FF:1310-23B1: Difference between revisions

Latest revision as of 18:51, 4 June 2020

Name:	epididymis and seminiferous tubule, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	CNhs11218
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	epididymis and seminiferous tubule
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		SAMD00004895

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11218		CAGE		DRX008951		DRR009825

Accession ID Mm9

Library id		BAM		CTSS
CNhs11218		DRZ001250		DRZ002633

Accession ID Mm10

Library id		BAM		CTSS
CNhs11218		DRZ012600		DRZ013983

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

CNhs11218

0	0
1	0
10	0
100	0
1000	0.0435
1001	0.0886
1002	0.85
1003	0.188
1004	0.305
1005	0
1006	-0.011
1007	0.141
1008	0
1009	0.331
101	0.0264
1010	0
1011	0.0021
1012	0.0421
1013	-0.141
1014	0.502
1015	0.171
1016	0.427
1017	0
1018	0.0421
1019	0
102	0
1020	0
1021	0.0805
1022	-0.0283
1023	0
1024	0.0585
1025	0.098
1026	0.0863
1027	0
1028	0
1029	0.226
103	0.671
1030	0
1031	0.701
1032	0.0174
1033	-0.0244
1034	0
1035	0
1036	0.0675
1037	0
1038	0.103
1039	-0.102
104	0
1040	0.31
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: CNhs11218

