FF:659-23C6: Difference between revisions

Latest revision as of 19:19, 4 June 2020

Name:	whole body, neonate N01
Species:	Mouse (Mus musculus)
Library ID:	CNhs10576
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	whole body
dev stage	1 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		SAMD00005246

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10576		CAGE		DRX009152		DRR010026

Accession ID Mm9

Library id		BAM		CTSS
CNhs10576		DRZ001451		DRZ002834

Accession ID Mm10

Library id		BAM		CTSS
CNhs10576		DRZ012801		DRZ014184

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

CNhs10576

0	0
1	0.076
10	0
100	0
1000	0.417
1001	0.228
1002	0.12
1003	0.323
1004	0
1005	0.0432
1006	0.464
1007	-0.0102
1008	0
1009	0.168
101	-0.0143
1010	0
1011	0.141
1012	0
1013	-0.0868
1014	0.425
1015	-0.101
1016	0.182
1017	0
1018	0.247
1019	0
102	0
1020	0
1021	0
1022	0.541
1023	0
1024	0.281
1025	0
1026	0.257
1027	0.186
1028	0
1029	0.217
103	0.856
1030	0
1031	0.335
1032	0.124
1033	0
1034	0
1035	0.076
1036	-0.0791
1037	0
1038	-0.0034
1039	0.142
104	0
1040	0.316
1041	0.247

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: CNhs10576

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.174
MA0003.1	MA0003.1	0.0662
MA0004.1	MA0004.1	0.052
MA0006.1	MA0006.1	0.247
MA0007.1	MA0007.1	0.926
MA0009.1	MA0009.1	0.573
MA0014.1	MA0014.1	0.315
MA0017.1	MA0017.1	9.00354e-5
MA0018.2	MA0018.2	0.00644
MA0019.1	MA0019.1	0.898
MA0024.1	MA0024.1	0.0061
MA0025.1	MA0025.1	0.328
MA0027.1	MA0027.1	0.292
MA0028.1	MA0028.1	5.64394e-10
MA0029.1	MA0029.1	0.595
MA0030.1	MA0030.1	0.502
MA0031.1	MA0031.1	0.437
MA0035.2	MA0035.2	0.0117
MA0038.1	MA0038.1	0.966
MA0039.2	MA0039.2	0.968
MA0040.1	MA0040.1	0.598
MA0041.1	MA0041.1	0.633
MA0042.1	MA0042.1	0.848
MA0043.1	MA0043.1	0.063
MA0046.1	MA0046.1	6.1736e-12
MA0047.2	MA0047.2	0.105
MA0048.1	MA0048.1	6.68495e-4
MA0050.1	MA0050.1	1.91433e-4
MA0051.1	MA0051.1	0.00408
MA0052.1	MA0052.1	1.06638e-35
MA0055.1	MA0055.1	9.53084e-6
MA0057.1	MA0057.1	0.794
MA0058.1	MA0058.1	0.0151
MA0059.1	MA0059.1	7.11451e-4
MA0060.1	MA0060.1	1.69234e-5
MA0061.1	MA0061.1	0.448
MA0062.2	MA0062.2	1.30901e-15
MA0065.2	MA0065.2	0.828
MA0066.1	MA0066.1	0.789
MA0067.1	MA0067.1	0.107
MA0068.1	MA0068.1	0.233
MA0069.1	MA0069.1	0.444
MA0070.1	MA0070.1	0.191
MA0071.1	MA0071.1	0.0726
MA0072.1	MA0072.1	0.0486
MA0073.1	MA0073.1	0.577
MA0074.1	MA0074.1	0.62
MA0076.1	MA0076.1	7.32157e-11
MA0077.1	MA0077.1	0.557
MA0078.1	MA0078.1	0.169
MA0079.2	MA0079.2	0.0107
MA0080.2	MA0080.2	4.62952e-5
MA0081.1	MA0081.1	0.21
MA0083.1	MA0083.1	5.89067e-11
MA0084.1	MA0084.1	0.619
MA0087.1	MA0087.1	0.239
MA0088.1	MA0088.1	0.0325
MA0090.1	MA0090.1	0.0297
MA0091.1	MA0091.1	0.782
MA0092.1	MA0092.1	0.372
MA0093.1	MA0093.1	0.0405
MA0099.2	MA0099.2	0.272
MA0100.1	MA0100.1	0.00265
MA0101.1	MA0101.1	0.0514
MA0102.2	MA0102.2	0.71
MA0103.1	MA0103.1	0.00886
MA0104.2	MA0104.2	0.0146
MA0105.1	MA0105.1	0.716
MA0106.1	MA0106.1	0.185
MA0107.1	MA0107.1	0.212
MA0108.2	MA0108.2	4.41876e-22
MA0111.1	MA0111.1	0.817
MA0112.2	MA0112.2	0.392
MA0113.1	MA0113.1	0.817
MA0114.1	MA0114.1	1.13502e-4
MA0115.1	MA0115.1	0.00237
MA0116.1	MA0116.1	0.831
MA0117.1	MA0117.1	0.395
MA0119.1	MA0119.1	0.905
MA0122.1	MA0122.1	0.794
MA0124.1	MA0124.1	0.254
MA0125.1	MA0125.1	0.125
MA0131.1	MA0131.1	0.288
MA0135.1	MA0135.1	0.148
MA0136.1	MA0136.1	6.89067e-8
MA0137.2	MA0137.2	0.00467
MA0138.2	MA0138.2	0.00144
MA0139.1	MA0139.1	0.157
MA0140.1	MA0140.1	0.00988
MA0141.1	MA0141.1	0.264
MA0142.1	MA0142.1	0.0375
MA0143.1	MA0143.1	0.14
MA0144.1	MA0144.1	0.204
MA0145.1	MA0145.1	0.0475
MA0146.1	MA0146.1	0.993
MA0147.1	MA0147.1	0.0188
MA0148.1	MA0148.1	0.092
MA0149.1	MA0149.1	0.00606
MA0150.1	MA0150.1	0.0976
MA0152.1	MA0152.1	0.34
MA0153.1	MA0153.1	2.91015e-12
MA0154.1	MA0154.1	0.438
MA0155.1	MA0155.1	0.0914
MA0156.1	MA0156.1	1.5524e-12
MA0157.1	MA0157.1	0.273
MA0159.1	MA0159.1	0.278
MA0160.1	MA0160.1	0.183
MA0162.1	MA0162.1	0.42
MA0163.1	MA0163.1	0.838
MA0164.1	MA0164.1	0.322
MA0258.1	MA0258.1	0.732
MA0259.1	MA0259.1	0.129

