FF:490-9F9: Difference between revisions

Latest revision as of 19:17, 4 June 2020

Name:	whole body, embryo E17.5
Species:	Mouse (Mus musculus)
Library ID:	CNhs10513
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	whole body
dev stage	17.5 days embryo
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		SAMD00004978

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10513		CAGE		DRX009148		DRR010022

Accession ID Mm9

Library id		BAM		CTSS
CNhs10513		DRZ001447		DRZ002830

Accession ID Mm10

Library id		BAM		CTSS
CNhs10513		DRZ012797		DRZ014180

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

CNhs10513

0	0
1	0.103
10	0
100	0.0766
1000	0.0737
1001	0.0651
1002	-0.0468
1003	0.0602
1004	0
1005	0.0479
1006	0.187
1007	0.00857
1008	0
1009	0.0353
101	-0.0221
1010	0
1011	0.1
1012	0.0438
1013	-0.0355
1014	0.401
1015	0.0117
1016	0.169
1017	0
1018	0.371
1019	0
102	0
1020	0
1021	0
1022	0.247
1023	0
1024	0.16
1025	0.437
1026	0.145
1027	0.15
1028	0
1029	-0.1
103	0.442
1030	0
1031	0.344
1032	-0.022
1033	0
1034	0.198
1035	0.129
1036	-0.0113
1037	0
1038	0.0613
1039	0.0638
104	0
1040	0.124
1041	0.198

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: CNhs10513

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.368
MA0003.1	MA0003.1	0.0865
MA0004.1	MA0004.1	0.0685
MA0006.1	MA0006.1	0.513
MA0007.1	MA0007.1	0.132
MA0009.1	MA0009.1	0.527
MA0014.1	MA0014.1	0.214
MA0017.1	MA0017.1	0.388
MA0018.2	MA0018.2	1.83182e-4
MA0019.1	MA0019.1	0.83
MA0024.1	MA0024.1	0.475
MA0025.1	MA0025.1	0.205
MA0027.1	MA0027.1	0.505
MA0028.1	MA0028.1	5.29781e-9
MA0029.1	MA0029.1	0.549
MA0030.1	MA0030.1	0.422
MA0031.1	MA0031.1	0.755
MA0035.2	MA0035.2	0.0998
MA0038.1	MA0038.1	0.0126
MA0039.2	MA0039.2	0.113
MA0040.1	MA0040.1	0.831
MA0041.1	MA0041.1	0.494
MA0042.1	MA0042.1	0.7
MA0043.1	MA0043.1	0.0627
MA0046.1	MA0046.1	1.97535e-19
MA0047.2	MA0047.2	0.0839
MA0048.1	MA0048.1	0.003
MA0050.1	MA0050.1	1.90546e-7
MA0051.1	MA0051.1	1.39622e-5
MA0052.1	MA0052.1	2.16537e-16
MA0055.1	MA0055.1	3.31586e-5
MA0057.1	MA0057.1	0.638
MA0058.1	MA0058.1	0.0104
MA0059.1	MA0059.1	0.00463
MA0060.1	MA0060.1	0.0385
MA0061.1	MA0061.1	0.106
MA0062.2	MA0062.2	1.94351e-16
MA0065.2	MA0065.2	0.66
MA0066.1	MA0066.1	0.694
MA0067.1	MA0067.1	0.0696
MA0068.1	MA0068.1	0.351
MA0069.1	MA0069.1	0.236
MA0070.1	MA0070.1	0.21
MA0071.1	MA0071.1	0.0247
MA0072.1	MA0072.1	0.175
MA0073.1	MA0073.1	0.986
MA0074.1	MA0074.1	0.192
MA0076.1	MA0076.1	4.3881e-10
MA0077.1	MA0077.1	0.717
MA0078.1	MA0078.1	0.0563
MA0079.2	MA0079.2	0.012
MA0080.2	MA0080.2	4.3656e-7
MA0081.1	MA0081.1	0.0311
MA0083.1	MA0083.1	5.08059e-10
MA0084.1	MA0084.1	0.818
MA0087.1	MA0087.1	0.113
MA0088.1	MA0088.1	0.132
MA0090.1	MA0090.1	0.0408
MA0091.1	MA0091.1	0.763
MA0092.1	MA0092.1	0.29
MA0093.1	MA0093.1	0.0589
MA0099.2	MA0099.2	0.683
MA0100.1	MA0100.1	0.00591
MA0101.1	MA0101.1	0.00669
MA0102.2	MA0102.2	0.199
MA0103.1	MA0103.1	0.804
MA0104.2	MA0104.2	0.0822
MA0105.1	MA0105.1	0.775
MA0106.1	MA0106.1	0.289
MA0107.1	MA0107.1	0.0361
MA0108.2	MA0108.2	1.05129e-53
MA0111.1	MA0111.1	0.647
MA0112.2	MA0112.2	0.664
MA0113.1	MA0113.1	0.15
MA0114.1	MA0114.1	0.846
MA0115.1	MA0115.1	0.169
MA0116.1	MA0116.1	0.873
MA0117.1	MA0117.1	0.165
MA0119.1	MA0119.1	0.211
MA0122.1	MA0122.1	0.73
MA0124.1	MA0124.1	0.871
MA0125.1	MA0125.1	0.0137
MA0131.1	MA0131.1	0.231
MA0135.1	MA0135.1	0.0571
MA0136.1	MA0136.1	1.06296e-13
MA0137.2	MA0137.2	0.00105
MA0138.2	MA0138.2	2.11122e-6
MA0139.1	MA0139.1	0.194
MA0140.1	MA0140.1	0.00369
MA0141.1	MA0141.1	0.0379
MA0142.1	MA0142.1	0.783
MA0143.1	MA0143.1	0.781
MA0144.1	MA0144.1	0.0941
MA0145.1	MA0145.1	0.0786
MA0146.1	MA0146.1	0.255
MA0147.1	MA0147.1	0.0633
MA0148.1	MA0148.1	0.0449
MA0149.1	MA0149.1	0.00532
MA0150.1	MA0150.1	0.183
MA0152.1	MA0152.1	0.932
MA0153.1	MA0153.1	3.53897e-9
MA0154.1	MA0154.1	0.377
MA0155.1	MA0155.1	0.145
MA0156.1	MA0156.1	1.26058e-12
MA0157.1	MA0157.1	0.932
MA0159.1	MA0159.1	0.0416
MA0160.1	MA0160.1	0.0516
MA0162.1	MA0162.1	0.965
MA0163.1	MA0163.1	0.232
MA0164.1	MA0164.1	0.16
MA0258.1	MA0258.1	0.377
MA0259.1	MA0259.1	0.207

