FF:633-15C6: Difference between revisions

Latest revision as of 19:18, 4 June 2020

Name:	eyeball, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	CNhs11207
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	eyeball
dev stage	0 day neonate
sex	mixture
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		SAMD00005813

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11207		CAGE		DRX008959		DRR009833

Accession ID Mm9

Library id		BAM		CTSS
CNhs11207		DRZ001258		DRZ002641

Accession ID Mm10

Library id		BAM		CTSS
CNhs11207		DRZ012608		DRZ013991

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

CNhs11207

0	0
1	0.169
10	0
100	0.149
1000	0.00486
1001	0.117
1002	0.262
1003	0.0222
1004	0.205
1005	-0.0101
1006	0.172
1007	0.143
1008	0
1009	0.0934
101	0.0287
1010	0
1011	0.0617
1012	0.127
1013	-0.105
1014	0.445
1015	0.19
1016	0.301
1017	0
1018	0.0807
1019	0
102	0
1020	0
1021	0.0558
1022	0.0103
1023	0
1024	0.0286
1025	-0.0611
1026	0.0286
1027	0.853
1028	0
1029	0.266
103	0.463
1030	0
1031	0.322
1032	0.0231
1033	0
1034	0
1035	0.0286
1036	0
1037	0
1038	0.0953
1039	-0.174
104	0
1040	0.0792
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: CNhs11207

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	6.99963e-5
MA0003.1	MA0003.1	0.254
MA0004.1	MA0004.1	0.371
MA0006.1	MA0006.1	0.347
MA0007.1	MA0007.1	0.292
MA0009.1	MA0009.1	0.355
MA0014.1	MA0014.1	0.138
MA0017.1	MA0017.1	1.94821e-7
MA0018.2	MA0018.2	0.464
MA0019.1	MA0019.1	0.571
MA0024.1	MA0024.1	0.0065
MA0025.1	MA0025.1	0.0959
MA0027.1	MA0027.1	0.331
MA0028.1	MA0028.1	0.173
MA0029.1	MA0029.1	0.447
MA0030.1	MA0030.1	0.843
MA0031.1	MA0031.1	0.448
MA0035.2	MA0035.2	8.95112e-4
MA0038.1	MA0038.1	0.00621
MA0039.2	MA0039.2	0.0475
MA0040.1	MA0040.1	0.0938
MA0041.1	MA0041.1	0.413
MA0042.1	MA0042.1	0.926
MA0043.1	MA0043.1	0.685
MA0046.1	MA0046.1	6.03816e-23
MA0047.2	MA0047.2	4.00589e-4
MA0048.1	MA0048.1	0.505
MA0050.1	MA0050.1	8.93772e-4
MA0051.1	MA0051.1	0.00624
MA0052.1	MA0052.1	0.733
MA0055.1	MA0055.1	0.641
MA0057.1	MA0057.1	0.129
MA0058.1	MA0058.1	0.349
MA0059.1	MA0059.1	0.245
MA0060.1	MA0060.1	7.96768e-8
MA0061.1	MA0061.1	0.0277
MA0062.2	MA0062.2	0.0028
MA0065.2	MA0065.2	7.51832e-7
MA0066.1	MA0066.1	0.233
MA0067.1	MA0067.1	0.954
MA0068.1	MA0068.1	0.387
MA0069.1	MA0069.1	0.0278
MA0070.1	MA0070.1	0.708
MA0071.1	MA0071.1	0.6
MA0072.1	MA0072.1	0.262
MA0073.1	MA0073.1	0.334
MA0074.1	MA0074.1	0.301
MA0076.1	MA0076.1	0.468
MA0077.1	MA0077.1	0.00755
MA0078.1	MA0078.1	0.833
MA0079.2	MA0079.2	0.528
MA0080.2	MA0080.2	5.42327e-12
MA0081.1	MA0081.1	0.0482
MA0083.1	MA0083.1	0.93
MA0084.1	MA0084.1	0.0734
MA0087.1	MA0087.1	0.185
MA0088.1	MA0088.1	0.0496
MA0090.1	MA0090.1	0.937
MA0091.1	MA0091.1	0.218
MA0092.1	MA0092.1	0.494
MA0093.1	MA0093.1	0.397
MA0099.2	MA0099.2	4.1374e-5
MA0100.1	MA0100.1	0.846
MA0101.1	MA0101.1	0.0657
MA0102.2	MA0102.2	0.489
MA0103.1	MA0103.1	0.00446
MA0104.2	MA0104.2	0.716
MA0105.1	MA0105.1	0.00128
MA0106.1	MA0106.1	0.311
MA0107.1	MA0107.1	0.0786
MA0108.2	MA0108.2	0.0171
MA0111.1	MA0111.1	0.71
MA0112.2	MA0112.2	2.53449e-4
MA0113.1	MA0113.1	0.31
MA0114.1	MA0114.1	3.21659e-6
MA0115.1	MA0115.1	1.91301e-5
MA0116.1	MA0116.1	0.0073
MA0117.1	MA0117.1	0.605
MA0119.1	MA0119.1	0.0498
MA0122.1	MA0122.1	0.894
MA0124.1	MA0124.1	0.522
MA0125.1	MA0125.1	0.00316
MA0131.1	MA0131.1	0.668
MA0135.1	MA0135.1	0.71
MA0136.1	MA0136.1	6.93397e-16
MA0137.2	MA0137.2	0.0111
MA0138.2	MA0138.2	0.856
MA0139.1	MA0139.1	0.0642
MA0140.1	MA0140.1	3.94882e-4
MA0141.1	MA0141.1	1.21139e-4
MA0142.1	MA0142.1	0.567
MA0143.1	MA0143.1	0.123
MA0144.1	MA0144.1	0.0308
MA0145.1	MA0145.1	0.0615
MA0146.1	MA0146.1	0.0587
MA0147.1	MA0147.1	0.5
MA0148.1	MA0148.1	3.90158e-4
MA0149.1	MA0149.1	0.0075
MA0150.1	MA0150.1	0.0348
MA0152.1	MA0152.1	0.335
MA0153.1	MA0153.1	8.08266e-26
MA0154.1	MA0154.1	0.00543
MA0155.1	MA0155.1	0.712
MA0156.1	MA0156.1	7.1723e-7
MA0157.1	MA0157.1	0.216
MA0159.1	MA0159.1	0.00685
MA0160.1	MA0160.1	0.00283
MA0162.1	MA0162.1	0.386
MA0163.1	MA0163.1	4.71896e-4
MA0164.1	MA0164.1	0.993
MA0258.1	MA0258.1	0.00832
MA0259.1	MA0259.1	0.802

