FF:726-26I4: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	testis, neonate N07
Species:	Mouse (Mus musculus)
Library ID:	CNhs11222
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	testis
dev stage	7 days neonate
sex	male
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005949

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11222		CAGE		DRX009108		DRR009982

Accession ID Mm9

Library id		BAM		CTSS
CNhs11222		DRZ001407		DRZ002790

Accession ID Mm10

Library id		BAM		CTSS
CNhs11222		DRZ012757		DRZ014140

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

CNhs11222

0	0
1	0
10	0
100	0
1000	0
1001	0.127
1002	0.398
1003	0.194
1004	0.122
1005	-0.117
1006	0.00663
1007	0.171
1008	0
1009	0.193
101	0.0911
1010	0
1011	-0.0307
1012	0.0842
1013	-0.116
1014	0.158
1015	0.14
1016	0.222
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.074
1022	0.0938
1023	0
1024	-0.039
1025	0.0394
1026	0
1027	0
1028	0
1029	0.274
103	0.337
1030	0
1031	0.211
1032	-0.00152
1033	0
1034	0.0532
1035	0.143
1036	0.0265
1037	0
1038	0.0544
1039	-0.0161
104	0
1040	-0.0508
1041	0.0532

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: CNhs11222

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	3.72239e-5
MA0003.1	MA0003.1	0.926
MA0004.1	MA0004.1	0.332
MA0006.1	MA0006.1	0.242
MA0007.1	MA0007.1	0.972
MA0009.1	MA0009.1	0.309
MA0014.1	MA0014.1	0.705
MA0017.1	MA0017.1	0.161
MA0018.2	MA0018.2	0.362
MA0019.1	MA0019.1	0.228
MA0024.1	MA0024.1	2.9624e-7
MA0025.1	MA0025.1	0.941
MA0027.1	MA0027.1	0.835
MA0028.1	MA0028.1	0.202
MA0029.1	MA0029.1	0.627
MA0030.1	MA0030.1	0.915
MA0031.1	MA0031.1	0.482
MA0035.2	MA0035.2	0.594
MA0038.1	MA0038.1	0.0596
MA0039.2	MA0039.2	0.187
MA0040.1	MA0040.1	0.468
MA0041.1	MA0041.1	0.532
MA0042.1	MA0042.1	0.786
MA0043.1	MA0043.1	0.737
MA0046.1	MA0046.1	0.464
MA0047.2	MA0047.2	0.574
MA0048.1	MA0048.1	0.107
MA0050.1	MA0050.1	0.257
MA0051.1	MA0051.1	0.275
MA0052.1	MA0052.1	0.00662
MA0055.1	MA0055.1	0.0249
MA0057.1	MA0057.1	0.425
MA0058.1	MA0058.1	0.299
MA0059.1	MA0059.1	0.537
MA0060.1	MA0060.1	2.86206e-12
MA0061.1	MA0061.1	0.0957
MA0062.2	MA0062.2	0.397
MA0065.2	MA0065.2	0.056
MA0066.1	MA0066.1	0.0376
MA0067.1	MA0067.1	0.961
MA0068.1	MA0068.1	0.861
MA0069.1	MA0069.1	0.674
MA0070.1	MA0070.1	0.28
MA0071.1	MA0071.1	0.7
MA0072.1	MA0072.1	0.846
MA0073.1	MA0073.1	0.457
MA0074.1	MA0074.1	0.276
MA0076.1	MA0076.1	0.0513
MA0077.1	MA0077.1	0.643
MA0078.1	MA0078.1	0.168
MA0079.2	MA0079.2	0.185
MA0080.2	MA0080.2	5.44773e-8
MA0081.1	MA0081.1	0.106
MA0083.1	MA0083.1	0.965
MA0084.1	MA0084.1	0.522
MA0087.1	MA0087.1	0.292
MA0088.1	MA0088.1	0.371
MA0090.1	MA0090.1	0.764
MA0091.1	MA0091.1	0.221
MA0092.1	MA0092.1	0.429
MA0093.1	MA0093.1	0.284
MA0099.2	MA0099.2	2.15536e-4
MA0100.1	MA0100.1	0.565
MA0101.1	MA0101.1	0.444
MA0102.2	MA0102.2	0.961
MA0103.1	MA0103.1	0.00637
MA0104.2	MA0104.2	0.136
MA0105.1	MA0105.1	9.10474e-6
MA0106.1	MA0106.1	0.927
MA0107.1	MA0107.1	0.284
MA0108.2	MA0108.2	0.158
MA0111.1	MA0111.1	0.243
MA0112.2	MA0112.2	1.1295e-4
MA0113.1	MA0113.1	0.434
MA0114.1	MA0114.1	0.13
MA0115.1	MA0115.1	0.545
MA0116.1	MA0116.1	0.00357
MA0117.1	MA0117.1	0.289
MA0119.1	MA0119.1	0.351
MA0122.1	MA0122.1	0.232
MA0124.1	MA0124.1	0.15
MA0125.1	MA0125.1	0.901
MA0131.1	MA0131.1	0.246
MA0135.1	MA0135.1	0.279
MA0136.1	MA0136.1	1.81738e-5
MA0137.2	MA0137.2	0.0959
MA0138.2	MA0138.2	0.0272
MA0139.1	MA0139.1	0.079
MA0140.1	MA0140.1	0.847
MA0141.1	MA0141.1	0.261
MA0142.1	MA0142.1	0.00807
MA0143.1	MA0143.1	0.83
MA0144.1	MA0144.1	0.1
MA0145.1	MA0145.1	0.0238
MA0146.1	MA0146.1	0.609
MA0147.1	MA0147.1	0.178
MA0148.1	MA0148.1	0.324
MA0149.1	MA0149.1	0.522
MA0150.1	MA0150.1	0.00233
MA0152.1	MA0152.1	0.0637
MA0153.1	MA0153.1	0.525
MA0154.1	MA0154.1	0.0096
MA0155.1	MA0155.1	0.551
MA0156.1	MA0156.1	0.085
MA0157.1	MA0157.1	0.221
MA0159.1	MA0159.1	2.90154e-4
MA0160.1	MA0160.1	0.883
MA0162.1	MA0162.1	0.0437
MA0163.1	MA0163.1	0.0983
MA0164.1	MA0164.1	0.711
MA0258.1	MA0258.1	5.958e-4
MA0259.1	MA0259.1	0.115