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: CNhs10576

Novel motif	Logo	P-value
1	1	0.337
10	10	0.157
100	100	0.997
101	101	0.316
102	102	0.995
103	103	0.0373
104	104	0.893
105	105	0.388
106	106	0.176
107	107	0.0598
108	108	0.374
109	109	0.625
11	11	0.402
110	110	0.515
111	111	0.262
112	112	0.139
113	113	0.751
114	114	0.951
115	115	0.259
116	116	0.287
117	117	0.0293
118	118	0.179
119	119	0.799
12	12	0.25
120	120	0.958
121	121	0.211
122	122	0.396
123	123	0.268
124	124	0.709
125	125	0.761
126	126	0.06
127	127	0.341
128	128	0.254
129	129	0.412
13	13	0.234
130	130	0.751
131	131	0.349
132	132	0.721
133	133	0.679
134	134	0.475
135	135	0.419
136	136	0.51
137	137	0.778
138	138	0.198
139	139	0.409
14	14	0.411
140	140	0.737
141	141	0.33
142	142	0.979
143	143	0.486
144	144	0.0249
145	145	0.127
146	146	0.996
147	147	0.911
148	148	0.351
149	149	0.532
15	15	0.0172
150	150	0.906
151	151	0.656
152	152	0.0468
153	153	0.242
154	154	0.564
155	155	0.27
156	156	0.021
157	157	0.482
158	158	0.0481
159	159	0.526
160	160	0.384
161	161	0.0232
162	162	0.894
163	163	0.638
164	164	0.111
165	165	0.913
166	166	0.316
167	167	0.0269
168	168	0.0324
169	169	0.0919
17	17	0.356
18	18	0.513
19	19	0.323
2	2	0.00814
20	20	0.0579
21	21	0.777
22	22	0.522
23	23	0.469
24	24	0.461
25	25	0.462
26	26	0.29
27	27	0.998
28	28	0.52
29	29	0.0146
3	3	0.218
30	30	0.214
31	31	0.541
32	32	0.139
33	33	0.176
34	34	0.134
35	35	0.11
36	36	0.0406
37	37	0.749
38	38	0.699
39	39	0.905
4	4	0.846
40	40	0.0688
41	41	0.211
42	42	0.264
43	43	0.901
44	44	0.343
45	45	0.162
46	46	0.927
47	47	0.47
48	48	0.22
49	49	0.31
5	5	0.991
50	50	0.194
51	51	0.966
52	52	0.185
53	53	0.398
54	54	0.355
55	55	0.881
56	56	0.552
57	57	0.42
58	58	0.766
59	59	0.0442
6	6	0.271
60	60	0.318
61	61	0.283
62	62	0.647
63	63	0.421
64	64	0.65
65	65	0.866
66	66	0.838
67	67	0.683
68	68	0.262
69	69	0.188
7	7	0.818
70	70	0.595
71	71	0.371
72	72	0.437
73	73	0.629
74	74	0.943
75	75	0.107
76	76	0.0359
77	77	0.224
78	78	0.659
79	79	0.171
8	8	0.289
80	80	0.557
81	81	0.355
82	82	0.345
83	83	0.876
84	84	0.453
85	85	0.117
86	86	0.709
87	87	0.739
88	88	0.856
89	89	0.476
9	9	0.247
90	90	0.0123
91	91	0.453
92	92	0.575
93	93	0.0405
94	94	0.882
95	95	0.536
96	96	0.76
97	97	0.518
98	98	0.599
99	99	0.381

