FF:662-22H3: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	skin, neonate N03
Species:	Mouse (Mus musculus)
Library ID:	CNhs11215
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	skin
dev stage	3 days 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		SAMD00004789

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11215		CAGE		DRX009079		DRR009953

Accession ID Mm9

Library id		BAM		CTSS
CNhs11215		DRZ001378		DRZ002761

Accession ID Mm10

Library id		BAM		CTSS
CNhs11215		DRZ012728		DRZ014111

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

CNhs11215

0	0
1	0
10	0
100	0
1000	0.0804
1001	0.0374
1002	-0.0566
1003	0.121
1004	0
1005	0
1006	0.0495
1007	0.0759
1008	0
1009	0.21
101	0.111
1010	0
1011	0.0254
1012	0
1013	-0.058
1014	0.0836
1015	-0.0122
1016	0.0979
1017	0
1018	0.467
1019	0
102	0
1020	0
1021	0.0254
1022	0.153
1023	0
1024	0.0984
1025	0
1026	0
1027	0.0113
1028	0
1029	-0.0267
103	0.389
1030	0
1031	0.245
1032	-0.0495
1033	0
1034	0.0495
1035	0.0254
1036	0.051
1037	0
1038	0.0376
1039	-0.0756
104	0
1040	0.14
1041	0.733

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: CNhs11215

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.123
MA0003.1	MA0003.1	0.446
MA0004.1	MA0004.1	0.496
MA0006.1	MA0006.1	0.101
MA0007.1	MA0007.1	0.303
MA0009.1	MA0009.1	0.164
MA0014.1	MA0014.1	0.725
MA0017.1	MA0017.1	2.1883e-9
MA0018.2	MA0018.2	0.239
MA0019.1	MA0019.1	0.175
MA0024.1	MA0024.1	0.161
MA0025.1	MA0025.1	0.9
MA0027.1	MA0027.1	0.995
MA0028.1	MA0028.1	0.00487
MA0029.1	MA0029.1	0.335
MA0030.1	MA0030.1	0.321
MA0031.1	MA0031.1	0.956
MA0035.2	MA0035.2	5.15306e-4
MA0038.1	MA0038.1	0.00233
MA0039.2	MA0039.2	0.00412
MA0040.1	MA0040.1	0.244
MA0041.1	MA0041.1	0.287
MA0042.1	MA0042.1	0.602
MA0043.1	MA0043.1	0.493
MA0046.1	MA0046.1	1.88659e-21
MA0047.2	MA0047.2	0.0487
MA0048.1	MA0048.1	0.438
MA0050.1	MA0050.1	0.0181
MA0051.1	MA0051.1	0.138
MA0052.1	MA0052.1	1.22503e-9
MA0055.1	MA0055.1	0.0449
MA0057.1	MA0057.1	0.312
MA0058.1	MA0058.1	0.262
MA0059.1	MA0059.1	0.013
MA0060.1	MA0060.1	0.00292
MA0061.1	MA0061.1	0.0559
MA0062.2	MA0062.2	9.58976e-5
MA0065.2	MA0065.2	0.0246
MA0066.1	MA0066.1	0.182
MA0067.1	MA0067.1	0.909
MA0068.1	MA0068.1	0.353
MA0069.1	MA0069.1	0.81
MA0070.1	MA0070.1	0.597
MA0071.1	MA0071.1	0.00188
MA0072.1	MA0072.1	0.615
MA0073.1	MA0073.1	0.871
MA0074.1	MA0074.1	0.0795
MA0076.1	MA0076.1	0.0134
MA0077.1	MA0077.1	0.56
MA0078.1	MA0078.1	0.0316
MA0079.2	MA0079.2	0.0326
MA0080.2	MA0080.2	7.35174e-7
MA0081.1	MA0081.1	0.00665
MA0083.1	MA0083.1	0.00417
MA0084.1	MA0084.1	0.88
MA0087.1	MA0087.1	0.466
MA0088.1	MA0088.1	0.647
MA0090.1	MA0090.1	0.0157
MA0091.1	MA0091.1	0.171
MA0092.1	MA0092.1	0.269
MA0093.1	MA0093.1	0.504
MA0099.2	MA0099.2	2.3907e-10
MA0100.1	MA0100.1	0.0469
MA0101.1	MA0101.1	0.712
MA0102.2	MA0102.2	0.111
MA0103.1	MA0103.1	0.788
MA0104.2	MA0104.2	0.049
MA0105.1	MA0105.1	0.00457
MA0106.1	MA0106.1	0.066
MA0107.1	MA0107.1	0.913
MA0108.2	MA0108.2	6.78402e-37
MA0111.1	MA0111.1	0.393
MA0112.2	MA0112.2	0.187
MA0113.1	MA0113.1	0.136
MA0114.1	MA0114.1	5.08266e-7
MA0115.1	MA0115.1	7.43795e-5
MA0116.1	MA0116.1	0.0179
MA0117.1	MA0117.1	0.647
MA0119.1	MA0119.1	0.776
MA0122.1	MA0122.1	0.436
MA0124.1	MA0124.1	0.404
MA0125.1	MA0125.1	8.73086e-4
MA0131.1	MA0131.1	0.827
MA0135.1	MA0135.1	0.0149
MA0136.1	MA0136.1	9.9065e-8
MA0137.2	MA0137.2	0.414
MA0138.2	MA0138.2	0.246
MA0139.1	MA0139.1	0.014
MA0140.1	MA0140.1	3.87348e-4
MA0141.1	MA0141.1	2.6763e-8
MA0142.1	MA0142.1	0.211
MA0143.1	MA0143.1	0.0973
MA0144.1	MA0144.1	0.973
MA0145.1	MA0145.1	0.275
MA0146.1	MA0146.1	0.352
MA0147.1	MA0147.1	0.0166
MA0148.1	MA0148.1	0.0378
MA0149.1	MA0149.1	0.348
MA0150.1	MA0150.1	0.392
MA0152.1	MA0152.1	0.105
MA0153.1	MA0153.1	4.97641e-13
MA0154.1	MA0154.1	0.268
MA0155.1	MA0155.1	0.664
MA0156.1	MA0156.1	2.22717e-4
MA0157.1	MA0157.1	0.346
MA0159.1	MA0159.1	0.00462
MA0160.1	MA0160.1	1.51697e-4
MA0162.1	MA0162.1	0.485
MA0163.1	MA0163.1	0.00929
MA0164.1	MA0164.1	0.137
MA0258.1	MA0258.1	0.0257
MA0259.1	MA0259.1	0.343