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00179
MA0003.1	MA0003.1	0.56
MA0004.1	MA0004.1	0.466
MA0006.1	MA0006.1	0.888
MA0007.1	MA0007.1	0.548
MA0009.1	MA0009.1	0.352
MA0014.1	MA0014.1	0.246
MA0017.1	MA0017.1	3.55163e-5
MA0018.2	MA0018.2	0.144
MA0019.1	MA0019.1	0.786
MA0024.1	MA0024.1	7.96657e-4
MA0025.1	MA0025.1	0.115
MA0027.1	MA0027.1	0.144
MA0028.1	MA0028.1	0.159
MA0029.1	MA0029.1	0.628
MA0030.1	MA0030.1	0.719
MA0031.1	MA0031.1	0.772
MA0035.2	MA0035.2	3.75903e-5
MA0038.1	MA0038.1	0.275
MA0039.2	MA0039.2	0.456
MA0040.1	MA0040.1	0.0773
MA0041.1	MA0041.1	0.0751
MA0042.1	MA0042.1	0.406
MA0043.1	MA0043.1	0.907
MA0046.1	MA0046.1	0.0196
MA0047.2	MA0047.2	0.0424
MA0048.1	MA0048.1	0.147
MA0050.1	MA0050.1	0.723
MA0051.1	MA0051.1	0.722
MA0052.1	MA0052.1	0.0679
MA0055.1	MA0055.1	0.158
MA0057.1	MA0057.1	0.59
MA0058.1	MA0058.1	0.394
MA0059.1	MA0059.1	0.167
MA0060.1	MA0060.1	0.291
MA0061.1	MA0061.1	0.542
MA0062.2	MA0062.2	0.00281
MA0065.2	MA0065.2	2.2295e-4
MA0066.1	MA0066.1	0.0194
MA0067.1	MA0067.1	0.276
MA0068.1	MA0068.1	0.798
MA0069.1	MA0069.1	0.537
MA0070.1	MA0070.1	0.99
MA0071.1	MA0071.1	0.00436
MA0072.1	MA0072.1	5.54261e-4
MA0073.1	MA0073.1	0.737
MA0074.1	MA0074.1	0.755
MA0076.1	MA0076.1	0.179
MA0077.1	MA0077.1	0.883
MA0078.1	MA0078.1	0.0578
MA0079.2	MA0079.2	0.11
MA0080.2	MA0080.2	2.23902e-5
MA0081.1	MA0081.1	0.0416
MA0083.1	MA0083.1	0.00113
MA0084.1	MA0084.1	0.904
MA0087.1	MA0087.1	0.351
MA0088.1	MA0088.1	0.0927
MA0090.1	MA0090.1	0.176
MA0091.1	MA0091.1	0.605
MA0092.1	MA0092.1	0.665
MA0093.1	MA0093.1	0.479
MA0099.2	MA0099.2	0.0252
MA0100.1	MA0100.1	0.276
MA0101.1	MA0101.1	0.853
MA0102.2	MA0102.2	0.618
MA0103.1	MA0103.1	0.00164
MA0104.2	MA0104.2	0.098
MA0105.1	MA0105.1	0.013
MA0106.1	MA0106.1	0.775
MA0107.1	MA0107.1	0.831
MA0108.2	MA0108.2	0.976
MA0111.1	MA0111.1	0.531
MA0112.2	MA0112.2	5.97573e-4
MA0113.1	MA0113.1	0.928
MA0114.1	MA0114.1	5.19039e-5
MA0115.1	MA0115.1	1.01068e-4
MA0116.1	MA0116.1	0.0275
MA0117.1	MA0117.1	0.168
MA0119.1	MA0119.1	0.298
MA0122.1	MA0122.1	0.403
MA0124.1	MA0124.1	0.098
MA0125.1	MA0125.1	0.287
MA0131.1	MA0131.1	0.583
MA0135.1	MA0135.1	0.863
MA0136.1	MA0136.1	9.23726e-6
MA0137.2	MA0137.2	0.406
MA0138.2	MA0138.2	0.00503
MA0139.1	MA0139.1	0.019
MA0140.1	MA0140.1	0.012
MA0141.1	MA0141.1	1.81188e-4
MA0142.1	MA0142.1	0.0122
MA0143.1	MA0143.1	0.935
MA0144.1	MA0144.1	0.777
MA0145.1	MA0145.1	0.333
MA0146.1	MA0146.1	0.76
MA0147.1	MA0147.1	0.0754
MA0148.1	MA0148.1	0.0193
MA0149.1	MA0149.1	0.0251
MA0150.1	MA0150.1	3.90525e-4
MA0152.1	MA0152.1	0.00173
MA0153.1	MA0153.1	0.00721
MA0154.1	MA0154.1	0.0521
MA0155.1	MA0155.1	0.529
MA0156.1	MA0156.1	0.0162
MA0157.1	MA0157.1	0.615
MA0159.1	MA0159.1	0.00129
MA0160.1	MA0160.1	7.77984e-4
MA0162.1	MA0162.1	0.702
MA0163.1	MA0163.1	0.859
MA0164.1	MA0164.1	0.905
MA0258.1	MA0258.1	1.76605e-4
MA0259.1	MA0259.1	0.744