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: CNhs10513

Novel motif	Logo	P-value
1	1	0.508
10	10	0.0806
100	100	0.532
101	101	0.1
102	102	0.0485
103	103	0.0386
104	104	0.73
105	105	0.462
106	106	0.581
107	107	0.024
108	108	0.813
109	109	0.372
11	11	0.313
110	110	0.292
111	111	0.018
112	112	0.106
113	113	0.633
114	114	0.196
115	115	0.863
116	116	0.371
117	117	0.00415
118	118	0.144
119	119	0.694
12	12	0.358
120	120	0.384
121	121	0.291
122	122	0.248
123	123	0.401
124	124	0.646
125	125	0.099
126	126	0.124
127	127	0.78
128	128	0.532
129	129	0.804
13	13	0.0371
130	130	0.471
131	131	0.0527
132	132	0.943
133	133	0.0828
134	134	0.482
135	135	0.739
136	136	0.176
137	137	0.55
138	138	0.762
139	139	0.696
14	14	0.389
140	140	0.725
141	141	0.838
142	142	0.749
143	143	0.144
144	144	0.817
145	145	0.359
146	146	0.204
147	147	0.95
148	148	0.28
149	149	0.858
15	15	0.0267
150	150	0.88
151	151	0.776
152	152	0.534
153	153	0.298
154	154	0.415
155	155	0.0295
156	156	0.0797
157	157	0.134
158	158	0.00395
159	159	0.0657
160	160	0.126
161	161	0.118
162	162	0.274
163	163	0.817
164	164	0.0362
165	165	0.395
166	166	0.118
167	167	0.00395
168	168	0.00139
169	169	0.639
17	17	0.966
18	18	0.245
19	19	0.444
2	2	0.0189
20	20	0.00368
21	21	0.342
22	22	0.834
23	23	0.274
24	24	0.156
25	25	0.695
26	26	0.511
27	27	0.464
28	28	0.819
29	29	0.0228
3	3	0.411
30	30	0.072
31	31	0.683
32	32	0.754
33	33	0.19
34	34	0.349
35	35	0.151
36	36	0.0629
37	37	0.257
38	38	0.702
39	39	0.711
4	4	0.914
40	40	0.211
41	41	0.205
42	42	0.619
43	43	0.999
44	44	0.205
45	45	0.201
46	46	0.737
47	47	0.827
48	48	0.415
49	49	0.515
5	5	0.536
50	50	0.683
51	51	0.857
52	52	0.199
53	53	0.14
54	54	0.476
55	55	0.743
56	56	0.586
57	57	0.529
58	58	0.833
59	59	0.133
6	6	0.91
60	60	0.804
61	61	0.308
62	62	0.792
63	63	0.865
64	64	0.951
65	65	0.87
66	66	0.999
67	67	0.916
68	68	0.53
69	69	0.771
7	7	0.794
70	70	0.0118
71	71	0.393
72	72	0.504
73	73	0.142
74	74	0.788
75	75	0.0411
76	76	0.0016
77	77	0.336
78	78	0.683
79	79	0.836
8	8	0.407
80	80	0.901
81	81	0.587
82	82	0.833
83	83	0.558
84	84	0.705
85	85	0.921
86	86	0.963
87	87	0.58
88	88	0.363
89	89	0.419
9	9	0.489
90	90	0.0119
91	91	0.505
92	92	0.684
93	93	0.0316
94	94	0.968
95	95	0.0238
96	96	0.866
97	97	0.576
98	98	0.748
99	99	0.138

