FF:761-6B4: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	whole body, neonate N10
Species:	Mouse (Mus musculus)
Library ID:	CNhs10518
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	whole body
dev stage	10 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		SAMD00005787

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10518		CAGE		DRX009154		DRR010028

Accession ID Mm9

Library id		BAM		CTSS
CNhs10518		DRZ001453		DRZ002836

Accession ID Mm10

Library id		BAM		CTSS
CNhs10518		DRZ012803		DRZ014186

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

CNhs10518

0	0
1	0.0646
10	0
100	0
1000	0.435
1001	0.182
1002	-0.0513
1003	0.162
1004	0
1005	0.0881
1006	0.491
1007	-0.0888
1008	0
1009	0.144
101	-0.0158
1010	0
1011	0.0366
1012	0
1013	-0.0689
1014	0.165
1015	-0.0559
1016	0.0298
1017	0
1018	0.0871
1019	0
102	0
1020	0
1021	0.0419
1022	0.55
1023	0
1024	0.239
1025	0
1026	0.136
1027	0.152
1028	0
1029	-0.0114
103	0.74
1030	0.165
1031	0.262
1032	0.197
1033	0
1034	0
1035	0.285
1036	-0.036
1037	0
1038	-0.0453
1039	0.244
104	0
1040	0.126
1041	0.49

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: CNhs10518

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0662
MA0003.1	MA0003.1	0.0108
MA0004.1	MA0004.1	0.0918
MA0006.1	MA0006.1	0.143
MA0007.1	MA0007.1	0.553
MA0009.1	MA0009.1	0.698
MA0014.1	MA0014.1	0.941
MA0017.1	MA0017.1	0.133
MA0018.2	MA0018.2	0.0181
MA0019.1	MA0019.1	0.112
MA0024.1	MA0024.1	0.0784
MA0025.1	MA0025.1	0.583
MA0027.1	MA0027.1	0.208
MA0028.1	MA0028.1	2.12603e-4
MA0029.1	MA0029.1	0.785
MA0030.1	MA0030.1	0.733
MA0031.1	MA0031.1	0.721
MA0035.2	MA0035.2	0.821
MA0038.1	MA0038.1	0.13
MA0039.2	MA0039.2	0.188
MA0040.1	MA0040.1	0.0696
MA0041.1	MA0041.1	0.309
MA0042.1	MA0042.1	0.49
MA0043.1	MA0043.1	0.0185
MA0046.1	MA0046.1	3.23452e-8
MA0047.2	MA0047.2	0.218
MA0048.1	MA0048.1	0.00154
MA0050.1	MA0050.1	0.147
MA0051.1	MA0051.1	0.665
MA0052.1	MA0052.1	2.10008e-53
MA0055.1	MA0055.1	4.83338e-4
MA0057.1	MA0057.1	0.503
MA0058.1	MA0058.1	0.0519
MA0059.1	MA0059.1	0.0157
MA0060.1	MA0060.1	0.192
MA0061.1	MA0061.1	0.709
MA0062.2	MA0062.2	1.98761e-7
MA0065.2	MA0065.2	0.0252
MA0066.1	MA0066.1	0.799
MA0067.1	MA0067.1	0.166
MA0068.1	MA0068.1	0.956
MA0069.1	MA0069.1	0.289
MA0070.1	MA0070.1	0.755
MA0071.1	MA0071.1	0.836
MA0072.1	MA0072.1	0.307
MA0073.1	MA0073.1	0.611
MA0074.1	MA0074.1	0.845
MA0076.1	MA0076.1	2.39175e-5
MA0077.1	MA0077.1	0.664
MA0078.1	MA0078.1	0.0317
MA0079.2	MA0079.2	0.0283
MA0080.2	MA0080.2	0.66
MA0081.1	MA0081.1	0.893
MA0083.1	MA0083.1	3.17325e-9
MA0084.1	MA0084.1	0.366
MA0087.1	MA0087.1	0.778
MA0088.1	MA0088.1	0.935
MA0090.1	MA0090.1	0.284
MA0091.1	MA0091.1	0.186
MA0092.1	MA0092.1	0.132
MA0093.1	MA0093.1	0.0995
MA0099.2	MA0099.2	0.576
MA0100.1	MA0100.1	0.0235
MA0101.1	MA0101.1	0.458
MA0102.2	MA0102.2	0.457
MA0103.1	MA0103.1	0.00435
MA0104.2	MA0104.2	0.0379
MA0105.1	MA0105.1	0.464
MA0106.1	MA0106.1	0.589
MA0107.1	MA0107.1	0.632
MA0108.2	MA0108.2	1.96658e-42
MA0111.1	MA0111.1	0.843
MA0112.2	MA0112.2	0.00159
MA0113.1	MA0113.1	0.74
MA0114.1	MA0114.1	0.242
MA0115.1	MA0115.1	0.0056
MA0116.1	MA0116.1	0.215
MA0117.1	MA0117.1	0.961
MA0119.1	MA0119.1	0.215
MA0122.1	MA0122.1	0.149
MA0124.1	MA0124.1	0.686
MA0125.1	MA0125.1	0.146
MA0131.1	MA0131.1	0.283
MA0135.1	MA0135.1	0.176
MA0136.1	MA0136.1	0.0036
MA0137.2	MA0137.2	0.0111
MA0138.2	MA0138.2	6.34727e-4
MA0139.1	MA0139.1	0.969
MA0140.1	MA0140.1	0.0119
MA0141.1	MA0141.1	0.178
MA0142.1	MA0142.1	0.226
MA0143.1	MA0143.1	0.107
MA0144.1	MA0144.1	0.381
MA0145.1	MA0145.1	0.0174
MA0146.1	MA0146.1	0.697
MA0147.1	MA0147.1	0.0655
MA0148.1	MA0148.1	0.794
MA0149.1	MA0149.1	0.0199
MA0150.1	MA0150.1	0.937
MA0152.1	MA0152.1	0.367
MA0153.1	MA0153.1	2.10136e-8
MA0154.1	MA0154.1	0.0348
MA0155.1	MA0155.1	0.095
MA0156.1	MA0156.1	0.0027
MA0157.1	MA0157.1	0.824
MA0159.1	MA0159.1	0.663
MA0160.1	MA0160.1	0.416
MA0162.1	MA0162.1	0.201
MA0163.1	MA0163.1	0.135
MA0164.1	MA0164.1	0.112
MA0258.1	MA0258.1	0.0539
MA0259.1	MA0259.1	0.116