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: CNhs10576

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000304 mouse neonate N0 sample
FF:0011399 mouse whole body- neonate N01 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)
0000304 (mouse neonate N0 sample)
0000734 (mouse neonate N1 sample)
0011399 (mouse whole body- neonate N01 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@SAMD00005246
+|accession_numbers=CAGE;DRX009152;DRR010026;DRZ001451;DRZ002834;DRZ012801;DRZ014184
 |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!1.80!62.74!Mef2c;;chr7:6649134..6649167,-!p1@Zim1!1.58!194.16!Zim1;;chr1:136186574..136186592,+!p1@Myog!1.45!27.16!Myog;;chr3:99057269..99057306,+!p1@Tbx15!1.44!32.14!Tbx15;;chr3:99057677..99057730,+!p2@Tbx15!1.43!26.02!Tbx15;;chr4:87452200..87452229,-!p2@Mllt3!1.40!50.31!Mllt3;;chr12:74147689..74147711,-!p1@Six1!1.39!50.12!Six1;;chr13:30841099..30841116,+!p1@Irf4!1.38!35.58!Irf4;;chr10:106931775..106931798,-!p1@Myf6!1.37!22.19!Myf6;;chr4:87452180..87452196,-!p3@Mllt3!1.35!41.13!Mllt3;;chr2:120365588..120365602,-!p2@Zfp106!1.33!33.86!Zfp106;;chr12:37835141..37835194,+!p1@Meox2!1.32!60.64!Meox2;;chr10:12810631..12810649,+!p1@Plagl1!1.30!482.81!Plagl1;;chr12:34642510..34642530,+!p1@Twist1!1.25!52.41!Twist1;;chr11:96143666..96143725,+!p1@Hoxb8!1.19!16.45!Hoxb8;;chr17:14011485..14011507,+!p2@Mllt4!1.18!14.16!Mllt4;;chr11:121380640..121380655,-!p1@Zfp750!1.16!22.38!Zfp750;;chr17:44951553..44951586,-!p2@Runx2!1.16!14.92!Runx2;;chr9:48644037..48644067,-!p2@Zbtb16!1.14!32.14!Zbtb16;;chr17:44951431..44951445,-!p3@Runx2!1.12!12.24!Runx2;;chr7:53631837..53631850,+!p1@Myod1!1.12!12.05!Myod1;;chr12:37835120..37835133,+!p2@Meox2!1.09!16.26!Meox2;;chr7:119885539..119885574,+!p3@Tead1!1.09!11.29!Tead1;;chr6:52190467..52190500,-!p1@Hoxa10!1.08!10.90!Hoxa10;;chr11:101755669..101755686,-!p1@Meox1!1.07!19.70!Meox1;;chr5:77543897..77543911,-!p2@Hopx!1.06!20.28!Hopx;;chr15:102197405..102197454,-!p1@Sp7!1.05!10.14!Sp7;;chr1:165243379..165243402,-!p3@Prrx1!1.01!13.96!Prrx1;;chr1:169548377..169548430,+!p1@Rxrg!0.99!8.80!Rxrg;;chr1:165243591..165243625,-!p2@Prrx1!0.98!13.39!Prrx1;;chr13:83643136..83643158,+!p7@Mef2c!0.97!8.42!Mef2c;;chr9:48644306..48644364,-!p1@Zbtb16!0.95!32.52!Zbtb16;;chr6:52176164..52176195,-!p1@Hoxa9!0.95!9.95!Hoxa9;;chr16:25801993..25802014,+!p1@Trp63!0.94!7.65!Trp63;;chr7:17647736..17647772,-!p1@Hif3a!0.92!27.16!Hif3a;;chr14:67853425..67853454,+!p1@Ebf2!0.92!10.52!Ebf2;;chr2:168427252..168427273,-!p2@Nfatc2!0.92!9.18!Nfatc2;;chr18:80909801..80909819,-!p1@Nfatc1!0.91!44.38!Nfatc1;;chr5:135582751..135582788,+!p1@Mlxipl!0.91!29.65!Mlxipl;;chr1:165243792..165243808,-!p1@Prrx1!0.91!26.02!Prrx1;;chrX:137135036..137135064,-!p4@Tsc22d3!0.91!14.35!Tsc22d3;;chr12:37835203..37835218,+!p3@Meox2!0.91!8.61!Meox2;;chr16:43363190..43363242,+!p2@Zbtb20!0.90!22