FF:1391-42E2: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	testis, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11130
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	testis
dev stage	30 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		SAMD00005568

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11130		CAGE		DRX009111		DRR009985

Accession ID Mm9

Library id		BAM		CTSS
CNhs11130		DRZ001410		DRZ002793

Accession ID Mm10

Library id		BAM		CTSS
CNhs11130		DRZ012760		DRZ014143

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

CNhs11130

0	1.145
1	0
10	0
100	0
1000	0.456
1001	0.339
1002	0
1003	-0.0132
1004	0
1005	-0.0389
1006	0.27
1007	0.336
1008	0
1009	0.276
101	0.0798
1010	0
1011	0.971
1012	0
1013	-0.174
1014	-0.0874
1015	0.494
1016	-0.261
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.312
1023	0
1024	-0.14
1025	0
1026	1.077
1027	0
1028	0
1029	-0.0661
103	0.0521
1030	0.198
1031	-0.517
1032	-0.232
1033	0
1034	0
1035	0.702
1036	-0.187
1037	0
1038	-0.188
1039	0.18
104	0
1040	-0.269
1041	0.333

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: CNhs11130

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.176
MA0003.1	MA0003.1	0.867
MA0004.1	MA0004.1	0.431
MA0006.1	MA0006.1	0.167
MA0007.1	MA0007.1	0.985
MA0009.1	MA0009.1	0.539
MA0014.1	MA0014.1	0.473
MA0017.1	MA0017.1	0.401
MA0018.2	MA0018.2	8.65971e-12
MA0019.1	MA0019.1	0.0575
MA0024.1	MA0024.1	0.447
MA0025.1	MA0025.1	0.73
MA0027.1	MA0027.1	0.455
MA0028.1	MA0028.1	0.00439
MA0029.1	MA0029.1	0.704
MA0030.1	MA0030.1	0.917
MA0031.1	MA0031.1	0.387
MA0035.2	MA0035.2	0.0216
MA0038.1	MA0038.1	0.912
MA0039.2	MA0039.2	0.118
MA0040.1	MA0040.1	0.402
MA0041.1	MA0041.1	0.206
MA0042.1	MA0042.1	0.976
MA0043.1	MA0043.1	9.71983e-4
MA0046.1	MA0046.1	5.9641e-11
MA0047.2	MA0047.2	0.00666
MA0048.1	MA0048.1	0.0731
MA0050.1	MA0050.1	1.88638e-4
MA0051.1	MA0051.1	0.505
MA0052.1	MA0052.1	0.824
MA0055.1	MA0055.1	6.25948e-5
MA0057.1	MA0057.1	0.546
MA0058.1	MA0058.1	0.397
MA0059.1	MA0059.1	0.0188
MA0060.1	MA0060.1	7.00114e-7
MA0061.1	MA0061.1	0.0124
MA0062.2	MA0062.2	0.00182
MA0065.2	MA0065.2	0.1
MA0066.1	MA0066.1	0.715
MA0067.1	MA0067.1	0.324
MA0068.1	MA0068.1	0.867
MA0069.1	MA0069.1	0.684
MA0070.1	MA0070.1	0.864
MA0071.1	MA0071.1	0.516
MA0072.1	MA0072.1	0.693
MA0073.1	MA0073.1	0.986
MA0074.1	MA0074.1	0.939
MA0076.1	MA0076.1	0.00156
MA0077.1	MA0077.1	4.68677e-4
MA0078.1	MA0078.1	8.22671e-10
MA0079.2	MA0079.2	0.185
MA0080.2	MA0080.2	2.22589e-7
MA0081.1	MA0081.1	0.0567
MA0083.1	MA0083.1	0.482
MA0084.1	MA0084.1	0.621
MA0087.1	MA0087.1	0.133
MA0088.1	MA0088.1	0.0416
MA0090.1	MA0090.1	0.687
MA0091.1	MA0091.1	0.498
MA0092.1	MA0092.1	0.0967
MA0093.1	MA0093.1	0.519
MA0099.2	MA0099.2	0.0721
MA0100.1	MA0100.1	8.59338e-18
MA0101.1	MA0101.1	0.181
MA0102.2	MA0102.2	0.185
MA0103.1	MA0103.1	0.874
MA0104.2	MA0104.2	0.00167
MA0105.1	MA0105.1	0.00694
MA0106.1	MA0106.1	0.0331
MA0107.1	MA0107.1	0.0128
MA0108.2	MA0108.2	0.041
MA0111.1	MA0111.1	0.365
MA0112.2	MA0112.2	0.987
MA0113.1	MA0113.1	0.72
MA0114.1	MA0114.1	0.22
MA0115.1	MA0115.1	0.27
MA0116.1	MA0116.1	0.162
MA0117.1	MA0117.1	0.851
MA0119.1	MA0119.1	0.13
MA0122.1	MA0122.1	0.868
MA0124.1	MA0124.1	0.933
MA0125.1	MA0125.1	0.149
MA0131.1	MA0131.1	0.0471
MA0135.1	MA0135.1	0.12
MA0136.1	MA0136.1	8.90673e-4
MA0137.2	MA0137.2	0.128
MA0138.2	MA0138.2	0.0721
MA0139.1	MA0139.1	0.194
MA0140.1	MA0140.1	5.92681e-4
MA0141.1	MA0141.1	0.387
MA0142.1	MA0142.1	0.948
MA0143.1	MA0143.1	3.43409e-4
MA0144.1	MA0144.1	0.106
MA0145.1	MA0145.1	0.00936
MA0146.1	MA0146.1	0.00207
MA0147.1	MA0147.1	0.00174
MA0148.1	MA0148.1	0.00175
MA0149.1	MA0149.1	0.387
MA0150.1	MA0150.1	0.876
MA0152.1	MA0152.1	0.212
MA0153.1	MA0153.1	2.82563e-5
MA0154.1	MA0154.1	0.0476
MA0155.1	MA0155.1	0.191
MA0156.1	MA0156.1	0.0534
MA0157.1	MA0157.1	0.304
MA0159.1	MA0159.1	0.234
MA0160.1	MA0160.1	2.83736e-4
MA0162.1	MA0162.1	0.928
MA0163.1	MA0163.1	0.0172
MA0164.1	MA0164.1	0.488
MA0258.1	MA0258.1	0.305
MA0259.1	MA0259.1	0.0236