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: CNhs11218

Novel motif	Logo	P-value
1	1	0.0454
10	10	0.119
100	100	0.857
101	101	0.405
102	102	0.997
103	103	0.269
104	104	0.928
105	105	0.555
106	106	0.445
107	107	0.788
108	108	0.693
109	109	0.159
11	11	0.124
110	110	0.24
111	111	0.0246
112	112	0.47
113	113	0.644
114	114	0.0106
115	115	0.682
116	116	0.945
117	117	0.00977
118	118	0.484
119	119	0.0399
12	12	0.58
120	120	0.294
121	121	0.395
122	122	0.705
123	123	0.188
124	124	0.287
125	125	0.46
126	126	0.409
127	127	0.201
128	128	0.244
129	129	0.349
13	13	0.459
130	130	0.468
131	131	0.728
132	132	0.748
133	133	0.192
134	134	0.754
135	135	0.106
136	136	0.469
137	137	0.846
138	138	0.0753
139	139	0.0125
14	14	0.466
140	140	0.434
141	141	0.374
142	142	0.589
143	143	0.387
144	144	0.189
145	145	0.625
146	146	0.521
147	147	0.715
148	148	0.574
149	149	0.853
15	15	0.0604
150	150	0.499
151	151	0.0575
152	152	0.727
153	153	0.912
154	154	0.669
155	155	0.701
156	156	0.00982
157	157	0.681
158	158	0.347
159	159	0.411
160	160	0.776
161	161	0.55
162	162	0.948
163	163	0.0571
164	164	0.539
165	165	0.164
166	166	0.0108
167	167	0.292
168	168	0.583
169	169	0.306
17	17	0.308
18	18	0.154
19	19	0.876
2	2	0.789
20	20	0.642
21	21	0.846
22	22	0.913
23	23	0.352
24	24	0.822
25	25	0.083
26	26	0.899
27	27	0.624
28	28	0.187
29	29	0.27
3	3	0.219
30	30	0.925
31	31	0.588
32	32	0.698
33	33	0.689
34	34	0.894
35	35	0.0207
36	36	0.0621
37	37	0.196
38	38	0.549
39	39	0.642
4	4	0.946
40	40	0.195
41	41	0.0171
42	42	0.511
43	43	0.205
44	44	0.0599
45	45	0.808
46	46	0.259
47	47	0.142
48	48	0.12
49	49	0.0624
5	5	0.136
50	50	0.462
51	51	0.754
52	52	0.882
53	53	0.97
54	54	0.402
55	55	0.459
56	56	0.313
57	57	0.527
58	58	0.22
59	59	0.457
6	6	0.906
60	60	0.506
61	61	0.567
62	62	0.0332
63	63	0.314
64	64	0.338
65	65	0.238
66	66	0.75
67	67	0.991
68	68	0.012
69	69	0.754
7	7	0.335
70	70	0.00114
71	71	0.122
72	72	0.467
73	73	0.206
74	74	0.877
75	75	0.0274
76	76	0.821
77	77	0.627
78	78	0.307
79	79	0.543
8	8	0.0218
80	80	0.111
81	81	0.257
82	82	0.389
83	83	0.434
84	84	0.829
85	85	0.0249
86	86	0.262
87	87	0.043
88	88	0.705
89	89	0.141
9	9	0.769
90	90	0.00453
91	91	0.486
92	92	0.404
93	93	0.916
94	94	0.239
95	95	0.112
96	96	0.0542
97	97	0.693
98	98	0.158
99	99	0.945

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: CNhs11218

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011506 mouse epididymis and seminiferous tubule- 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)
0001301 (epididymis)
0001343 (seminiferous tubule of testis)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0005904 (duct of male reproductive system)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)
0006947 (male genital duct)
0004054 (internal male genitalia)