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: CNhs11222

Novel motif	Logo	P-value
1	1	0.125
10	10	0.425
100	100	0.642
101	101	0.42
102	102	0.9
103	103	0.655
104	104	0.758
105	105	0.505
106	106	0.00581
107	107	0.0825
108	108	0.335
109	109	0.554
11	11	0.19
110	110	0.752
111	111	0.362
112	112	0.797
113	113	0.607
114	114	0.0225
115	115	0.344
116	116	0.124
117	117	0.88
118	118	0.911
119	119	0.153
12	12	0.445
120	120	0.135
121	121	0.727
122	122	0.834
123	123	0.151
124	124	0.613
125	125	0.0513
126	126	0.859
127	127	0.159
128	128	0.00658
129	129	0.326
13	13	0.99
130	130	0.572
131	131	0.708
132	132	0.416
133	133	0.0485
134	134	0.781
135	135	0.331
136	136	0.0479
137	137	0.856
138	138	0.227
139	139	0.0457
14	14	0.142
140	140	0.656
141	141	0.0461
142	142	0.176
143	143	0.0319
144	144	0.12
145	145	0.766
146	146	0.488
147	147	0.791
148	148	0.0494
149	149	0.209
15	15	0.0743
150	150	0.984
151	151	0.0488
152	152	0.407
153	153	0.29
154	154	0.988
155	155	0.32
156	156	0.00292
157	157	0.57
158	158	0.443
159	159	0.394
160	160	0.587
161	161	0.845
162	162	0.583
163	163	0.0426
164	164	0.806
165	165	0.05
166	166	0.238
167	167	0.363
168	168	0.367
169	169	0.185
17	17	0.142
18	18	0.164
19	19	0.769
2	2	0.559
20	20	0.779
21	21	0.707
22	22	0.75
23	23	0.187
24	24	0.986
25	25	0.427
26	26	0.908
27	27	0.255
28	28	0.359
29	29	0.974
3	3	0.233
30	30	0.739
31	31	0.162
32	32	0.332
33	33	0.8
34	34	0.726
35	35	0.0637
36	36	0.0985
37	37	0.136
38	38	0.869
39	39	0.812
4	4	0.959
40	40	0.587
41	41	0.0195
42	42	0.4
43	43	0.223
44	44	0.128
45	45	0.448
46	46	0.107
47	47	0.241
48	48	0.344
49	49	0.211
5	5	0.078
50	50	0.972
51	51	0.828
52	52	0.215
53	53	0.544
54	54	0.513
55	55	0.392
56	56	0.145
57	57	0.465
58	58	0.19
59	59	0.111
6	6	0.613
60	60	0.0696
61	61	0.543
62	62	0.0667
63	63	0.185
64	64	0.619
65	65	0.155
66	66	0.537
67	67	0.935
68	68	0.024
69	69	0.388
7	7	0.476
70	70	0.00679
71	71	0.215
72	72	0.517
73	73	0.379
74	74	0.913
75	75	0.219
76	76	0.986
77	77	0.434
78	78	0.3
79	79	0.64
8	8	0.148
80	80	0.102
81	81	0.27
82	82	0.399
83	83	0.668
84	84	0.441
85	85	0.0122
86	86	0.153
87	87	0.774
88	88	0.87
89	89	0.0582
9	9	0.858
90	90	0.205
91	91	0.411
92	92	0.354
93	93	0.74
94	94	0.233
95	95	0.772
96	96	0.254
97	97	0.609
98	98	0.0742
99	99	0.822