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: CNhs11207

Novel motif	Logo	P-value
1	1	0.08
10	10	0.105
100	100	0.786
101	101	0.644
102	102	0.779
103	103	0.0248
104	104	0.712
105	105	0.536
106	106	0.11
107	107	0.373
108	108	0.938
109	109	0.00856
11	11	0.0357
110	110	0.095
111	111	0.00114
112	112	0.00508
113	113	0.99
114	114	0.0321
115	115	0.88
116	116	0.177
117	117	0.0189
118	118	0.455
119	119	0.0543
12	12	0.445
120	120	0.318
121	121	0.515
122	122	0.888
123	123	0.666
124	124	0.588
125	125	0.0804
126	126	0.183
127	127	0.0968
128	128	0.179
129	129	0.409
13	13	0.00515
130	130	0.943
131	131	0.225
132	132	0.615
133	133	0.741
134	134	0.527
135	135	0.284
136	136	0.168
137	137	0.794
138	138	0.338
139	139	0.0292
14	14	0.9
140	140	0.191
141	141	0.0281
142	142	0.764
143	143	0.184
144	144	0.709
145	145	0.0721
146	146	0.385
147	147	0.498
148	148	0.283
149	149	0.231
15	15	0.0462
150	150	0.376
151	151	0.343
152	152	0.0788
153	153	0.608
154	154	0.973
155	155	0.296
156	156	0.941
157	157	0.924
158	158	0.353
159	159	0.748
160	160	0.404
161	161	0.143
162	162	0.979
163	163	0.577
164	164	0.0111
165	165	0.0154
166	166	0.593
167	167	0.739
168	168	0.694
169	169	0.00352
17	17	0.0459
18	18	0.467
19	19	0.296
2	2	0.717
20	20	0.499
21	21	0.307
22	22	0.256
23	23	0.351
24	24	0.0687
25	25	0.403
26	26	0.0257
27	27	0.473
28	28	0.317
29	29	0.0445
3	3	0.0557
30	30	0.84
31	31	0.52
32	32	0.282
33	33	0.235
34	34	0.768
35	35	0.523
36	36	0.074
37	37	0.0229
38	38	0.238
39	39	0.544
4	4	0.699
40	40	0.151
41	41	0.253
42	42	0.212
43	43	0.157
44	44	0.0533
45	45	0.537
46	46	0.142
47	47	0.0627
48	48	0.0637
49	49	0.156
5	5	0.0988
50	50	0.746
51	51	0.578
52	52	0.485
53	53	0.964
54	54	0.65
55	55	0.353
56	56	0.26
57	57	0.55
58	58	0.214
59	59	0.0337
6	6	0.47
60	60	0.0749
61	61	0.298
62	62	0.0845
63	63	0.0905
64	64	0.4
65	65	0.117
66	66	0.842
67	67	0.983
68	68	0.104
69	69	0.804
7	7	0.0906
70	70	0.00462
71	71	0.0181
72	72	0.164
73	73	0.0288
74	74	0.566
75	75	0.0272
76	76	0.564
77	77	0.135
78	78	0.0384
79	79	0.201
8	8	0.0353
80	80	0.256
81	81	0.295
82	82	0.0104
83	83	0.414
84	84	0.445
85	85	0.0333
86	86	0.167
87	87	0.0656
88	88	0.6
89	89	0.0843
9	9	0.627
90	90	0.0885
91	91	0.855
92	92	0.108
93	93	0.277
94	94	0.393
95	95	0.0459
96	96	0.413
97	97	0.823
98	98	0.439
99	99	0.518