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: CNhs10513

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011374 mouse whole body- embryo E17.5 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)
0000922 (embryo)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000301 (mouse embryonic day 17.5 sample)
0011374 (mouse whole body- embryo E17.5 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
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004978
+|accession_numbers=CAGE;DRX009148;DRR010022;DRZ001447;DRZ002830;DRZ012797;DRZ014180
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
 |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=chr13:83643159..83643226,+!p3@Mef2c!1.51!31.25!Mef2c;;chr12:34642510..34642530,+!p1@Twist1!1.37!69.83!Twist1;;chr5:77543897..77543911,-!p2@Hopx!1.36!41.28!Hopx;;chr3:99057269..99057306,+!p1@Tbx15!1.31!23.73!Tbx15;;chr11:121380640..121380655,-!p1@Zfp750!1.30!30.87!Zfp750;;chr6:55631042..55631102,-!p1@Neurod6!1.30!19.10!Neurod6;;chr7:6649134..6649167,-!p1@Zim1!1.29!97.61!Zim1;;chr1:136186574..136186592,+!p1@Myog!1.29!18.33!Myog;;chr16:25801993..25802014,+!p1@Trp63!1.27!17.75!Trp63;;chr10:106931775..106931798,-!p1@Myf6!1.25!16.78!Myf6;;chr4:87452200..87452229,-!p2@Mllt3!1.20!31.25!Mllt3;;chr4:87452180..87452196,-!p3@Mllt3!1.20!29.13!Mllt3;;chr15:103085660..103085681,-!p1@Nfe2!1.20!22.18!Nfe2;;chr12:74147689..74147711,-!p1@Six1!1.17!29.90!Six1;;chr7:17647736..17647772,-!p1@Hif3a!1.15!45.91!Hif3a;;chr2:120365588..120365602,-!p2@Zfp106!1.15!21.99!Zfp106;;chr13:40829137..40829205,-!p1@Tfap2a!1.14!14.28!Tfap2a;;chr9:74709695..74709722,+!p1@Onecut1!1.13!12.54!Onecut1;;chr13:72766250..72766273,+!p1@Irx2!1.12!19.10!Irx2;;chr11:94981424..94981439,+!p1@Dlx3!1.12!13.89!Dlx3;;chr8:87425854..87425891,+!p1@Klf1!1.10!11.57!Klf1;;chr10:12810631..12810649,+!p1@Plagl1!1.09!294.38!Plagl1;;chr17:44951553..44951586,-!p2@Runx2!1.09!12.54!Runx2;;chr4:135129538..135129558,-!p1@Grhl3!1.08!16.78!Grhl3;;chr9:31720843..31720888,-!p1@Barx2!1.08!12.15!Barx2;;chr19:5560600..5560617,-!p1@Ovol1!1.06!12.73!Ovol1;;chr10:22539932..22539956,-!p1@Tcf21!1.05!27.59!Tcf21;;chr9:91260616..91260653,-!p2@Zic1!1.05!10.22!Zic1;;chr12:37835141..37835194,+!p1@Meox2!1.04!31.64!Meox2;;chr11:121380594..121380609,-!p2@Zfp750!1.02!16.78!Zfp750;;chr10:80555320..80555378,-!p1@Creb3l3!1.01!10.80!Creb3l3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.00!11.57!Pou3f3;;chr1:165243591..165243625,-!p2@Prrx1!0.99!13.70!Prrx1;;chr13:72766279..72766296,+!p2@Irx2!0.99!13.31!Irx2;;chr12:37835120..37835133,+!p2@Meox2!0.99!12.73!Meox2;;chr17:44951431..44951445,-!p3@Runx2!0.99!8.87!Runx2;;chr3:3634145..3634161,+!p1@Hnf4g!0.99!8.87!Hnf4g;;chr15:102828658..102828678,+!p1@Hoxc6!0.99!8.68!Hoxc6;;chr15:102197405..102197454,-!p1@Sp7!0.99!8.68!Sp7;;chr9:91260594..91260612,-!p1@Zic1!0.98!8.49!Zic1;;chr7:53631837..53631850,+!p1@Myod1!0.98!8.49!Myod1;;chr12:30213247..30213333,+!p1@Myt1l!0.97!8.29!Myt1l;;chr13:55932591..55932622,-!p1@Pitx1!0.96!9.84!Pitx1;;chr1:179374784..179374800,+!p2@Zfp238!0.94!9.07!Zfp238;;chr7:19608891..19608895,-!p1@Foxa3!0.93!9.84!Foxa3;;chr11:96143666..96143725,+!p1@Hoxb8!0.92!8.49!Hoxb8;;chr5:77543935..77543947,-!p4@Hopx!0.91!7.14!Hopx;;chr10:126778916..126778974,-!p1@Gli1!0.90!16.01!Gli1;;chr2:103143336..103143367,-!p1@Ehf!0.90!11.38!Ehf;;chr7:122989594..122989626,-!p1@Sox6!0.90!6.94!Sox6;;chr11:121380611..121380625,-!p3@Zfp750!0.89!8.29!Zfp750;;chr6:6832076..6832092,-!p1@Dlx5!0.89!8.10!Dlx5;;chr7:122989632..122989668,-!p2@Sox6!0.89!6.75!Sox6;;chr9:43013917..43013968,-!p1@Pou2f3!0.89!6.75!Pou2f3;;chr11:98190918..98190951,-!p1@Neurod2!0.89!6.75!Neurod2;;chr8:59799772..59799789,+!p1@Hand2!0.88!19.87!Hand2;;chr10:88969376..88969395,-!p1@Nr1h4!0.88!6.56!Nr1h4;;chr3:95032091..95032183,-!p1@Mllt11!0.87!57.29!Mllt11;;chr2:9800207..9800234,-!p1@Gata3!0.87!20.64!Gata3;;chr1:93698030..93698064,+!p1@Twist2!0.87!13.31!Twist2;;chr7:119885539..119885574,+!p3@Tead1!0.87!6.37!Tead1;;chr6:52190467..52190500,-!p1@Hoxa10!0.87!6.37!Hoxa10;;chr12:109242266..109242295,-!p1@Bcl11b!0.86!54.98!Bcl11b;;chr10:44178521..44178557,-!p1@Prdm1!0.86!11.38!Prdm1;;chr12:54349410..54349461,+!p1@Npas3!0.86!7.72!Npas3;;chr2:172375081..172375105,+!p1@Tfap2c!0.86!6.17!Tfap2c;;chrX:7544943..7545001,-!p1@Gata1!0.86!6.17!Gata1;;chr1:165243379..165243402,-!p3@Prrx1!0.85!9.45!Prrx1;;chr2:28477452..28477483,-!p1@Gfi1b!0.85!7.72!Gfi1b;;chr12:28027561..28027591,-!p1@Sox11!0.83!40.70!Sox11;;chr2:65683890..65683907,+!p1@Csrnp3!0.83!11.38!Csrnp3;;chr17:48015839..48015915,-!p3@Foxp4!0.83!6.94!Foxp4;;chr2:79296783..79296801,-!p1@Neurod1!0.83!5.79!Neurod1;;chr7:116154364..116154444,+!p1@Tub!0.82!10.03!Tub;;chr16:91270004..91270023,+!p1@Olig1!0.82!6.56!Olig1;;chr2:71384802..71384815,-!p1@Dlx2!0.81!6.94!Dlx2;;chr11:85699862..85699920,+!p1@Tbx4!0.81!5.40!Tbx4;;chr19:19185671..19185693,-!p1@Rorb!0.79!13.12!Rorb;;chr13:72101178..72101203,-!p1@Irx1!0.79!8.29!Irx1;;chr15:85566184..85566238,+!p1@Ppara!0.79!7.91!Ppara;;chr13:83643232..83643254,+!p5@Mef2c!0.79!5.21!Mef2c;;chr19:55969923..55969944,+!p6@Tcf7l2!0.79!5.21!Tcf7l2;;chr1:19199236..19199258,+!p1@Tfap2b!0.79!5.21!Tfap2b;;chr11:96880072..96880079,+!p1@Sp6!0.79!5.21!Sp6;;chr5:148118639..148118715,-!p1@Cdx2!0.79!5.21!Cdx2;;chr6:70906450..70906454,+!p1@Foxi3!0.79!5.21!Foxi3;;chr12:37835203..37835218,+!p3@Meox2!0.78!6.17!Meox2;;chr2:163372884..163372904,+!p1@Hnf4a!0.78!5.02!Hnf4a;;chr4:114732112..114732158,+!p1@Tal1!0.77!11.38!Tal1;;chr1:140739014..140739032,-!p1@Lhx9!0.77!6.37!Lhx9;;chr1:169548377..169548430,+!p1@Rxrg!0.77!4.82!Rxrg;;chr12:57796615..57796687,+!p1@Pax9!0.77!4.82!Pax9;;chr3:99057256..99057268,+!p3@Tbx15!0.77!4.82!Tbx15;;chrX:108009761..108009788,+!p1@Pou3f4!0.77!4.82!Pou3f4;;chr1:137155026..137155042,-!p1@Elf3!0.76!30.09!Elf3;;chr15:35225845..35225867,+!p1@Osr2!0.76!12.92!Osr2;;chr9:96159147..96159204,+!p2@Tfdp2!0.76!9.45!Tfdp2;;chr11:101755669..101755686,-!p1@Meox1!0.76!9.07!Meox1;;chr13:99124189..99124205,+!p1@Foxd1!0.76!7.52!Foxd1;;chr6:128250380..128250442,-!p2@Tead4!0.76!6.17!Tead4;;chr2:38206580..38206600,+!p2@Lhx2!0.76!5.98!Lhx2;;chr1:57028125..57028149,-!p2@Satb2!0.75!4.63!Satb2;;chr12:30219426..30219506,+!p2@Myt1l!0.75!4.63!Myt1l;;chr16:38294860..38294924,-!p1@Nr1i2!0.75!4.63!Nr1i2;;chr13:40825465..40825469,-!p2@Tfap2a!0.74!4.44!Tfap2a;;chr3:99057677..99057730,+!p2@Tbx15!0.74!4.44!Tbx15;;chr4:87452167..87452178,-!p8@Mllt3!0.74!4.44!Mllt3;;chr18:80909801..80909819,-!p1@Nfatc1!0.73!28.55!Nfatc1;;chr14:67853632..67853674,+!p3@Ebf2!0.73!5.40!Ebf2;;chr14:99697871..99697934,+!p1@Klf5!0.72!93.75!Klf5;;chr15:102087737..102087801,-!p3@Rarg!0.72!7.33!Rarg;;chr15:102196745..102196769,-!p2@Sp7!0.72!4.24!Sp7;;chr8:94881733..94881790,+!p1@Irx5!0.71!8.68!Irx5;;chr6:6831950..6831985,-!p2@Dlx5!0.71!4.63!Dlx5;;chr9:87626083..87626108,-!p1@Tbx18!0.70!9.65!Tbx18;;chr3:66785857..66785873,-!p1@Shox2!0.70!4.05!Shox2;;chr2:61642631..61642684,+!p1@Tbr1!0.70!4.05!Tbr1;;chr12:37835248..37835260,+!p4@Meox2!0.70!4.05!Meox2;;chr12:25257265..25257294,+!p2@Grhl1!0.70!4.05!Grhl1;;chr2:160192793..160192809,-!p1@Mafb!0.69!67.13!Mafb;;chr4:55545337..55545357,-!p1@Klf4!0.69!65.40!Klf4;;chr1:57029281..57029326,-!p1@Satb2!0.69!6.37!Satb2;;chr2:38206744..38206766,+!p1@Lhx2!0.69!4.82!Lhx2;;chr4:139388835..139388867,-!p1@Pax7!0.69!3.86!Pax7;;chr15:103082088..103082136,-!p2@Nfe2!0.69!3.86!Nfe2;;chr9:71743854..71743909,-!p1@Tcf12!0.68!33.95!Tcf12;;chr7:144506077..144506128,-!p1@Ebf3!0.68!9.65!Ebf3;;chr14:56443806..56443848,+!p1@Nfatc4!0.68!8.29!Nfatc4;;chr3:34548909..34548927,+!p1@Sox2!0.68!6.94!Sox2;;chr15:103085690..103085710,-!p3@Nfe2!0.68!4.24!Nfe2;;chr18:64499674..64499696,+!p1@Onecut2!0.67!6.75!Onecut2;;chrX:90531838..90531861,+!p1@Arx!0.67!4.82!Arx;;chr19:59533221..59533271,+!p1@Emx2!0.67!4.63!Emx2;;chr11:83664365..83664383,+!p1@Hnf1b!0.67!3.67!Hnf1b;;chr10:106923133..106923146,-!p1@Myf5!0.67!3.67!Myf5;;chr3:101814061..101814094,+!p1@Nhlh2!0.67!3.67!Nhlh2;;chr2:71367871..71367898,+!p1@Dlx1!0.67!3.67!Dlx1;;chr9:69137716..69137744,+!p1@Rora!0.66!25.85!Rora;;chr2:91864449..91864492,-!p3@Creb3l1!0.66!6.17!Creb3l1;;chr14:67853425..67853454,+!p1@Ebf2!0.66!5.40!Ebf2;;chr6:52176164..52176195,-!p1@Hoxa9!0.66!4.63!Hoxa9;;chr6:14851440..14851497,+!p2@Foxp2!0.65!9.45!Foxp2;;chr8:87297280..87297326,-!p2@Nfix!0.65!9.07!Nfix;;chr18:64499706..64499721,+!p2@Onecut2!0.65!5.21!Onecut2;;chr9:24578720..24578735,-!p1@Tbx20!0.65!3.47!Tbx20;;chr2:103143315..103143328,-!p2@Ehf!0.65!3.47!Ehf;;chr6:30908793..30908815,-!p1@Klf14!0.65!3.47!Klf14;;chr1:165243792..165243808,-!p1@Prrx1!0.64!