1	0.775
MA0068.1	MA0068.1	0.15
MA0069.1	MA0069.1	0.777
MA0070.1	MA0070.1	0.154
MA0071.1	MA0071.1	0.682
MA0072.1	MA0072.1	0.413
MA0073.1	MA0073.1	0.931
MA0074.1	MA0074.1	0.633
MA0076.1	MA0076.1	0.0313
MA0077.1	MA0077.1	0.929
MA0078.1	MA0078.1	0.132
MA0079.2	MA0079.2	0.0947
MA0080.2	MA0080.2	1.16179e-4
MA0081.1	MA0081.1	0.633
MA0083.1	MA0083.1	0.588
MA0084.1	MA0084.1	0.979
MA0087.1	MA0087.1	0.518
MA0088.1	MA0088.1	0.995
MA0090.1	MA0090.1	0.933
MA0091.1	MA0091.1	0.307
MA0092.1	MA0092.1	0.333
MA0093.1	MA0093.1	0.216
MA0099.2	MA0099.2	5.83726e-4
MA0100.1	MA0100.1	0.334
MA0101.1	MA0101.1	0.518
MA0102.2	MA0102.2	0.76
MA0103.1	MA0103.1	0.00125
MA0104.2	MA0104.2	0.0566
MA0105.1	MA0105.1	9.40138e-5
MA0106.1	MA0106.1	0.345
MA0107.1	MA0107.1	0.343
MA0108.2	MA0108.2	0.0716
MA0111.1	MA0111.1	0.368
MA0112.2	MA0112.2	8.67024e-5
MA0113.1	MA0113.1	0.338
MA0114.1	MA0114.1	0.00297
MA0115.1	MA0115.1	0.052
MA0116.1	MA0116.1	0.0201
MA0117.1	MA0117.1	0.206
MA0119.1	MA0119.1	0.314
MA0122.1	MA0122.1	0.965
MA0124.1	MA0124.1	0.169
MA0125.1	MA0125.1	0.929
MA0131.1	MA0131.1	0.632
MA0135.1	MA0135.1	0.625
MA0136.1	MA0136.1	0.0213
MA0137.2	MA0137.2	0.261
MA0138.2	MA0138.2	0.006
MA0139.1	MA0139.1	0.56
MA0140.1	MA0140.1	0.839
MA0141.1	MA0141.1	0.537
MA0142.1	MA0142.1	0.00344
MA0143.1	MA0143.1	0.828
MA0144.1	MA0144.1	0.156
MA0145.1	MA0145.1	0.0463
MA0146.1	MA0146.1	0.346
MA0147.1	MA0147.1	0.137
MA0148.1	MA0148.1	0.00176
MA0149.1	MA0149.1	0.0869
MA0150.1	MA0150.1	0.00299
MA0152.1	MA0152.1	0.235
MA0153.1	MA0153.1	6.02754e-18
MA0154.1	MA0154.1	0.00597
MA0155.1	MA0155.1	0.709
MA0156.1	MA0156.1	0.769
MA0157.1	MA0157.1	0.264
MA0159.1	MA0159.1	6.64849e-5
MA0160.1	MA0160.1	0.968
MA0162.1	MA0162.1	0.0387
MA0163.1	MA0163.1	0.163
MA0164.1	MA0164.1	0.339
MA0258.1	MA0258.1	3.72e-4
MA0259.1	MA0259.1	0.0828

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: CNhs11033

Novel motif	Logo	P-value
1	1	0.108
10	10	0.229
100	100	0.725
101	101	0.569
102	102	0.648
103	103	0.291
104	104	0.834
105	105	0.395
106	106	2.95835e-4
107	107	0.00349
108	108	0.722
109	109	0.697
11	11	0.343
110	110	0.792
111	111	0.415
112	112	0.431
113	113	0.397
114	114	0.035
115	115	0.613
116	116	0.478
117	117	0.642
118	118	0.909
119	119	0.169
12	12	0.463
120	120	0.463
121	121	0.51
122	122	0.716
123	123	0.127
124	124	0.119
125	125	0.0584
126	126	0.939
127	127	0.261
128	128	1.61625e-4
129	129	0.142
13	13	0.471
130	130	0.423
131	131	0.829
132	132	0.568
133	133	0.962
134	134	0.645
135	135	0.491
136	136	0.0657
137	137	0.852
138	138	0.538
139	139	0.0532
14	14	0.171
140	140	0.5
141	141	0.125
142	142	0.888
143	143	0.109
144	144	0.133
145	145	0.627
146	146	0.429
