FF:1300-22B7: Difference between revisions

Latest revision as of 18:48, 4 June 2020

Name:	testis, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	CNhs11189
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	testis
dev stage	0 day 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		SAMD00005755

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11189		CAGE		DRX009107		DRR009981

Accession ID Mm9

Library id		BAM		CTSS
CNhs11189		DRZ001406		DRZ002789

Accession ID Mm10

Library id		BAM		CTSS
CNhs11189		DRZ012756		DRZ014139

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

CNhs11189

0	0
1	0
10	0
100	0
1000	0
1001	0.0398
1002	0.695
1003	0.167
1004	0.0482
1005	-0.0249
1006	0.0482
1007	0.121
1008	0
1009	0.147
101	0.0758
1010	0
1011	0.0268
1012	0.0482
1013	-0.16
1014	0.556
1015	0.102
1016	0.336
1017	0
1018	0
1019	0
102	0
1020	0.00655
1021	0.0932
1022	0.0482
1023	0
1024	-0.0064
1025	0.0482
1026	0.0188
1027	0.0482
1028	0
1029	0.226
103	0.313
1030	0
1031	0.348
1032	-0.0928
1033	0.0369
1034	0
1035	0.131
1036	0.0184
1037	0
1038	0.0745
1039	-0.071
104	0
1040	0.216
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: CNhs11189

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00106
MA0003.1	MA0003.1	0.811
MA0004.1	MA0004.1	0.683
MA0006.1	MA0006.1	0.264
MA0007.1	MA0007.1	0.681
MA0009.1	MA0009.1	0.565
MA0014.1	MA0014.1	0.73
MA0017.1	MA0017.1	4.30614e-4
MA0018.2	MA0018.2	0.143
MA0019.1	MA0019.1	0.56
MA0024.1	MA0024.1	1.97254e-5
MA0025.1	MA0025.1	0.769
MA0027.1	MA0027.1	0.748
MA0028.1	MA0028.1	0.736
MA0029.1	MA0029.1	0.929
MA0030.1	MA0030.1	0.435
MA0031.1	MA0031.1	0.643
MA0035.2	MA0035.2	0.437
MA0038.1	MA0038.1	0.231
MA0039.2	MA0039.2	0.854
MA0040.1	MA0040.1	0.27
MA0041.1	MA0041.1	0.243
MA0042.1	MA0042.1	0.396
MA0043.1	MA0043.1	0.955
MA0046.1	MA0046.1	1.07324e-24
MA0047.2	MA0047.2	0.0646
MA0048.1	MA0048.1	0.0784
MA0050.1	MA0050.1	0.232
MA0051.1	MA0051.1	0.188
MA0052.1	MA0052.1	3.61132e-4
MA0055.1	MA0055.1	0.0947
MA0057.1	MA0057.1	0.064
MA0058.1	MA0058.1	0.603
MA0059.1	MA0059.1	0.885
MA0060.1	MA0060.1	0.00428
MA0061.1	MA0061.1	0.265
MA0062.2	MA0062.2	0.482
MA0065.2	MA0065.2	0.00315
MA0066.1	MA0066.1	0.067
MA0067.1	MA0067.1	0.666
MA0068.1	MA0068.1	0.144
MA0069.1	MA0069.1	0.995
MA0070.1	MA0070.1	0.963
MA0071.1	MA0071.1	0.915
MA0072.1	MA0072.1	0.283
MA0073.1	MA0073.1	0.322
MA0074.1	MA0074.1	0.464
MA0076.1	MA0076.1	0.532
MA0077.1	MA0077.1	0.677
MA0078.1	MA0078.1	0.109
MA0079.2	MA0079.2	0.353
MA0080.2	MA0080.2	8.55654e-6
MA0081.1	MA0081.1	0.243
MA0083.1	MA0083.1	0.762
MA0084.1	MA0084.1	0.738
MA0087.1	MA0087.1	0.36
MA0088.1	MA0088.1	0.142
MA0090.1	MA0090.1	0.573
MA0091.1	MA0091.1	0.912
MA0092.1	MA0092.1	0.403
MA0093.1	MA0093.1	0.626
MA0099.2	MA0099.2	3.40157e-4
MA0100.1	MA0100.1	0.776
MA0101.1	MA0101.1	0.571
MA0102.2	MA0102.2	0.826
MA0103.1	MA0103.1	2.21859e-4
MA0104.2	MA0104.2	0.467
MA0105.1	MA0105.1	9.61683e-4
MA0106.1	MA0106.1	0.811
MA0107.1	MA0107.1	0.525
MA0108.2	MA0108.2	2.32371e-4
MA0111.1	MA0111.1	0.303
MA0112.2	MA0112.2	0.00255
MA0113.1	MA0113.1	0.763
MA0114.1	MA0114.1	2.66168e-4
MA0115.1	MA0115.1	0.0731
MA0116.1	MA0116.1	0.0383
MA0117.1	MA0117.1	0.251
MA0119.1	MA0119.1	0.438
MA0122.1	MA0122.1	0.432
MA0124.1	MA0124.1	0.148
MA0125.1	MA0125.1	0.331
MA0131.1	MA0131.1	0.456
MA0135.1	MA0135.1	0.214
MA0136.1	MA0136.1	6.87064e-5
MA0137.2	MA0137.2	0.202
MA0138.2	MA0138.2	0.00182
MA0139.1	MA0139.1	0.234
MA0140.1	MA0140.1	0.566
MA0141.1	MA0141.1	0.175
MA0142.1	MA0142.1	0.0282
MA0143.1	MA0143.1	0.983
MA0144.1	MA0144.1	0.191
MA0145.1	MA0145.1	0.03
MA0146.1	MA0146.1	0.825
MA0147.1	MA0147.1	0.518
MA0148.1	MA0148.1	0.0174
MA0149.1	MA0149.1	0.195
MA0150.1	MA0150.1	6.74283e-4
MA0152.1	MA0152.1	0.0149
MA0153.1	MA0153.1	7.25968e-14
MA0154.1	MA0154.1	0.0248
MA0155.1	MA0155.1	0.586
MA0156.1	MA0156.1	0.0575
MA0157.1	MA0157.1	0.838
MA0159.1	MA0159.1	1.8363e-5
MA0160.1	MA0160.1	0.997
MA0162.1	MA0162.1	0.0412
MA0163.1	MA0163.1	0.572
MA0164.1	MA0164.1	0.522
MA0258.1	MA0258.1	0.00259
MA0259.1	MA0259.1	0.332