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: CNhs11207

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011264 mouse eyeball- 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)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

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)
0011264 (mouse eyeball- 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005813
+|accession_numbers=CAGE;DRX008959;DRR009833;DRZ001258;DRZ002641;DRZ012608;DRZ013991
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000970,UBERON:0000019,UBERON:0000033,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0000047,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0001032,UBERON:0010317,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0002104,UBERON:0004456,UBERON:0001456
 |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=chr19:19185671..19185693,-!p1@Rorb!2.57!848.14!Rorb;;chr2:79296783..79296801,-!p1@Neurod1!2.32!205.81!Neurod1;;chr18:66098702..66098742,-!p1@Rax!2.22!165.40!Rax;;chr7:16465229..16465249,-!p1@Crx!2.20!155.87!Crx;;chr10:86956396..86956411,-!p1@Ascl1!2.06!172.00!Ascl1;;chr4:154335024..154335039,+!p1@Hes5!2.06!135.05!Hes5;;chr10:129717274..129717298,-!p1@Neurod4!2.05!111.72!Neurod4;;chr10:76285563..76285576,-!p2@Pcbp3!1.95!87.15!Pcbp3;;chr2:105509045..105509071,+!p1@Pax6!1.93!84.91!Pax6;;chr2:105522662..105522687,+!p2@Pax6!1.91!80.22!Pax6;;chr14:49287186..49287225,-!p1@Otx2!1.89!77.15!Otx2;;chr17:86020115..86020128,+!p2@Six3!1.81!64.16!Six3;;chr3:127336052..127336058,+!p1@Neurog2!1.78!58.99!Neurog2;;chr14:49284773..49284790,-!p2@Otx2!1.78!58.78!Otx2;;chr2:38206744..38206766,+!p1@Lhx2!1.76!67.02!Lhx2;;chr1:19199236..19199258,+!p1@Tfap2b!1.76!56.20!Tfap2b;;chr17:86020156..86020183,+!p1@Six3!1.74!54.57!Six3;;chr12:85910771..85910785,+!p1@Vsx2!1.72!51.57!Vsx2;;chr2:38206580..38206600,+!p2@Lhx2!1.64!51.84!Lhx2;;chr9:59797875..59797929,-!p1@Nr2e3!1.60!38.85!Nr2e3;;chr12:74040861..74040875,+!p1@Six6!1.58!37.15!Six6;;chr17:86020510..86020589,+!p3@Six3!1.56!35.52!Six3;;chr3:101814061..101814094,+!p1@Nhlh2!1.53!32.86!Nhlh2;;chr4:21612929..21612952,-!p1@Prdm13!1.51!31.02!Prdm13;;chr3:34548909..34548927,+!p1@Sox2!1.50!50.42!Sox2;;chr4:150503457..150503498,-!p3@Camta1!1.48!32.93!Camta1;;chr2:146047829..146047847,+!p1@Insm1!1.47!50.96!Insm1;;chr12:74040895..74040916,+!p2@Six6!1.47!28.30!Six6;;chr17:25707623..25707639,-!p1@Sox8!1.44!110.90!Sox8;;chr19:19185697..19185711,-!p2@Rorb!1.43!33.13!Rorb;;chr2:163028808..163028869,+!p1@Tox2!1.41!86.81!Tox2;;chr14:104867201..104867258,-!p1@Pou4f1!1.41!34.02!Pou4f1;;chr10:62562530..62562540,+!p1@Atoh7!1.41!24.43!Atoh7;;chr13:40826150..40826167,-!p3@Tfap2a!1.38!25.45!Tfap2a;;chr5:35731493..35731531,+!p1@Hmx1!1.34!20.68!Hmx1;;chr10:20880731..20880775,-!p2@Myb!1.33!42.05!Myb;;chr17:86012772..86012