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: CNhs11130

Novel motif	Logo	P-value
1	1	0.585
10	10	0.107
100	100	0.0524
101	101	0.952
102	102	0.182
103	103	0.67
104	104	0.739
105	105	0.399
106	106	4.07231e-4
107	107	5.70932e-4
108	108	0.27
109	109	0.184
11	11	0.412
110	110	0.285
111	111	0.0206
112	112	0.248
113	113	0.405
114	114	0.255
115	115	0.951
116	116	0.895
117	117	0.00499
118	118	0.142
119	119	0.892
12	12	0.836
120	120	0.968
121	121	0.0404
122	122	0.765
123	123	0.33
124	124	0.224
125	125	0.927
126	126	0.167
127	127	0.878
128	128	0.00326
129	129	0.45
13	13	0.085
130	130	0.983
131	131	0.184
132	132	0.699
133	133	0.771
134	134	0.575
135	135	0.0318
136	136	0.00101
137	137	0.543
138	138	0.614
139	139	0.363
14	14	0.31
140	140	0.949
141	141	0.142
142	142	0.713
143	143	0.697
144	144	0.163
145	145	0.267
146	146	0.796
147	147	0.241
148	148	0.0751
149	149	0.0743
15	15	0.701
150	150	0.2
151	151	0.192
152	152	0.431
153	153	0.299
154	154	0.725
155	155	0.225
156	156	0.0352
157	157	0.783
158	158	6.68628e-6
159	159	0.22
160	160	0.161
161	161	0.166
162	162	0.732
163	163	0.366
164	164	0.19
165	165	0.469
166	166	0.602
167	167	0.67
168	168	0.438
169	169	0.515
17	17	0.646
18	18	0.884
19	19	0.762
2	2	6.26518e-4
20	20	0.00436
21	21	0.429
22	22	0.986
23	23	0.416
24	24	0.118
25	25	0.336
26	26	0.886
27	27	0.00867
28	28	0.9
29	29	0.0559
3	3	0.911
30	30	0.246
31	31	0.28
32	32	0.745
33	33	0.268
34	34	0.839
35	35	0.631
36	36	0.187
37	37	0.822
38	38	0.866
39	39	0.52
4	4	0.759
40	40	0.129
41	41	4.24996e-4
42	42	0.8
43	43	0.639
44	44	0.823
45	45	0.366
46	46	0.891
47	47	0.328
48	48	0.379
49	49	0.944
5	5	0.821
50	50	0.886
51	51	0.55
52	52	0.174
53	53	0.267
54	54	0.508
55	55	0.677
56	56	0.233
57	57	0.974
58	58	0.557
59	59	0.222
6	6	0.556
60	60	0.447
61	61	0.649
62	62	0.744
63	63	0.695
64	64	0.661
65	65	0.229
66	66	0.0452
67	67	0.639
68	68	0.319
69	69	0.192
7	7	0.637
70	70	0.374
71	71	0.983
72	72	0.262
73	73	0.523
74	74	0.894
75	75	0.366
76	76	0.0186
77	77	0.671
78	78	0.0079
79	79	0.604
8	8	0.0423
80	80	0.306
81	81	0.2
82	82	0.989
83	83	0.899
84	84	0.627
85	85	0.889
86	86	0.855
87	87	0.0214
88	88	0.78
89	89	0.578
9	9	0.738
90	90	0.591
91	91	0.211
92	92	0.666
93	93	0.237
94	94	0.824
95	95	0.0866
96	96	0.39
97	97	0.256
98	98	0.976
99	99	0.247