.19!Zbtb20;;chr15:35225845..35225867,+!p1@Osr2!0.90!17.98!Osr2;;chr14:56443806..56443848,+!p1@Nfatc4!0.90!14.54!Nfatc4;;chr14:67853632..67853674,+!p3@Ebf2!0.90!8.61!Ebf2;;chr15:75578637..75578669,-!p2@Mafa!0.90!7.84!Mafa;;chr13:83643232..83643254,+!p5@Mef2c!0.90!6.89!Mef2c;;chr6:6831950..6831985,-!p2@Dlx5!0.88!7.27!Dlx5;;chr4:148178559..148178603,+!p1@Casz1!0.87!19.13!Casz1;;chr10:126778916..126778974,-!p1@Gli1!0.87!14.92!Gli1;;chr10:106923133..106923146,-!p1@Myf5!0.86!6.31!Myf5;;chr10:106931839..106931851,-!p3@Myf6!0.85!6.12!Myf6;;chr10:106931803..106931817,-!p2@Myf6!0.85!6.12!Myf6;;chr15:102828658..102828678,+!p1@Hoxc6!0.85!6.12!Hoxc6;;chr7:123182248..123182264,-!p3@Sox6!0.84!7.27!Sox6;;chr11:121380594..121380609,-!p2@Zfp750!0.82!10.14!Zfp750;;chr6:30908793..30908815,-!p1@Klf14!0.82!5.55!Klf14;;chr12:37835248..37835260,+!p4@Meox2!0.82!5.55!Meox2;;chr7:144505980..144506010,-!p3@Ebf3!0.81!6.70!Ebf3;;chr8:87297280..87297326,-!p2@Nfix!0.80!13.20!Nfix;;chr5:138199361..138199441,+!p2@Tsc22d4!0.80!10.52!Tsc22d4;;chr3:99057256..99057268,+!p3@Tbx15!0.80!5.36!Tbx15;;chr4:55545337..55545357,-!p1@Klf4!0.79!82.25!Klf4;;chr19:25746898..25746910,+!p1@Dmrt2!0.79!7.84!Dmrt2;;chr6:6832076..6832092,-!p1@Dlx5!0.79!6.12!Dlx5;;chr9:31720843..31720888,-!p1@Barx2!0.79!5.74!Barx2;;chr12:37835219..37835230,+!p5@Meox2!0.79!5.16!Meox2;;chr16:25684232..25684285,+!p2@Trp63!0.79!5.16!Trp63;;chr11:94981424..94981439,+!p1@Dlx3!0.78!5.74!Dlx3;;chr9:91260616..91260653,-!p2@Zic1!0.78!4.97!Zic1;;chr12:34642682..34642753,+!p2@Twist1!0.77!13.96!Twist1;;chr13:99124189..99124205,+!p1@Foxd1!0.77!7.84!Foxd1;;chr19:5560600..5560617,-!p1@Ovol1!0.77!6.12!Ovol1;;chr11:98636373..98636387,-!p5@Nr1d1!0.77!5.74!Nr1d1;;chr11:44431687..44431706,+!p2@Ebf1!0.76!24.10!Ebf1;;chr17:25707623..25707639,-!p1@Sox8!0.76!22.19!Sox8;;chr7:144506077..144506128,-!p1@Ebf3!0.76!11.86!Ebf3;;chr2:65683890..65683907,+!p1@Csrnp3!0.76!9.76!Csrnp3;;chr15:102087737..102087801,-!p3@Rarg!0.76!8.23!Rarg;;chr15:102196745..102196769,-!p2@Sp7!0.76!4.78!Sp7;;chr4:139388835..139388867,-!p1@Pax7!0.76!4.78!Pax7;;chr19:23215673..23215753,+!p1@Klf9!0.75!74.03!Klf9;;chr3:95032091..95032183,-!p1@Mllt11!0.75!43.42!Mllt11;;chr7:144505957..144505972,-!p2@Ebf3!0.75!5.93!Ebf3;;chr9:91260594..91260612,-!p1@Zic1!0.75!4.59!Zic1;;chr11:96153767..96153822,+!p1@Hoxb6!0.74!7.27!Hoxb6;;chr11:96145450..96145517,+!p2@Hoxb7!0.74!7.08!Hoxb7;;chr6:128250380..128250442,-!p2@Tead4!0.74!5.93!Tead4;;chr8:90328310..90328362,-!p3@Zfp423!0.73!5.16!Zfp423;;chr6:52195795..52195825,-!p1@Hoxa11!0.73!4.40!Hoxa11;;chr1:169528720..169528749,+!p6@Rxrg!0.73!4.40!Rxrg;;chr19:46222739..46222745,-!p2@Pitx3!0.73!4.40!Pitx3;;chr4:135840573..135840601,+!p1@Zfp46!0.72!37.30!Zfp46;;chr8:94881733..94881790,+!p1@Irx5!0.72!8.99!Irx5;;chr15:85566184..85566238,+!p1@Ppara!0.72!6.70!Ppara;;chr6:115311270..115311298,+!p1@Pparg!0.72!6.50!Pparg;;chr11:98636400..98636418,-!p4@Nr1d1!0.72!5.74!Nr1d1;;chr4:99322820..99322845,+!p1@Foxd3!0.72!5.55!Foxd3;;chr3:99044284..99044308,+!p4@Tbx15!0.72!4.21!Tbx15;;chr11:100553754..100553787,-!p1@Zfp385c!0.72!4.21!Zfp385c;;chr2:147190725..147190747,+!p2@Pax1!0.72!4.21!Pax1;;chr15:102820964..102821006,+!p1@Hoxc8!0.72!4.21!Hoxc8;;chr15:102751603..102751630,+!p1@Hoxc13!0.72!4.21!Hoxc13;;chr5:24107779..24107825,-!p1@Smarcd3!0.71!30.99!Smarcd3;;chr15:76287876..76287894,+!p1@Scx!0.71!25.06!Scx;;chr9:71743854..71743909,-!p1@Tcf12!0.70!35.58!Tcf12;;chr3:94176733..94176794,+!p1@Rorc!0.70!34.81!Rorc;;chr2:91864449..91864492,-!p3@Creb3l1!0.70!6.89!Creb3l1;;chr13:72766279..72766296,+!p2@Irx2!0.70!6.31!Irx2;;chr6:52167513..52167549,-!p2@Hoxa7!0.70!5.93!Hoxa7;;chr13:40829137..40829205,-!p1@Tfap2a!0.70!4.59!Tfap2a;;chr9:43013917..43013968,-!p1@Pou2f3!0.70!4.02!Pou2f3;;chr7:119822957..119822980,+!p2@Tead1!0.69!21.23!Tead1;;chr2:91864300..91864379,-!p2@Creb3l1!0.69!12.43!Creb3l1;;chr8:124984566..124984595,-!p1@Snai3!0.69!6.31!Snai3;;chr3:5218516..5218544,+!p2@Zfhx4!0.69!6.12!Zfhx4;;chr16:91270004..91270023,+!p1@Olig1!0.69!4.59!Olig1;;chr7:6683123..6683142,-!p1@Peg3!0.68!226.68!Peg3;;chr16:43363152..43363186,+!p3@Zbtb20!0.68!9.56!Zbtb20;;chr11:44430989..44431015,+!p4@Ebf1!0.68!7.27!Ebf1;;chr2:147190749..147190769,+!p1@Pax1!0.68!3.83!Pax1;;chr11:96690797..96690813,-!p1@Nfe2l1!0.67!81.87!Nfe2l1;;chr9:69137716..69137744,+!p1@Rora!0.67!26.59!Rora;;chr11:98636531..98636559,-!p1@Nr1d1!0.67!24.10!Nr1d1;;chr5:125538737..125538781,-!p2@Ncor2!0.67!14.92!Ncor2;;chr5:138187583..138187602,+!p6@Tsc22d4!0.67!7.27!Tsc22d4;;chr7:116154364..116154444,+!p1@Tub!0.67!6.89!Tub;;chr2:74542918..74542971,+!p1@Hoxd8!0.67!5.93!Hoxd8;;chr13:55932591..55932622,-!p1@Pitx1!0.67!4.59!Pitx1;;chr11:96143962..96144035,+!p2@Hoxb8!0.67!3.63!Hoxb8;;chr9:55388997..55389016,+!p1@Isl2!0.67!3.63!Isl2;;chr7:35904304..35904320,+!p1@Cebpa!0.66!83.98!Cebpa;;chr18:7004715..7004731,-!p1@Mkx!0.66!9.56!Mkx;;chr4:148178529..148178548,+!p3@Casz1!0.66!9.37!Casz1;;chr6:52163319..52163342,-!p1@Hoxa3!0.66!5.55!Hoxa3;;chr11:44431016..44431045,+!p5@Ebf1!0.66!5.36!Ebf1;;chr11:98636508..98636524,-!p3@Nr1d1!0.66!4.59!Nr1d1;;chr15:78994907..78994926,-!p1@Sox10!0.65!9.95!Sox10;;chr11:96690779..96690790,-!p3@Nfe2l1!0.65!9.37!Nfe2l1;;chr6:90412608..90412630,+!p2@Klf15!0.65!7.84!Klf15;;chr11:44431710..44431725,+!p7@Ebf1!0.65!5.93!Ebf1;;chr15:97738692..97738747,-!p1@Vdr!0.64!21.23!Vdr;;chr1:93698030..93698064,+!p1@Twist2!0.64!7.46!Twist2;;chr1:135557526..135557551,-!p1@Zbed6!0.64!5.74!Zbed6;;chr4:55545051..55545110,-!p2@Klf4!0.64!4.40!Klf4;;chr1:165243638..165243649,-!p5@Prrx1!0.64!4.21!Prrx1;;chr16:15887371..15887385,+!p1@Cebpd!0.63!131.03!Cebpd;;chr18:14131126..14131211,-!p1@Zfp521!0.63!82.06!Zfp521;;chr10:67599319..67599360,-!p2@Arid5b!0.63!42.47!Arid5b;;chr6:90412582..90412601,+!p1@Klf15!0.63!17.98!Klf15;;chr15:102301130..102301147,+!p3@Pcbp2!0.63!11.29!Pcbp2;;chr4:135129538..135129558,-!p1@Grhl3!0.63!5.36!Grhl3;;chr4:55545152..55545194,-!p3@Klf4!0.63!4.02!Klf4;;chr1:19199236..19199258,+!p1@Tfap2b!0.63!3.25!Tfap2b;;chr2:172375081..172375105,+!p1@Tfap2c!0.63!3.25!Tfap2c;;chr2:31495237..31495243,+!p1@Prdm12!0.63!3.25!Prdm12;;chr6:53523358..53523388,+!p1@Creb5!0.62!45.53!Creb5;;chr11:44430812..44430838,+!p1@Ebf1!0.62!36.73!Ebf1;;chrX:137077653..137077669,-!p3@Tsc22d3!0.62!16.83!Tsc22d3;;chr14:104867201..104867258,-!p1@Pou4f1!0.62!4.78!Pou4f1;;chr9:48644284..48644305,-!p4@Zbtb16!0.62!4.40!Zbtb16;;chr6:131338435..131338482,-!p1@Csda!0.61!348.91!Csda;;chr3:5218629..5218684,+!p1@Zfhx4!0.61!11.67!Zfhx4;;chr18:14130694..14130697,-!p2@Zfp521!0.61!8.03!Zfp521;;chr15:85566014..85566045,+!p3@Ppara!0.61!4.40!Ppara;;chr16:91225808..91225824,+!p1@Olig2!0.61!3.06!Olig2;;chr4:87452167..87452178,-!p8@Mllt3!0.61!3.06!Mllt3;;chr14:67853682..67853702,+!p4@Ebf2!0.61!3.06!Ebf2;;chr15:102828642..102828653,+!p2@Hoxc6!0.61!3.06!Hoxc6;;chr12:57796615..57796687,+!p1@Pax9!0.61!3.06!Pax9;;chr5:77543935..77543947,-!p4@Hopx!0.61!3.06!Hopx;;chr2:32229906..32229942,+!p3@Ciz1!0.61!3.06!Ciz1;;chr2:160192793..160192809,-!p1@Mafb!0.60!55.09!Mafb;;chr13:31898729..31898761,+!p1@Foxc1!0.60!8.42!Foxc1;;chr8:87297878..87297935,-!p3@Nfix!0.60!7.46!Nfix;;chr3:128917187..128917223,+!p2@Pitx2!0.60!3.63!Pitx2;;chr4:150482563..150482655,-!p2@Camta1!0.59!12.24!Camta1;;chr4:97444537..97444555,+!p8@Nfia!0.59!8.23!Nfia;;chr14:67853457..67853482,+!p2@Ebf2!0.59!4.40!Ebf2;;chr4:124334894..124334899,+!p1@Pou3f1!0.59!4.02!Pou3f1;;chr6:52167459..52167492,-!p1@Hoxa7!0.59!3.63!Hoxa7;;chr6:52184901..52184959,-!p2@Hoxa10!0.59!2.87!Hoxa10;;chr15:102797183..102797205,+!p4@Hoxc10!0.59!2.87!Hoxc10;;chr1:169528823..169528860,+!p5@Rxrg!0.59!2.87!Rxrg;;chr1:136186599..136186608,+!p3@Myog!0.59!2.87!Myog;;chr16:14705925..14705951,+!p1@Snai2!0.58!23.72!Snai2;;chr2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+|ffid_belonging_in_development=FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000304;;FF:0011399
 |is_obsolete=
+|library_id=CNhs10576
+|library_id_phase_based=2:CNhs10576
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;659
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;659
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N01.CNhs10576.659-23C6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N01.CNhs10576.659-23C6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N01.CNhs10576.659-23C6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N01.CNhs10576.659-23C6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520neonate%2520N01.CNhs10576.659-23C6.mm9.nobarcode.rdna.fa.gz
 |name=whole body, neonate N01