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)
0011506 (mouse epididymis and seminiferous tubule- 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:0004871 (somatic layer of lateral plate mesoderm)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0007297 (presumptive pronephric mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008814
+|DRA_sample_Accession=CAGE@SAMD00004895
+|accession_numbers=CAGE;DRX008951;DRR009825;DRZ001250;DRZ002633;DRZ012600;DRZ013983
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000473,UBERON:0000991,UBERON:0001301,UBERON:0001343,UBERON:0000479,UBERON:0000058,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0005904,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0004175,UBERON:0010317,UBERON:0003101,UBERON:0000079,UBERON:0006947,UBERON:0004054
 |ancestors_in_cell_lineage_facet=
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:22539932..22539956,-!p1@Tcf21!2.02!265.50!Tcf21;;chr15:35225845..35225867,+!p1@Osr2!1.69!116.50!Osr2;;chr2:104966766..104966786,+!p1@Wt1!1.60!60.49!Wt1;;chr15:102828658..102828678,+!p1@Hoxc6!1.57!36.46!Hoxc6;;chr6:52190467..52190500,-!p1@Hoxa10!1.49!29.84!Hoxa10;;chrX:90531838..90531861,+!p1@Arx!1.46!34.42!Arx;;chr19:59533221..59533271,+!p1@Emx2!1.44!32.38!Emx2;;chr2:104966874..104966907,+!p2@Wt1!1.35!21.18!Wt1;;chr6:88148650..88148669,+!p1@Gata2!1.33!164.37!Gata2;;chr16:43247391..43247422,+!p12@Zbtb20!1.31!19.35!Zbtb20;;chr7:6649134..6649167,-!p1@Zim1!1.27!92.88!Zim1;;chr11:83664365..83664383,+!p1@Hnf1b!1.26!17.21!Hnf1b;;chr6:52176164..52176195,-!p1@Hoxa9!1.25!20.98!Hoxa9;;chr6:52195795..52195825,-!p1@Hoxa11!1.24!16.40!Hoxa11;;chr10:12810631..12810649,+!p1@Plagl1!1.21!387.60!Plagl1;;chr19:25746898..25746910,+!p1@Dmrt2!1.20!22.20!Dmrt2;;chr6:52163319..52163342,-!p1@Hoxa3!1.19!21.28!Hoxa3;;chr1:140739014..140739032,-!p1@Lhx9!1.17!17.62!Lhx9;;chr15:102820946..102820961,+!p3@Hoxc8!1.16!13.44!Hoxc8;;chr15:102820964..102821006,+!p1@Hoxc8!1.16!13.34!Hoxc8;;chr11:96153767..96153822,+!p1@Hoxb6!1.15!20.16!Hoxb6;;chr2:104966933..104966966,+!p3@Wt1!1.13!12.63!Wt1;;chr6:52184901..52184959,-!p2@Hoxa10!1.12!12.22!Hoxa10;;chr15:102828642..102828653,+!p2@Hoxc6!1.11!11.81!Hoxc6;;chr10:126778916..126778974,-!p1@Gli1!1.10!26.38!Gli1;;chr6:52195763..52195792,-!p2@Hoxa11!1.09!11.20!Hoxa11;;chr2:70313168..70313184,+!p1@Sp5!1.08!16.80!Sp5;;chr2:103143336..103143367,-!p1@Ehf!1.07!17.72!Ehf;;chr10:5636374..5636421,-!p1@Esr1!1.06!13.34!Esr1;;chr11:96143666..96143725,+!p1@Hoxb8!1.06!12.02!Hoxb8;;chr2:74529970..74529997,+!p1@Hoxd10!1.05!10.29!Hoxd10;;chr2:24331085..24331100,-!p1@Pax8!1.02!9.37!Pax8;;chr15:102821007..102821021,+!p2@Hoxc8!1.01!9.17!Hoxc8;;chr2:74549968..74