147	147	0.763
148	148	0.0513
149	149	0.326
15	15	0.111
150	150	0.858
151	151	0.0713
152	152	0.266
153	153	0.315
154	154	0.799
155	155	0.71
156	156	5.53283e-4
157	157	0.293
158	158	0.215
159	159	0.0388
160	160	0.79
161	161	0.659
162	162	0.609
163	163	0.128
164	164	0.937
165	165	0.0354
166	166	0.846
167	167	0.268
168	168	0.215
169	169	0.453
17	17	0.0895
18	18	0.185
19	19	0.975
2	2	0.556
20	20	0.731
21	21	0.674
22	22	0.803
23	23	0.134
24	24	0.983
25	25	0.42
26	26	0.39
27	27	0.313
28	28	0.339
29	29	0.957
3	3	0.199
30	30	0.93
31	31	0.148
32	32	0.467
33	33	0.726
34	34	0.957
35	35	0.0477
36	36	0.204
37	37	0.127
38	38	0.663
39	39	0.801
4	4	0.637
40	40	0.722
41	41	0.139
42	42	0.466
43	43	0.183
44	44	0.276
45	45	0.496
46	46	0.132
47	47	0.47
48	48	0.358
49	49	0.104
5	5	0.0561
50	50	0.913
51	51	0.784
52	52	0.0999
53	53	0.912
54	54	0.428
55	55	0.236
56	56	0.196
57	57	0.561
58	58	0.292
59	59	0.174
6	6	0.815
60	60	0.0345
61	61	0.967
62	62	0.0849
63	63	0.179
64	64	0.734
65	65	0.218
66	66	0.286
67	67	0.8
68	68	1.1007e-4
69	69	0.461
7	7	0.401
70	70	0.0139
71	71	0.114
72	72	0.765
73	73	0.302
74	74	0.654
75	75	0.275
76	76	0.787
77	77	0.316
78	78	0.341
79	79	0.533
8	8	0.0957
80	80	0.118
81	81	0.237
82	82	0.504
83	83	0.426
84	84	0.302
85	85	0.00602
86	86	0.09
87	87	0.411
88	88	0.857
89	89	0.0434
9	9	0.737
90	90	0.179
91	91	0.45
92	92	0.117
93	93	0.667
94	94	0.24
95	95	0.933
96	96	0.235
97	97	0.639
98	98	0.118
99	99	0.975

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: CNhs11033

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011364 mouse testis- embryo E16 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)
0000299 (mouse embryonic day 16 sample)
0011364 (mouse testis- embryo E16 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@SAMD00005676
+|accession_numbers=CAGE;DRX009104;DRR009978;DRZ001403;DRZ002786;DRZ012753;DRZ014136
+|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:0000299,FF:0011364
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:140739014..140739032,-!p1@Lhx9!2.32!261.15!Lhx9;;chr10:22539932..22539956,-!p1@Tcf21!2.17!377.82!Tcf21;;chr2:38570011..38570034,-!p1@Nr5a1!2.10!125.62!Nr5a1;;chrX:90531838..90531861,+!p1@Arx!2.09!152.84!Arx;;chr7:147129712..147129774,+!p1@Utf1!1.99!96.45!Utf1;;chr14:63864056..63864102,-!p1@Gata4!1.96!154.01!Gata4;;chr1:168168856..168168893,-!p1@Mael!1.69!48.22!Mael;;chr15:102828658..102828678,+!p1@Hoxc6!1.65!43.17!Hoxc6;;chr1:168168817..168168850,-!p2@Mael!1.62!40.45!Mael;;chr2:74529970..74529997,+!p1@Hoxd10!1.42!25.08!Hoxd10;;chr2:74549968..74549996,+!p1@Hoxd3!1.35!26.45!Hoxd3;;chr2:104966766..104966786,+!p1@Wt1!1.34!32.