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: CNhs11189

Novel motif	Logo	P-value
1	1	0.151
10	10	0.444
100	100	0.602
101	101	0.618
102	102	0.789
103	103	0.937
104	104	0.995
105	105	0.286
106	106	0.0184
107	107	0.143
108	108	0.685
109	109	0.419
11	11	0.211
110	110	0.857
111	111	0.311
112	112	0.604
113	113	0.406
114	114	0.0914
115	115	0.512
116	116	0.218
117	117	0.915
118	118	0.723
119	119	0.0879
12	12	0.189
120	120	0.325
121	121	0.601
122	122	0.863
123	123	0.152
124	124	0.457
125	125	0.135
126	126	0.608
127	127	0.119
128	128	0.00531
129	129	0.291
13	13	0.667
130	130	0.493
131	131	0.34
132	132	0.549
133	133	0.429
134	134	0.835
135	135	0.615
136	136	0.294
137	137	0.808
138	138	0.466
139	139	0.238
14	14	0.199
140	140	0.695
141	141	0.304
142	142	0.209
143	143	0.028
144	144	0.0223
145	145	0.837
146	146	0.369
147	147	0.639
148	148	0.228
149	149	0.494
15	15	0.0879
150	150	0.897
151	151	0.0423
152	152	0.417
153	153	0.639
154	154	0.981
155	155	0.252
156	156	0.902
157	157	0.597
158	158	0.417
159	159	0.478
160	160	0.752
161	161	0.835
162	162	0.523
163	163	0.0472
164	164	0.801
165	165	0.0531
166	166	0.605
167	167	0.974
168	168	0.271
169	169	0.556
17	17	0.167
18	18	0.212
19	19	0.738
2	2	0.547
20	20	0.8
21	21	0.383
22	22	0.727
23	23	0.125
24	24	0.73
25	25	0.226
26	26	0.814
27	27	0.326
28	28	0.287
29	29	0.858
3	3	0.316
30	30	0.64
31	31	0.293
32	32	0.418
33	33	0.749
34	34	0.793
35	35	0.117
36	36	0.377
37	37	0.133
38	38	0.609
39	39	0.847
4	4	0.773
40	40	0.481
41	41	0.0183
42	42	0.585
43	43	0.32
44	44	0.109
45	45	0.35
46	46	0.225
47	47	0.274
48	48	0.188
49	49	0.166
5	5	0.0973
50	50	0.896
51	51	0.798
52	52	0.277
53	53	0.712
54	54	0.371
55	55	0.197
56	56	0.284
57	57	0.766
58	58	0.262
59	59	0.163
6	6	0.577
60	60	0.109
61	61	0.796
62	62	0.0613
63	63	0.241
64	64	0.553
65	65	0.162
66	66	0.903
67	67	0.617
68	68	9.4639e-5
69	69	0.487
7	7	0.431
70	70	0.00823
71	71	0.213
72	72	0.484
73	73	0.34
74	74	0.669
75	75	0.254
76	76	0.383
77	77	0.326
78	78	0.403
79	79	0.892
8	8	0.143
80	80	0.0398
81	81	0.396
82	82	0.656
83	83	0.826
84	84	0.435
85	85	0.00877
86	86	0.122
87	87	0.106
88	88	0.985
89	89	0.0335
9	9	0.835
90	90	0.127
91	91	0.535
92	92	0.264
93	93	0.798
94	94	0.411
95	95	0.672
96	96	0.204
97	97	0.507
98	98	0.111
99	99	0.929