13.50!Prrx1;;chr17:25707623..25707639,-!p1@Sox8!0.63!16.40!Sox8;;chr11:116196664..116196679,-!p1@Foxj1!0.63!5.40!Foxj1;;chr19:25746898..25746910,+!p1@Dmrt2!0.63!5.21!Dmrt2;;chr3:5218516..5218544,+!p2@Zfhx4!0.63!5.21!Zfhx4;;chr11:11584970..11585030,+!p2@Ikzf1!0.63!5.02!Ikzf1;;chr7:144505957..144505972,-!p2@Ebf3!0.63!4.24!Ebf3;;chr6:6831928..6831949,-!p3@Dlx5!0.63!3.28!Dlx5;;chr1:57028538..57028553,-!p6@Satb2!0.63!3.28!Satb2;;chr14:49287186..49287225,-!p1@Otx2!0.63!3.28!Otx2;;chr10:106931803..106931817,-!p2@Myf6!0.63!3.28!Myf6;;chr17:86087592..86087615,-!p1@Six2!0.63!3.28!Six2;;chr7:35904304..35904320,+!p1@Cebpa!0.62!77.36!Cebpa;;chr12:34642682..34642753,+!p2@Twist1!0.62!9.45!Twist1;;chr8:94325321..94325366,-!p1@Irx3!0.62!8.68!Irx3;;chr13:31717548..31717596,+!p1@Foxf2!0.62!6.94!Foxf2;;chr12:58646974..58647003,-!p1@Foxa1!0.62!4.44!Foxa1;;chr8:94325814..94325839,-!p2@Irx3!0.61!7.14!Irx3;;chr7:144505980..144506010,-!p3@Ebf3!0.61!3.86!Ebf3;;chr16:91225808..91225824,+!p1@Olig2!0.61!3.09!Olig2;;chr1:169528720..169528749,+!p6@Rxrg!0.61!3.09!Rxrg;;chr1:57028556..57028583,-!p5@Satb2!0.61!3.09!Satb2;;chr2:103264213..103264233,+!p1@Elf5!0.61!3.09!Elf5;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.60!13.89!Ppp1r13l;;chr4:148178559..148178603,+!p1@Casz1!0.60!9.84!Casz1;;chr4:13670571..13670625,+!p1@Runx1t1!0.60!9.45!Runx1t1;;chr2:74542918..74542971,+!p1@Hoxd8!0.60!4.82!Hoxd8;;chr8:123608252..123608268,+!p1@Foxf1a!0.60!4.82!Foxf1a;;chr7:6683123..6683142,-!p1@Peg3!0.59!182.49!Peg3;;chr13:117099847..117099907,-!p1@Isl1!0.59!5.98!Isl1;;chr1:14746065..14746079,-!p1@Msc!0.59!3.67!Msc;;chr1:93698068..93698085,+!p2@Twist2!0.59!3.47!Twist2;;chr2:164228702..164228719,+!p1@Rbpjl!0.59!2.89!Rbpjl;;chr15:76352832..76352900,-!p1@Scrt1!0.59!2.89!Scrt1;;chr15:50714356..50714368,-!p14@Trps1!0.59!2.89!Trps1;;chr7:17642177..17642223,-!p3@Hif3a!0.59!2.89!Hif3a;;chr6:52195795..52195825,-!p1@Hoxa11!0.59!2.89!Hoxa11;;chr6:52184901..52184959,-!p2@Hoxa10!0.59!2.89!Hoxa10;;chr3:5218629..5218684,+!p1@Zfhx4!0.58!10.80!Zfhx4;;chr12:25257141..25257173,+!p1@Grhl1!0.58!6.56!Grhl1;;chr11:44430989..44431015,+!p4@Ebf1!0.58!5.59!Ebf1;;chr14:63864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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011374
 |is_obsolete=
+|library_id=CNhs10513
+|library_id_phase_based=2:CNhs10513
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;490
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;490
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5.CNhs10513.490-9F9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5.CNhs10513.490-9F9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5.CNhs10513.490-9F9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5.CNhs10513.490-9F9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5.CNhs10513.490-9F9.mm9.nobarcode.rdna.fa.gz