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: CNhs10518

Novel motif	Logo	P-value
1	1	0.966
10	10	0.546
100	100	0.983
101	101	0.149
102	102	0.758
103	103	0.406
104	104	0.515
105	105	0.105
106	106	0.138
107	107	0.189
108	108	0.678
109	109	0.235
11	11	0.691
110	110	0.852
111	111	0.242
112	112	0.663
113	113	0.269
114	114	0.776
115	115	0.823
116	116	0.0882
117	117	0.1
118	118	0.384
119	119	0.412
12	12	0.0662
120	120	0.68
121	121	0.754
122	122	0.846
123	123	0.11
124	124	0.725
125	125	0.784
126	126	0.493
127	127	0.377
128	128	0.282
129	129	0.519
13	13	0.566
130	130	0.603
131	131	0.312
132	132	0.972
133	133	0.138
134	134	0.827
135	135	0.211
136	136	0.772
137	137	0.168
138	138	0.451
139	139	0.365
14	14	0.191
140	140	0.935
141	141	0.241
142	142	0.102
143	143	0.934
144	144	0.0844
145	145	0.309
146	146	0.407
147	147	0.978
148	148	0.98
149	149	0.137
15	15	0.549
150	150	0.818
151	151	0.127
152	152	0.0495
153	153	0.539
154	154	0.555
155	155	0.511
156	156	0.798
157	157	0.114
158	158	0.274
159	159	0.146
160	160	0.12
161	161	0.287
162	162	0.811
163	163	0.78
164	164	0.165
165	165	0.191
166	166	0.56
167	167	0.0202
168	168	0.0457
169	169	0.00677
17	17	0.437
18	18	0.504
19	19	0.049
2	2	0.0385
20	20	0.0289
21	21	0.616
22	22	0.243
23	23	0.36
24	24	0.715
25	25	0.545
26	26	0.63
27	27	0.486
28	28	0.823
29	29	0.156
3	3	0.894
30	30	0.306
31	31	0.501
32	32	0.032
33	33	0.339
34	34	0.098
35	35	0.243
36	36	0.163
37	37	0.263
38	38	0.644
39	39	0.539
4	4	0.881
40	40	0.975
41	41	0.278
42	42	0.68
43	43	0.576
44	44	0.92
45	45	0.214
46	46	0.842
47	47	0.758
48	48	0.94
49	49	0.795
5	5	0.4
50	50	0.48
51	51	0.734
52	52	0.212
53	53	0.142
54	54	0.29
55	55	0.908
56	56	0.399
57	57	0.672
58	58	0.621
59	59	0.00787
6	6	0.628
60	60	0.349
61	61	0.416
62	62	0.482
63	63	0.336
64	64	0.787
65	65	0.471
66	66	0.465
67	67	0.526
68	68	0.449
69	69	0.305
7	7	0.381
70	70	0.875
71	71	0.425
72	72	0.998
73	73	0.187
74	74	0.435
75	75	0.513
76	76	0.0181
77	77	0.245
78	78	0.111
79	79	0.308
8	8	0.897
80	80	0.208
81	81	0.166
82	82	0.204
83	83	0.213
84	84	0.493
85	85	0.0969
86	86	0.671
87	87	0.175
88	88	0.551
89	89	0.347
9	9	0.22
90	90	0.0614
91	91	0.143
92	92	0.378
93	93	0.385
94	94	0.761
95	95	0.361
96	96	0.808
97	97	0.873
98	98	0.981
99	99	0.342