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10576,LSID653,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.154135593839832,0,0,0,0,0,0.537415056943422,0,0.00490160122573029,0,0,1.03131003724672,0,0,0,0,0,0,-0.0512041285269321,0,0,0,0.0760168881589905,0,0.0760168881589905,0,0,0,0,0,0,0,0.257643536619135,0,0,0,0.0760168881589905,0.0656662892494309,0.055150853734678,0.0477652844665076,0.0300385607949085,1.35256009739251,0.0621110439632683,0,0,0,0,0,0,0,0,0,0,0.196967476487388,0,0.0746836747922021,0.196967476487388,0,0,0,0.0331699330761157,0,0.128261455839583,0.0760168881589905,0,0.0216978904587876,-0.00903674765100965,0.0925225006653957,0.245082115233699,0.0677835670288048,0.140689222355642,0.140689222355642,0.0853308009456679,0,0.196967476487388,0,0.0265983200074845,-0.0695076295232434,0.0517800020035163,-0.0788315948399074,0,0,0,0,0,0,-0.0660154575426048,-0.146146895065624,-0.0860611071085196,0,0,0,0,0
 |rna_box=23
 |rna_catalog_number=
@@ Line 60: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
 |top_motifs=TFAP4:2.51694928964;ESR1:2.26547511963;MEF2{A,B,C,D}:2.26071325147;FOXL1:2.19972438626;TFCP2:2.16638852236;TBP:2.13764941834;TFAP2{A,C}:2.11148475452;EP300:2.09711430681;SMAD1..7,9:2.00504136179;MYOD1:2.00175686666;HOX{A4,D4}:1.96014047097;SOX5:1.92786336754;IKZF1:1.92697936953;GCM1,2:1.90888577026;ZNF238:1.89772892224;TGIF1:1.83253963191;ZNF148:1.73892814933;NFATC1..3:1.60026752985;TEAD1:1.5833689742;MAFB:1.55144231311;NKX2-3_NKX2-5:1.54638863941;GLI1..3:1.45824689632;FOSL2:1.44762760335;NHLH1,2:1.41051429842;TOPORS:1.39816189897;RXR{A,B,G}:1.38831484967;MAZ:1.37090405622;NR3C1:1.35224137226;FOS_FOS{B,L1}_JUN{B,D}:1.32479494003;SRF:1.32013412459;RXRA_VDR{dimer}:1.3196539041;TAL1_TCF{3,4,12}:1.29477982955;NKX3-2:1.26369757431;MYFfamily:1.25783644447;TLX2:1.23225760368;HMX1:1.21375572088;ATF6:1.19634106554;EBF1:1.16429379295;FOXO1,3,4:1.1566384299;AR:1.1009574494;UFEwm:1.08694963874;PAX5:1.08562438766;PRDM1:1.08176836748;KLF4:1.07446952815;PATZ1:1.06943806947;MYBL2:1.06296173417;STAT2,4,6:1.05217995633;HMGA1,2:1.02801466668;PAX2:1.02649620293;GFI1B:0.994046636156;MTF1:0.97651407591;ZNF423:0.971122253623;GTF2I:0.939610410094;XCPE1{core}:0.939506826484;NKX2-1,4:0.937731218217;RREB1:0.918502024911;HIC1:0.904569444339;TLX1..3_NFIC{dimer}:0.882035709024;ZIC1..3:0.86689199111;MZF1:0.862796895744;SP1:0.8600587009;NR1H4:0.856753804955;MTE{core}:0.793317256469;GATA4:0.790707251669;NANOG{mouse}:0.780413148149;NFE2L2:0.767380733353;HES1:0.74380071131;SOX{8,9,10}:0.718090342367;FOXP3:0.716715831656;NFE2L1:0.701762461808;TFAP2B:0.665397262316;FOX{D1,D2}:0.658740019078;VSX1,2:0.658245758185;TP53:0.625777418192;ESRRA:0.586626957742;HIF1A:0.540582144826;PITX1..3:0.539418338742;NR5A1,2:0.537035934585;LEF1_TCF7_TCF7L1,2:0.514628305058;GTF2A1,2:0.513476197919;NFE2:0.511842621287;ATF2:0.502356558408;ZBTB6:0.468724051671;STAT5{A,B}:0.456313314589;HSF1,2:0.442