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: CNhs11222

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011412 mouse testis- neonate N07 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)
0000313 (mouse neonate N7 sample)
0011412 (mouse testis- neonate N07 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@SAMD00005949
+|accession_numbers=CAGE;DRX009108;DRR009982;DRZ001407;DRZ002790;DRZ012757;DRZ014140
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000473,UBERON:0000991,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000313,FF:0011412
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:38570011..38570034,-!p1@Nr5a1!1.95!88.67!Nr5a1;;chr14:63864056..63864102,-!p1@Gata4!1.83!113.02!Gata4;;chr10:22539932..22539956,-!p1@Tcf21!1.82!166.14!Tcf21;;chr2:104966766..104966786,+!p1@Wt1!1.65!67.32!Wt1;;chr1:140739014..140739032,-!p1@Lhx9!1.65!54.56!Lhx9;;chr19:25580110..25580163,+!p1@Dmrt1!1.59!38.02!Dmrt1;;chrX:90531838..90531861,+!p1@Arx!1.53!40.75!Arx;;chrX:83437105..83437121,+!p1@Nr0b1!1.53!32.55!Nr0b1;;chr1:168168856..168168893,-!p1@Mael!1.51!31.51!Mael;;chr19:25580226..25580261,+!p2@Dmrt1!1.51!31.38!Dmrt1;;chr2:104966874..104966907,+!p2@Wt1!1.40!24.22!Wt1;;chr19:25580272..25580305,+!p3@Dmrt1!1.40!23.96!Dmrt1;;chr17:25707623..25707639,-!p1@Sox8!1.39!97.91!Sox8;;chrX:58146612..58146615,-!p1@Sox3!1.39!23.83!Sox3;;chr15:102828658..102828678,+!p1@Hoxc6!1.39!23.57!Hoxc6;;chr6:85463580..85463585,-!p1@Egr4!1.36!22.00!Egr4;;chr15:35225845..35225867,+!p1@Osr2!1.32!49.61!Osr2;;chr4:89354729..89354776,+!p1@Dmrta1!1.27!17.58!Dmrta1;;chrX:137135036..137135064,-!p4@Tsc22d3!1.17!26.95!Tsc22d3;;chr14:63890459..63890484,-!p4@Gata4!1.15!13.02!Gata4;;chr3:54985946..54985981,+!p1@Sohlh2!1.13!12.37!Sohlh2;;chr14:69808725..69808748,+!p1@Nkx3-1!1.11!11.85!Nkx3-1;;chr14:63890491..63890516,-!p2@Gata4!1.10!11.59!Gata4;;chr2:104966933..104966966,+!p3@Wt1!1.10!11.59!Wt1;;chr2:152758901..152758925,-!p1@Foxs1!1.08!48.70!Foxs1;;chr2:74529970..74529997,+!p1@Hoxd10!1.06!10.55!Hoxd10;;chr2:104966662..104966673,+!p4@Wt1!1.06!10.42!Wt1;;chr5:135582751..135582788,+!p1@Mlxipl!1.05!41.80!Mlxipl;;chr4:119960301..119960359,-!p1@Foxo6!1.02!31.25!Foxo6;;chr15:75578748..75578752,-!p1@Mafa!1.02!9.37!Mafa;;chr10:126778916..126778974,-!p1@Gli1!1.00!20.44!Gli1;;chr10:80809447..80809515,-!p5@Hmg20b!0.96!9.90!Hmg20b;;chr2:74549968..74549996,+!p1@Hoxd3!0.95!9.90!Hoxd3;;chr16:43247391..43247422,+!p12@Zbtb20!0.95!7.94!Zbtb20;;chr1:168168817..168168850,-!p2@Mael!0.95!7.81!Mael;;chr15:75578637..75578669,-!p2@Mafa!0.94!8.72!Mafa;;chr2:74536026..74536039,+!p1@Hoxd9!0.93!7.55!Hoxd9;;chr15:102828642..102828653,+!p2@Hoxc