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: CNhs11215

Novel motif	Logo	P-value
1	1	0.235
10	10	0.356
100	100	0.975
101	101	0.93
102	102	0.818
103	103	0.0437
104	104	0.176
105	105	0.381
106	106	0.526
107	107	0.156
108	108	0.943
109	109	0.286
11	11	0.256
110	110	0.429
111	111	0.118
112	112	0.106
113	113	0.947
114	114	0.233
115	115	0.131
116	116	0.637
117	117	0.129
118	118	0.0177
119	119	0.374
12	12	0.497
120	120	0.485
121	121	0.446
122	122	0.645
123	123	0.726
124	124	0.159
125	125	0.533
126	126	0.754
127	127	0.352
128	128	0.751
129	129	0.433
13	13	0.172
130	130	0.666
131	131	0.277
132	132	0.569
133	133	0.35
134	134	0.806
135	135	0.215
136	136	0.204
137	137	0.465
138	138	0.394
139	139	0.0612
14	14	0.706
140	140	0.388
141	141	0.386
142	142	0.948
143	143	0.179
144	144	0.93
145	145	0.889
146	146	0.816
147	147	0.194
148	148	0.0936
149	149	0.462
15	15	0.0131
150	150	0.526
151	151	0.393
152	152	0.0195
153	153	0.675
154	154	0.609
155	155	0.434
156	156	0.345
157	157	0.00324
158	158	0.132
159	159	0.0794
160	160	0.711
161	161	0.2
162	162	0.587
163	163	0.764
164	164	0.199
165	165	0.273
166	166	0.183
167	167	0.00789
168	168	0.322
169	169	0.148
17	17	0.494
18	18	0.0978
19	19	0.763
2	2	0.197
20	20	0.141
21	21	0.99
22	22	0.869
23	23	0.371
24	24	0.971
25	25	0.224
26	26	0.0545
27	27	0.435
28	28	0.81
29	29	0.0583
3	3	0.158
30	30	0.0373
31	31	0.209
32	32	0.504
33	33	0.346
34	34	0.646
35	35	2.56414e-4
36	36	0.00992
37	37	0.769
38	38	0.586
39	39	0.272
4	4	0.615
40	40	0.223
41	41	0.473
42	42	0.694
43	43	0.269
44	44	0.0806
45	45	0.332
46	46	0.739
47	47	0.381
48	48	0.515
49	49	0.0414
5	5	0.151
50	50	0.571
51	51	0.781
52	52	0.139
53	53	0.287
54	54	0.885
55	55	0.745
56	56	0.719
57	57	0.776
58	58	0.833
59	59	0.758
6	6	0.977
60	60	0.29
61	61	0.998
62	62	0.363
63	63	0.921
64	64	0.184
65	65	0.329
66	66	0.871
67	67	0.985
68	68	0.0169
69	69	0.591
7	7	0.674
70	70	0.0854
71	71	0.527
72	72	0.648
73	73	0.499
74	74	0.823
75	75	0.0384
76	76	0.0012
77	77	0.427
78	78	0.0754
79	79	0.516
8	8	0.0744
80	80	0.22
81	81	0.29
82	82	0.271
83	83	0.251
84	84	0.61
85	85	0.912
86	86	0.232
87	87	0.0439
88	88	0.757
89	89	0.0963
9	9	0.528
90	90	0.186
91	91	0.484
92	92	0.394
93	93	0.674
94	94	0.673
95	95	0.72
96	96	0.622
97	97	0.0663
98	98	0.276
99	99	0.399