825,+!p4@Six3!1.33!20.34!Six3;;chr10:42303385..42303401,-!p1@Nr2e1!1.33!20.27!Nr2e1;;chr6:83661226..83661282,+!p1@Vax2!1.31!19.59!Vax2;;chr10:129717308..129717319,-!p2@Neurod4!1.30!18.91!Neurod4;;chr2:105515793..105515808,+!p3@Pax6!1.29!18.71!Pax6;;chr2:19367259..19367278,+!p1@Ptf1a!1.28!18.10!Ptf1a;;chr1:140739014..140739032,-!p1@Lhx9!1.27!22.45!Lhx9;;chr8:12395603..12395621,+!p1@Sox1!1.26!17.21!Sox1;;chr16:91225808..91225824,+!p1@Olig2!1.24!16.19!Olig2;;chr14:34791937..34791977,-!p1@Zfp488!1.24!16.19!Zfp488;;chr10:20880698..20880717,-!p3@Myb!1.23!25.17!Myb;;chr13:40829137..40829205,-!p1@Tfap2a!1.22!17.55!Tfap2a;;chr14:49282415..49282426,-!p4@Otx2!1.21!15.10!Otx2;;chr14:122874619..122874634,+!p1@Zic2!1.21!15.10!Zic2;;chr5:106887474..106887489,-!p1@Barhl2!1.20!14.70!Barhl2;;chr10:20880629..20880683,-!p1@Myb!1.19!41.57!Myb;;chr2:151907546..151907561,+!p1@Scrt2!1.19!14.49!Scrt2;;chr17:86020137..86020149,+!p5@Six3!1.19!14.49!Six3;;chrX:58146612..58146615,-!p1@Sox3!1.19!14.42!Sox3;;chr14:49287107..49287125,-!p3@Otx2!1.18!14.15!Otx2;;chr10:12810631..12810649,+!p1@Plagl1!1.12!313.99!Plagl1;;chr10:44178375..44178390,-!p2@Prdm1!1.11!16.26!Prdm1;;chr15:103164702..103164778,-!p3@Zfp385a!1.11!14.08!Zfp385a;;chr2:105515586..105515606,+!p4@Pax6!1.11!11.97!Pax6;;chr5:98609885..98609900,+!p1@Prdm8!1.11!11.77!Prdm8;;chr4:148178559..148178603,+!p1@Casz1!1.10!33.20!Casz1;;chr1:19202352..19202354,+!p2@Tfap2b!1.10!11.63!Tfap2b;;chr13:40825465..40825469,-!p2@Tfap2a!1.10!11.50!Tfap2a;;chr13:117099847..117099907,-!p1@Isl1!1.09!20.75!Isl1;;chr7:38554763..38554780,-!p1@Zfp536!1.09!20.75!Zfp536;;chr9:74709695..74709722,+!p1@Onecut1!1.09!11.36!Onecut1;;chr4:97248607..97248649,+!p15@Nfia!1.09!11.23!Nfia;;chr10:44178521..44178557,-!p1@Prdm1!1.08!19.93!Prdm1;;chr5:114723781..114723795,-!p1@Foxn4!1.08!11.16!Foxn4;;chr1:19199119..19199134,+!p4@Tfap2b!1.08!11.02!Tfap2b;;chr4:114598669..114598674,-!p1@Foxe3!1.07!10.82!Foxe3;;chr18:66098673..66098684,-!p2@Rax!1.05!10.34!Rax;;chr9:55388997..55389016,+!p1@Isl2!1.05!10.34!Isl2;;chr2:65683890..65683907,+!p1@Csrnp3!1.04!19.05!Csrnp3;;chr17:48015645..48015689,-!p9@Foxp4!1.04!13.06!Foxp4;;chr10:42303452..42303470,-!p2@Nr2e1!1.04!10.07!Nr2e1;;chr14:56143046..56143060,-!p1@Nrl!1.04!9.93!Nrl;;chr2:105515635..105515661,+!p5@Pax6!1.04!9.87!Pax6;;chr11:85646303..85646329,+!p1@Tbx2!1.03!64.57!Tbx2;;chr11:101755669..101755686,-!p1@Meox1!1.03!17.83!Meox1;;chr3:128916868..128916890,+!p1@Pitx2!1.03!13.61!Pitx2;;chr1:9690398..9690410,-!p2@Mybl1!1.03!11.77!Mybl1;;chr8:107793737..107793757,+!p2@Hsf4!1.01!10.61!Hsf4;;chr1:19199095..19199114,+!p5@Tfap2b!1.01!9.32!Tfap2b;;chr7:6649134..6649167,-!p1@Zim1!0.99!48.44!Zim1;;chr13:83643159..83643226,+!p3@Mef2c!0.99!8.84!Mef2c;;chr12:28027561..28027591,-!p1@Sox11!0.98!57.35!Sox11;;chr11:85646263..85646278,+!p