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: CNhs10518

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011420 mouse whole body- neonate N10 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011420 (mouse whole body- neonate N10 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@SAMD00005787
+|accession_numbers=CAGE;DRX009154;DRR010028;DRZ001453;DRZ002836;DRZ012803;DRZ014186
 |ancestors_in_anatomy_facet=UBERON:0000468,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!1.93!83.94!Mef2c;;chr2:120365588..120365602,-!p2@Zfp106!1.59!62.60!Zfp106;;chr7:119885539..119885574,+!p3@Tead1!1.48!29.45!Tead1;;chr17:14011485..14011507,+!p2@Mllt4!1.42!25.27!Mllt4;;chr10:106931775..106931798,-!p1@Myf6!1.41!24.81!Myf6;;chr12:37835141..37835194,+!p1@Meox2!1.37!67.94!Meox2;;chr4:87452200..87452229,-!p2@Mllt3!1.36!45.68!Mllt3;;chr1:136186574..136186592,+!p1@Myog!1.36!21.80!Myog;;chr3:99057677..99057730,+!p2@Tbx15!1.35!21.56!Tbx15;;chr11:100683839..100683890,-!p2@Stat5b!1.31!44.52!Stat5b;;chr15:102197405..102197454,-!p1@Sp7!1.31!19.25!Sp7;;chr3:99057269..99057306,+!p1@Tbx15!1.30!22.95!Tbx15;;chr12:74147689..74147711,-!p1@Six1!1.29!39.88!Six1;;chr17:44951431..44951445,-!p3@Runx2!1.29!18.32!Runx2;;chr8:87425854..87425891,+!p1@Klf1!1.26!17.16!Klf1;;chr16:43363190..43363242,+!p2@Zbtb20!1.25!51.01!Zbtb20;;chr17:44951553..44951586,-!p2@Runx2!1.25!18.55!Runx2;;chr4:87452180..87452196,-!p3@Mllt3!1.24!32.23!Mllt3;;chr7:53631837..53631850,+!p1@Myod1!1.21!15.30!Myod1;;chr12:37835120..37835133,+!p2@Meox2!1.16!19.48!Meox2;;chr6:52190467..52190500,-!p1@Hoxa10!1.15!13.22!Hoxa10;;chr15:103085660..103085681,-!p1@Nfe2!1.14!19.01!Nfe2;;chr7:6649134..6649167,-!p1@Zim1!1.13!67.24!Zim1;;chr11:101755669..101755686,-!p1@Meox1!1.13!22.72!Meox1;;chr12:37835203..37835218,+!p3@Meox2!1.12!14.61!Meox2;;chr1:169548377..169548430,+!p1@Rxrg!1.12!12.06!Rxrg;;chr2:28477452..28477483,-!p1@Gfi1b!1.11!14.61!Gfi1b;;chr15:103164702..103164778,-!p3@Zfp385a!1.09!13.45!Zfp385a;;chr12:34642510..34642530,+!p1@Twist1!1.05!33.16!Twist1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.05!19.48!Tsc22d4;;chr5:135582751..135582788,+!p1@Mlxipl!1.01!37.56!Mlxipl;;chr7:122989594..122989626,-!p1@Sox6!1.00!9.04!Sox6;;chr13:83643136..83643158,+!p7@Mef2c!1.00!9.04!Mef2c;;chr16:91270004..91270023,+!p1@Olig1!0.99!10.20!Olig1;;chr1:38721792..38721845,-!p1@Aff3!0.98!10.90!Aff3;;chr9:51021788..51021802,+!p1@Pou2af1!0.98!10.20!Pou2af1;;chr16:25684232..25684285,+!p2@Trp63!0.98!8.58!Trp63;;chr2:74542918..74542971,+!p1@Hoxd8!0.96!12.52!Hoxd8;;chr12:37835248..37835260,+!p4@Meox2!0.96!8.12!Meox2;;chr1:165243792..165243808,-!p1@Prrx1!0.94!27.82!Prrx1;;chr9:96159147..96159204,+!p2@Tfdp2!0.94!14.61!Tfdp2;;chr6:115372058..115372085,+!p3@Pparg!0.94!7.65!Pparg;;chr10:5636374..5636421,-!p1@Esr1!0.93!9.51!Esr1;;chrX:7544943..7545001,-!p1@Gata1!0.93!7.42!Gata1;;chr13:30841099..30841116,+!p1@Irf4!0.92!11.59!Irf4;;chr11:94981424..94981439,+!p1@Dlx3!0.92!8.35!Dlx3;;chr15:102828658..102828678,+!p1@Hoxc6!0.91!7.19!Hoxc6;;chr1:165243379..165243402,-!p3@Prrx1!0.89!10.43!Prrx1;;chr6:52176164..52176195,-!p1@Hoxa9!0.89!8.58!Hoxa9;;chr16:43363152..43363186,+!p3@Zbtb20!0.88!15.77!Zbtb20;;chr18:80909801..80909819,-!p1@Nfatc1!0.87!39.65!Nfatc1;;chr7:51787434..51787448,-!p1@Spib!0.87!9.51!Spib;;chr4:44723559..44723593,-!p1@Pax5!0.87!6.49!Pax5;;chr13:83643232..83643254,+!p5@Mef2c!0.87!6.49!Mef2c;;chr7:122989632..122989668,-!p2@Sox6!0.87!6.49!Sox6;;chr6:115372099..115372121,+!p5@Pparg!0.87!6.49!Pparg;;chr15:102196745..102196769,-!p2@Sp7!0.86!6.26!Sp7;;chr17:25707623..25707639,-!p1@Sox8!0.85!27.59!Sox8;;chr10:106931803..106931817,-!p2@Myf6!0.85!6.03!Myf6;;chr6:6832076..6832092,-!p1@Dlx5!0.84!6.96!Dlx5;;chr2:151969288..151969294,+!p1@Tcf15!0.83!9.27!Tcf15;;chr4:114732112..114732158,+!p1@Tal1!0.82!12.75!Tal1;;chr14:67853632..67853674,+!p3@Ebf2!0.82!6.96!Ebf2;;chr12:37835219..37835230,+!p5@Meox2!0.82!5.56!Meox2;;chr15:75578748..75578752,-!p1@Mafa!0.82!5.56!Mafa;;chr4:139388835..139388867,-!p1@Pax7!0.82!5.56!Pax7;;chr10:106931839..106931851,-!p3@Myf6!0.82!5.56!Myf6;;chr1:57029281..57029326,-!p1@Satb2!0.81!8.81!Satb2;;chr15:76287876..76287894,+!p1@Scx!0.80!31.53!Scx;;chr4:87452167..87452178,-!p8@Mllt3!0.80!5.33!Mllt3;;chr8:87297280..87297326,-!p2@Nfix!0.79!12.75!Nfix;;chr14:67853425..67853454,+!p1@Ebf2!0.79!7.65!Ebf2;;chr15:103082088..103082136,-!p2@Nfe2!0.79!5.10!Nfe2;;chr1:165243591..165243625,-!p2@Prrx1!0.78!7.88!Prrx1;;chr6:6831950..6831985,-!p2@Dlx5!0.78!5.56!Dlx5;;chr10:12810631..12810649,+!p1@Plagl1!0.77!140.28!Plagl1;;chr10:5636354..5636373,-!p2@Esr1!0.77!4.87!Esr1;;chr9:63514630..63514652,-!p8@Smad3!0.77!4.87!Smad3;;chr19:25746898..25746910,+!p1@Dmrt2!0.76!7.42!Dmrt2;;chr15:103085690..103085710,-!p3@Nfe2!0.75!5.10!Nfe2;;chr11:96143666..96143725,+!p1@Hoxb8!0.73!5.10!Hoxb8;;chr11:98636531..98636559,-!p1@Nr1d1!0.72!26.90!Nr1d1;;chr5:24108047..24108106,-!p3@Smarcd3!0.72!7.88!Smarcd3;;chr14:67853457..67853482,+!p2@Ebf2!0.72!6.26!Ebf2;;chr11:96690779..96690790,-!p3@Nfe2l1!0.71!10.90!Nfe2l1;;chr3:99057256..99057268,+!p3@Tbx15!0.71!4.17!Tbx15;;chr6:6831928..6831949,-!p3@Dlx5!0.71!4.17!Dlx5;;chr16:92826249..92826325,-!p1@Runx1!0.70!10.90!Runx1;;chr5:24107993..24108036,-!p2@Smarcd3!0.70!10.43!Smarcd3;;chr11:44430812..44430838,+!p1@Ebf1!0.69!43.13!Ebf1;;chr15:97738692..97738747,-!p1@Vdr!0.69!23.88!Vdr;;chr2:152758901..152758925,-!p1@Foxs1!0.69!19.48!Foxs1;;chr10:67000609..67000625,+!p1@Egr2!0.69!9.74!Egr2;;chr7:52963269..52963305,+!p4@Dbp!0.69!5.80!Dbp;;chr10:106923133..106923146,-!p1@Myf5!0.69!3.94!Myf5;;chr11:96690797..96690813,-!p1@Nfe2l1!0.68!84.17!Nfe2l1;;chr14:19071466..19071550