6!0.92!7.29!Hoxc6;;chr12:34642510..34642530,+!p1@Twist1!0.91!23.57!Twist1;;chr15:76287876..76287894,+!p1@Scx!0.90!40.10!Scx;;chr2:104966436..104966455,+!p7@Wt1!0.90!7.03!Wt1;;chr11:98826178..98826197,+!p7@Rara!0.90!6.90!Rara;;chr7:6649134..6649167,-!p1@Zim1!0.88!37.24!Zim1;;chr5:31271028..31271040,+!p1@Tcf23!0.88!6.51!Tcf23;;chr4:89354785..89354801,+!p2@Dmrta1!0.87!6.38!Dmrta1;;chr11:98826125..98826141,+!p12@Rara!0.86!6.25!Rara;;chr2:104966465..104966479,+!p6@Wt1!0.86!6.25!Wt1;;chr18:11052485..11052508,+!p2@Gata6!0.85!18.10!Gata6;;chr14:63890660..63890687,-!p7@Gata4!0.84!5.99!Gata4;;chr2:38567715..38567730,-!p2@Nr5a1!0.83!5.73!Nr5a1;;chr15:81633165..81633188,+!p2@Tef!0.82!49.35!Tef;;chr2:105003277..105003280,+!p5@Wt1!0.82!5.60!Wt1;;chr2:152223441..152223465,-!p2@Sox12!0.81!24.09!Sox12;;chr2:169458799..169458832,+!p5@Tshz2!0.81!9.37!Tshz2;;chr11:101755669..101755686,-!p1@Meox1!0.80!9.90!Meox1;;chr2:180377386..180377462,-!p1@Tcfl5!0.79!6.38!Tcfl5;;chr19:25580353..25580364,+!p4@Dmrt1!0.79!5.21!Dmrt1;;chr18:11052456..11052477,+!p3@Gata6!0.78!16.93!Gata6;;chrX:7544943..7545001,-!p1@Gata1!0.78!5.08!Gata1;;chr13:83712735..83712761,+!p9@Mef2c!0.78!5.08!Mef2c;;chrX:45245679..45245702,-!p1@Smarca1!0.77!23.57!Smarca1;;chr2:74550015..74550057,+!p2@Hoxd3!0.77!4.95!Hoxd3;;chr4:107356833..107356836,-!p7@Dmrtb1!0.77!4.95!Dmrtb1;;chr12:77278238..77278252,-!p1@Esr2!0.77!4.95!Esr2;;chr11:52096804..52096896,-!p1@Tcf7!0.76!41.93!Tcf7;;chr14:63890519..63890539,-!p3@Gata4!0.76!4.82!Gata4;;chr12:12948633..12948651,-!p1@Mycn!0.73!46.87!Mycn;;chr11:96143666..96143725,+!p1@Hoxb8!0.73!5.08!Hoxb8;;chrX:35232210..35232214,-!p1@Rhox8!0.73!4.43!Rhox8;;chr19:59533221..59533271,+!p1@Emx2!0.72!5.34!Emx2;;chr2:25702844..25702859,-!p1@Sohlh1!0.72!4.30!Sohlh1;;chr10:12810631..12810649,+!p1@Plagl1!0.71!123.17!Plagl1;;chr19:28754692..28754757,-!p1@Glis3!0.71!19.01!Glis3;;chr14:63864337..63864381,-!p6@Gata4!0.71!4.17!Gata4;;chr2:74536050..74536065,+!p2@Hoxd9!0.71!4.17!Hoxd9;;chr11:112643496..112643562,+!p1@Sox9!0.70!168.48!Sox9;;chr14:55711114..55711159,-!p2@Zfhx2!0.70!9.64!Zfhx2;;chr2:181194069..181194144,-!p1@Zbtb46!0.69!24.74!Zbtb46;;chr7:77511403..77511450,-!p3@Nr2f2!0.69!9.11!Nr2f2;;chr2:77654815..77654872,-!p2@Zfp385b!0.69!5.08!Zfp385b;;chr2:169458838..169458859,+!p4@Tshz2!0.68!8.20!Tshz2;;chr8:72676653..72676668,+!p4@2310045N01Rik,p4@Mef2b!0.68!3.78!Mef2b;;chr4:133109285..133109308,+!p1@Nr0b2!0.68!3.78!Nr0b2;;chr11:83664365..83664383,+!p1@Hnf1b!0.68!3.78!Hnf1b;;chr1:38684260..38684312,-!p2@Aff3!0.67!29.43!Aff3;;chr11:85646303..85646329,+!p1@Tbx2!0.67!28.12!Tbx2;;chr2:103143336..103143367,-!p1@Ehf!0.67!6.38!Ehf;;chr15:81633