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: CNhs11189

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011509 mouse testis- neonate N00 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)
0000304 (mouse neonate N0 sample)
0011509 (mouse testis- neonate N00 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
+|DRA_sample_Accession=CAGE@SAMD00005755
+|accession_numbers=CAGE;DRX009107;DRR009981;DRZ001406;DRZ002789;DRZ012756;DRZ014139
 |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=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:140739014..140739032,-!p1@Lhx9!2.18!189.18!Lhx9;;chr14:63864056..63864102,-!p1@Gata4!2.14!230.84!Gata4;;chrX:90531838..90531861,+!p1@Arx!2.11!160.19!Arx;;chr10:22539932..22539956,-!p1@Tcf21!2.09!313.58!Tcf21;;chr2:38570011..38570034,-!p1@Nr5a1!2.08!117.94!Nr5a1;;chr2:104966766..104966786,+!p1@Wt1!1.57!55.98!Wt1;;chr2:74529970..74529997,+!p1@Hoxd10!1.47!28.40!Hoxd10;;chr15:102828658..102828678,+!p1@Hoxc6!1.46!27.58!Hoxc6;;chr2:104966874..104966907,+!p2@Wt1!1.45!27.11!Wt1;;chr15:35225845..35225867,+!p1@Osr2!1.44!65.60!Osr2;;chr10:126778916..126778974,-!p1@Gli1!1.41!54.69!Gli1;;chrX:83437105..83437121,+!p1@Nr0b1!1.39!23.59!Nr0b1;;chr17:25707623..25707639,-!p1@Sox8!1.30!79.92!Sox8;;chr2:74536026..74536039,+!p1@Hoxd9!1.29!18.54!Hoxd9;;chr1:168168817..168168850,-!p2@Mael!1.29!18.54!Mael;;chr19:25580110..25580163,+!p1@Dmrt1!1.26!17.02!Dmrt1;;chr1:168168856..168168893,-!p1@Mael!1.19!14.55!Mael;;chr2:74536050..74536065,+!p2@Hoxd9!1.16!13.50!Hoxd9;;chr2:104966662..104966673,+!p4@Wt1!1.14!12.67!Wt1;;chr2:104966933..104966966,+!p3@Wt1!1.12!12.09!Wt1;;chr2:74529998..74530020,+!p2@Hoxd10!1.11!11.74!Hoxd10;;chr12:34642510..34642530,+!p1@Twist1!1.10!37.08!Twist1;;chr2:152758938..152758954,-!p2@Foxs1!1.08!15.26!Foxs1;;chr19:25580226..25580261,+!p2@Dmrt1!1.08!11.15!Dmrt1;;chr11:85646303..85646329,+!p1@Tbx2!1.07!71.12!Tbx2;;chr2:74549968..74549996,+!p1@Hoxd3!1.07!13.38!Hoxd3;;chr14:63864337..63864381,-!p6@Gata4!1.07!10.80!Gata4;;chr2:152758901..152758925,-!p1@Foxs1!1.05!45.65!Foxs1;;chr14:63890459..63890484,-!p4@Gata4!1.05!10.21!Gata4;;chr7:147129712..147129774,+!p1@Utf1!1.05!10.21!Utf1;;chr15:102828642..102828653,+!p2@Hoxc6!1.04!9.86!Hoxc6;;chr7:6649134..6649167,-!p1@Zim1!1.02!51.75!Zim1;;chr10:12810631..12810649,+!p1@Plagl1!1.01!246.10!Plagl1;;chr12:77278238..77278252,-!p1@Esr2!0.99!8.68!Esr2;;chrX:45245679..45245702,-!p1@Smarca1!0.98!39.67!Smarca1;;chr13:83712735..83712761,+!p9@Mef2c!0.96!8.22!Mef2c;;chr2:104966465..104966479,+!p6@Wt1!0.94!7.63!Wt1;;chr2:169458192..169458247,+!p1@Tshz2!0.92!68.30!Tshz2;;chrX:45245644..45245666,-!p2@Smarca1!0.92!24.53!Smarca1;;chr11:85646341..85646352,+!p3@Tbx2!0.92!14.79!Tbx2;;chr2:105003277..105003280,+!p5@Wt1!0.92!7.39!Wt1;;chr2:74550015..74550057,+!p2@Hoxd3!0.92!7.28!Hoxd3;;chr1:38684260..38684312,-!p2@Aff3!0.91!51.87!Aff3;;chr1:140739042..140739054,-!p2@Lhx9!0.91!7.04!Lhx9;;chr10:80809447..80809515,-!p5@Hmg20b!0.89!8.45!Hmg20b;;chr4:3865501..3865548,-!p1@Plag1!0.87!34.39!Plag1;;chr2:169458838..169458859,+!p4@Tshz2!0.87!13.38!Tshz2;;chr2:169458519..169458555,+!p2@Tshz2!0.86!26.76!Tshz2;;chr5:135582751..135582788,+!p1@Mlxipl!0.85!25.94!Mlxipl;;chr11:85646263..85646278,+!p2@Tbx2!0.84!15.96!Tbx2;;chr10:5734525..5734569,-!p3@Esr1!0.84!10.09!Esr1;;chr15:35225873..35225889,+!p2@Osr2!0.84!5.87!Osr2;;chr19:25580272..25580305,+!p3@Dmrt1!0.84!5.87!Dmrt1;;chr19:59533221..59533271,+!p1@Emx2!0.83!7.16!Emx2;;chr14:63890660..63890687,-!p7@Gata4!0.83!5.75!Gata4;;chr11:52096804..52096896,-!p1@Tcf7!0.82!49.29!Tcf7;;chr14:63890491..63890516,-!p2@Gata4!0.82!5.63!Gata4;;chr15:76287876..76287894,+!p1@Scx!0.81!32.04!Scx;;chr7:77511403..77511450,-!p3@Nr2f2!0.81!12.32!Nr2f2;;chr2:74543397..74543435,+!p2@Hoxd8!0.81!5.52!Hoxd8;;chr15:75578748..75578752,-!p1@Mafa!0.81!5.40!Mafa;;chr11:98826178..98826197,+!p7@Rara!0.81!5.40!Rara;;chr4:119960301..119960359,-!p1@Foxo6!0.80!18.54!Foxo6;;chr2:169458799..169458832,+!p5@Tshz2!0.80!9.15!Tshz2;;chr12:9581262..9581282,+!p1@Osr1!0.79!68.07!Osr1;;chr18:11052456..11052477,+!p3@Gata6!0.79!17.37!Gata6;;chr2:38567715..38567730,-!p2@Nr5a1!0.79!5.16!Nr5a1;;chr11:98826125..98826141,+!p12@Rara!0.79!5.16!Rara;;chr2:74536071..74536083,+!p4@Hoxd9!0.79!5.16!Hoxd9;;chr19:26822880..26822964,+!p2@Smarca2!0.78!46.47!Smarca2;;chr2:181194069..181194144,-!p1@Zbtb46!0.78!31.22!Zbtb46;;chr12:34642682..34642753,+!p2@Twist1!0.77!13.85!Twist1;;chr1:38684383..38684394,-!p4@Aff3!0.77!6.81!Aff3;;chr2:152223441..152223465,-!p2@Sox12!0.76!21.24!Sox12;;chr14:63890519..63890539,-!p3@Gata4!0.76!4.69!Gata4;;chr9:36954842..36954908,-!p1@Pknox2!0.75!59.38!Pknox2;;chr18:11052485..11052508,+!p2@Gata6!0.75!14.08!Gata6;;chr7:77505617..77505632,-!p1@Nr2f2!0.74!234.36!Nr2f2;;chr15:81633165..81633188,+!p2@Tef!0.74!40.96!Tef;;chr15:75578637..75578669,-!p2@Mafa!0.74!5.16!Mafa;;chr12:12948633..12948651,-!p1@Mycn!0.71!44.60!Mycn;;chr7:17647736..17647772,-!p1@Hif3a!0.70!15.96!Hif3a;;chr1:120879128..120879183,-!p3@Gli2!0.70!8.22!Gli2;;chr