,-!p1@Nr1d2!0.68!29.68!Nr1d2;;chr6:52167513..52167549,-!p2@Hoxa7!0.68!5.56!Hoxa7;;chr10:80889867..80889924,-!p1@Nfic!0.67!120.11!Nfic;;chr18:7004715..7004731,-!p1@Mkx!0.67!9.74!Mkx;;chr15:85566184..85566238,+!p1@Ppara!0.67!5.80!Ppara;;chr3:5218516..5218544,+!p2@Zfhx4!0.67!5.80!Zfhx4;;chr15:75578637..75578669,-!p2@Mafa!0.67!4.17!Mafa;;chr11:44431687..44431706,+!p2@Ebf1!0.66!19.01!Ebf1;;chr5:24107903..24107917,-!p6@Smarcd3!0.66!4.64!Smarcd3;;chr12:34642682..34642753,+!p2@Twist1!0.65!10.20!Twist1;;chr11:100683794..100683805,-!p4@Stat5b!0.65!3.48!Stat5b;;chr1:57028125..57028149,-!p2@Satb2!0.65!3.48!Satb2;;chr1:57028538..57028553,-!p6@Satb2!0.65!3.48!Satb2;;chr14:64562503..64562524,+!p1@Sox7!0.63!22.26!Sox7;;chr18:69681483..69681514,+!p11@Tcf4!0.63!6.03!Tcf4;;chr2:168427252..168427273,-!p2@Nfatc2!0.63!4.17!Nfatc2;;chr9:91260616..91260653,-!p2@Zic1!0.63!3.25!Zic1;;chr7:53631818..53631829,+!p2@Myod1!0.63!3.25!Myod1;;chr16:91225808..91225824,+!p1@Olig2!0.63!3.25!Olig2;;chr1:92895299..92895373,+!p2@Lrrfip1!0.62!78.37!Lrrfip1;;chr4:63064364..63064384,-!p1@Akna!0.62!10.67!Akna;;chr15:78994907..78994926,-!p1@Sox10!0.62!9.27!Sox10;;chr6:52163319..52163342,-!p1@Hoxa3!0.62!4.87!Hoxa3;;chr17:48015645..48015689,-!p9@Foxp4!0.61!4.17!Foxp4;;chr13:83663902..83663927,+!p1@Mef2c!0.60!86.72!Mef2c;;chr7:144506077..144506128,-!p1@Ebf3!0.60!7.88!Ebf3;;chr10:5734525..5734569,-!p3@Esr1!0.60!5.33!Esr1;;chr3:99044284..99044308,+!p4@Tbx15!0.60!3.01!Tbx15;;chr16:43363968..43364001,+!p7@Zbtb20!0.59!5.80!Zbtb20;;chr11:11584970..11585030,+!p2@Ikzf1!0.59!4.41!Ikzf1;;chr8:90328310..90328362,-!p3@Zfp423!0.59!3.48!Zfp423;;chr4:135840573..135840601,+!p1@Zfp46!0.58!26.90!Zfp46;;chr2:90936901..90936945,+!p1@Sfpi1!0.58!17.85!Sfpi1;;chr11:44430989..44431015,+!p4@Ebf1!0.58!5.56!Ebf1;;chr7:123177377..123177409,-!p7@Sox6!0.58!3.71!Sox6;;chr6:30908793..30908815,-!p1@Klf14!0.58!2.78!Klf14;;chr5:20361092..20361119,-!p4@Phtf2!0.58!2.78!Phtf2;;chr17:14011569..14011589,+!p8@Mllt4!0.58!2.78!Mllt4;;chr1:122498955..122498968,+!p1@En1!0.58!2.78!En1;;chr2:74529970..74529997,+!p1@Hoxd10!0.58!2.78!Hoxd10;;chr9:96159133..96159145,+!p9@Tfdp2!0.58!2.78!Tfdp2;;chr8:87324243..87324277,-!p1@Nfix!0.57!81.39!Nfix;;chr16:95680889..95680991,-!p1@Erg!0.57!26.90!Erg;;chr11:11586218..11586285,+!p1@Ikzf1!0.57!10.20!Ikzf1;;chr2:65683890..65683907,+!p1@Csrnp3!0.57!5.80!Csrnp3;;chr16:18587076..18587106,-!p1@Tbx1!0.57!4.17!Tbx1;;chr11:44430877..44430899,+!p6@Ebf1!0.57!3.71!Ebf1;;chr5:24107779..24107825,-!p1@Smarcd3!0.56!21.80!Smarcd3;;chr8:87225329..87225396,+!p1@Lyl1!0.56!11.83!Lyl1;;chr15:103085802..103085817,-!p4@Nfe2!0.56!3.48!Nfe2;;chr2:181406327..181406350,-!p1@Sox18!0.55!101.56!Sox18;;chr11:16908650..16908690,-!p1@Plek!0.55!19.48!Plek;;chr17:87153462..87153473,+!p3@Epas1!0.55!11.59!Epas1;;chr6:145814003..145814056,-