FF:372-23H2: Difference between revisions

Latest revision as of 19:13, 4 June 2020

Name:	whole body, embryo E13
Species:	Mouse (Mus musculus)
Library ID:	CNhs10512
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	whole body
dev stage	13 days embryo
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		SAMD00006017

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10512		CAGE		DRX009144		DRR010018

Accession ID Mm9

Library id		BAM		CTSS
CNhs10512		DRZ001443		DRZ002826

Accession ID Mm10

Library id		BAM		CTSS
CNhs10512		DRZ012793		DRZ014176

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

CNhs10512

0	0
1	0.114
10	0
100	0.18
1000	-0.00125
1001	-0.0749
1002	0.0979
1003	0.0046
1004	0.154
1005	-0.0402
1006	0.0468
1007	0.0839
1008	0
1009	-0.0105
101	0.101
1010	0
1011	0.0424
1012	0
1013	-0.169
1014	0.338
1015	0.27
1016	0.193
1017	0
1018	0.0685
1019	0
102	0
1020	0
1021	-7.232784e-4
1022	-0.0188
1023	0
1024	-0.066
1025	0.18
1026	0.039
1027	0.268
1028	0
1029	-0.0553
103	0.104
1030	0
1031	0.317
1032	-0.177
1033	0.104
1034	0
1035	0
1036	0.197
1037	0
1038	-0.0722
1039	-0.123
104	0
1040	-0.00904
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression Analyst: Michiel de Hoon link to dataset. data