12:9581317..9581333,+!p3@Osr1!0.69!6.22!Osr1;;chr5:31271028..31271040,+!p1@Tcf23!0.69!3.87!Tcf23;;chr18:11052642..11052659,+!p1@Gata6!0.68!21.95!Gata6;;chr2:169458352..169458397,+!p3@Tshz2!0.68!10.44!Tshz2;;chr2:30700788..30700824,+!p2@Prrx2!0.68!6.22!Prrx2;;chr4:97439519..97439539,+!p11@Nfia!0.67!8.45!Nfia;;chr2:74542918..74542971,+!p1@Hoxd8!0.67!5.87!Hoxd8;;chr2:104966436..104966455,+!p7@Wt1!0.67!3.64!Wt1;;chrX:35232210..35232214,-!p1@Rhox8!0.67!3.64!Rhox8;;chr4:122911086..122911112,+!p1@Heyl!0.66!48.82!Heyl;;chr7:37483231..37483263,+!p2@Tshz3!0.66!5.75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Hoxa11;;chr4:150482353..150482386,-!p6@Camta1!0.23!0.70!Camta1;;chr2:74520048..74520064,+!p1@Hoxd11!0.23!0.70!Hoxd11;;chr5:104182725..104182737,+!p17@Aff1!0.23!0.70!Aff1;;chr2:74517742..74517758,+!p2@Hoxd11!0.23!0.70!Hoxd11;;chrX:133654245..133654253,-!p3@Esx1!0.23!0.70!Esx1;;chr7:25655099..25655143,+!p1@Dmrtc2!0.23!0.70!Dmrtc2;;chr15:102839912..102839938,+!p5@Hoxc6!0.23!0.70!Hoxc6;;chr15:102797170..102797182,+!p3@Hoxc10!0.23!0.70!Hoxc10;;chr13:83663500..83663519,+!p8@Mef2c!0.23!0.70!Mef2c;;chr12:30525072..30525115,+!p14@Myt1l!0.23!0.70!Myt1l;;chr16:30064250..30064282,+!p6@Hes1!0.23!0.70!Hes1;;chr18:35721854..35721914,+!p1@Matr3!0.22!112.19!Matr3;;chr18:60720384..60720450,+!p1@Rbm22!0.22!76.75!Rbm22;;chr9:110034519..110034606,+!p1@Smarcc1!0.22!63.84!Smarcc1;;chr5:106305551..106305604,+!p1@Zfp326!0.22!55.51!Zfp326;;chr14:57397138..57397189,-!p1@Pspc1!0.22!46.59!Pspc1;;chrX:45947560..45947670,-!p1@Zfp280c!0.22!27.93!Zfp280c;;chr12:16817746..16817784,+!p1@E2f6!0.22!25.82!E2f6;;chr5:107125549..107125605,-!p1@Zfp644!0.22!25.70!Zfp644;;chr15:102034070..102034124,+!p1@Zfp740!0.22!24.88!Zfp740;;chr12:4484016..4484074,-!p1@Ncoa1!0.22!24.29!Ncoa1;;chr11:3189883..3189925,+!p1@Patz1!0.22!20.19!Patz1;;chr2:181327438..181327495,-!p1@Znf512b!0.22!19.60!Znf512b;;chr10:30522881..30522960,-!p1@Ncoa7!0.22!17.49!Ncoa7;;chr7:4866804..4866832,+!p1@Zfp628!0.22!16.43!Zfp628;;chr13:67784412..67784499,-!p1@Zfp738!0.22!13.14!Zfp738;;chr1:167932744..167932778,-!p1@Pou2f1!0.22!12.79!Pou2f1;;chr2:72817320..72817399,-!p2@Sp3!0.22!12.21!Sp3;;chr7:30739068..30739108,-!p1@Zfp74!0.22!10.68!Zfp74;;chr18:76401314..76401395,+!p2@Smad2!0.22!9.98!Smad2;;chr17:48061409..48061431,-!p4@Foxp4!0.22!7.16!Foxp4;;chr10:20032330..20032345,+!p3@Bclaf1!0.22!6.45!Bclaf1;;chr19:5637501..5637517,+!p4@Rela!0.22!5.40!Rela;;chr6:47785748..47785776,+!p3@Zfp398!0.22!4.93!Zfp398;;chr2:168032763..168