549996,+!p1@Hoxd3!1.00!11.20!Hoxd3;;chr1:93698030..93698064,+!p1@Twist2!0.98!17.72!Twist2;;chr10:5636354..5636373,-!p2@Esr1!0.98!8.55!Esr1;;chr2:74536026..74536039,+!p1@Hoxd9!0.98!8.55!Hoxd9;;chr2:104966662..104966673,+!p4@Wt1!0.96!8.15!Wt1;;chr2:74550015..74550057,+!p2@Hoxd3!0.96!8.05!Hoxd3;;chr8:59799772..59799789,+!p1@Hand2!0.95!23.12!Hand2;;chr15:102865131..102865151,+!p2@Hoxc4!0.94!8.76!Hoxc4;;chr4:3865501..3865548,-!p1@Plag1!0.91!38.19!Plag1;;chr7:17647736..17647772,-!p1@Hif3a!0.91!25.97!Hif3a;;chr14:63864056..63864102,-!p1@Gata4!0.91!12.73!Gata4;;chr18:11052485..11052508,+!p2@Gata6!0.90!20.37!Gata6;;chr2:74517742..74517758,+!p2@Hoxd11!0.89!6.82!Hoxd11;;chr15:102839948..102839975,+!p3@Hoxc6!0.89!6.72!Hoxc6;;chr2:74542918..74542971,+!p1@Hoxd8!0.88!10.08!Hoxd8;;chr2:169458192..169458247,+!p1@Tshz2!0.87!59.88!Tshz2;;chr2:169458838..169458859,+!p4@Tshz2!0.87!13.24!Tshz2;;chr5:120121020..120121049,+!p1@Tbx3!0.86!40.63!Tbx3;;chr15:102865088..102865107,+!p1@Hoxc4!0.86!8.45!Hoxc4;;chr11:96147952..96147967,+!p1@Hoxb7!0.86!7.84!Hoxb7;;chr15:102797288..102797302,+!p1@Hoxc10!0.86!6.21!Hoxc10;;chr6:52190668..52190682,-!p3@Hoxa10!0.86!6.21!Hoxa10;;chr14:22807083..22807104,-!p1@Zfp503!0.85!113.65!Zfp503;;chr17:28487603..28487626,-!p2@Tead3!0.85!13.44!Tead3;;chr10:102491237..102491291,-!p2@Alx1!0.85!6.01!Alx1;;chr10:5734525..5734569,-!p3@Esr1!0.84!10.08!Esr1;;chr15:35225873..35225889,+!p2@Osr2!0.84!5.91!Osr2;;chr15:102839976..102839989,+!p4@Hoxc6!0.84!5.91!Hoxc6;;chr19:59533163..59533185,+!p3@Emx2!0.83!5.80!Emx2;;chr2:91864300..91864379,-!p2@Creb3l1!0.82!17.21!Creb3l1;;chr19:10315179..10315241,-!p1@Gm98!0.81!61.41!Gm98;;chr1:38684260..38684312,-!p2@Aff3!0.81!41.55!Aff3;;chr11:85646303..85646329,+!p1@Tbx2!0.81!39.31!Tbx2;;chr18:11052642..11052659,+!p1@Gata6!0.81!29.64!Gata6;;chr7:77511403..77511450,-!p3@Nr2f2!0.81!12.12!Nr2f2;;chr11:84339016..84339044,-!p1@Lhx1!0.81!5.50!Lhx1;;chr2:74520343..74520383,+!p4@Hoxd11!0.81!5.50!Hoxd11;;chr15:40486566..40486600,+!p1@Zfpm2!0.80!34.12!Zfpm2;;chr5:120121446..120121461,+!p2@Tbx3!0.80!18.84!Tbx3;;chr11:5761889..5761969,+!p1@Aebp1!0.79!235.55!Aebp1;;chr18:11052456..11052477,+!p3@Gata6!0.78!16.70!Gata6;;chr1:93698068..93698085,+!p2@Twist2!0.78!6.01!Twist2;;chr2:169458352..169458397,+!p3@Tshz2!0.77!13.04!Tshz2;;chr19:59533139..59533152,+!p2@Emx2!0.77!4.89!Emx2;;chr11:18918917..18918944,-!p1@Meis1!0.76!67.32!Meis1;;chr12:34642682..34642753,+!p2@Twist1!0.76!13.54!Twist1;;chr14:56443806..56443848,+!p1@Nfatc4!0.76!10.18!Nfatc4;;chr2:91864449..91864492,-!p3@Creb3l1!0.76!8.05!Creb3l1;;chrX:45245679..45245702,-!p1@Smarca1!0.75!22.51!Smarca1;;chr13:96093557..96093561,+!p6@Zbed3!0.75!4.68!Zbed3;;chr2:105003277..