67!Wt1;;chr15:35225845..35225867,+!p1@Osr2!1.30!47.25!Osr2;;chr2:104966874..104966907,+!p2@Wt1!1.29!18.47!Wt1;;chr2:74536026..74536039,+!p1@Hoxd9!1.29!18.47!Hoxd9;;chr12:3891810..3891829,+!p2@Dnmt3a!1.25!26.25!Dnmt3a;;chr2:180377386..180377462,-!p1@Tcfl5!1.23!19.06!Tcfl5;;chr12:34642510..34642530,+!p1@Twist1!1.22!49.00!Twist1;;chr10:126778916..126778974,-!p1@Gli1!1.21!34.22!Gli1;;chr19:25580110..25580163,+!p1@Dmrt1!1.18!14.19!Dmrt1;;chrX:83437105..83437121,+!p1@Nr0b1!1.18!14.00!Nr0b1;;chr11:85646303..85646329,+!p1@Tbx2!1.17!90.03!Tbx2;;chr17:25707623..25707639,-!p1@Sox8!1.17!58.34!Sox8;;chr2:152758901..152758925,-!p1@Foxs1!1.12!54.25!Foxs1;;chr17:35642997..35643014,+!p1@Pou5f1!1.11!11.86!Pou5f1;;chr17:35642973..35642994,+!p2@Pou5f1!1.07!10.69!Pou5f1;;chr15:102828642..102828653,+!p2@Hoxc6!1.05!10.31!Hoxc6;;chr2:104966933..104966966,+!p3@Wt1!1.05!10.11!Wt1;;chr2:74536050..74536065,+!p2@Hoxd9!1.05!10.11!Hoxd9;;chr12:3891753..3891801,+!p4@Dnmt3a!1.04!16.33!Dnmt3a;;chr5:31271028..31271040,+!p1@Tcf23!1.04!9.92!Tcf23;;chr2:74550015..74550057,+!p2@Hoxd3!1.02!9.53!Hoxd3;;chr11:85646263..85646278,+!p2@Tbx2!0.99!22.75!Tbx2;;chr19:59533221..59533271,+!p1@Emx2!0.98!10.69!Emx2;;chr14:63890660..63890687,-!p7@Gata4!0.98!8.56!Gata4;;chr14:63890491..63890516,-!p2@Gata4!0.98!8.56!Gata4;;chrX:45245679..45245702,-!p1@Smarca1!0.94!35.97!Smarca1;;chr2:38567715..38567730,-!p2@Nr5a1!0.92!7.39!Nr5a1;;chr2:74529998..74530020,+!p2@Hoxd10!0.92!7.39!Hoxd10;;chr10:12810631..12810649,+!p1@Plagl1!0.91!194.06!Plagl1;;chr14:63890459..63890484,-!p4@Gata4!0.91!7.19!Gata4;;chr7:6615049..6615056,-!p1@uc009fbu.1!0.91!7.19!Zim2;;chr1:38684260..38684312,-!p2@Aff3!0.90!50.75!Aff3;;chr4:133109285..133109308,+!p1@Nr0b2!0.90!7.00!Nr0b2;;chr7:6649134..6649167,-!p1@Zim1!0.89!38.31!Zim1;;chr15:75578748..75578752,-!p1@Mafa!0.89!6.81!Mafa;;chr4:122911086..122911112,+!p1@Heyl!0.88!81.09!Heyl;;chr2:152758938..152758954,-!p2@Foxs1!0.88!9.33!Foxs1;;chr1:140739042..140739054,-!p2@Lhx9!0.88!6.61!Lhx9;;chr14:63864337..63864381,-!p6@Gata4!0.88!6.61!Gata4;;chr8:26958093..26958148,-!p2@Ash2l!0.88!6.61!Ash2l;;chr10:77512581..77512592,+!p3@Dnmt3l!0.88!6.61!Dnmt3l;;chr2:104966465..104966479,+!p6@Wt1!0.87!6.42!Wt1;;chr2:104966662..104966673,+!p4@Wt1!0.85!6.03!Wt1;;chr19:25580226..25580261,+!p2@Dmrt1!0.85!6.03!Dmrt1;;chr11:85646341..85646352,+!p3@Tbx2!0.84!12.06!Tbx2;;chr2:169458799..169458832,+!p5@Tshz2!0.83!9.92!Tshz2;;chr1:120879128..120879183,-!p3@Gli2!0.82!11.08!Gli2;;chr2:74536071..74536083,+!p4@Hoxd9!0.81!5.44!Hoxd9;;chr7:147129777..147129814,+!p2@Utf1!0.81!5.44!Utf1;;chr2:74535796..74535808,+!p3@Hoxd9!0.80!5.25!Hoxd9;;chr2:169458