032802,-!p3@Adnp!0.22!4.46!Adnp;;chr17:21520689..21520730,+!p1@Zfp677!0.22!4.46!Zfp677;;chr13:15555496..15555544,+!p1@Gli3!0.22!4.46!Gli3;;chr17:84587167..84587239,-!p2@Zfp36l2!0.22!4.34!Zfp36l2;;chr1:52176378..52176401,+!p3@Stat1!0.22!3.76!Stat1;;chr4:133276698..133276743,-!p6@Arid1a!0.22!3.40!Arid1a;;chr10:85379814..85379844,-!p2@Prdm4!0.22!2.82!Prdm4;;chr5:107125778..107125803,-!p4@Zfp644!0.22!2.58!Zfp644;;chr6:47780508..47780583,-!p1@Zfp786!0.22!2.00!Zfp786;;chr11:106993257..106993268,-!p4@Bptf!0.22!1.88!Bptf;;chr14:100684036..100684068,-!p5@Klf12!0.22!1.76!Klf12;;chr11:98821858..98821907,+!p6@Rara!0.22!1.64!Rara;;chr16:42875918..42875940,+!p13@Zbtb20!0.22!1.64!Zbtb20;;chr16:50429979..50429997,-!p4@Bbx!0.22!1.53!Bbx;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.22!1.53!Ncoa4;;chr4:135840552..135840567,+!p4@Zfp46!0.22!1.53!Zfp46;;chr10:107769719..107769745,+!p4@Pawr!0.22!1.41!Pawr;;chr2:44965761..44965785,-!p13@Zeb2!0.22!1.41!Zeb2;;chr12:25336286..25336297,+!p2@Klf11!0.22!1.41!Klf11;;chr6:47785727..47785738,+!p6@Zfp398!0.22!1.29!Zfp398;;chr4:135840623..135840632,+!p5@Zfp46!0.22!1.17!Zfp46;;chr18:76219161..76219176,+!p4@Zbtb7c!0.22!1.17!Zbtb7c;;chrX:103070960..103070973,-!p7@Atrx!0.22!1.17!Atrx;;chr15:102865048..102865073,+!p3@Hoxc4!0.22!1.06!Hoxc4;;chr15:81575472..81575481,+!p4@Zc3h7b!0.22!1.06!Zc3h7b;;chr10:79896360..79896400,-!p1@Tcf3!0.21!59.97!Tcf3;;chr1:15795720..15795756,+!p1@Terf1!0.21!42.95!Terf1;;chr4:94645754..94645797,-!p1@LOC100047941,p1@Mysm1!0.21!37.55!Mysm1;;chr17:35653725..35653780,-!p1@Tcf19!0.21!24.41!Tcf19;;chr6:47998498..47998527,-!p1@Zfp777!0.21!23.94!Zfp777;;chr10:41170169..41170227,+!p1@Zbtb24!0.21!19.72!Zbtb24;;chr1:136456734..136456757,+!p3@Kdm5b!0.21!17.84!Kdm5b;;chr5:32438831..32438878,+!p1@Fosl2!0.21!14.67!Fosl2;;chr7:28645585..28645659,+!p1@Zfp607!0.21!13.26!Zfp607;;chr17:25325325..25325363,+!p1@Unkl!0.21!10.09!Unkl;;chr17:48061692..48061723,-!p5@Foxp4!0.21!6.34!Foxp4;;chr11:50872733..50872809,+!p1@Zfp354a!0.21!5.99!Zfp354a;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.21!5.05!Ppp1r13l;;chr18:74376000..74376061,+!p3@Cxxc1!0.21!4.58!Cxxc1;;chr18:84255804..84255832,-!p2@Tshz1!0.21!4.46!Tshz1;;chr2:83499707..83499708,+!p6@Zc3h15!0.21!4.34!Zc3h15;;chr13:67914714..67914768,+!p1@Zfp273!0.21!4.11!Zfp273;;chr18:74375772..74375799,+!p2@Cxxc1!0.21!3.52!Cxxc1;;chr19:26681865..26681900,+!p6@Smarca2!0.21!3.52!Smarca2;;chr8:59799772..59799789,+!p1@Hand2!0.21!3.40!Hand2;;chr11:59285966..59285990,-!p2@Zfp867!