203..81633215,+!p3@Tef!0.67!6.12!Tef;;chr14:65977324..65977372,+!p2@Zfp395!0.66!23.44!Zfp395;;chr6:53018700..53018759,-!p2@Jazf1!0.65!14.45!Jazf1;;chr2:30700788..30700824,+!p2@Prrx2!0.65!5.73!Prrx2;;chr2:152758938..152758954,-!p2@Foxs1!0.65!5.08!Foxs1;;chr15:76701495..76701535,-!p3@Zfp251!0.65!3.52!Zfp251;;chr2:16945819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@Crebzf!0.18!44.14!Crebzf;;chr4:97444471..97444514,+!p1@Nfia!0.18!36.20!Nfia;;chr7:26035739..26035757,-!p1@Erf!0.18!33.07!Erf;;chr12:32635078..32635111,-!p1@Hbp1!0.18!28.38!Hbp1;;chr6:83391606..83391658,-!p1@Tet3!0.18!22.66!Tet3;;chr3:9610090..9610124,-!p1@Zfp704!0.18!17.58!Zfp704;;chr15:101097270..101097290,+!p1@Nr4a1!0.18!13.54!Nr4a1;;chr17:23723181..23723236,-!p1@Zfp13!0.18!12.50!Zfp13;;chr4:136604692..136604722,-!p1@Zbtb40!0.18!12.37!Zbtb40;;chr7:17200422..17200487,-!p3@Grlf1!0.18!8.20!Grlf1;;chrX:98728074..98728116,+!p2@Taf1!0.18!8.20!Taf1;;chr17:35031460..35031518,+!p1@Zbtb12!0.18!6.12!Zbtb12;;chr4:119406389..119406411,+!p1@Hivep3!0.18!5.99!Hivep3;;chr2:92886297..92886329,-!p1@Prdm11!0.18!5.60!Prdm11;;chr15:100325682..100325698,-!p1@Csrnp2!0.18!5.60!Csrnp2;;chr2:72817659..72817725,-!p5@Sp3!0.18!4.95!Sp3;;chr15:102034446..102034506,+!p2@Zfp740!0.18!4.04!Zfp740;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!0.18!3.78!Atf1;;chr7:134489096..134489123,-!p2@Zfp768!0.18!3.52!Zfp768;;chr11:102178937..102178956,-!p5@Ubtf!0.18!3.39!Ubtf;;chr12:77470461..77470504,-!p3@Zbtb25!0.18!3.39!Zbtb25;;chr12:110031207..110031224,+!p5@Yy1!0.18!3.26!Yy1;;chr4:82151148..82151159,-!p5@Nfib!0.18!3.12!Nfib;;chr15:100058289..100058300,+!p3@Atf1!0.18!2.86!Atf1;;chr9:55785981..55786009,-!p2@Scaper!0.18!2.86!Scaper;;chr13:67433461..67433489,-!p2@Zfp595!0.18!2.60!Zfp595;;chr6:72739234..72739256,-!p2@Tcf7l1!0.18!2.34!Tcf7l1;;chr8:72498246..72498263,-!p11@Gatad2a!0.18!2.34!Gatad2a;;chr1:170361826..170361844,-!p9@Pbx1!0.18!2.21!Pbx1;;chr1:95651267..95651284,-!p4@Thap4!0.18!1.69!Thap4;;chr16:43363968..43364001,+!p7@Zbtb20!0.18!1.69!Zbtb20;;chr1:170361777..170361797,-!p10@Pbx1!0.18!1.56!Pbx1;;chr7:4947625..4947634,-!p6@Zfp579!0.18!1.43!Zfp579;;chr5:134741947..134741948,-!p9@Gtf2i!0.18!1.30!Gtf2i;;chr3:51144477..51144506,-!p6@Elf2!0.18!1.30!Elf2;;chr12:32635051..32635062,-!p2@Hbp1!0.18!1.17!Hbp1;;chr11:102177921..102177960,-!p9@Ubtf!0.18!1.17!Ubtf;;chr7:17200615..17200625,-!p9@Grlf1!0.18!1.04!Grlf1;;chr8:87324203..87324206,-!p10@Nfix!0.18!1.04!Nfix;;chr6:92041372..92041383,+!p6@Nr2c2!0.18!0.91!Nr2c2;;chr7:123174606..123174636,-!p5@Sox6!0.18!0.91!Sox6;;chr11:44430877..44430899,+!p6@Ebf1!0.18!0.91!Ebf1;;chr17:48015839..48015915,-!p3@Foxp4!0.18!0.78