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: CNhs11215

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011400 mouse skin- neonate N03 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)
0000014 (zone of skin)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0007029 (surface)
0000483 (epithelium)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003102 (surface structure)
0007376 (outer epithelium)
0010371 (ecto-epithelium)
0010317 (germ layer / neural crest derived structure)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000311 (mouse neonate N3 sample)
0011400 (mouse skin- neonate N03 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004789
+|accession_numbers=CAGE;DRX009079;DRR009953;DRZ001378;DRZ002761;DRZ012728;DRZ014111
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000014,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0007029,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0010317,UBERON:0002416
 |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=chr11:94981424..94981439,+!p1@Dlx3!2.18!170.99!Dlx3;;chr16:25801993..25802014,+!p1@Trp63!2.14!138.36!Trp63;;chr11:121380640..121380655,-!p1@Zfp750!2.01!165.14!Zfp750;;chr2:9800207..9800234,-!p1@Gata3!1.82!189.08!Gata3;;chr13:53568104..53568156,-!p1@Msx2!1.79!88.00!Msx2;;chr15:102751603..102751630,+!p1@Hoxc13!1.76!56.81!Hoxc13;;chr9:31720843..31720888,-!p1@Barx2!1.74!59.47!Barx2;;chr13:72766250..72766273,+!p1@Irx2!1.72!77.32!Irx2;;chr11:121380594..121380609,-!p2@Zfp750!1.71!84.98!Zfp750;;chr13:40829137..40829205,-!p1@Tfap2a!1.71!56.33!Tfap2a;;chr13:72766279..72766296,+!p2@Irx2!1.59!55.79!Irx2;;chr4:135129538..135129558,-!p1@Grhl3!1.58!54.58!Grhl3;;chr9:43013917..43013968,-!p1@Pou2f3!1.58!37.27!Pou2f3;;chr11:121380611..121380625,-!p3@Zfp750!1.55!41.25!Zfp750;;chr5:77543897..77543911,-!p2@Hopx!1.54!63.51!Hopx;;chr19:5560600..5560617,-!p1@Ovol1!1.50!37.21!Ovol1;;chr4:46356509..46356527,+!p1@Foxe1!1.46!27.99!Foxe1;;chr14:118636214..118636235,-!p1@Sox21!1.44!31.85!Sox21;;chr12:34642510..34642530,+!p1@Twist1!1.43!80.52!Twist1;;chr3:99057269..99057306,+!p1@Tbx15!1.43!31.00!Tbx15;;chr11:96880072..96880079,+!p1@Sp6!1.41!24.49!Sp6;;chr2:38206580..38206600,+!p2@Lhx2!1.40!29.49!Lhx2;;chr12:25257141..25257173,+!p1@Grhl1!1.39!47.65!Grhl1;;chr2:172375081..172375105,+!p1@Tfap2c!1.37!22.32!Tfap2c;;chr2:38206744..38206766,+!p1@Lhx2!1.34!25.21!Lhx2;;chr6:70906450..70906454,+!p1@Foxi3!1.30!19.00!Foxi3;;chr15:97738692..97738747,-!p1@Vdr!1.25!90.11!Vdr;;chr11:78200071..78200100,-!p1@Foxn1!1.25!16.71!Foxn1;;chr19:5560570..5560582,-!p2@Ovol1!1.24!16.53!Ovol1;;chr13:40826961..40827001,-!p4@Tfap2a!1.22!15.62!Tfap2a;;chr4:55545337..55545357,-!p1@Klf4!1.21!218.57!Klf4;;chr7:19946556..19946611,+!p1@Ppp1r13l!1.20!58.38!Ppp1r13l;;chr12:25257265..25257294,+!p2@Grhl1!1.19!14.48!Grhl1;;chr13:83643159..83643226,+!p3@Mef2c!1.18!13.99!Mef2c;;chr4:124334894..124334899,+!p1@Pou3f1!1.16!17.31!Pou3f1;;chr7:6649134..6649167,-!p1@Zim1!1