0.21!2.93!Zfp867;;chrX:35542909..35542927,+!p4@Zbtb33!0.21!2.93!Zbtb33;;chr12:3807001..3807016,+!p5@Dnmt3a!0.21!2.82!Dnmt3a;;chr10:26093876..26093894,-!p2@L3mbtl3!0.21!2.70!L3mbtl3;;chr18:3337612..3337644,-!p8@Crem!0.21!2.00!Crem;;chr15:61818965..61819046,+!p3@Myc!0.21!1.76!Myc;;chr1:135557526..135557551,-!p1@Zbed6!0.21!1.53!Zbed6;;chr8:109868335..109868338,+!p3@Nfat5!0.21!1.41!Nfat5;;chr3:5218546..5218561,+!p4@Zfhx4!0.21!1.41!Zfhx4;;chr2:91489942..91489953,-!p3@Zfp408!0.21!1.06!Zfp408;;chr19:9016729..9016740,+!p6@Mta2!0.21!0.94!Mta2;;chr1:93698095..93698113,+!p3@Twist2!0.21!0.94!Twist2;;chr9:63869705..63869713,-!p8@Smad6!0.21!0.94!Smad6;;chr11:95171500.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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011509
 |is_obsolete=
+|library_id=CNhs11189
+|library_id_phase_based=2:CNhs11189
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1300
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1300
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N00.CNhs11189.1300-22B7.mm9.nobarcode.rdna.fa.gz
 |name=testis, neonate N00
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11189,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.139036365589797,0.0245443149212458,0.000872398333124675,0,0,0.0240960234281546,0.334107710669411,0,0.0564890445021211,0,0,1.12981019485805,0,0,0.0481920468563092,0,0,0,0.249072151133289,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0491703472549133,0,0,0.0481920468563092,0,0.0421247630166749,0.0817905893820813,0.0437531961542221,-0.155971557848438,0.794161976255299,0.0431999161937057,0,0,0,0,0,0,0,0,0,0,0.2005184129827,0.459047904046733,0.165500597474121,0.0915665403705771,0,0,0,0,0,0.0770576900529798,0.0481920468563092,0.130999727855463,0.0496377268915849,0.102051246347877,0.148397246707347,-0.109898995914773,0.181887640665224,0,0.0891399924614136,0.0486421533429187,0,0.402372152531402,0,0.0644076824969094,-0.0568283611842636,-0.258740772668467,0.0521681330155555,0,0,0,0,0,0.130999727855463,0,0.255112911599161,0.0539758632399234,0.0252665629655529,0,0,0,0.0481920468563092
 |rna_box=22
 |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=table111:1300-22B7;search_select_hide=table117:1300-22B7
 }}

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FF:1300-22B7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:48, 4 June 2020

CNhs11189

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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