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: CNhs11130

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011495 mouse testis- neonate N30 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)
0000310 (mouse neonate N30 sample)
0011495 (mouse testis- neonate N30 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
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+|DRA_sample_Accession=CAGE@SAMD00005568
+|accession_numbers=CAGE;DRX009111;DRR009985;DRZ001410;DRZ002793;DRZ012760;DRZ014143
+|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:0000310,FF:0011495
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr4:107356135..107356179,-!p1@Dmrtb1!3.18!1514.46!Dmrtb1;;chr1:168168856..168168893,-!p1@Mael!3.04!1108.05!Mael;;chr5:38611867..38611888,+!p2@Lyar!2.92!838.46!Lyar;;chr13:93346120..93346155,-!p1@Spz1!2.92!836.15!Spz1;;chr6:131338278..131338362,-!p2@Csda!2.83!1903.59!Csda;;chr3:90046414..90046476,-!p1@Creb3l4!2.76!568.86!Creb3l4;;chr11:69749396..69749433,+!p1@Ybx2!2.72!529.69!Ybx2;;chr1:52065054..52065098,+!p4@Stat4!2.38!236.76!Stat4;;chr4:107356181..107356197,-!p2@Dmrtb1!2.38!236.47!Dmrtb1;;chr10:22451680..22451722,-!p3@Tbpl1!2.37!235.90!Tbpl1;;chr18:52775562..52775650,+!p1@Zfp474!2.37!231.58!Zfp474;;chr6:143895612..143895631,-!p3@Sox5!2.31!201.62!Sox5;;chr16:50331100..50331130,-!p3@Bbx!2.26!179.73!Bbx;;chr18:50438025..50438057,+!p1@Fam170a!2.25!178.58!Fam170a;;chr12:100009228..100009251,+!p2@Zc3h14!2.23!167.63!Zc3h14;;chr18:3309876..3309914,-!p9@Crem!2.20!157.84!Crem;;chr2:17985983..17986035,+!p4@Mllt10!2.18!149.49!Mllt10;;chr10:22451724..22451752,-!p4@Tbpl1!2.17!146.03!Tbpl1;;chr2:180377386..180377462,-!p1@Tcfl5!2.13!158.70!Tcfl5;;chr5:138202908..138202942,+!p10@Tsc22d4!2.13!134.22!Tsc22d4;;chr1:52043967..52043976,+!p5@Stat4!2.11!128.46!Stat4;;chr1:168168817..168168850,-!p2@Mael!2.10!125.01!Mael;;chr18:3299535..3299565,-!p10@Crem!2.10!124.43!Crem;;chr10:70701022..70701036,-!p3@Tfam!2.08!120.11!Tfam;;chr16:50331135..50331178,-!p5@Bbx!2.07!115.50!Bbx;;chr6:143895581..143895604,-!p6@Sox5!2.04!107.72!Sox5;;chr10:84224957..84224991,+!p3@Rfx4!2.03!106.57!Rfx4;;chr5:38611831..38611842,+!p3@Lyar!2.03!105.13!Lyar;;chr1:56694305..56694324,-!p1@Hsfy2!2.01!101.39!Hsfy2;;chr6:52663997..52664043,+!p2@Tax1bp1!1.99!96.49!Tax1bp1;;chr7:19953851..19953902,+!p4@Ppp1r13l!1.91!80.36!Ppp1r13l;;chr6:131338363..131338383,-!p4@Csda!1.90!330.95!Csda;;chr4:149610794..149610876,+!p2@LOC100045967,p2@LOC100503183,p3@Eno1,p3@Gm5506!1.89!102.25!Eno1;;chr11:69749437..69749467,+!p3@Ybx2!1.89!76.33!Ybx2;;chr7:135020660..135020688,+!p3@Zfp646!1.88!102.54!Zfp646;;chr7:25655099..25655143,+!p1@Dmrtc2!1.87!73.45!Dmrtc2;;chr18:3299485..3299513,-!p12@Crem!1.87!72.87!Crem;;chr11:69749367..69749385,+!p4@Ybx2!1.86!71.72!Ybx2;;chr7:29552143..29552173,-!p4@Nfkbib!1.85!70.28!Nfkbib;;chr12:100009260..100009274,+!p3@Zc3h14!1.84!67.98!Zc3h14;;chr10:70698065..70698087,-!p4@Tfam!1.84!67.69!Tfam;;chr7:31383850..31383