192..169458247,+!p1@Tshz2!0.79!50.36!Tshz2;;chr7:17647736..17647772,-!p1@Hif3a!0.79!19.83!Hif3a;;chr2:91864300..91864379,-!p2@Creb3l1!0.79!15.75!Creb3l1;;chr10:80809447..80809515,-!p5@Hmg20b!0.79!6.42!Hmg20b;;chr9:36954842..36954908,-!p1@Pknox2!0.77!63.00!Pknox2;;chr7:147129680..147129693,+!p3@Utf1!0.77!4.86!Utf1;;chr11:98826125..98826141,+!p12@Rara!0.77!4.86!Rara;;chr7:77511403..77511450,-!p3@Nr2f2!0.75!10.50!Nr2f2;;chr2:91864449..91864492,-!p3@Creb3l1!0.75!7.97!Creb3l1;;chr2:25702844..25702859,-!p1@Sohlh1!0.75!4.67!Sohlh1;;chr12:77278238..77278252,-!p1@Esr2!0.75!4.67!Esr2;;chr4:119960301..119960359,-!p1@Foxo6!0.74!15.75!Foxo6;;chr18:11052485..11052508,+!p2@Gata6!0.74!13.61!Gata6;;chr15:35225873..35225889,+!p2@Osr2!0.74!4.47!Osr2;;chr2:105003277..105003280,+!p5@Wt1!0.74!4.47!Wt1;;chr7:77505617..77505632,-!p1@Nr2f2!0.73!227.12!Nr2f2;;chr11:52096804..52096896,-!p1@Tcf7!0.73!39.47!Tcf7;;chr2:30700788..30700824,+!p2@Prrx2!0.73!7.00!Prrx2;;chrX:45245644..45245666,-!p2@Smarca1!0.71!14.58!Smarca1;;chr4:84320893..84320910,-!p1@Bnc2!0.71!9.92!Bnc2;;chr2:74549945..74549965,+!p4@Hoxd3!0.71!4.08!Hoxd3;;chr2:152223441..152223465,-!p2@Sox12!0.70!18.47!Sox12;;chr12:34642682..34642753,+!p2@Twist1!0.70!11.67!Twist1;;chr18:11052456..11052477,+!p3@Gata6!0.69!13.42!Gata6;;chr11:5761889..5761969,+!p1@Aebp1!0.67!178.31!Aebp1;;chr2:169458519..169458555,+!p2@Tshz2!0.67!16.72!Tshz2;;chr2:74542918..74542971,+!p1@Hoxd8!0.67!5.83!Hoxd8;;chr4:3865501..3865548,-!p1@Plag1!0.66!21.20!Plag1;;chr2:181194069..181194144,-!p1@Zbtb46!0.65!22.95!Zbtb46;;chr11:5761979..5761992,+!p2@Aebp1!0.65!7.78!Aebp1;;chr11:98826178..98826197,+!p7@Rara!0.65!3.50!Rara;;chr14:63890519..63890539,-!p3@Gata4!0.65!3.50!Gata4;;chr14:63890691..63890718,-!p8@Gata4!0.65!3.50!Gata4;;chr9:44249274..44249313,-!p1@Foxr1!0.65!3.50!Foxr1;;chr15:76701495..76701535,-!p3@Zfp251!0.65!3.50!Zfp251;;chr5:31270977..31270988,+!p3@Tcf23!0.65!3.50!Tcf23;;chr1:38684383..38684394,-!p4@Aff3!0.64!4.86!Aff3;;chr7:52471143..52471186,+!p1@Tead2!0.63!40.64!Tead2;;chr10:5734525..5734569,-!p3@Esr1!0.63!5.83!Esr1;;chr7:89137163..89137200,-!p1@Bnc1!0.63!4.08!Bnc1;;chr1:120949949..120950000,-!p1@Gli2!0.62!16.14!Gli2;;chr15:81633203..81633215,+!p3@Tef!0.62!5.44!Tef;;chr15:103164702..103164778,-!p3@Zfp385a!0.62!3.89!Zfp385a;;chr14:76904313..76904328,+!p1@Tsc22d1!0.61!711.50!Tsc22d1;;chr11:74981654..74981658,-!p1@Hic1!0.61!14.19!Hic1;;chr7:19679964..19679982,+!p1@Six5!0.61!10.11!Six5;;chr7:77511622..77511657,-!p5@Nr2f2!0.61!4.08!Nr2f2;;chr2:74543202..74543213,+!p3@Hoxd8!0.61!3.11!Hoxd8;;chr2:104966436..104966455,+!p7@Wt1!0.61!3.11!Wt1;;chr15:40486566..40486600,+!