 |name=whole body, embryo E17.5
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10513,LSID649,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0446937034125132,0,0,0,0,0,0.345914173748315,0,0,0,0,0.635318924211553,0,0,0,0,0,0,-0.191893350882575,0,0,0,0.0766064454112358,0,0.0766064454112358,0,0,0,0,0,0,0,0.308804097076043,0,0,0,0.198305064902181,0.0657431673334649,0.0364594772431945,0.0864592980374361,0.262033004853749,0.678048065827105,0.275164445339063,0,0,0,0,0,0,0,0,0,0,0.0766064454112358,0,0.18236660653111,0.141704700595215,0,0,0,0,0,0.0766064454112358,0,0,0.0529716444806845,0.0960946639295665,-0.0622785032448363,0.175847616476514,0.0218016164856,0,0.193444040164534,0.0882033481136048,0,0.198305064902181,0,0.0636157139586853,0.0430544904615036,-0.00556364067308368,-0.0788315948399074,0,0,0,0,0,0,-0.0327098497339402,-0.214041398596072,-0.160647429228173,0,0,0.0766064454112358,0,0
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
 |top_motifs=TBP:2.6850142093;NKX3-2:2.37811303976;HOX{A4,D4}:2.36068813716;NKX2-3_NKX2-5:2.04089288333;TLX2:1.9125918365;T:1.89297391386;ZNF148:1.79247478273;TFCP2:1.77535163857;TFAP4:1.74356531856;FOXL1:1.53756330703;ZNF238:1.50860345391;SMAD1..7,9:1.49987026851;MYOD1:1.45722980739;PAX1,9:1.4475552124;TBX4,5:1.44457629417;TAL1_TCF{3,4,12}:1.44112681751;MAZ:1.42718211063;TGIF1:1.41530869124;LEF1_TCF7_TCF7L1,2:1.38737691928;FOXA2:1.38608429473;GLI1..3:1.36998436728;EP300:1.36207484059;MYFfamily:1.35487343841;GTF2I:1.26364477379;FOSL2:1.26327795158;FOX{F1,F2,J1}:1.25620553355;EN1,2:1.21741988694;MEF2{A,B,C,D}:1.2155751139;FOS_FOS{B,L1}_JUN{B,D}:1.13592733587;GFI1:1.11095916258;MZF1:1.10995404591;VSX1,2:1.10605103645;TLX1..3_NFIC{dimer}:1.06794488151;SRF:1.04224635417;XCPE1{core}:1.03099766356;GATA6:1.0177631088;PATZ1:0.98894839485;PBX1:0.984819430629;TEAD1:0.980350132349;SP1:0.978892851237;SOX{8,9,10}:0.978687152584;GFI1B:0.970298572182;MAFB:0.959298424435;HMX1:0.956793664854;SNAI1..3:0.947303256636;TFAP2{A,C}:0.941306413622;EBF1:0.93915101267;NKX2-1,4:0.923441209423;ESR1:0.906699863218;NHLH1,2:0.899340281616;GCM1,2:0.885736199046;RREB1:0.858132083687;ADNP_IRX_SIX_ZHX:0.833565648055;MTF1:0.820600276349;FOX{D1,D2}:0.78016320146;NANOG:0.777465422361;ATF6:0.770559593889;NFE2L2:0.766288330025;SOX5:0.752080504062;HNF1A:0.75010612326;POU5F1:0.741598162313;CEBPA,B_DDIT3:0.740378339133;ZNF423:0.718503038254;HOXA9_MEIS1:0.715047339908;HMGA1,2:0.711822153046;TP53:0.698779860005;TOPORS:0.680909676045;DBP:0.667298369711;LMO2:0.666518004936;PAX6:0.664925260546;HSF1,2:0.662555915766;PRDM1:0.65129214323;KLF4:0.637963185875;HLF:0.627066920766;HOX{A5,B5}:0.624295870571;GTF2A1,2:0.621321911109;CUX2:0.606429362118;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.593744753066;HIC1:0.590984488617;HIF1A:0.546092114223;NFIX:0.54582649402;MTE{core}:0.500857397565;POU3F1..4