2@Tbx2!0.98!22.45!Tbx2;;chr13:99124189..99124205,+!p1@Foxd1!0.98!13.13!Foxd1;;chr10:42303410..42303422,-!p3@Nr2e1!0.98!8.57!Nr2e1;;chr5:114724042..114724090,-!p2@Foxn4!0.98!8.50!Foxn4;;chr10:44178493..44178520,-!p3@Prdm1!0.97!11.91!Prdm1;;chr9:91260616..91260653,-!p2@Zic1!0.97!8.44!Zic1;;chr1:6720216..6720232,+!p1@St18!0.97!8.37!St18;;chr4:150482563..150482655,-!p2@Camta1!0.96!29.87!Camta1;;chr18:55149735..55149776,-!p4@Zfp608!0.96!20.07!Zfp608;;chr10:44178474..44178487,-!p4@Prdm1!0.96!11.77!Prdm1;;chr3:34548946..34548972,+!p2@Sox2!0.96!8.98!Sox2;;chr10:126778916..126778974,-!p1@Gli1!0.95!18.37!Gli1;;chr15:76352832..76352900,-!p1@Scrt1!0.95!7.96!Scrt1;;chr17:86020468..86020504,+!p6@Six3!0.94!7.76!Six3;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.93!19.39!Hmga1;;chr1:189821714..189821761,+!p1@Esrrg!0.93!14.29!Esrrg;;chr2:163028888..163028905,+!p3@Tox2!0.92!8.91!Tox2;;chr4:153708892..153708904,-!p13@Prdm16!0.92!7.35!Prdm16;;chr7:17647736..17647772,-!p1@Hif3a!0.91!26.33!Hif3a;;chr4:6917921..6917970,-!p2@Tox!0.91!20.68!Tox;;chr1:9690424..9690467,-!p1@Mybl1!0.91!15.44!Mybl1;;chr8:94881733..94881790,+!p1@Irx5!0.91!14.42!Irx5;;chr9:91260594..91260612,-!p1@Zic1!0.91!7.21!Zic1;;chr5:106887496..106887515,-!p2@Barhl2!0.91!7.14!Barhl2;;chr14:98568971..98569025,-!p1@Dach1!0.89!54.36!Dach1;;chr9:96159147..96159204,+!p2@Tfdp2!0.89!13.20!Tfdp2;;chr7:116154364..116154444,+!p1@Tub!0.89!11.97!Tub;;chr18:64499706..64499721,+!p2@Onecut2!0.89!9.59!Onecut2;;chr17:86020293..86020318,+!p7@Six3!0.89!6.80!Six3;;chr19:46222859..46222876,-!p1@Pitx3!0.89!6.74!Pitx3;;chr4:97248652..97248671,+!p19@Nfia!0.89!6.74!Nfia;;chr8:24780125..24780143,+!p1@Zmat4!0.88!9.87!Zmat4;;chr1:19199151..19199170,+!p3@Tfap2b!0.88!6.67!Tfap2b;;chr16:25801993..25802014,+!p1@Trp63!0.88!6.53!Trp63;;chr7:130644017..130644092,-!p1@Zkscan2!0.87!12.72!Zkscan2;;chr4:97248473..97248496,+!p16@Nfia!0.87!6.46!Nfia;;chr10:67364011..67364018,-!p5@Zfp365!0.87!6.40!Zfp365;;chr12:30219426..30219506,+!p2@Myt1l!0.86!6.19!Myt1l;;chr19:7342725..7342784,+!p1@Rcor2!0.85!26.19!Rcor2;;chr4:148178529..148178548,+!p3@Casz1!0.85!15.17!Casz1;;chr4:13670499..13670526,+!p2@Runx1t1!0.85!14.08!Runx1t1;;chr11:85646341..85646352,+!p3@Tbx2!0.85!12.38!Tbx2;;chr8:94881872..94881887,+!p2@Irx5!0.85!6.60!Irx5;;chr2:181501988..181502026,+!p3@Myt1!0.85!6.12!Myt1;;chr1:19199079..19199092,+!p7@Tfap2b!0.85!6.06!Tfap2b;;chr3:99057269..99057306,+!p1@Tbx15!0.84!7.35!Tbx15;;chr9:118387300..118387317,+!p1@Eomes!0.84!5.92!Eomes;;chr15:76352677..76352737,-!p3@Scrt1!0.84!5.92!Scrt1;;chr14:122874593..122874610,+!p2@Zic2!0.84!5.85!Zic2;;chr13:40826119..40826131,-!p7@Tfap2a!0.84!5.85!Tfap2a;;chr9:106356211..106356242,+!p1@Pcbp4!0.83!119.34!Pcbp4;;chr4:122673278..122673336,+!p1@Mycl1!0.83!19.12!Mycl1;;chr17:27693746..27693759,+!p6@Hmga1-rs1,p7@Hmga1!0.83!11.77!Hmga1;;chr4:82351566..82351607,-!p10@Nfib!0.83!5.78!Nfib;;chr12:56700411..56700416,+!p@chr12:56700411..56700416,+!0.83!5.78!Insm2;;chr18:66098752..66098757,-!p3@Rax!0.83!5.72!Rax;;chr1:19202185..19202187,+!p9@Tfap2b!0.83!5.72!Tfap2b;;chr1:93309740..93309811,-!p1@Hes6!0.82!121.72!Hes6;;chr3:95032091..95032183,-!p1@Mllt11!0.82!51.71!Mllt11;;chr17:86020186..86020195,+!p9@Six3!0.82!5.65!Six3;;chr1:19199221..19199234,+!p6@Tfap2b!0.82!5.58!Tfap2b;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.81!26.53!Hmga1;;chr1:179374784..179374800,+!p2@Zfp238!0.81!6.46!Zfp238;;chr2:181501745..181501778,+!p1@Myt1!0.81!5.44!Myt1;;chr4:82351527..82351541,-!p16@Nfib!0.81!5.44!Nfib;;chr6:70906450..70906454,+!p1@Foxi3!0.81!5.44!Foxi3;;chr18:65741935..65741964,+!p2@Zfp532!0.80!15.72!Zfp532;;chr15:35225845..35225867,+!p1@Osr2!0.80!14.08!Osr2;;chr13:72766279..72766296,+!p2@Irx2!0.80!8.10!Irx2;;chr7:144505957..144505972,-!p2@Ebf3!0.80!6.80!Ebf3;;chr9:59797847..59797858,-!p5@Nr2e3!0.80!5.37!Nr2e3;;chr17:86020336..86020352,+!p8@Six3!0.79!5.10!Six3;;chr2:65768174..65768247,+!p2@Csrnp3!0.79!5.10!Csrnp3;;chr12:12948633..12948651,-!p1@Mycn!0.77!51.71!Mycn;;chr14:98568761..98568814,-!p2@Dach1!0.77!36.40!Dach1;;chr9:106356243..106356264,+!p2@Pcbp4!0.77!23.06!Pcbp4;;chr7:38557752..38557793,-!p3@Zfp536!0.77!5.92!Zfp536;;chr2:172375081..172375105,+!p1@Tfap2c!0.77!4.90!Tfap2c;;chr1:191994550..191994623,-!p1@Prox1!0.76!35.99!Prox1;;chr14:98569030..98569059,-!p3@Dach1!0.76!25.31!Dach1;;chr10:44178575..44178590,-!p5@Prdm1!0.76!6.06!Prdm1;;chr10:42303434..42303445,-!p4@Nr2e1!0.76!4.69!Nr2e1;;chr15:76352740..76352781,-!p5@Scrt1!0.76!4.69!Scrt1;;chr9:96159665..96159680,+!p3@Tfdp2!0.75!23.06!Tfdp2;;chr4:54960870..54960926,+!p1@Zfp462!0.75!18.17!Zfp462;;chr9:96159116..96159130,+!p6@Tfdp2!0.75!5.92!Tfdp2;;chr17:48015839..48015915,-!p3@Foxp4!0.74!5.37!Foxp4;;chr15:76353005..76353021,-!p2@Scrt1!0.74!4.56!Scrt1;;chr1:136186574..136186592,+!p1@Myog!0.74!4.56!Myog;;chr4:82351544..82351563,-!p15@Nfib!0.74!4.56!Nfib;;chr15:103170533..103170556,-!p1@Zfp385a!0.73!17.76!Zfp385a;;chr2:103143336..103143367,-!p1@Ehf!0.73!7.42!Ehf;;chr19:7342786..7342803,+!p2@Rcor2!0.73!6.12!Rcor2;;chr7:144505980..144506010,-!p3@Ebf3!0.73!5.37!Ebf3;;chr1:157589131..157589176,-!p1@Lhx4!0.73!4.42!Lhx4;;chr11:21901608..21901634,-!p1@Otx1!0.73!4.42!Otx1;;chr10:106931775..106931798,-!p1@Myf6!0.73!4.42!Myf6;;chr14:18814020..18814023,+!p3@Thrb!0.73!4.42!Thrb;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ik;;chr1:93698030..93698064,+!p1@Twist2!0.28!2.65!Twist2;;chr2:30700881..30700916,+!p1@Prrx2!0.28!2.45!Prrx2;;chr11:90250944..90250982,-!p2@Hlf!0.28!2.11!Hlf;;chr7:134758722..134758733,-!p2@Zfp629!0.28!1.97!Zfp629;;chr11:16952347..16952366,-!p2@Plek!0.28!1.77!Plek;;chr6:53523346..53523353,+!p3@Creb5!0.28!