library id: CNhs10512

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	9.71032e-5
MA0003.1	MA0003.1	0.276
MA0004.1	MA0004.1	0.651
MA0006.1	MA0006.1	0.267
MA0007.1	MA0007.1	0.141
MA0009.1	MA0009.1	0.182
MA0014.1	MA0014.1	0.188
MA0017.1	MA0017.1	1.45862e-5
MA0018.2	MA0018.2	0.496
MA0019.1	MA0019.1	0.866
MA0024.1	MA0024.1	4.24535e-4
MA0025.1	MA0025.1	0.01
MA0027.1	MA0027.1	0.0335
MA0028.1	MA0028.1	0.534
MA0029.1	MA0029.1	0.944
MA0030.1	MA0030.1	0.135
MA0031.1	MA0031.1	0.00862
MA0035.2	MA0035.2	0.327
MA0038.1	MA0038.1	0.00734
MA0039.2	MA0039.2	0.14
MA0040.1	MA0040.1	0.343
MA0041.1	MA0041.1	0.515
MA0042.1	MA0042.1	0.567
MA0043.1	MA0043.1	0.389
MA0046.1	MA0046.1	0.0135
MA0047.2	MA0047.2	0.00531
MA0048.1	MA0048.1	0.573
MA0050.1	MA0050.1	6.33008e-6
MA0051.1	MA0051.1	4.16219e-5
MA0052.1	MA0052.1	0.845
MA0055.1	MA0055.1	0.686
MA0057.1	MA0057.1	0.0745
MA0058.1	MA0058.1	0.758
MA0059.1	MA0059.1	0.435
MA0060.1	MA0060.1	2.05506e-16
MA0061.1	MA0061.1	0.101
MA0062.2	MA0062.2	0.052
MA0065.2	MA0065.2	1.99506e-6
MA0066.1	MA0066.1	0.0697
MA0067.1	MA0067.1	0.488
MA0068.1	MA0068.1	0.0731
MA0069.1	MA0069.1	0.635
MA0070.1	MA0070.1	0.114
MA0071.1	MA0071.1	0.0334
MA0072.1	MA0072.1	0.0146
MA0073.1	MA0073.1	0.929
MA0074.1	MA0074.1	0.281
MA0076.1	MA0076.1	0.832
MA0077.1	MA0077.1	0.0867
MA0078.1	MA0078.1	0.896
MA0079.2	MA0079.2	0.542
MA0080.2	MA0080.2	1.45991e-10
MA0081.1	MA0081.1	0.226
MA0083.1	MA0083.1	0.331
MA0084.1	MA0084.1	0.825
MA0087.1	MA0087.1	0.323
MA0088.1	MA0088.1	0.263
MA0090.1	MA0090.1	0.533
MA0091.1	MA0091.1	0.915
MA0092.1	MA0092.1	0.466
MA0093.1	MA0093.1	0.743
MA0099.2	MA0099.2	2.86669e-5
MA0100.1	MA0100.1	0.694
MA0101.1	MA0101.1	0.145
MA0102.2	MA0102.2	0.533
MA0103.1	MA0103.1	0.0013
MA0104.2	MA0104.2	0.821
MA0105.1	MA0105.1	0.121
MA0106.1	MA0106.1	0.0431
MA0107.1	MA0107.1	0.108
MA0108.2	MA0108.2	2.16709e-4
MA0111.1	MA0111.1	0.424
MA0112.2	MA0112.2	2.13946e-6
MA0113.1	MA0113.1	0.245
MA0114.1	MA0114.1	6.07343e-5
MA0115.1	MA0115.1	0.0048
MA0116.1	MA0116.1	0.0397
MA0117.1	MA0117.1	0.424
MA0119.1	MA0119.1	0.0992
MA0122.1	MA0122.1	0.74
MA0124.1	MA0124.1	0.94
MA0125.1	MA0125.1	0.00591
MA0131.1	MA0131.1	0.57
MA0135.1	MA0135.1	0.214
MA0136.1	MA0136.1	7.29847e-10
MA0137.2	MA0137.2	0.0275
MA0138.2	MA0138.2	0.435
MA0139.1	MA0139.1	0.0895
MA0140.1	MA0140.1	0.00415
MA0141.1	MA0141.1	9.61289e-5
MA0142.1	MA0142.1	0.186
MA0143.1	MA0143.1	0.0249
MA0144.1	MA0144.1	0.0551
MA0145.1	MA0145.1	0.0316
MA0146.1	MA0146.1	0.0229
MA0147.1	MA0147.1	0.988
MA0148.1	MA0148.1	0.00299
MA0149.1	MA0149.1	8.17113e-4
MA0150.1	MA0150.1	0.00659
MA0152.1	MA0152.1	0.915
MA0153.1	MA0153.1	0.0174
MA0154.1	MA0154.1	0.00365
MA0155.1	MA0155.1	0.768
MA0156.1	MA0156.1	6.41909e-5
MA0157.1	MA0157.1	0.0107
MA0159.1	MA0159.1	3.26423e-4
MA0160.1	MA0160.1	0.00126
MA0162.1	MA0162.1	0.435
MA0163.1	MA0163.1	0.00234
MA0164.1	MA0164.1	0.952
MA0258.1	MA0258.1	1.14377e-4
MA0259.1	MA0259.1	0.909