!Foxp4;;chr7:123182248..123182264,-!p3@Sox6!0.18!0.78!Sox6;;chr6:52167459..52167492,-!p1@Hoxa7!0.18!0.78!Hoxa7;;chr13:40826150..40826167,-!p3@Tfap2a!0.18!0.65!Tfap2a;;chr15:102821007..102821021,+!p2@Hoxc8!0.18!0.52!Hoxc8;;chr13:40826236..40826248,-!p8@Tfap2a!0.18!0.52!Tfap2a;;chr15:102797183..102797205,+!p4@Hoxc10!0.18!0.52!Hoxc10;;chr15:100058744..100058772,+!p4@Gm1862,p6@Atf1!0.18!0.52!Atf1;;chr6:85967211..85967223,+!p1@Figla!0.18!0.52!Figla;;chr5:92391970..92391984,+!p5@Thap6!0.18!0.52!Thap6;;chr6:115372099..115372121,+!p5@Pparg!0.18!0.52!Pparg;;chr6:52184880..52184893,-!p6@Hoxa10!0.18!0.52!Hoxa10;;chr2:9809402..9809422,-!p5@Gata3!0.18!0.52!Gata3;;chr4:53792566..53792578,+!p1@Tal2!0.18!0.52!Tal2;;chr2:17976830..17976848,+!p12@Mllt10!0.18!0.52!Mllt10;;chr2:115874845..115874865,-!p20@Meis2!0.18!0.52!Meis2;;chr19:59533429..59533470,+!p4@Emx2!0.18!0.52!Emx2;;chr10:30522660..30522671,-!p10@Ncoa7!0.18!0.52!Ncoa7;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.18!0.52!Hoxb2;;chr10:5734717..5734727,-!p12@Esr1!0.18!0.52!Esr1;;chr11:96132767..96132796,+!p2@Hoxb9!0.18!0.52!Hoxb9;;chr11:52096305..52096328,-!p11@Tcf7!0.18!0.52!Tcf7;;chr16:43236088..43236099,+!p43@Zbtb20!0.18!0.52!Zbtb20;;chr16:38294860..38294924,-!p1@Nr1i2!0.18!0.52!Nr1i2;;chrX:35419715..35419724,+!p1@Rhox10!0.18!0.52!Rhox10;;
+|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:726-26I4
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011412
+|is_a=EFO:0002091;;FF:0011412
+|is_obsolete=
+|library_id=CNhs11222
+|library_id_phase_based=2:CNhs11222
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;726
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;726
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N07.CNhs11222.726-26I4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N07.CNhs11222.726-26I4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N07.CNhs11222.726-26I4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N07.CNhs11222.726-26I4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N07.CNhs11222.726-26I4.mm9.nobarcode.rdna.fa.gz
 |name=testis, neonate N07
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11222,LSID748,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.136788033622223,0,0.0136629991291724,0,0,0.0560627173528152,0.232577857685053,0,0.0768342020728291,0,0,1.01110859342963,0,0,0,0,0,0,0.144934369366052,0,0,0,0.0531569878936061,0,0,0,0,0,0,0,0,0,0.154777030255665,0,0,0,0.100511416252052,0.0496588369707553,0.149994255851041,0.0531569878936061,-0.100618014465822,0.580170614717067,0.254355930145453,0,0,0,0,0,0,0,0,0,0,0.100511416252052,0.36211359164562,0.116071564980297,0,0,0,0,0,