p1@Zfpm2!0.60!21.00!Zfpm2;;chr8:90483459..90483475,-!p1@Zfp423!0.60!9.53!Zfp423;;chr17:47278081..47278103,+!p1@Trerf1!0.60!7.78!Trerf1;;chr8:90483433..90483457,-!p2@Zfp423!0.60!4.28!Zfp423;;chr6:52176164..52176195,-!p1@Hoxa9!0.60!3.89!Hoxa9;;chr10:126779021..126779032,-!p2@Gli1!0.60!3.89!Gli1;;chr18:11052642..11052659,+!p1@Gata6!0.59!17.31!Gata6;;chr19:25580272..25580305,+!p3@Dmrt1!0.59!2.92!Dmrt1;;chrX:35419715..35419724,+!p1@Rhox10!0.59!2.92!Rhox10;;chr2:74542974..74542986,+!p5@Hoxd8!0.59!2.92!Hoxd8;;chr4:84321280..84321298,-!p5@Bnc2!0.59!2.92!Bnc2;;chr16:14705925..14705951,+!p1@Snai2!0.58!23.92!Snai2;;chr14:65977324..65977372,+!p2@Zfp395!0.58!19.25!Zfp395;;chr2:169458352..169458397,+!p3@Tshz2!0.58!8.17!Tshz2;;chr15:40486427..40486437,+!p5@Zfpm2!0.58!3.89!Zfpm2;;chr10:5636374..5636421,-!p1@Esr1!0.58!3.69!Esr1;;chr15:81633165..81633188,+!p2@Tef!0.57!27.61!Tef;;chr13:22036953..22037009,+!p1@Zfp184!0.57!8.56!Zfp184;;chr16:55966407..55966447,+!p6@Rpl24,p6@Zbtb11!0.57!7.58!Zbtb11;;chr1:120949925..120949947,-!p4@Gli2!0.57!6.03!Gli2;;chr11:85646469..85646488,+!p5@Tbx2!0.57!4.47!Tbx2;;chr15:40486883..40486903,+!p4@Zfpm2!0.57!3.89!Zfpm2;;chr14:69808725..69808748,+!p1@Nkx3-1!0.57!2.72!Nkx3-1;;chr2:104966909..104966920,+!p8@Wt1!0.57!2.72!Wt1;;chr3:130815472..130815497,+!p6@Lef1!0.57!2.72!Lef1;;chr2:74543397..74543435,+!p2@Hoxd8!0.57!2.72!Hoxd8;;chr4:84321317..84321332,-!p4@Bnc2!0.57!2.72!Bnc2;;chr2:25562346..25562433,+!p1@Bmyc!0.56!60.67!Bmyc;;chr19:26822880..26822964,+!p2@Smarca2!0.56!27.81!Smarca2;;chr2:152223469..152223512,-!p1@Sox12!0.56!16.72!Sox12;;chr5:125538737..125538781,-!p2@Ncor2!0.56!11.47!Ncor2;;chr2:152223783..152223812,-!p4@Sox12!0.56!7.00!Sox12;;chr17:37139472..37139514,+!p1@Zfp57!0.55!21.39!Zfp57;;chr14:56443806..56443848,+!p1@Nfatc4!0.55!5.83!Nfatc4;;chr7:17642053..17642066,-!p2@Hif3a!0.55!3.89!Hif3a;;chr4:84321300..84321315,-!p2@Bnc2!0.55!3.31!Bnc2;;chr2:74529942..74529953,+!p4@Hoxd10!0.55!2.53!Hoxd10;;chr2:24331085..24331100,-!p1@Pax8!0.55!2.53!Pax8;;chr5:31271010..31271019,+!p2@Tcf23!0.55!2.53!Tcf23;;chr15:102820964..102821006,+!p1@Hoxc8!0.55!2.53!Hoxc8;;chr13:83712735..83712761,+!p9@Mef2c!0.55!2.53!Mef2c;;chr15:102821007..102821021,+!p2@Hoxc8!0.55!2.53!Hoxc8;;chr2:91864661..91864686,-!p1@Creb3l1!0.54!68.64!Creb3l1;;chr12:9581262..9581282,+!p1@Osr1!0.54!37.33!Osr1;;chr7:37483021..37483078,+!p1@Tshz3!0.54!9.14!Tshz3;;chr16:14705961..14705978,+!p2@Snai2!0.53!14.00!Snai2;;chr12:12948633..12948651,-!p1@Mycn!0.52!28.78!Mycn;;chr4:128483534..128483613,-!p1@Zfp362!0.52!20.61!Zfp362;;chr12:28027561..28027591,-!p1@Sox11!0.52!19.45!Sox11;;chr2:130120884..130120972,+!p1@