633730851;EGR1..3:0.439632949368;T:0.409726483881;CRX:0.342514699752;BACH2:0.328198719268;EN1,2:0.324024688848;HLF:0.323724309397;IKZF2:0.319630756899;ALX1:0.289917159535;PAX1,9:0.282471386538;IRF7:0.280569390974;MED-1{core}:0.27577320944;SPZ1:0.271486733823;ALX4:0.266620755289;HOX{A5,B5}:0.264536053162;CEBPA,B_DDIT3:0.262093241958;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.240933330629;REST:0.23917363529;HOXA9_MEIS1:0.201766771538;TBX4,5:0.195726580497;RORA:0.194045812183;FOXA2:0.190751634146;CUX2:0.16653888466;SREBF1,2:0.161616663433;DMAP1_NCOR{1,2}_SMARC:0.0698298434068;EVI1:0.0477857236312;BREu{core}:0.0473513314726;SPIB:0.0466557001843;FOX{I1,J2}:0.0360270572048;POU3F1..4:0.00940868754311;LMO2:-0.0194866050421;SPI1:-0.0261900733885;GFI1:-0.0268147175253;ZFP161:-0.0585324350081;AHR_ARNT_ARNT2:-0.0617945096682;JUN:-0.0691235598392;RUNX1..3:-0.0755626065006;HBP1_HMGB_SSRP1_UBTF:-0.0805907224212;SNAI1..3:-0.113355876405;SOX2:-0.128038852425;PPARG:-0.151420816707;POU5F1:-0.167937727208;RBPJ:-0.193736378463;NKX2-2,8:-0.198503875691;NANOG:-0.207576018599;ETS1,2:-0.210438596647;RFX2..5_RFXANK_RFXAP:-0.233479414266;NFKB1_REL_RELA:-0.233699690006;HAND1,2:-0.237671754232;DBP:-0.243114637207;PDX1:-0.249306659472;FOX{F1,F2,J1}:-0.263193564486;YY1:-0.271518541427;POU6F1:-0.28959568322;PAX4:-0.302919635341;ZNF384:-0.308920911431;NR6A1:-0.349161632346;SOX17:-0.357977360552;ATF4:-0.361953418629;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.387540012294;PAX6:-0.388094076392;PBX1:-0.420887043775;CDC5L:-0.442860127514;HNF4A_NR2F1,2:-0.470035988473;IRF1,2:-0.479768381131;TFDP1:-0.505424957899;GZF1:-0.512539366696;FOXP1:-0.520225936746;NFIX:-0.530027701261;RFX1:-0.541246469225;AIRE:-0.577486524225;FOXN1:-0.617583101921;ZEB1:-0.625300904731;FOXM1:-0.634955639589;HNF1A:-0.64052647165;FOXQ1:-0.644366357508;NFIL3:-0.651352001855;ZNF143:-0.654807208404;CREB1:-0.659809199982;ELF1,2,4:-0.663415793029;ATF5_CREB3:-0.673574702374;BPTF:-0.673664190287;E2F1..5:-0.675154556136;MYB:-0.688887763283;OCT4_SOX2{dimer}:-0.717354620627;PRRX1,2:-0.721331678311;NKX6-1,2:-0.724313724402;POU2F1..3:-0.729642292144;TEF:-0.740199815228;NKX3-1:-0.740357114303;bHLH_family:-0.801213859164;NRF1:-0.838381272283;PAX8:-0.840605638737;LHX3,4:-0.89603774208;ADNP_IRX_SIX_ZHX:-1.01623518293;GATA6:-1.02352008478;POU1F1:-1.05598122455;FOXD3:-1.08818385015;ONECUT1,2:-1.11112885224;CDX1,2,4:-1.2289400909;ELK1,4_GABP{A,B1}:-1.25047189217;NFY{A,B,C}:-1.44320082993;ARID5B:-1.55904029073;ZBTB16:-1.60361447555;STAT1,3:-1.98729079086
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:659-23C6;search_select_hide=table117:659-23C6
 }}

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FF:659-23C6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:19, 4 June 2020

CNhs10576

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