874,-!p1@Zbtb32!1.82!64.52!Zbtb32;;chr14:55489750..55489784,-!p2@Homez!1.81!64.23!Homez;;chr1:52043983..52043995,+!p6@Stat4!1.80!62.21!Stat4;;chr2:180377307..180377330,-!p2@Tcfl5!1.79!61.35!Tcfl5;;chr11:116196714..116196729,-!p2@Foxj1!1.79!60.49!Foxj1;;chr9:18282807..18282821,+!p1@Mbd3l1!1.78!58.76!Mbd3l1;;chr1:56694274..56694293,-!p2@Hsfy2!1.77!58.18!Hsfy2;;chr11:116196698..116196713,-!p3@Foxj1!1.76!57.03!Foxj1;;chr1:39777834..39777860,-!p1@Rfx8!1.76!56.45!Rfx8;;chr11:87430678..87430702,+!p1@Hsf5!1.75!54.73!Hsf5;;chr3:90046478..90046489,-!p5@Creb3l4!1.75!54.73!Creb3l4;;chr5:38611816..38611827,+!p4@Lyar!1.74!60.49!Lyar;;chr4:118967319..118967330,-!p6@Ybx1!1.74!53.57!Ybx1;;chr3:95032515..95032553,-!p5@Mllt11!1.73!62.79!Mllt11;;chr14:32979060..32979091,+!p4@Gm6768,p4@Ncoa4!1.71!50.12!Ncoa4;;chr8:26950937..26950991,-!p3@Ash2l!1.70!57.89!Ash2l;;chr17:15637108..15637147,+!p3@Tbp!1.69!48.39!Tbp;;chr9:18282826..18282845,+!p2@Mbd3l1!1.69!48.10!Mbd3l1;;chr15:36937522..36937543,-!p4@Gm10193,p4@Zfp706!1.69!47.81!Zfp706;;chr8:26958093..26958148,-!p2@Ash2l!1.66!45.22!Ash2l;;chr2:160685337..160685366,-!p5@Zhx3!1.66!44.36!Zhx3;;chr7:86937900..86937933,-!p@chr7:86937900..86937933,-!1.64!42.63!Mesp1;;chr11:95170996..95171026,-!p3@Myst2!1.64!42.63!Myst2;;chr7:88007115..88007129,+!p2@Zscan2!1.63!41.48!Zscan2;;chr14:32979026..32979042,+!p5@Gm6768,p5@Ncoa4!1.63!41.19!Ncoa4;;chr17:56970481..56970551,-!p2@Rfx2!1.62!122.70!Rfx2;;chr14:69789996..69790021,+!p1@Nkx2-6!1.62!40.61!Nkx2-6;;chr5:134782473..134782486,-!p12@Gtf2i!1.60!38.88!Gtf2i;;chr7:31383882..31383903,-!p2@Zbtb32!1.57!36.58!Zbtb32;;chr10:22451660..22451678,-!p7@Tbpl1!1.57!36.29!Tbpl1;;chrX:83437105..83437121,+!p1@Nr0b1!1.56!35.72!Nr0b1;;chr4:117438155..117438175,-!p1@Klf17,p1@LOC100504967!1.56!35.43!Klf17;;chr12:81214217..81214219,-!p2@Zfp36l1!1.56!35.14!Zfp36l1;;chrX:113562567..113562578,+!p1@Cpxcr1!1.55!34.85!Cpxcr1;;chr1:52065106..52065124,+!p7@Stat4!1.55!34.56!Stat4;;chr15:100410635..100410667,-!p4@Pou6f1!1.54!33.99!Pou6f1;;chr18:3309750..3309787,-!p21@Crem!1.54!33.99!Crem;;chr18:3337503..3337536,-!p7@Crem!1.53!55.88!Crem;;chr8:72356384..72356434,+!p2@Pbx4!1.53!49.54!Pbx4;;chr9:111020746..111020768,+!p5@Lrrfip2!1.53!32.55!Lrrfip2;;chr4:63042249..63042287,-!p10@Akna!1.52!32.26!Akna;;chr11:45793811..45793839,+!p1@Sox30!1.52!31.97!Sox30;;chr2:27565816..27565828,+!p10@Rxra!1.52!31.97!Rxra;;chr13:96094769..96094829,+!p4@Zbed3!1.51!44.64!Zbed3;;chr11:87430653..87430666,+!p2@Hsf5!1.51!31.68!Hsf5;;chr10:22451765..22451795,-!p6@Tbpl1!1.50!45.22!Tbpl1;;chr4:61869708..61869732,-!p5@Zfp37!1.50!30.53!Zfp37;;chr1:56694252..56694259,-!p3@Hsfy2!1.50!30.53!Hsfy2;;chr12:86438030..86438041,-!p@chr12:86438030..86438041,-!1.49!30.24!Prox2;;chr7:25655066..25655080,+!p2@Dmrtc2!1.49!29.96!Dmrtc2;;chr6:52664044..52664072,+!p5@Tax1bp1!1.49!29.67!Tax1bp1;;chr14:32979005..32979017,+!p7@Gm6768,p7@Ncoa4!1.49!29.67!Ncoa4;;chr15:100058744..100058772,+!p4@Gm1862,p6@Atf1!1.48!29.38