0,0.050255708126026,0,0,0.0531569878936061,0.0603475238357281,0.0980051863337668,-0.104934054877476,0.207232129831538,0.0531569878936061,0.159139908756646,0.0642428078865897,0.0160389288693858,0.100511416252052,0,0.100511416252052,0.0548175493201899,-0.187259037067417,0.138921245536416,0,0,0,0,0,0.0531569878936061,-0.0847931891315178,-0.0629526946036516,-0.134348088096434,0.0531569878936061,0,0.182077112543737,0,0
 |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=HIF1A:2.15170673447;NR6A1:1.77873871563;PITX1..3:1.65265990034;NFIX:1.46779483077;NANOG{mouse}:1.39623771868;MYBL2:1.313888663;NKX3-1:1.29077232615;SP1:1.25124194678;NFY{A,B,C}:1.18085739687;NRF1:1.08940025965;ZNF384:1.07228273805;E2F1..5:0.99323590391;TEF:0.949462055343;XCPE1{core}:0.944086475319;GCM1,2:0.939062440295;ZNF238:0.937546233732;FOXQ1:0.902616654603;ZBTB16:0.88863974494;TFAP2{A,C}:0.884634421496;NR1H4:0.860680989196;GLI1..3:0.855434132633;GFI1B:0.842826149771;RXR{A,B,G}:0.815277329432;FOXP1:0.809824669982;TOPORS:0.782951202331;ZNF143:0.781568237758;GATA4:0.735297216843;CRX:0.722799172591;EGR1..3:0.718882463528;ZIC1..3:0.716812076731;SOX5:0.677507286304;PATZ1:0.674089214718;NR5A1,2:0.671627511376;TFDP1:0.6670837131;bHLH_family:0.649980781363;GFI1:0.642245112645;TEAD1:0.633144665494;TLX1..3_NFIC{dimer}:0.594584167322;EVI1:0.572363498049;ONECUT1,2:0.546367015024;POU1F1:0.531762697075;TFAP2B:0.530755116271;FOXD3:0.518309874416;ELK1,4_GABP{A,B1}:0.492195758572;CDX1,2,4:0.484039234175;MAZ:0.475520590363;FOXP3:0.475346022593;EN1,2:0.470743701481;ZNF423:0.458462683657;MTE{core}:0.441382821581;IKZF2:0.432407185182;PAX5:0.418063731807;GTF2I:0.406505205366;PAX1,9:0.358448227468;FOXA2:0.35132549218;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.347877573966;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.339057487852;BREu{core}:0.336499463392;RBPJ:0.325063340303;PAX4:0.323321706412;IKZF1:0.308152983909;HIC1:0.295152035773;STAT1,3:0.285402873063;TAL1_TCF{3,4,12}:0.279980141353;NFIL3:0.266490786521;NKX2-2,8:0.262493531497;AIRE:0.256992379962;NKX6-1,2:0.256286858027;HNF1A:0.249047033061;EP300:0.228704172599;CEBPA,B_DDIT3:0.2249339903;RREB1:0.213685161275;HMGA1,2:0.210452538167;ZFP161:0.200355556257;SRF:0.195759680547;MED-1{core}:0.187414286724;HSF1,2:0.184740248499;BPTF:0.180490285699;POU6F1:0.163208337758;SOX17:0.100659344037;MZF1:0.0994054100639;KLF4:0.0971337981764;CREB1:0.0941886506662;AR:0.0923364989222;MYB:0.0914992956498;ESRRA:0.0823345986938;TFCP2:0.0748102301469;HBP1_HMGB_SSRP1_UBTF:0.0729426426234;NFATC1..3:0.0598768257867;ADNP_IRX_SIX_ZHX:0.0415454510343;LEF1_TCF7_TCF7L1,2:0.0291610978503;PAX6:0.0187435