.15!70.20!Zim1;;chr14:70477113..70477173,+!p1@Egr3!1.15!12.97!Egr3;;chr4:148178559..148178603,+!p1@Casz1!1.14!36.61!Casz1;;chr15:35225845..35225867,+!p1@Osr2!1.14!32.57!Osr2;;chr10:44178521..44178557,-!p1@Prdm1!1.13!22.01!Prdm1;;chr15:102087880..102087927,-!p2@Rarg!1.12!27.99!Rarg;;chr13:72101178..72101203,-!p1@Irx1!1.12!19.06!Irx1;;chr15:102828658..102828678,+!p1@Hoxc6!1.12!12.18!Hoxc6;;chr12:109242266..109242295,-!p1@Bcl11b!1.11!98.55!Bcl11b;;chr16:18587076..18587106,-!p1@Tbx1!1.11!16.83!Tbx1;;chr2:71384802..71384815,-!p1@Dlx2!1.11!14.84!Dlx2;;chr12:37835141..37835194,+!p1@Meox2!1.10!36.19!Meox2;;chr18:80909801..80909819,-!p1@Nfatc1!1.09!67.13!Nfatc1;;chr12:25257176..25257190,+!p3@Grhl1!1.09!12.67!Grhl1;;chr15:102751578..102751600,+!p2@Hoxc13!1.09!11.40!Hoxc13;;chr13:73397958..73397994,+!p1@Irx4!1.09!11.34!Irx4;;chr10:126778916..126778974,-!p1@Gli1!1.08!24.79!Gli1;;chr1:93698030..93698064,+!p1@Twist2!1.07!21.59!Twist2;;chr6:115372058..115372085,+!p3@Pparg!1.05!10.19!Pparg;;chr6:52176164..52176195,-!p1@Hoxa9!1.04!12.48!Hoxa9;;chr13:40825465..40825469,-!p2@Tfap2a!1.03!9.83!Tfap2a;;chr13:53568191..53568219,-!p2@Msx2!1.03!9.71!Msx2;;chr5:77543935..77543947,-!p4@Hopx!1.03!9.71!Hopx;;chr6:97941770..97941784,+!p4@Mitf!1.02!9.47!Mitf;;chr1:165243792..165243808,-!p1@Prrx1!1.01!32.69!Prrx1;;chr1:19199236..19199258,+!p1@Tfap2b!1.01!9.17!Tfap2b;;chr15:50714356..50714368,-!p14@Trps1!1.01!9.17!Trps1;;chr9:69137716..69137744,+!p1@Rora!1.00!57.78!Rora;;chr9:31721051..31721068,-!p3@Barx2!0.99!8.69!Barx2;;chr14:99697871..99697934,+!p1@Klf5!0.97!170.93!Klf5;;chr3:130813200..130813252,+!p1@Lef1!0.97!38.06!Lef1;;chr10:67000609..67000625,+!p1@Egr2!0.97!19.90!Egr2;;chr17:14011485..14011507,+!p2@Mllt4!0.97!8.38!Mllt4;;chr6:115372099..115372121,+!p5@Pparg!0.97!8.32!Pparg;;chr1:194979315..194979359,+!p1@Irf6!0.96!50.78!Irf6;;chr12:37835120..37835133,+!p2@Meox2!0.96!11.70!Meox2;;chr11:106128936..106128955,-!p4@Smarcd2!0.96!9.41!Smarcd2;;chr2:120365588..120365602,-!p2@Zfp106!0.94!13.21!Zfp106;;chr2:160192793..160192809,-!p1@Mafb!0.93!118.39!Mafb;;chr15:103170533..103170556,-!p1@Zfp385a!0.93!29.01!Zfp385a;;chr15:103170516..103170531,-!p2@Zfp385a!0.93!18.52!Zfp385a;;chr3:130813736..130813752,+!p3@Lef1!0.93!10.80!Lef1;;chr17:14011569..14011589,+!p8@Mllt4!0.93!7.42!Mllt4;;chr12:25257114..25257131,+!p4@Grhl1!0.92!9.59!Grhl1;;chr13:40829337..40829360,-!p5@Tfap2a!0.92!7.24!Tfap2a;;chr6:51382677..51382783,+!p1@Nfe2l3!0.91!18.82!Nfe2l3;;chr1:194979361..194979373,+!p2@Irf6!0.91!9.71!Irf6;;chr13:72766234..72766243,+!p3@Irx2!0.91!7.06!Irx2;;chr17:14011545..14011564,+!p6@Mllt4!0.91!7.06!Mllt4;;chr6:53523358..53523388,+!p1@Creb5!0.90!87.33!Creb5;;chr4:126413480..126413489,-!p1@Tfap2e!0.90!6.94!Tfap2e;;chr11:96143666..96143725,+!p1@Hoxb8!0.89!7.78!Hoxb8;;chr4:84321300..84321315,-!p2@Bnc2!0.88!8.26!Bnc2;;chr5:38215819..38215823,-!p1@Msx1!0.87!17.43!Msx1;;chr17:14011529..14011544,+!p7@Mllt4!0.87!6.45!Mllt4;;chr11:23980664..23980706,+!p