Ebf4!0.52!17.11!Ebf4;;chr8:59799772..59799789,+!p1@Hand2!0.52!7.97!Hand2;;chr1:9690424..9690467,-!p1@Mybl1!0.52!5.64!Mybl1;;chr4:122911056..122911065,+!p2@Heyl!0.52!3.89!Heyl;;chr15:50720589..50720600,-!p12@Trps1!0.52!3.31!Trps1;;chr6:72850124..72850210,-!p7@Kcmf1!0.52!3.31!Kcmf1;;chr19:59533139..59533152,+!p2@Emx2!0.52!2.33!Emx2;;chr15:102839948..102839975,+!p3@Hoxc6!0.52!2.33!Hoxc6;;chr2:74543103..74543135,+!p4@Hoxd8!0.52!2.33!Hoxd8;;chr4:62626594..62626651,+!p1@Zfp618!0.51!10.50!Zfp618;;chr2:169458838..169458859,+!p4@Tshz2!0.51!5.25!Tshz2;;chr7:26067619..26067702,+!p2@Cic!0.50!15.75!Cic;;chr17:28487603..28487626,-!p2@Tead3!0.50!5.44!Tead3;;chr7:37483231..37483263,+!p2@Tshz3!0.50!3.69!Tshz3;;chr1:9690398..9690410,-!p2@Mybl1!0.50!2.72!Mybl1;;chr19:59533429..59533470,+!p4@Emx2!0.50!2.14!Emx2;;chr10:77512605..77512612,+!p7@Dnmt3l!0.50!2.14!Dnmt3l;;chr2:74543235..74543246,+!p7@Hoxd8!0.50!2.14!Hoxd8;;chr2:74560109..74560131,+!p1@Hoxd4!0.50!2.14!Hoxd4;;chr14:32979060..32979091,+!p4@Gm6768,p4@Ncoa4!0.50!2.14!Ncoa4;;chr12:30525072..30525115,+!p14@Myt1l!0.50!2.14!Myt1l;;chrX:154006915..154006923,-!p1@Yy2!0.50!2.14!Yy2;;chr7:77511234..77511302,-!p2@Nr2f2!0.49!18.08!Nr2f2;;chr19:7342725..7342784,+!p1@Rcor2!0.49!11.08!Rcor2;;chr2:34227446..34227511,-!p1@Pbx3!0.49!5.83!Pbx3;;chr2:156666727..156666753,+!p2@Tgif2!0.49!3.50!Tgif2;;chr5:138187341..138187406,+!p3@Tsc22d4!0.48!28.97!Tsc22d4;;chr14:65977498..65977528,+!p1@Zfp395!0.48!17.70!Zfp395;;chr11:102177921..102177960,-!p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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 36: / Line 42: @@
 |has_quality=
 |id=FF:470-26G5
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011364
+|is_a=EFO:0002091;;FF:0011364
+|is_obsolete=
+|library_id=CNhs11033
+|library_id_phase_based=2:CNhs11033
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;470
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;470
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm9.nobarcode.rdna.fa.gz
 |name=testis, embryo E16
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11033,LSID732,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0464597358026166,0,0,0,0.0771684068561175,0,-0.00847950629557195,0,0.0054773605742938,0,0,0.323155254622498,0,0,0,0,0,0,0.0579907121703936,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.0355335033535007,0,0.142671721075526,0,0,0.00877032694715313,0.145139934744884,0.0648703845393668,-0.167976697156123,0.213848576162502,0.199144673371508,0,0,0,0,0,0,0,0,0,0,0,0.199577904247741,0.1335723566843,0.0771684068561175,0,0,0,-0.0428469550828748,0,-0.00575453392430265,0,0,0.00221372931839045,0.0660749550892359,-0.0156873842270003,-0.080922635914965,0.115576165236432,0,0.0771684068561175,0.0152132736318376,0.108332862260126,0.142671721075526,0,0.0209149751458576,0.03467687860968,-0.396336976492829,0.0638401262356187,0,0,0,0,0,0,-0.166362444370259,-0.247730463716719,-0.0021139438691129,0,0,0,0,0