!p1@Bhlhe41!0.55!8.81!Bhlhe41;;chr6:52141694..52141715,-!p1@Hoxa4!0.55!3.48!Hoxa4;;chr16:43364215..43364252,+!p14@Zbtb20!0.55!3.48!Zbtb20;;chr6:52167459..52167492,-!p1@Hoxa7!0.55!3.25!Hoxa7;;chr15:85566537..85566552,+!p2@Ppara!0.55!2.55!Ppara;;chr17:14011545..14011564,+!p6@Mllt4!0.55!2.55!Mllt4;;chr9:63514609..63514620,-!p10@Smad3!0.55!2.55!Smad3;;chr2:147190725..147190747,+!p2@Pax1!0.55!2.55!Pax1;;chr1:136186599..136186608,+!p3@Myog!0.55!2.55!Myog;;chr10:79884592..79884621,-!p5@Tcf3!0.55!2.55!Tcf3;;chr7:35904304..35904320,+!p1@Cebpa!0.54!64.46!Cebpa;;chr4:135728581..135728668,+!p1@E2f2!0.54!14.61!E2f2;;chr2:91864661..91864686,-!p1@Creb3l1!0.53!67.47!Creb3l1;;chr2:91864300..91864379,-!p2@Creb3l1!0.53!8.35!Creb3l1;;chr7:144505980..144506010,-!p3@Ebf3!0.53!3.01!Ebf3;;chr9:69137716..69137744,+!p1@Rora!0.52!18.32!Rora;;chr9:91260594..91260612,-!p1@Zic1!0.52!2.32!Zic1;;chr3:66785181..66785199,-!p2@Shox2!0.52!2.32!Shox2;;chr11:101755710..101755715,-!p2@Meox1!0.52!2.32!Meox1;;chr11:98407264..98407295,-!p1@Ikzf3!0.52!2.32!Ikzf3;;chr16:91270091..91270143,+!p2@Olig1!0.52!2.32!Olig1;;chr15:102751603..102751630,+!p1@Hoxc13!0.52!2.32!Hoxc13;;chr16:42907676..42907797,+!p1@Zbtb20!0.51!37.56!Zbtb20;;chr3:95032091..95032183,-!p1@Mllt11!0.51!24.58!Mllt11;;chr16:44173384..44173407,+!p2@Gm608!0.51!6.96!Gm608;;chr5:20387832..20387841,-!p2@Phtf2!0.51!4.41!Phtf2;;chr11:96145450..96145517,+!p2@Hoxb7!0.51!3.71!Hoxb7;;chr6:52154386..52154407,-!p2@Hoxa5!0.51!3.01!Hoxa5;;chr4:99322820..99322845,+!p1@Foxd3!0.51!3.01!Foxd3;;chr7:52960780..52960793,+!p5@Dbp!0.51!2.78!Dbp;;chr4:122911086..122911112,+!p1@Heyl!0.50!33.62!Heyl;;chr5:20387850..20387869,-!p1@Phtf2!0.50!28.75!Phtf2;;chr11:44430788..44430804,+!p3@Ebf1!0.50!6.49!Ebf1;;chr3:30408603..30408668,-!p1@Mecom!0.50!6.03!Mecom;;chr2:91035197..91035237,-!p1@Nr1h3!0.50!5.33!Nr1h3;;chr8:124984566..124984595,-!p1@Snai3!0.50!3.71!Snai3;;chr4:32325445..32325468,+!p4@Bach2!0.50!3.48!Bach2;;chr11:11585912..11585950,+!p6@Ikzf1!0.50!3.01!Ikzf1;;chr7:123174606..123174636,-!p5@Sox6!0.50!3.01!Sox6;;chr1:1474606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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011420
 |is_obsolete=
+|library_id=CNhs10518
+|library_id_phase_based=2:CNhs10518
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;761
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;761
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N10.CNhs10518.761-6B4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N10.CNhs10518.761-6B4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N10.CNhs10518.761-6B4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N10.CNhs10518.761-6B4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N10.CNhs10518.761-6B4.mm9.nobarcode.rdna.fa.gz
 |name=whole body, neonate N10