1.63!Creb5;;chr18:65741911..65741929,+!p3@Zfp532!0.28!1.50!Zfp532;;chr1:69732511..69732540,-!p2@Ikzf2!0.28!1.43!Ikzf2;;chr4:133309775..133309784,-!p15@Arid1a!0.28!1.36!Arid1a;;chr14:67853632..67853674,+!p3@Ebf2!0.28!1.29!Ebf2;;chr4:13670661..13670681,+!p12@Runx1t1!0.28!1.16!Runx1t1;;chr3:107398056..107398082,+!p1@Alx3!0.28!0.88!Alx3;;chr3:128916838..128916856,+!p4@Pitx2!0.28!0.88!Pitx2;;chr2:93482426..93482434,+!p3@Alx4!0.28!0.88!Alx4;;chr4:139388835..139388867,-!p1@Pax7!0.28!0.88!Pax7;;chr3:17954233..17954249,+!p1@Bhlhe22!0.28!0.88!Bhlhe22;;chr4:114581497..114581519,-!p2@Foxd2!0.28!0.88!Foxd2;;chr1:19093112..19093124,+!p1@Tfap2d!0.28!0.88!Tfap2d;;chr2:26063801..26063813,-!p2@Lhx3!0.28!0.88!Lhx3;;chr2:105522351..105522362,+!p19@Pax6!0.28!0.88!Pax6;;chr1:57028125..57028149,-!p2@Satb2!0.28!0.88!Satb2;;chr16:91225654..91225671,+!p2@Olig2!0.28!0.88!Olig2;;chr9:118387742..118387753,+!p3@Eomes!0.28!0.88!Eomes;;chr9:59797133..59797145,-!p7@Nr2e3!0.28!0.88!Nr2e3;;chr13:83643232..83643254,+!p5@Mef2c!0.28!0.88!Mef2c;;chr12:12947406..12947418,-!p5@Mycn!0.28!0.88!Mycn;;chr14:56143812..56143822,-!p5@Nrl!0.28!0.88!Nrl;;chr14:122874718..122874729,+!p3@Zic2!0.28!0.88!Zic2;;chr5:125659525..125659599,-!p1@Ncor2!0.27!102.74!Ncor2;;chr11:112643496..112643562,+!p1@Sox9!0.27!62.80!Sox9;;chr7:105851749..105851802,+!p1@Prkrir!0.27!57.56!Prkrir;;chr12:117285924..117286018,+!p1@Zfp386!0.27!47.83!Zfp386;;chr7:13404186..13404214,-!p1@Zfp329!0.27!32.93!Zfp329;;chr7:4966247..4966286,-!p1@Fiz1!0.27!32.25!Fiz1;;chr17:33766023..33766059,+!p1@Zfp414!0.27!24.90!Zfp414;;chr19:23215673..23215753,+!p1@Klf9!0.27!24.15!Klf9;;chr9:19426523..19426584,+!p1@Zfp317!0.27!24.15!Zfp317;;chr3:94641350..94641380,+!p1@Pogz!0.27!16.33!Pogz;;chr17:23004085..23004108,-!p1@Zfp945!0.27!15.99!Zfp945;;chr10:20032304..20032324,+!p2@Bclaf1!0.27!15.44!Bclaf1;;chr11:98821749..98821799,+!p2@Rara!0.27!9.93!Rara;;chr7:6336020..6336068,+!p1@Zfp28!0.27!6.80!Zfp28;;chr11:50700965..50701027,-!p1@Zfp454!0.27!5.17!Zfp454;;chrX:45245644..45245666,-!p2@Smarca1!0.27!4.69!Smarca1;;chr15:76755836..76755867,-!p1@Zfp647!0.27!4.15!Zfp647;;chr14:100684075..100684098,-!p3@Klf12!0.27!3.47!Klf12;;chr18:75979828..75979864,+!p2@Zbtb7c!0.27!3.06!Zbtb7c;;chr18:3337612..3337644,-!p8@Crem!0.27!2.52!Crem;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.27!2.38!D630045J12Rik;;chr10:127896265..127896276,+!p4@Smarcc2!0.27!2.18!Smarcc2;;chr4:13712168..13712218,+!p4@Runx1t1!0.27!2.04!Runx1t1;;chr1:170361633..170361644,-!p11@Pbx1!0.27!2.04!Pbx1;;chr14:65568567..65568588,-!p3@Hmbox1!0.27!1.77!Hmbox1;;chr1:13364153..13364156,-!p5@Ncoa2!0.27!1.70!Ncoa2;;chr4:114581524..114581551,-!p1@Foxd2!0.27!1.70!Foxd2;;chr12:72149325..72149343,+!p2@Arid4a!0.27!1.56!Arid4a;;chr14:67853425..67853454,+!p1@Ebf2!0.27!1.56!Ebf2;;chr5:22939909..22939948,+!p6