 |rna_box=26
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=testis
 |top_motifs=ZNF238:1.71318797065;NRF1:1.59805739667;NFY{A,B,C}:1.59117764862;HIF1A:1.56853702536;ZNF143:1.49677732259;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.40205623801;SP1:1.22952395609;TEF:1.14291699078;MYBL2:1.12999524618;RXR{A,B,G}:1.05634633607;HOX{A5,B5}:1.05066113214;XCPE1{core}:1.03893714315;GFI1B:1.03267403354;GFI1:1.01525283632;FOXP3:1.00777249271;EGR1..3:0.99354669202;ZNF384:0.967524090029;PATZ1:0.951173117978;STAT1,3:0.918099007759;E2F1..5:0.878776175253;GLI1..3:0.855769735349;EP300:0.793521237051;GATA4:0.785884758185;RBPJ:0.783244577348;TFAP2{A,C}:0.769967702062;FOXP1:0.744596414337;CRX:0.743305267722;NANOG{mouse}:0.736353161316;GCM1,2:0.718290607591;NKX3-1:0.642050144347;IKZF1:0.624488707762;NKX6-1,2:0.616332136108;ZNF423:0.606074680575;ZBTB16:0.605704640422;NR5A1,2:0.564422147618;TEAD1:0.556073052082;PITX1..3:0.548915545989;TLX1..3_NFIC{dimer}:0.545162837693;FOXD3:0.531531396909;NR1H4:0.523335025329;NR6A1:0.509230346986;RREB1:0.499142649137;ELK1,4_GABP{A,B1}:0.46798703633;IKZF2:0.456518794077;GTF2I:0.435007481622;ZIC1..3:0.401066237272;SOX5:0.39495887861;SOX17:0.390269764325;ESR1:0.381477236904;CDC5L:0.378740399396;BREu{core}:0.355407396208;TFDP1:0.338772124745;MZF1:0.333061137833;RFX2..5_RFXANK_RFXAP:0.318208589763;TOPORS:0.3050309949;YY1:0.29872637927;MAZ:0.284751806824;bHLH_family:0.2844677815;HBP1_HMGB_SSRP1_UBTF:0.249718828589;TFAP4:0.246196567573;ZFP161:0.243039725241;AIRE:0.237761702544;EN1,2:0.233670285453;ADNP_IRX_SIX_ZHX:0.218020736214;ESRRA:0.204234992245;MTE{core}:0.194357193528;MYB:0.190348258504;PRRX1,2:0.189208141623;PBX1:0.189175613306;NFATC1..3:0.182917539294;HSF1,2:0.180795877316;CREB1:0.168508649575;RFX1:0.161346559996;MED-1{core}:0.147636743924;POU2F1..3:0.143927348925;SOX2:0.131470622227;ATF2:0.130554816707;MTF1:0.125519990963;LEF1_TCF7_TCF7L1,2:0.112165649685;NFIX:0.104372014007;PAX5:0.097691006642;PAX4:0.093352895065;GATA6:0.090125006963;AHR_ARNT_ARNT2:0.0847424639413;TFAP2B:0.0830847131073;HIC1:0.071597193187;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0492949544536;ARID5B:0.0475230785938;DBP:0.0186642102252;TAL1_TCF{3,4,12}:0.0119432580566;HOXA9_MEIS1:-0.0190240387859;GTF2A1,2:-0.0368998943114;SPZ1:-0.0370860562