!Atf1;;chr11:87430728..87430749,+!p3@Hsf5!1.48!29.38!Hsf5;;chr3:95032802..95032830,-!p7@Mllt11!1.48!29.38!Mllt11;;chr4:102815657..102815676,+!p16@Mier1!1.48!29.09!Mier1;;chr2:180377331..180377344,-!p3@Tcfl5!1.48!29.09!Tcfl5;;chr8:72356532..72356611,+!p1@Pbx4!1.47!114.35!Pbx4;;chr11:69749320..69749345,+!p2@Ybx2!1.47!45.80!Ybx2;;chr4:61869757..61869771,-!p6@Zfp37!1.47!28.23!Zfp37;;chr13:78164153..78164174,+!p1@Pou5f2!1.46!27.65!Pou5f2;;chr7:13420092..13420160,+!p2@Zfp110!1.45!50.98!Zfp110;;chr10:84300848..84300879,+!p6@Rfx4!1.45!27.07!Rfx4;;chr11:58717647..58717659,-!p3@Zfp39!1.44!26.79!Zfp39;;chr6:52859625..52859638,-!p3@Jazf1!1.43!25.92!Jazf1;;chr4:61869681..61869704,-!p3@Zfp37!1.43!25.63!Zfp37;;chr14:69790035..69790050,+!p2@Nkx2-6!1.43!25.63!Nkx2-6;;chr8:86590318..86590330,+!p3@Rfx1!1.43!25.63!Rfx1;;chr6:72850124..72850210,-!p7@Kcmf1!1.42!32.84!Kcmf1;;chr11:69749491..69749502,+!p6@Ybx2!1.42!25.35!Ybx2;;chrX:133656674..133656710,-!p4@Esx1!1.40!24.19!Esx1;;chr11:59319921..59319944,-!p5@Zkscan17!1.40!23.91!Zkscan17;;chr7:86938093..86938119,-!p@chr7:86938093..86938119,-!1.39!23.62!Mesp1;;chr2:38570011..38570034,-!p1@Nr5a1!1.38!23.04!Nr5a1;;chr5:136778385..136778407,-!p7@Cux1!1.38!23.04!Cux1;;chr6:52859575..52859603,-!p4@Jazf1!1.37!22.47!Jazf1;;chr9:63864838..63864856,-!p14@Smad6!1.37!22.47!Smad6;;chr6:83303212..83303243,+!p5@Bola3!1.37!22.18!Bola3;;chr11:87430713..87430724,+!p4@Hsf5!1.37!22.18!Hsf5;;chr8:107033774..107033794,-!p1@Ccdc79!1.36!26.79!Ccdc79;;chr16:55966407..55966447,+!p6@Rpl24,p6@Zbtb11!1.35!51.27!Zbtb11;;chr10:85379907..85379936,-!p7@Prdm4!1.35!21.60!Prdm4;;chr13:83643159..83643226,+!p3@Mef2c!1.35!21.31!Mef2c;;chr16:3872255..3872283,-!p4@Zfp597!1.34!29.96!Zfp597;;chr2:74543397..74543435,+!p2@Hoxd8!1.34!21.03!Hoxd8;;chr2:144157107..144157128,-!p3@Ovol2!1.34!20.74!Ovol2;;chr10:75384163..75384185,-!p3@Smarcb1!1.33!20.16!Smarcb1;;chr11:58717675..58717719,-!p1@Zfp39!1.32!136.53!Zfp39;;chr11:69749299..69749319,+!p5@Ybx2!1.31!23.62!Ybx2;;chr9:111020795..111020816,+!p3@Lrrfip2!1.31!20.74!Lrrfip2;;chr18:48204983..48205002,+!p5@LOC100045967,p5@LOC100503183,p6@Eno1,p7@Gm5506!1.31!19.59!Eno1;;chr10:102491694..102491714,-!p3@Alx1!1.31!19.30!Alx1;;chr8:86590801..86590818,+!p2@Rfx1!1.31!19.30!Rfx1;;chr10:76424613..76424689,-!p1@Pcbp3!1.30!389.99!Pcbp3;;chr13:44829403..44829438,+!p11@Jarid2!1.30!22.18!Jarid2;;chr2:17986043..17986056,+!p17@Mllt10!1.30!19.01!Mllt10;;chr5:38611720..38611799,+!p1@Lyar!1.29!479.57!Lyar;;chr5:125342568..125342602,+!p2@Zfp664!1.29!30.24!Zfp664;;chr2:144157091..144157103,-!p4@Ovol2!1.29!18.43!Ovol2;;chr8:74842792..74842814,+!p2@Klf2!1.29!18.43!Klf2;;chr8:86590283..86590297,+!p5@Rfx1!1.29!18.43!Rfx1;;chr2:38781916..38781974,-!p1@Nr6a1!1.28!54.44!Nr6a1;;chr11:69749347..69749356,+!p8@Ybx2!1.28!17.86!Ybx2;;chr4:89354729..89354776,+!p1@Dmrta1!1.28!17.86!Dmrta1;;chr3:51144477..51144506,-!p6@Elf2!1.27!26.79!Elf2;;chr4:61869733..61869751,-!p8@Zfp37!1.27!17.57!Zfp37;;chr12:113