@Mll5!0.27!1.36!Mll5;;chr3:95032184..95032195,-!p4@Mllt11!0.27!1.29!Mllt11;;chr4:107107175..107107204,+!p1@Glis1!0.27!1.22!Glis1;;chr13:31898529..31898542,+!p5@Foxc1!0.27!1.22!Foxc1;;chr14:57397138..57397189,-!p1@Pspc1!0.26!50.42!Pspc1;;chr11:87881744..87881791,+!p1@Vezf1!0.26!46.13!Vezf1;;chr9:72122773..72122820,+!p1@Zfp280d!0.26!43.34!Zfp280d;;chr7:117205217..117205246,+!p1@Zfp143!0.26!31.71!Zfp143;;chr10:126725907..126725974,-!p1@Mbd6!0.26!21.57!Mbd6;;chr7:48888915..48888973,+!p1@Zfp788!0.26!20.07!Zfp788;;chr3:100773567..100773599,-!p1@Ttf2!0.26!17.42!Ttf2;;chr10:57206160..57206220,+!p1@Hsf2!0.26!17.28!Hsf2;;chr5:145965392..145965443,+!p1@Zkscan5!0.26!14.15!Zkscan5;;chr7:13563183..13563249,+!p1@Zfp446!0.26!10.95!Zfp446;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011264
 |is_obsolete=
+|library_id=CNhs11207
+|library_id_phase_based=2:CNhs11207
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;633
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;633
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N00.CNhs11207.633-15C6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N00.CNhs11207.633-15C6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N00.CNhs11207.633-15C6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N00.CNhs11207.633-15C6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/eyeball%252c%2520neonate%2520N00.CNhs11207.633-15C6.mm9.nobarcode.rdna.fa.gz
 |name=eyeball, neonate N00
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11207,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.15531222543474,0.0285860945550467,0,0,0,0,0.513951999980207,0.0285860945550467,0.0680361098787663,0,0,0.633186718944118,0,0,0,0,0.0142930472775233,0,0.217166839258061,0,0,0,0,0,0,0,0.0173314149839321,0,0,0,0,0,0.164728968116342,0,0,0,0,0.0831941736365484,0.0887085487015116,0.130046708154826,0.0877828307705357,0.60721392291843,0.795101736006463,0,0,0,0,0,0,0,0,0,0.0285860945550467,0.127163941277894,0,0.0146604343565212,0.0806659819199616,0,0,0,0,0,0.0929646499778043,0.055406237837571,0.169161526902821,0.0976177829125495,0.0837011534800704,0.172379326196554,0.954997038659153,0.206889822834207,0,0.112905675137174,0.151457818094133,0,0.169161526902821,0,0.173794197565293,-0.0020796935064377,-0.210529119898715,0.0483323464379869,0.00073294000058241,0,0,0,0.0277031189187855,0,-0.125090247242678,-0.217063561448671,-0.0252962668496776,0.0285860945550467,0,0,0,0.0285860945550467
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:633-15C6;search_select_hide=table117:633-15C6
 }}

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FF:633-15C6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:18, 4 June 2020

CNhs11207

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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