105003280,+!p5@Wt1!0.75!4.58!Wt1;;chr12:9581262..9581282,+!p1@Osr1!0.74!59.88!Osr1;;chr2:77654936..77654988,-!p4@Zfp385b!0.74!5.60!Zfp385b;;chr6:52167459..52167492,-!p1@Hoxa7!0.74!5.60!Hoxa7;;chr2:74529998..74530020,+!p2@Hoxd10!0.74!4.48!Hoxd10;;chr2:169458799..169458832,+!p5@Tshz2!0.73!7.54!Tshz2;;chrX:45245644..45245666,-!p2@Smarca1!0.72!15.07!Smarca1;;chr18:7004715..7004731,-!p1@Mkx!0.72!10.90!Mkx;;chrX:110411840..110411860,+!p1@Dach2!0.72!5.30!Dach2;;chr12:34642510..34642530,+!p1@Twist1!0.71!14.36!Twist1;;chr1:170361777..170361797,-!p10@Pbx1!0.71!7.74!Pbx1;;chr6:88143711..88143717,+!p2@Gata2!0.71!7.03!Gata2;;chr2:74520048..74520064,+!p1@Hoxd11!0.71!4.18!Hoxd11;;chr11:96143843..96143868,+!p3@Hoxb8!0.71!4.18!Hoxb8;;chr11:96160426..96160443,+!p2@Hoxb6!0.71!4.07!Hoxb6;;chr11:18918959..18918976,-!p2@Meis1!0.70!62.02!Meis1;;chr7:77511234..77511302,-!p2@Nr2f2!0.70!30.35!Nr2f2;;chr2:130120884..130120972,+!p1@Ebf4!0.70!26.38!Ebf4;;chr2:152223441..152223465,-!p2@Sox12!0.70!18.33!Sox12;;chr11:5761871..5761882,+!p3@Aebp1!0.70!11.51!Aebp1;;chr6:52167513..52167549,-!p2@Hoxa7!0.70!5.91!Hoxa7;;chr7:89137163..89137200,-!p1@Bnc1!0.70!4.99!Bnc1;;chr2:74536050..74536065,+!p2@Hoxd9!0.70!3.97!Hoxd9;;chr15:102820912..102820923,+!p5@Hoxc8!0.69!3.87!Hoxc8;;chr7:77505617..77505632,-!p1@Nr2f2!0.68!202.25!Nr2f2;;chr2:9800207..9800234,-!p1@Gata3!0.68!12.93!Gata3;;chr11:5761979..5761992,+!p2@Aebp1!0.68!8.25!Aebp1;;chr2:180069370..180069409,-!p1@Gata5!0.68!4.58!Gata5;;chr19:59533429..59533470,+!p4@Emx2!0.68!3.77!Emx2;;chr11:85646263..85646278,+!p2@Tbx2!0.67!10.39!Tbx2;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.67!4.89!Pou3f3;;chr14:22807107..22807119,-!p2@Zfp503!0.66!18.03!Zfp503;;chr2:169458519..169458555,+!p2@Tshz2!0.66!16.40!Tshz2;;chr2:74543202..74543213,+!p3@Hoxd8!0.66!3.56!Hoxd8;;chr15:40486754..40486771,+!p2@Zfpm2!0.65!6.52!Zfpm2;;chr12:9581317..9581333,+!p3@Osr1!0.65!5.60!Osr1;;chr2:38570011..38570034,-!p1@Nr5a1!0.65!3.46!Nr5a1;;chr2:115891534..115891589,-!p1@Meis2!0.64!56.22!Meis2;;chr1:170362040..170362113,-!p2@Pbx1!0.64!30.55!Pbx1;;chr5:38215819..38215823,-!p1@Msx1!0.64!9.88!Msx1;;chr11:85646427..85646451,+!p4@Tbx2!0.64!6.31!Tbx2;;chr11:18918434..18918489,-!p3@Meis1!0.64!5.80!Meis1;;chr7:17642053..17642066,-!p2@Hif3a!0.64!5.09!Hif3a;;chr7:77511622..77511657,-!p5@Nr2f2!0.64!4.48!Nr2f2;;chr2:74517609..74517621,+!p3@Hoxd11!0.64!3.36!Hoxd11;;chr6:53523358..53523388,+!p1@Creb5!0.63!46.44!Creb5;;chr15:76287876..76287894,+!p1@Scx!0.63!20.78!Scx;;chr1:170361730..170361769,-!p7@Pbx1!0.63!8.35!Pbx1;;chr12:9581284..9581303,+!p2@Osr1!0.63!7.03!Osr1;;chr15:40486458..40486467,+!p9@Zfpm2!0.63!3.97!Zfpm2;;chr2:74513125..74513143,+!p1@Hoxd12!0.63!3.26!Hoxd12;;chr1:137155026..137155042,-!p1@Elf3!0.62!21.59!Elf3;;chr1:4483679..4483695,-!p1@Sox17!0.62!17.31!Sox17;;chr1:165243792..165243808,-!p1@Prrx1!0.62!12.73!Prrx1;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.62!10.29!Tfcp2l1;;chr13:53568104..53568156,-!p1@Msx2!0.62!4.99!Msx2;;chr6:52190858..52190873,-!p4@Hoxa10!0.62!3.16!Hoxa10;;chr2:152223881..152223933,-!p3@Sox12!0.61!11.92!Sox12;;chr7:25372631..25372684,-!p1@Zfp575!0.61!10.69!Zfp575;;chr4:84320893..84320910,-!p1@Bnc2!0.61!7.64!Bnc2;;chr11:18918820..18918831,-!p4@Meis1!0.61!6.42!Meis1;;chr12:9581243..9581254,+!p4@Osr1!0.61!4.58!Osr1;;chr2:103123925..103123959,-!p3@Ehf!0.61!3.06!Ehf;;chr7:52471143..52471186,+!p1@Tead2!0.60!38.70!Tead2;;chr19:26822880..26822964,+!p2@Smarca2!0.60!30.65!Smarca2;;chr1:165243379..165243402,-!p3@Prrx1!0.60!4.79!Prrx1;;chr15:40486427..40486437,+!p5@Zfpm2!0.60!4.07!Zfpm2;;chr2:104966465..104966479,+!p6@Wt1!0.60!2.95!Wt1;;chr10:126778639..126778670,-!p3@Gli1!0.60!2.95!Gli1;;chr1:93698095..93698113,+!p3@Twist2!0.59!3.67!Twist2;;chr6:88143570..88143590,+!p4@Gata2!0.59!2.85!Gata2;;chr17:37139472..37139514,+!p1@Zfp57!0.58!23.22!Zfp57;;chr4:82151622..82151643,-!p4@Nfib!0.58!13.95!Nfib;;chr2:169458496..169458516,+!p6@Tshz2!0.58!6.72!Tshz2;;chr11:18918982..18918993,-!p5@Meis1!0.58!6.62!Meis1;;chr11:85646341..85646352,+!p3@Tbx2!0.58!6.21!Tbx2;;chr1:120949925..120949947,-!p4@Gli2!0.58!6.11!Gli2;;chr7:19895354..19895369,-!p1@Fosb!0.58!4.18!Fosb;;chr7:37483021..37483078,+!p1@Tshz3!0.57!9.78!Tshz3;;chr1:120879128..120879183,-!p3@Gli2!0.57!5.80!Gli2;;chr13:72101178..72101203,-!p1@Irx1!0.57!4.58!Irx1;;chr7:37483231..37483263,+!p2@Tshz3!0.57!4.48!Tshz3;;chr15:102844431..102844445,+!p1@Hoxc5!0.57!2.75!Hoxc5;;chr2:74543103..74543135,+!p4@Hoxd8!0.57!2.75!Hoxd8;;chrX:95345005..95345053,+!p1@Ar!0.57!2.75!Ar;;chr11:96132767..96132796,+!p2@Hoxb9!0.57!2.75!Hoxb9;;chr7:6683123..6683142,-!p1@Peg3!0.56!171.80!Peg3;;chr16:4594740..4594759,+!p1@Glis2!0.56!37.17!Glis2;;chr6:72739185..72739232,-!p1@Tcf7l1!0.56!34.12!Tcf7l1;;chr2:152758901..152758925,-!p1@Foxs1!0.56!14.26!Foxs1;;chr17:47278081..47278103,+!p1@Trerf1!0.56!7.13!Trerf1;;chr15:40486883..40486903,+!p4@Zfpm2!0.56!3.77!Zfpm2;;chr2:74543397..74543435,+!p2@Hoxd8!0.56!2.65!Hoxd8;;chr16:14705925..14705951,+!p1@Snai2!0.55!22.30!Snai2;;chr7:19679964..19679982,+!p1@Six5!0.55!8.55!Six5;;chr11:116196664..116196679,-!p1@Foxj1!0.55!4.28!Foxj1;;chr11:96145450..96145517,+!p2@Hoxb7!0.55!4.18!Hoxb7;;chr7:77511311..77511352,-!p4@Nr2f2!0.54!5.70!Nr2f2;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.54!4.79!Hoxb2;;chr15:40486615..40486628,+!p3@Zfpm2!0.54!4.38!Zfpm2;;chr9:98855847..98855866,+!p3@Foxl2!0.54!2.44!Foxl2;;chr5:31271028..31271040,+!p1@Tcf23!0.54!2.44!Tcf23;;chr8:87324243..87324277,-!p1@Nfix!0.53!73.63!Nfix;;chr11:50641183..50641244,-!p1@Zfp354c!0.53!23.32!Zfp354c;;chr1:1652436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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011506