931;KLF4:-0.0523296304429;SRF:-0.0854210546632;EVI1:-0.101079617112;PAX1,9:-0.113313537984;HES1:-0.120338847785;SOX{8,9,10}:-0.122776339616;T:-0.124035750818;FOXL1:-0.129943437708;REST:-0.139831089857;ZNF148:-0.153758145023;BPTF:-0.160390549278;FOXN1:-0.161848797728;SPIB:-0.18893441236;PAX6:-0.201132840239;POU5F1:-0.208209274588;ELF1,2,4:-0.213040732506;HMGA1,2:-0.223004695251;RUNX1..3:-0.225217173569;MEF2{A,B,C,D}:-0.231744075176;TFCP2:-0.232076999893;RORA:-0.247495133614;MYFfamily:-0.251561315918;ATF4:-0.256691202232;STAT5{A,B}:-0.263495531245;TBX4,5:-0.263901085708;POU6F1:-0.278059511732;UFEwm:-0.286955924571;SREBF1,2:-0.306059646266;ALX4:-0.314206179836;CUX2:-0.323766102685;ETS1,2:-0.355468146447;NKX2-2,8:-0.364633559342;NKX2-1,4:-0.367081147289;NKX2-3_NKX2-5:-0.391775338921;HOX{A4,D4}:-0.4194019557;FOX{D1,D2}:-0.420071050228;FOXQ1:-0.421418871029;PRDM1:-0.43006260266;SMAD1..7,9:-0.459242209535;ONECUT1,2:-0.462884422014;HLF:-0.493001009527;BACH2:-0.500745626452;HNF4A_NR2F1,2:-0.514121707372;SPI1:-0.527213614342;FOXA2:-0.531705533302;HAND1,2:-0.53893789241;CDX1,2,4:-0.540697386939;VSX1,2:-0.551262244181;TBP:-0.568376984656;NFKB1_REL_RELA:-0.575712555512;NKX3-2:-0.588502742457;AR:-0.604600784486;POU1F1:-0.605135737896;POU3F1..4:-0.631295496677;HMX1:-0.631343273167;FOXO1,3,4:-0.632709813068;TP53:-0.633197425782;PAX2:-0.652374701532;MAFB:-0.667947916955;LHX3,4:-0.670474464869;NANOG:-0.674818201922;ALX1:-0.676828786832;HNF1A:-0.689712112765;NHLH1,2:-0.719765217739;CEBPA,B_DDIT3:-0.721365386271;NFE2L2:-0.746613593596;PDX1:-0.750011725066;ATF6:-0.758478581644;ZBTB6:-0.769323208782;PAX8:-0.788634003679;GZF1:-0.805251132994;RXRA_VDR{dimer}:-0.805287354807;EBF1:-0.808254525451;DMAP1_NCOR{1,2}_SMARC:-0.811612410404;OCT4_SOX2{dimer}:-0.814960917863;LMO2:-0.818774334515;JUN:-0.820486966023;NFE2:-0.841445434759;PPARG:-0.860240716448;TGIF1:-0.861699279147;IRF1,2:-0.875993529898;IRF7:-0.944472285486;FOX{F1,F2,J1}:-0.95508881045;FOS_FOS{B,L1}_JUN{B,D}:-0.957682633686;FOXM1:-0.989024126232;NFIL3:-0.999805470176;SNAI1..3:-1.00515793743;STAT2,4,6:-1.13012401213;FOSL2:-1.17202186054;ZEB1:-1.2236799585;TLX2:-1.29693315827;ATF5_CREB3:-1.38508990236;FOX{I1,J2}:-1.41393813098;MYOD1:-1.47340657852;NFE2L1:-1.49023379139;NR3C1:-1.63043064071
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:470-26G5;search_select_hide=table117:470-26G5
 }}

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FF:470-26G5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:17, 4 June 2020

CNhs11033

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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