917774..113917792,+!p5@Zbtb42!1.27!17.57!Zbtb42;;chr10:84300905..84300919,+!p7@Rfx4!1.27!17.57!Rfx4;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!1.26!56.74!Atf1;;chr18:3337465..3337498,-!p6@Crem!1.26!33.12!Crem;;chr13:21454766..21454791,+!p3@Zscan12!1.26!19.59!Zscan12;;chr1:39777805..39777820,-!p2@Rfx8!1.26!17.28!Rfx8;;chr11:62271076..62271096,-!p19@Ncor1!1.26!17.28!Ncor1;;chrX:133654667..133654672,-!p1@Esx1!1.26!16.99!Esx1;;chr8:26950912..26950933,-!p4@Ash2l!1.26!16.99!Ash2l;;chr17:3557785..3557797,-!p3@Tfb1m!1.25!31.97!Tfb1m;;chr16:3872378..3872411,-!p6@Zfp597!1.25!19.01!Zfp597;;chr17:3557813..3557824,-!p4@Tfb1m!1.25!16.71!Tfb1m;;chr3:130815455..130815467,+!p10@Lef1!1.25!16.71!Lef1;;chr10:77518072..77518110,+!p2@Dnmt3l!1.23!16.13!Dnmt3l;;chr7:31421533..31421548,-!p1@Etv2!1.23!15.84!Etv2;;chr3:130815433..130815454,+!p15@Lef1!1.23!15.84!Lef1;;chr17:68663935..68663949,+!p@chr17:68663935..68663949,+!1.23!15.84!L3mbtl4;;chr1:56694299..56694304,-!p4@Hsfy2!1.23!15.84!Hsfy2;;chr18:5334765..5334833,-!p2@Zfp438!1.22!41.76!Zfp438;;chr7:135020644..135020659,+!p6@Zfp646!1.22!15.55!Zfp646;;chr15:10400245..10400282,-!p2@Dnajc21!1.21!50.69!Dnajc21;;chr11:100683839..100683890,-!p2@Stat5b!1.21!35.72!Stat5b;;chr11:116196664..116196679,-!p1@Foxj1!1.21!23.33!Foxj1;;chr3:103772552..103772584,+!p2@Phtf1!1.21!23.33!Phtf1;;chr1:9690424..9690467,-!p1@Mybl1!1.20!30.82!Mybl1;;chr13:112476407..112476418,+!p6@Mier3!1.20!14.98!Mier3;;chrX:131559846..131559883,-!p3@Zmat1!1.20!14.98!Zmat1;;chr11:45793757..45793775,+!p2@Sox30!1.20!14.98!Sox30;;chr2:180377022..180377040,-!p4@Tcfl5!1.20!14.69!Tcfl5;;chr8:26958153..26958170,-!p5@Ash2l!1.19!14.40!Ash2l;;chr3:51144465..51144476,-!p12@Elf2!1.19!14.40!Elf2;;chr3:51144446..51144456,-!p11@Elf2!1.19!14.40!Elf2;;chr8:72356661..72356680,+!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f9!0.24!1.15!Klf9;;chr16:43364215..43364252,+!p14@Zbtb20!0.24!1.15!Zbtb20;;chr4:141000572..141000629,+!p1@Zbtb17!0.23!28.51!Zbtb17;;chr19:26679654..26679675,+!p1@Smarca2!0.23!13.83!Smarca2;;chr4:133801453..133801492,-!p1@Zfp593!0.23!12.10!Zfp593;;chr7:50835064..50835134,+!p1@Zfp719!0.23!11.52!Zfp719;;chr1:138521528..138521572,+!p1@Zfp281!0.23!8.35!Zfp281;;chr11:23670953..23671028,-!p1@Rel!0.23!8.06!Rel;;chr7:26067619..26067702,+!p2@Cic!0.23!8.06!Cic;;chr10:41996550..41996569,-!p2@Foxo3!0.23!6.34!Foxo3;;chr7:17200019..17200060,-!p4@Grlf1!0.23!6.05!Grlf1;;chr18:11052456..11052477,+!p3@Gata6!0.23!4.03!Gata6;;chr8:72520225..72520248,-!p9@Gatad2a!0.23!3.46!Gatad2a;;chr7:13063643..13063662,+!p2@Zfp606!0.23!3.17!Zfp606;;chr19:55816278..55816287,+!p10@Tcf7l2!0.23!2.30!Tcf7l2;;chr12:32635051..32635062,-!p2@Hbp1!0.23!1.44!Hbp1;;chr16:98073382..98073395,-!p4@Prdm15!0.23!1.15!Prdm15;;chr7:19608891..19608895,-!p1@Foxa3!0.23!1.15!Foxa3;;chr5:107125549..107125605,-!p1@Zfp644!0.22!25.63!Zfp644;;chr14:76814539..76814600,+!p2@Tsc22d1!0.22!20.74!Tsc22d1;;chr2:28915759..28915807,+!p1@Ttf1!0.22!20.16!Ttf1;;