 |is_obsolete=
-|library_ids=CNhs11218
+|library_id=CNhs11218
+|library_id_phase_based=2:CNhs11218
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1310
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1310
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/epididymis%2520and%2520seminiferous%2520tubule%252c%2520neonate%2520N00.CNhs11218.1310-23B1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/epididymis%2520and%2520seminiferous%2520tubule%252c%2520neonate%2520N00.CNhs11218.1310-23B1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/epididymis%2520and%2520seminiferous%2520tubule%252c%2520neonate%2520N00.CNhs11218.1310-23B1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/epididymis%2520and%2520seminiferous%2520tubule%252c%2520neonate%2520N00.CNhs11218.1310-23B1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/epididymis%2520and%2520seminiferous%2520tubule%252c%2520neonate%2520N00.CNhs11218.1310-23B1.mm9.nobarcode.rdna.fa.gz
 |name=epididymis and seminiferous tubule, neonate N00
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11218,LSID748,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.086373359564732,0,0,0,0,0.0540323423167005,0.20088990862573,0,0.0210591418683525,0,0,1.09330783072155,0,0,0,0,0,0,0.0669150567869665,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.106159577683106,0,0,0,0,0.0421182837367051,0.00945441894938743,0.118929708322798,-0.0381674268072587,0.830439952660832,-0.0627633434353137,0,0,0,0,0,0,0,0,0,0,0.452263214640926,0,0.0497773469841137,0.0805105854221362,0,0,0,0,0,0,0.0805105854221362,0.178745881220886,0.0421182837367051,0.0292569764529317,0.186088999405705,-0.00968662465988351,0.162846311654124,0,0.0811205961775602,0.0868592521120238,0.0829902820647535,0.0805105854221362,0,0.0954693596906797,-0.0472031640661284,-0.313393758246739,0.0369512997076467,0,0,0,0,0,0,-0.0730404042754446,0.0123579972824466,-0.0594086205982574,0,0,0,0,0
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1310-23B1;search_select_hide=table117:1310-23B1
-|DRA_sample_Accession=CAGE@DRS008814
-|accession_numbers=DRX008951;DRR009825;DRZ001250;DRZ002633;CAGE
-|library_id=CNhs11218
 }}

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From FANTOM5_SSTAR

Latest revision as of 18:51, 4 June 2020

CNhs11218

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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