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10518,LSID649,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0102177899346491,0,0,0,0.0905641158318875,0,0.259614759884698,0,0,0,0,0.200648689312399,0,0,0,0,0,0,-0.101329235050687,0,0,0,0,0.0905641158318875,0,0,0,0,0,0,0,0,0.114587544992956,0,0,0,0,0.0019864638002432,0.015902567717729,0,0.0481895839150237,0.752674696354357,0.108748537865188,0,0,0,0,0,0,0,0,0,0,0.0905641158318875,0,0.0245585682684472,0,0,0,0,0,0,0,0,0.28498792970894,0,0.047603818851104,0.0236702071387552,-0.067526926939195,-0.0579563549082079,0.0905641158318875,-0.0162887987723509,0.0217471200735115,-0.0602516976002627,0.16546265671817,0,0,-0.108544004395034,0.0551709090467852,-0.0788315948399074,0.0062333564272886,0,0,0,0,0,0.0605908231418785,-0.142431030047728,0.086666017945441,0,0,0,0,0
 |rna_box=6
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
 |top_motifs=MEF2{A,B,C,D}:2.80323910383;FOXL1:2.72468084339;TBP:2.47606531534;ESR1:2.2433557508;SMAD1..7,9:2.20985432401;HOX{A4,D4}:2.20495899248;TFAP4:2.13592758709;TLX2:1.94807032519;TFCP2:1.91300412354;GCM1,2:1.70515688105;NFE2L2:1.70159875066;ZNF238:1.66602352621;NFATC1..3:1.66068905205;TFAP2{A,C}:1.58905909781;GLI1..3:1.52432422895;NKX2-3_NKX2-5:1.51051223567;EBF1:1.50129678498;TAL1_TCF{3,4,12}:1.46770968639;SOX5:1.44543554135;NR5A1,2:1.35337656013;FOSL2:1.30556586257;FOXP3:1.29607807461;ZNF148:1.29595107254;MAFB:1.29320512701;TOPORS:1.29223790227;TGIF1:1.27710959651;STAT2,4,6:1.22827755255;SRF:1.21066375291;MYFfamily:1.21041108672;TLX1..3_NFIC{dimer}:1.17244341913;MYOD1:1.14473076544;SOX{8,9,10}:1.14221378804;NHLH1,2:1.12470227594;HES1:1.10864112159;RXRA_VDR{dimer}:1.10293844155;TEAD1:1.08219124716;PAX1,9:1.02916651666;GFI1:0.957963622087;RXR{A,B,G}:0.933063802209;NR3C1:0.930698855749;EP300:0.884640029966;MYBL2:0.824743845232;MTF1:0.805007064923;ATF6:0.800055514575;GTF2A1,2:0.781441130419;NFE2L1:0.752719247282;ESRRA:0.735284898356;IKZF1:0.658133237052;HSF1,2:0.639159317767;PPARG:0.628854369099;GATA6:0.609188070029;ALX4:0.607860826218;TP53:0.59948501821;RORA:0.585734695703;CEBPA,B_DDIT3:0.582942685641;KLF4:0.581816751212;MAZ:0.580198421903;PAX5:0.565113970601;FOS_FOS{B,L1}_JUN{B,D}:0.529783316323;GFI1B:0.517386894328;FOXQ1:0.494074883555;PATZ1:0.493163602032;SP1:0.476686051157;XCPE1{core}:0.474131716993;PRDM1:0.469553718445;HIC1:0.452432253473;HLF:0.444738186271;FOXA2:0.419192342001;GTF2I:0.404422504369;NFE2:0.398360449629;HIF1A:0.398312381944;YY1:0.391583452498;ALX1:0.34379148953;SPZ1:0.339504372265;RUNX1..3:0.33064269021;LEF1_TCF7_TCF7L1,2:0.324705649786;CRX:0.324081649535;LMO2:0.322427521787;PBX1:0.317288311439;IRF7:0.316463990561;SPIB:0.290663452512;ZIC1..3:0.288409942086;SPI1:0.278859218893;FOX{I1,J2}:0.267351280936;BACH2:0.252679082507;DMAP1_NCOR{1,2}_SMARC:0.247747467672;RREB1:0.24458727361;PAX2:0.24006667197;SREBF1,2:0.237799490082;MTE{core}:0.233478645614;STAT5{A,B}:0.186110615242;ETS1,2:0.178205264117;NR1H4:0.171204727348;UFEwm:0.148804870144;VSX1,2:0.136537284073;TFAP2B:0.135902212097;HMGA1,2:0.126494148817;AR:0.123260863627;EN1,2:0.093912414872;HMX1:0.0896004064106;PDX1:0.0743148773323;MZF1:0.0655682518132;TBX4,5:0.0571134419723;FOXO1,3,4:0.0520125325742;NR6A1:0.0197210710121;GATA4:0.0129181380287;POU3F1..4:0.00203304528926;NFIL3:-0.005117094985;NKX2-2,8:-0.0211067389043;REST:-0.0233686684871;IRF1,2:-0.0244318619339;POU5F1:-0.027977462379;ZNF423:-0.0357569815057;POU2F1..3:-0.0771069247004;NFKB1_REL_RELA:-0.0810517803638;ZNF143:-0.0821965557977;ELF1,2,4:-0.085644613349;NKX3-2:-0.0928423275228;HBP1_HMGB_SSRP1_UBTF:-0.0944845052777;IKZF2:-0.112593896668;E2F1..5:-0.120851597821;FOX{F1,F2,J1}:-0.121671363584;NANOG{mouse}:-0.121822615294;EVI1:-0.136694479445;T:-0.143560217044;NKX2-1,4:-0.15328672953;JUN:-0.156523191962;ZFP161:-0.165166924088;ATF2:-0.18365394511;ZBTB6:-0.196718485877;EGR1..3:-0.217014698799;HOXA9_MEIS1:-0.232190567364;NANOG:-0.232395069508;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.27256277422;MED-1{core}:-0.326008583104;SOX2:-0.339199432212;SOX17:-0.36698232171;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.376405580598;FOX{D1,D2}:-0.378281622971;ATF4:-0.384834730705;PITX1..3:-0.390513067031;CDC5L:-0.406248824278;PRRX1,2:-0.412568508485;HNF4A_NR2F1,2:-0.426607727516;bHLH_family:-0.439112082428;ZNF384:-0.439856759627;HOX{A5,B5}:-0.4442957746;MYB:-0.451983548648;ARID5B:-0.495226030114;BREu{core}:-0.49878689591;POU6F1:-0.498995077124;HNF1A:-0.515677026114;LHX3,4:-0.522415682626;NRF1:-0.523280863556;RFX1:-0.528299385598;CUX2:-0.529691589305;PAX8:-0.555104176871;RFX2..5_RFXANK_RFXAP:-0.562664379562;RBPJ:-0.578033079071;HAND1,2:-0.58013047477;NFY{A,B,C}:-0.592028891047;DBP:-0.594272815287;ATF5_CREB3:-0.599629772239;POU1F1:-0.631508106767;FOXM1:-0.688686850916;TEF:-0.716846063983;SNAI1..3:-0.748978068609;GZF1:-0.761334356603;AHR_ARNT_ARNT2:-0.788260366886;NKX3-1:-0.791075641707;TFDP1:-0.794000718577;ZEB1:-0.856894907041;PAX6:-0.894967752471;PAX4:-0.912921155951;FOXP1:-0.969288184802;OCT4_SOX2{dimer}:-0.97129757895;CREB1:-1.01713215188;NFIX:-1.01871816744;AIRE:-1.14860198871;ELK1,4_GABP{A,B1}:-1.20488981648;ADNP_IRX_SIX_ZHX:-1.27675756429;FOXD3:-1.28134194755;FOXN1:-1.29079430229;STAT1,3:-1.33236730547;NKX6-1,2:-1.36228821431;CDX1,2,4:-1.52092002853;ZBTB16:-1.56603721766;BPTF:-1.69274181558;ONECUT1,2:-1.78540902025
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:761-6B4;search_select_hide=table117:761-6B4
 }}

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FF:761-6B4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs10518

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