2@Bcl11a!0.86!28.83!Bcl11a;;chr6:52167459..52167492,-!p1@Hoxa7!0.86!7.54!Hoxa7;;chr3:99057677..99057730,+!p2@Tbx15!0.86!6.27!Tbx15;;chr13:53568081..53568094,-!p3@Msx2!0.86!6.27!Msx2;;chr4:135129447..135129467,-!p2@Grhl3!0.85!7.42!Grhl3;;chr1:93698068..93698085,+!p2@Twist2!0.85!7.24!Twist2;;chr14:118636238..118636257,-!p2@Sox21!0.85!6.09!Sox21;;chr9:31720903..31720918,-!p2@Barx2!0.85!6.03!Barx2;;chr7:35904304..35904320,+!p1@Cebpa!0.84!127.86!Cebpa;;chr1:165243591..165243625,-!p2@Prrx1!0.84!9.29!Prrx1;;chr2:103143336..103143367,-!p1@Ehf!0.83!9.65!Ehf;;chr2:74542918..74542971,+!p1@Hoxd8!0.82!8.75!Hoxd8;;chr19:25746898..25746910,+!p1@Dmrt2!0.82!8.69!Dmrt2;;chr1:19202352..19202354,+!p2@Tfap2b!0.82!5.67!Tfap2b;;chr11:94981134..94981147,+!p2@Dlx3!0.81!5.49!Dlx3;;chr18:76219118..76219155,+!p1@Zbtb7c!0.80!9.65!Zbtb7c;;chr2:9800094..9800108,-!p3@Gata3!0.80!5.31!Gata3;;chr13:73398004..73398017,+!p2@Irx4!0.80!5.25!Irx4;;chr10:44178493..44178520,-!p3@Prdm1!0.79!7.36!Prdm1;;chr7:89137163..89137200,-!p1@Bnc1!0.79!6.39!Bnc1;;chr4:148178459..148178482,+!p4@Casz1!0.79!5.13!Casz1;;chr10:66998241..66998263,+!p2@Egr2!0.79!5.13!Egr2;;chr1:19199021..19199048,+!p8@Tfap2b!0.79!5.13!Tfap2b;;chr4:148178529..148178548,+!p3@Casz1!0.78!12.55!Casz1;;chr1:120950098..120950132,-!p2@Gli2!0.78!12.24!Gli2;;chr10:44178375..44178390,-!p2@Prdm1!0.78!7.00!Prdm1;;chr6:128250380..128250442,-!p2@Tead4!0.78!6.51!Tead4;;chr6:52190467..52190500,-!p1@Hoxa10!0.78!5.07!Hoxa10;;chr4:87452200..87452229,-!p2@Mllt3!0.77!10.98!Mllt3;;chr13:72101161..72101177,-!p2@Irx1!0.76!6.82!Irx1;;chr14:64562503..64562524,+!p1@Sox7!0.75!29.67!Sox7;;chr4:148275237..148275311,+!p2@Casz1!0.75!20.81!Casz1;;chr13:40826150..40826167,-!p3@Tfap2a!0.75!5.25!Tfap2a;;chr13:40824310..40824314,-!p6@Tfap2a!0.75!4.64!Tfap2a;;chr4:82151653..82151706,-!p2@Nfib!0.74!139.50!Nfib;;chr15:37162796..37162828,+!p1@Grhl2!0.74!7.96!Grhl2;;chr8:90328310..90328362,-!p3@Zfp423!0.74!5.31!Zfp423;;chr9:31720746..31720762,-!p4@Barx2!0.74!4.52!Barx2;;chr12:25257298..25257323,+!p5@Grhl1!0.74!4.52!Grhl1;;chr3:99057256..99057268,+!p3@Tbx15!0.74!4.52!Tbx15;;chr3:99044284..99044308,+!p4@Tbx15!0.74!4.46!Tbx15;;chr12:34642682..34642753,+!p2@Twist1!0.73!12.61!Twist1;;chr13:31898496..31898519,+!p3@Foxc1!0.73!7.42!Foxc1;;chr10:44178575..44178590,-!p5@Prdm1!0.72!5.37!Prdm1;;chr15:37163124..37163153,+!p3@Grhl2!0.72!4.22!Grhl2;;chr15:102087737..102087801,-!p3@Rarg!0.71!7.18!Rarg;;chr13:72101141..72101158,-!p3@Irx1!0.71!5.31!Irx1;;chr9:31720817..31720829,-!p5@Barx2!0.71!4.10!Barx2;;chr1:19199119..19199134,+!p4@Tfap2b!0.71!4.10!Tfap2b;;chr1:19199221..19199234,+!p6@Tfap2b!0.71!4.10!Tfap2b;;chr16:92697560..92697592,-!p2@Runx1!0.70!28.23!Runx1;;chr8:94881733..94881790,+!p1@Irx5!0.70!8.38!Irx5;;chr15:37163065..37163092,+!p4@Grhl2!0.70!3.98!Grhl2;;chr10:12810631..12810649,+!p1@Plagl1!0.69!116.16!Plagl1;;chr6:52167434..52167450,-!p3@Hoxa7!0.69!3.92!Hoxa7;;chr6:131338435..131338482,-!p1@Csda!0.68!414.11!Csda;;chr4:87