chr3:94819338..94819384,-!p1@Zfp687!0.22!13.54!Zfp687;;chr9:57684520..57684612,-!p1@Arid3b!0.22!12.67!Arid3b;;chr2:44965593..44965624,-!p3@Zeb2!0.22!7.78!Zeb2;;chr5:104121453..104121479,+!p4@Aff1!0.22!6.05!Aff1;;chr17:87153462..87153473,+!p3@Epas1!0.22!4.90!Epas1;;chr17:24592183..24592202,-!p2@E4f1!0.22!4.61!E4f1;;chr2:163028808..163028869,+!p1@Tox2!0.22!4.61!Tox2;;chr9:65675474..65675503,-!p3@Zfp609!0.22!3.74!Zfp609;;chr7:148008023..148008092,-!p1@Zfp941!0.22!2.88!Zfp941;;chr14:55711114..55711159,-!p2@Zfhx2!0.22!2.59!Zfhx2;;chr8:109868335..109868338,+!p3@Nfat5!0.22!1.44!Nfat5;;chr6:134780337..134780355,+!p3@Crebl2!0.22!1.15!Crebl2;;chr1:120950269..120950287,-!p6@Gli2!0.22!1.15!Gli2;;chr15:102865088..102865107,+!p1@Hoxc4!0.22!1.15!Hoxc4;;chr5:34530319..34530398,-!p1@Mxd4!0.21!70.86!Mxd4;;chr19:53384985..53385042,+!p1@Mxi1!0.21!44.64!Mxi1;;chr10:80889867..80889924,-!p1@Nfic!0.21!40.61!Nfic;;chr15:76701830..76701883,-!p1@Zfp251!0.21!19.30!Zfp251;;chr19:5637708..5637730,+!p3@Rela!0.21!14.11!Rela;;chr12:110031207..110031224,+!p5@Yy1!0.21!3.46!Yy1;;chrX:92906980..92907024,+!p2@Zc3h12b!0.21!2.88!Zc3h12b;;chr16:42907554..42907591,+!p5@Zbtb20!0.21!2.88!Zbtb20;;chr4:97439519..97439539,+!p11@Nfia!0.21!2.30!Nfia;;chr11:58717721..58717738,-!p2@Zfp39!0.21!2.02!Zfp39;;chr17:51951634..51951651,-!p6@Satb1!0.21!2.02!Satb1;;chr18:24113207..24113218,+!p3@Zfp397!0.21!1.44!Zfp397;;chr12:3891810..3891829,+!p2@Dnmt3a!0.21!1.44!Dnmt3a;;chr8:124984566..124984595,-!p1@Snai3!0.21!1.44!Snai3;;chr1:135551736..135551746,-!p3@Zc3h11a!0.21!1.44!Zc3h11a;;chr19:23215554..23215567,+!p5@Klf9!0.21!1.15!Klf9;;chr18:5334737..5334749,-!p5@Zfp438!0.21!0.86!Zfp438;;chr1:36364572..36364580,+!p2@Arid5a!0.21!0.86!Arid5a;;chr8:90328310..90328362,-!p3@Zfp423!0.21!0.86!Zfp423;;chr7:52253119..52253130,+!p4@Irf3!0.21!0.86!Irf3;;chr10:67599450..67599456,-!p8@Arid5b!0.21!0.86!Arid5b;;chr12:117285924..117286018,+!p1@Zfp386!0.20!40.61!Zfp386;;chr19:5637736..5637766,+!p1@Rela!0.20!37.73!Rela;;chr7:4966247..4966286,-!p1@Fiz1!0.20!27.65!Fiz1;;chr7:26006436..26006488,+!p1@Zfp526!0.20!15.84!Zfp526;;chr10:127176572..127176648,+!p1@Zbtb39!0.20!8.35!Zbtb39;;chr19:5637528..5637548,+!p2@Rela!0.20!7.78!Rela;;chr11:50872733..50872809,+!p1@Zfp354a!0.20!5.76!Zfp354a;;chr13:58503894..58503895,-!p4@Hnrnpk!0.20!4.03!Hnrnpk;;chr19:26681226..26681299,+!p7@Smarca2!0.20!2.59!Smarca2;;chr17:37140628..37140631,+!p2@Zfp57!0.20!2.02!Zfp57;;chr6:47545052..47545064,-!p2@Ezh2!0.20!2.02!Ezh2;;chr13:58501849..58501853,-!p5@Hnrnpk!0.20!1.73!Hnrnpk;;chr17:87153505..87153516,+!p6@Epas1!0.20!1.15!Epas1;;chr7:30088977..30089002,+!p2@Dpf1!0.20!1.15!Dpf1;;chr9:96159427..96159432,+!p11@Tfdp2!0.20!0.86!Tfdp2;;chr15:103164702..103164778,-!p3@Zfp385a!0.20!0.86!Zfp385a;;chr10:88996295..88996335,-!p3@Nr1h4!0.20!0.86!Nr1h4;;chr11:98636568..98636574,-!p9@Nr1d1!0.20!0.86!Nr1d1;;chr19:23215446..23215457,+!p8@Klf9!0.20!0.86!Klf9;;chr17:44951539..44951544,-!p28@Runx2!0.20!0.58!Runx2;;chr17:34784066..34784067,+!p5@Atf6b!0.20!0.58!Atf6b;;chr16:43364258..43364270,+!p27@Zbtb20!0.20!0.58!Zbtb20;;chr15:81494404..81494415,+!p2@L3mbtl2!0.20!0.58!L3mbtl2;;chr16:25865862..25865871,+!p8@Trp63!0.20!0.58!Trp63;;chr16:25801993..25802014,+!p1@Trp63!0.20!0.58!Trp63;;chr16:43364103..43364130,+!p30@Zbtb20!0.20!0.58!Zbtb20;;chr16:43364036..43364047,+!p28@Zbtb20!0.20!0.58!Zbtb20;;chr19:46222739..46222745,-!p2@Pitx3!0.20!0.58!Pitx3;;chr14:69808725..69808748,+!p1@Nkx3-1!0.20!0.58!Nkx3-1;;chr15:102797288..102797302,+!p1@Hoxc10!0.20!0.58!Hoxc10;;chr12:37835248..37835260,+!p4@Meox2!0.20!0.58!Meox2;;
+|ffid_belonging_in_development=UBERON:0009117,UBERON:0002532,UBERON:0006603,UBERON:0005564,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011495
 |is_obsolete=
+|library_id=CNhs11130
+|library_id_phase_based=2:CNhs11130
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1391
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1391
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N30.CNhs11130.1391-42E2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N30.CNhs11130.1391-42E2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N30.CNhs11130.1391-42E2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N30.CNhs11130.1391-42E2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/testis%252c%2520neonate%2520N30.CNhs11130.1391-42E2.mm9.nobarcode.rdna.fa.gz
 |name=testis, neonate N30
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11130,LSID735,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.152671284699399,0,0.0979869192257792,0,0,0,0.305097487688664,0,0.0218561474315863,0,0,0.303077289121669,0,0,0,0,0.89438918450275,0,0.195523178635636,1.10752303252632,0.504660850804005,0,0,0,0,0,0,0.970944906348099,0,0.701776887229741,0.00106806571448121,0,-0.0393512014266878,0,1.54032335122267,1.28856041956842,0,0,0.220343370409231,-0.069692989129467,-0.25338545435266,-0.504749784688184,-0.269868638010351,0,0,0,0.109925980570702,0,0,0,1.80081657908472,0,0,0.270466881039779,0.332866488534905,0.0439204330072621,0,0,0.109925980570702,0,-0.031778720024513,0,0.183802220283236,0,0.197572750341488,0.0294203382206404,0.154201462579013,0.168810924450256,0.0394817075704053,0.126555283854059,0.109925980570702,0,-0.0526799078233515,-0.00528504046963496,0.197572750341488,0,0,0.100412749325846,-0.208498351222359,0.031094385730795,0,1.30124666352267,0,0.414100901966413,0,0,-0.079312591815807,-0.0770705969106933,-0.116053636775304,0.03013587364168,0,0,0,0
 |rna_box=42
 |rna_catalog_number=
@@ Line 56: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=42E2
+|rna_tube_id=4.20E+03
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1391-42E2;search_select_hide=table117:1391-42E2
 }}

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FF:1391-42E2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11130

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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