:0.498836694549;NANOG{mouse}:0.473114494529;RXRA_VDR{dimer}:0.472376966676;POU6F1:0.465598148061;PRRX1,2:0.450935526355;NFATC1..3:0.448193933513;RBPJ:0.422950040181;EGR1..3:0.417758806707;MYBL2:0.407329504817;HNF4A_NR2F1,2:0.401070999458;IKZF1:0.358938649412;ATF2:0.358126034093;PAX2:0.351615411874;LHX3,4:0.326023627747;TFAP2B:0.319210724407;REST:0.31068353677;PAX5:0.304105817144;OCT4_SOX2{dimer}:0.282607174835;ZIC1..3:0.265136809059;MED-1{core}:0.2482325969;CRX:0.234358044809;NR5A1,2:0.212800242421;NFE2:0.208676365585;NR3C1:0.183479517535;ZBTB6:0.181952107495;CDC5L:0.17843678879;ALX1:0.168622165351;SOX2:0.167502354522;HES1:0.160097454574;GATA4:0.145619227697;ZFP161:0.1275879085;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.126370970424;GZF1:0.115673005405;STAT2,4,6:0.114628268515;ONECUT1,2:0.088977234119;IKZF2:0.0773840414383;ESRRA:0.0741397776927;ZNF384:0.0434722227975;HBP1_HMGB_SSRP1_UBTF:0.0417199004268;ZEB1:0.0374287407985;NFY{A,B,C}:0.029039270471;TFDP1:0.020528172937;RFX2..5_RFXANK_RFXAP:0.0201056889428;BREu{core}:0.00879290986179;NR1H4:-0.0423159962581;RFX1:-0.0482620595649;SPZ1:-0.0494209649773;POU2F1..3:-0.0632622962985;E2F1..5:-0.066528630355;BACH2:-0.100507260231;SOX17:-0.106780875378;FOXD3:-0.108392352686;PPARG:-0.108958842587;NKX3-1:-0.115249164652;DMAP1_NCOR{1,2}_SMARC:-0.120004676195;AHR_ARNT_ARNT2:-0.127735859425;FOXP3:-0.144299090205;FOXM1:-0.153033587977;RORA:-0.154243929092;FOXP1:-0.181996048593;PITX1..3:-0.21400065745;ZNF143:-0.241393937709;JUN:-0.248880145008;IRF7:-0.258849457933;HAND1,2:-0.275573521625;ALX4:-0.300475868102;NFIL3:-0.311321527905;CDX1,2,4:-0.312736101072;SPI1:-0.337161909565;SPIB:-0.344121076628;PAX4:-0.345212856024;AR:-0.362353832298;ETS1,2:-0.37020492736;NKX6-1,2:-0.387727079377;RUNX1..3:-0.39509254819;FOX{I1,J2}:-0.429232586644;NKX2-2,8:-0.46937050112;RXR{A,B,G}:-0.487090355836;NFKB1_REL_RELA:-0.50786999436;UFEwm:-0.510497707444;FOXN1:-0.531364177569;EVI1:-0.545723753035;PDX1:-0.547250780912;NRF1:-0.557141679838;NR6A1:-0.573925088548;STAT5{A,B}:-0.58128291293;MYB:-0.583879237319;bHLH_family:-0.587056108511;POU1F1:-0.601255808284;FOXQ1:-0.641751713859;YY1:-0.644974146427;NFE2L1:-0.654794184123;ATF5_CREB3:-0.660944167281;TEF:-0.723172495196;FOXO1,3,4:-0.728063218883;ARID5B:-0.742834194205;ATF4:-0.767628654357;ELF1,2,4:-0.774832604613;IRF1,2:-0.797203254906;SREBF1,2:-0.902893119351;CREB1:-0.908568198255;AIRE:-0.953418609683;PAX8:-1.01310150597;ELK1,4_GABP{A,B1}:-1.32600479299;STAT1,3:-1.36708256771;BPTF:-1.36737295946;ZBTB16:-1.51278459687
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:490-9F9;search_select_hide=table117:490-9F9
 }}

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FF:490-9F9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:17, 4 June 2020

CNhs10513

	FAQ
	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0