452180..87452196,-!p3@Mllt3!0.68!8.08!Mllt3;;chr2:74543397..74543435,+!p2@Hoxd8!0.68!3.80!Hoxd8;;chr2:38194778..38194798,+!p3@Lhx2!0.68!3.80!Lhx2;;chr7:119885539..119885574,+!p3@Tead1!0.68!3.74!Tead1;;chr11:69468531..69468557,+!p1@Sox15!0.68!3.74!Sox15;;chr16:14705925..14705951,+!p1@Snai2!0.67!29.73!Snai2;;chr2:133377954..133377973,+!p1@Bmp2!0.67!13.15!Bmp2;;chr4:122673187..122673201,+!p2@Mycl1!0.67!7.06!Mycl1;;chr10:44178474..44178487,-!p4@Prdm1!0.67!5.61!Prdm1;;chr5:32438831..32438878,+!p1@Fosl2!0.66!42.46!Fosl2;;chr4:134708451..134708469,+!p1@Runx3!0.66!6.82!Runx3;;chr6:52167513..52167549,-!p2@Hoxa7!0.66!5.31!Hoxa7;;chr11:101646127..101646147,-!p5@Etv4!0.66!4.28!Etv4;;chr15:50721942..50721987,-!p13@Trps1!0.66!4.22!Trps1;;chr13:53568169..53568179,-!p4@Msx2!0.66!3.62!Msx2;;chr15:102828642..102828653,+!p2@Hoxc6!0.66!3.62!Hoxc6;;chr4:84321317..84321332,-!p4@Bnc2!0.66!3.62!Bnc2;;chr2:93482464..93482491,+!p1@Alx4!0.66!3.56!Alx4;;chr6:88143711..88143717,+!p2@Gata2!0.65!5.97!Gata2;;chr11:96145450..96145517,+!p2@Hoxb7!0.65!5.61!Hoxb7;;chr12:37835203..37835218,+!p3@Meox2!0.65!4.22!Meox2;;chr13:73397921..73397935,+!p3@Irx4!0.65!3.50!Irx4;;chr15:102820964..102821006,+!p1@Hoxc8!0.65!3.44!Hoxc8;;chr17:28409136..28409150,+!p3@Ppard!0.65!3.44!Ppard;;chr4:32325688..32325777,+!p1@Bach2!0.64!34.32!Bach2;;chr8:87297280..87297326,-!p2@Nfix!0.64!8.93!Nfix;;chr10:80599248..80599261,+!p3@Zbtb7a!0.64!6.57!Zbtb7a;;chr2:30700857..30700873,+!p3@Prrx2!0.64!4.89!Prrx2;;chr7:89137554..89137565,-!p2@Bnc1!0.64!3.38!Bnc1;;chr16:25684232..25684285,+!p2@Trp63!0.64!3.38!Trp63;;chr4:82151274..82151290,-!p3@Nfib!0.63!62.48!Nfib;;chr4:82151622..82151643,-!p4@Nfib!0.63!15.74!Nfib;;chr2:27532479..27532509,+!p3@Rxra!0.63!7.36!Rxra;;chr15:37162834..37162849,+!p2@Grhl2!0.63!3.98!Grhl2;;chr11:44430812..44430838,+!p1@Ebf1!0.62!36.37!Ebf1;;chr6:86619104..86619119,-!p1@Mxd1!0.62!31.00!Mxd1;;chr5:135582751..135582788,+!p1@Mlxipl!0.62!14.90!Mlxipl;;chr6:6832076..6832092,-!p1@Dlx5!0.62!3.86!Dlx5;;chr1:19199095..19199114,+!p5@Tfap2b!0.62!3.20!Tfap2b;;chr15:102839948..102839975,+!p3@Hoxc6!0.62!3.14!Hoxc6;;chr18:35020854..35020869,+!p1@Egr1!0.61!144.15!Egr1;;chr5: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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011400
 |is_obsolete=
+|library_id=CNhs11215
+|library_id_phase_based=2:CNhs11215
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;662
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;662
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/skin%252c%2520neonate%2520N03.CNhs11215.662-22H3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/skin%252c%2520neonate%2520N03.CNhs11215.662-22H3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/skin%252c%2520neonate%2520N03.CNhs11215.662-22H3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/skin%252c%2520neonate%2520N03.CNhs11215.662-22H3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/skin%252c%2520neonate%2520N03.CNhs11215.662-22H3.mm9.nobarcode.rdna.fa.gz
 |name=skin, neonate N03
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11215,LSID748,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0278467451705003,0.00235103671480408,0.0251263865439911,0,0,0,0.223051545998322,0,0.0127170276859676,0,0,0.373497359144941,0,0,0,0,0,0,-0.11966596847864,0,0.0764788827549915,0,0,0.0984901092893304,0.114465736354675,0,0,0,0,0,0,0,0.393948519410203,0,0,0,0.0254340553719351,0.0254340553719351,0.0807432542768479,0.024090350300185,0.241217765902752,0.300778880136835,-0.220408001745238,0,0,0,0,0,0,0.429552345187898,0,0,0,0,0,-0.0165449112983274,0,0,0,0,-0.0174128997109397,0,0.10416279628064,0.0254340553719351,0.134138060633146,0.03890672919511,0.0963612560866523,-0.0592392479308416,0.367239406546284,0.0916376252833914,0.0722273824039347,0.102137373480485,0.0534669101522038,0.0494606362651129,0.134138060633146,0,0.0254340553719351,-0.0802089801932449,-0.316089695768103,0.142176113365755,0,0,0,0,0,0,-0.205802727800294,-0.375487151222427,-0.232355656412875,0,0,0,0,0
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
 |top_motifs=HOX{A4,D4}:3.04039727014;FOS_FOS{B,L1}_JUN{B,D}:2.84529433955;TBP:2.6883336281;NANOG:2.57268020987;VSX1,2:2.5067209033;LEF1_TCF7_TCF7L1,2:2.31691500811;FOSL2:2.26970409476;TP53:2.09510165515;TFCP2:1.97052056551;T:1.92425996086;SPZ1:1.85247350355;BACH2:1.85035814239;GLI1..3:1.80595867919;TOPORS:1.78422602823;PDX1:1.52745828502;GCM1,2:1.52051451254;HMX1:1.48442287506;ZNF148:1.466240846;NKX2-3_NKX2-5:1.45545868842;ZNF238:1.39257008715;TEAD1:1.38606657579;FOX{I1,J2}:1.36297082091;EN1,2:1.33594508201;SP1:1.32264470134;GFI1:1.30624347073;TFAP4:1.29222577945;SMAD1..7,9:1.26742064055;TFAP2{A,C}:1.25448685074;GFI1B:1.21768226022;HLF:1.19470509554;XCPE1{core}:1.17727239033;NFATC1..3:1.13729446011;NKX2-1,4:1.10387372831;PITX1..3:1.09673235437;MYOD1:1.07135313962;CDC5L:1.0452463468;IKZF1:1.04442089576;GATA4:1.04282925772;TBX4,5:1.02831458988;TAL1_TCF{3,4,12}:1.00489404743;SOX5:0.965839671341;ATF2:0.956320187422;EP300:0.935003799468;FOXO1,3,4:0.89156619908;CRX:0.879737138717;TEF:0.875677590725;HSF1,2:0.845427853222;NFE2:0.837183022509;GTF2I:0.799684346276;AIRE:0.780776507204;SNAI1..3:0.734709928531;NKX3-2:0.721960649375;FOXQ1:0.705554025978;ATF4:0.703646099735;CEBPA,B_DDIT3:0.699378241349;PAX5:0.696767181952;EBF1:0.695051689417;SREBF1,2:0.684866533405;MAZ:0.66674081357;ZNF384:0.660579380492;MYFfamily:0.647936753686;MEF2{A,B,C,D}:0.641857524837;NFE2L2:0.638326465553;ESR1:0.624617210473;ALX4:0.607841067305;TLX1..3_NFIC{dimer}:0.592855991497;ALX1:0.567861403968;RBPJ:0.542967878938;MYBL2:0.542902429168;GTF2A1,2:0.539255375933;PAX2:0.538589474346;ZEB1:0.538581826196;TGIF1:0.538180914812;E2F1..5:0.534083695591;POU3F1..4:0.527329551835;ATF6:0.517265171263;SRF:0.514014763904;POU2F1..3:0.474662118651;HIC1:0.446416429188;MAFB:0.441415269838;POU6F1:0.393598933503;IKZF2:0.381001681206;FOXP3:0.365668772645;FOXP1:0.