983437;FOXO1,3,4:-0.00926418833559;ESR1:-0.0140139614717;SOX2:-0.032011186063;FOX{D1,D2}:-0.033803547773;HOX{A5,B5}:-0.036973798771;GZF1:-0.0522214941948;GATA6:-0.0617007213344;HNF4A_NR2F1,2:-0.0996272220196;DBP:-0.104959708434;RFX1:-0.106080017384;TFAP4:-0.109223139699;ATF4:-0.111042620788;CUX2:-0.116828057541;POU2F1..3:-0.116959458537;RORA:-0.140030959224;FOXN1:-0.145519986308;NR3C1:-0.152354400652;MTF1:-0.156775684509;AHR_ARNT_ARNT2:-0.163608007248;MYFfamily:-0.166937328637;IRF1,2:-0.192902013766;STAT2,4,6:-0.192987405629;NKX2-1,4:-0.212905663097;YY1:-0.221756445462;UFEwm:-0.226711348434;T:-0.228842909193;MEF2{A,B,C,D}:-0.24136288696;HOXA9_MEIS1:-0.249469794132;CDC5L:-0.268653353194;REST:-0.277845742204;RFX2..5_RFXANK_RFXAP:-0.283182523108;ZBTB6:-0.299226021312;TBP:-0.325642280826;PRRX1,2:-0.337962646706;SREBF1,2:-0.344882514995;HES1:-0.348590640992;ALX4:-0.35803533851;PRDM1:-0.363364289035;ATF2:-0.375234806617;TLX2:-0.376584027114;FOXL1:-0.3997390886;LMO2:-0.402907695311;OCT4_SOX2{dimer}:-0.419800603802;ELF1,2,4:-0.426247432578;POU5F1:-0.437882933523;HLF:-0.439340212044;RUNX1..3:-0.457256891652;NANOG:-0.460464984356;SPIB:-0.473342023332;FOX{F1,F2,J1}:-0.495312535645;HOX{A4,D4}:-0.505166195524;POU3F1..4:-0.505242648449;SOX{8,9,10}:-0.519013275874;TBX4,5:-0.52349895888;NFKB1_REL_RELA:-0.525430815453;NKX2-3_NKX2-5:-0.538757453132;PBX1:-0.538910847962;GTF2A1,2:-0.539391950964;EBF1:-0.541396805546;STAT5{A,B}:-0.541681556722;BACH2:-0.568573293246;HAND1,2:-0.570196576578;TP53:-0.576450957414;MAFB:-0.577456552918;ARID5B:-0.578958696836;ETS1,2:-0.588803511378;PAX8:-0.618073751894;PAX2:-0.62690196307;NFE2:-0.668335505496;SPI1:-0.677539236156;VSX1,2:-0.693370013934;IRF7:-0.700384998257;FOS_FOS{B,L1}_JUN{B,D}:-0.749619723005;ZNF148:-0.754149404225;DMAP1_NCOR{1,2}_SMARC:-0.795780146875;LHX3,4:-0.817973757847;SNAI1..3:-0.877214100982;SMAD1..7,9:-0.898461126607;FOXM1:-0.900696088;NFE2L2:-0.90168494103;ZEB1:-0.907999500755;NKX3-2:-0.950203168157;NHLH1,2:-0.958750601911;RXRA_VDR{dimer}:-0.985908680772;ATF6:-0.99833092923;SPZ1:-1.00306378054;PDX1:-1.03083477668;JUN:-1.03763847221;HMX1:-1.05039231142;FOX{I1,J2}:-1.09329294729;ATF5_CREB3:-1.12639233912;ALX1:-1.13832848942;TGIF1:-1.14887808803;MYOD1:-1.25805522056;FOSL2:-1.52714823541;PPARG:-1.9996169969;NFE2L1:-2.13816913156
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:726-26I4;search_select_hide=table117:726-26I4
 }}

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FF:726-26I4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs11222

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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