359432211668;FOXL1:0.357638487493;RORA:0.354980260994;HIF1A:0.350298380536;KLF4:0.343027480179;TFDP1:0.300599015649;bHLH_family:0.300309269731;PATZ1:0.292444515534;EGR1..3:0.272967860543;PRRX1,2:0.260074524099;TFAP2B:0.205804366754;SOX{8,9,10}:0.195425367975;FOXN1:0.185663539279;ZNF143:0.180341447523;MZF1:0.173619621794;MTF1:0.169551438811;STAT5{A,B}:0.155411389739;BREu{core}:0.147623256561;TLX2:0.145480100168;LHX3,4:0.118487236313;NFY{A,B,C}:0.0751596238714;SOX2:0.0740621863699;DBP:0.0708930547375;PRDM1:0.0667419540969;NKX2-2,8:0.0643411888979;IRF7:0.0486119267562;NKX3-1:0.0395140423936;NFE2L1:0.0237473421742;PAX8:0.0187644851032;MTE{core}:0.00570206143988;STAT2,4,6:0.000679199482281;HES1:-0.000954904356127;ZIC1..3:-0.0109025207419;NR3C1:-0.0121893732823;SOX17:-0.0162641877109;RFX2..5_RFXANK_RFXAP:-0.0318441442504;NHLH1,2:-0.041280738926;NFKB1_REL_RELA:-0.0468400655122;SPI1:-0.0610464534056;MED-1{core}:-0.0662626025678;POU5F1:-0.0678853144443;NKX6-1,2:-0.0756572125683;PAX6:-0.0862092446056;SPIB:-0.090391521966;HAND1,2:-0.111309214846;HOX{A5,B5}:-0.11404666908;HOXA9_MEIS1:-0.125375940153;ELK1,4_GABP{A,B1}:-0.130015367743;RREB1:-0.139585542635;HMGA1,2:-0.154241727796;NFIX:-0.177995141843;STAT1,3:-0.189899594691;NANOG{mouse}:-0.192924911044;ELF1,2,4:-0.19811834263;FOX{D1,D2}:-0.230412844764;ETS1,2:-0.23437810454;DMAP1_NCOR{1,2}_SMARC:-0.271507729799;NRF1:-0.283437408583;ZFP161:-0.292336245229;IRF1,2:-0.295162820185;REST:-0.313605763114;POU1F1:-0.322898347653;MYB:-0.333883024893;PAX1,9:-0.346356945996;RUNX1..3:-0.395251645904;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.406821000876;FOX{F1,F2,J1}:-0.412911982272;ATF5_CREB3:-0.45711517489;GZF1:-0.462704365993;ADNP_IRX_SIX_ZHX:-0.479033898152;HNF4A_NR2F1,2:-0.492685874704;ZBTB6:-0.496740336497;CREB1:-0.504040697599;AHR_ARNT_ARNT2:-0.526985816328;CUX2:-0.535586045849;ESRRA:-0.562184537495;HBP1_HMGB_SSRP1_UBTF:-0.571287701205;FOXA2:-0.573717226859;ZNF423:-0.588046353222;PPARG:-0.591619049743;RXRA_VDR{dimer}:-0.597858135725;LMO2:-0.63264245846;NR6A1:-0.65107579567;RFX1:-0.704384888664;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.715017254791;PAX4:-0.716701713052;ONECUT1,2:-0.726019364749;RXR{A,B,G}:-0.732469211594;HNF1A:-0.733406307321;GATA6:-0.745750759927;FOXM1:-0.780997455429;NFIL3:-0.804347789435;CDX1,2,4:-0.812887877986;ZBTB16:-0.826623468315;AR:-0.878066495125;FOXD3:-0.891258488935;JUN:-0.904649552749;BPTF:-0.913663067208;NR5A1,2:-0.940726501014;OCT4_SOX2{dimer}:-0.941001267233;UFEwm:-1.01446979168;PBX1:-1.23270941873;YY1:-1.29091270401;NR1H4:-1.33405805479;ARID5B:-1.39650508089;EVI1:-1.54901879254
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:662-22H3;search_select_hide=table117:662-22H3
 }}

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FF:662-22H3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs11215

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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