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: CNhs10512

Novel motif	Logo	P-value
1	1	0.0575
10	10	0.0793
100	100	0.952
101	101	0.766
102	102	0.44
103	103	0.0294
104	104	0.662
105	105	0.484
106	106	0.0168
107	107	0.119
108	108	0.887
109	109	0.0324
11	11	0.0645
110	110	0.105
111	111	0.0052
112	112	0.00662
113	113	0.901
114	114	0.0101
115	115	0.41
116	116	0.47
117	117	0.0194
118	118	0.539
119	119	0.107
12	12	0.846
120	120	0.885
121	121	0.677
122	122	0.817
123	123	0.987
124	124	0.667
125	125	0.0933
126	126	0.116
127	127	0.065
128	128	0.0674
129	129	0.236
13	13	0.00961
130	130	0.196
131	131	0.748
132	132	0.285
133	133	0.434
134	134	0.966
135	135	0.668
136	136	0.0951
137	137	0.562
138	138	0.838
139	139	0.0269
14	14	0.572
140	140	0.0152
141	141	0.0535
142	142	0.623
143	143	0.216
144	144	0.652
145	145	0.0881
146	146	0.72
147	147	0.617
148	148	0.227
149	149	0.341
15	15	0.0496
150	150	0.284
151	151	0.23
152	152	0.0399
153	153	0.162
154	154	0.566
155	155	0.179
156	156	8.55989e-6
157	157	0.847
158	158	0.0885
159	159	0.0966
160	160	0.538
161	161	0.29
162	162	0.827
163	163	0.299
164	164	0.0269
165	165	0.155
166	166	0.39
167	167	0.744
168	168	0.608
169	169	0.00257
17	17	0.0444
18	18	0.467
19	19	0.175
2	2	0.914
20	20	0.45
21	21	0.671
22	22	0.173
23	23	0.264
24	24	0.177
25	25	0.412
26	26	0.0147
27	27	0.563
28	28	0.337
29	29	0.0982
3	3	0.0957
30	30	0.843
31	31	0.528
32	32	0.215
33	33	0.215
34	34	0.963
35	35	0.25
36	36	0.222
37	37	0.018
38	38	0.311
39	39	0.36
4	4	0.626
40	40	0.236
41	41	0.346
42	42	0.354
43	43	0.118
44	44	0.0398
45	45	0.55
46	46	0.121
47	47	0.13
48	48	0.0768
49	49	0.0991
5	5	0.151
50	50	0.898
51	51	0.599
52	52	0.411
53	53	0.985
54	54	0.639
55	55	0.382
56	56	0.403
57	57	0.488
58	58	0.214
59	59	0.0699
6	6	0.65
60	60	0.0429
61	61	0.22
62	62	0.0718
63	63	0.13
64	64	0.5
65	65	0.18
66	66	0.679
67	67	0.984
68	68	0.176
69	69	0.488
7	7	0.116
70	70	1.78847e-4
71	71	0.0508
72	72	0.384
73	73	0.0205
74	74	0.367
75	75	0.0146
76	76	0.552
77	77	0.12
78	78	0.0911
79	79	0.715
8	8	0.0866
80	80	0.386
81	81	0.558
82	82	0.0305
83	83	0.322
84	84	0.252
85	85	0.0166
86	86	0.232
87	87	0.514
88	88	0.434
89	89	0.209
9	9	0.614
90	90	0.084
91	91	0.464
92	92	0.0798
93	93	0.119
94	94	0.898
95	95	0.0231
96	96	0.408
97	97	0.556
98	98	0.395
99	99	0.745

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: CNhs10512

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011326 mouse whole body- embryo E13 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)
0000293 (mouse embryonic day 13 sample)
0011326 (mouse whole body- embryo E13 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
-|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0000922,UBERON:0001062
+|DRA_sample_Accession=CAGE@SAMD00006017
+|accession_numbers=CAGE;DRX009144;DRR010018;DRZ001443;DRZ002826;DRZ012793;DRZ014176
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000293,FF:0011326
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr12:34642510..34642530,+!p1@Twist1!1.62!123.44!Twist1;;chr8:87425854..87425891,+!p1@Klf1!1.55!34.49!Klf1;;chr11:96143666..96143725,+!p1@Hoxb8!1.54!38.76!Hoxb8;;chr1:136186574..136186592,+!p1@Myog!1.44!26.81!Myog;;chr3:127336052..127336058,+!p1@Neurog2!1.42!25.27!Neurog2;;chr9:91260594..91260612,-!p1@Zic1!1.36!21.85!Zic1;;chr6:55631042..55631102,-!p1@Neurod6!1.34!20.66!Neurod6;;chr15:103085660..103085681,-!p1@Nfe2!1.30!28.17!Nfe2;;chr1:140739014..140739032,-!p1@Lhx9!1.29!23.22!Lhx9;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.29!23.22!Pou3f3;;chr9:91260616..91260653,-!p2@Zic1!1.28!17.93!Zic1;;chr12:28027561..28027591,-!p1@Sox11!1.27!112.17!Sox11;;chr4:154335024..154335039,+!p1@Hes5!1.26!21.00!Hes5;;chr3:99057269..99057306,+!p1@Tbx15!1.26!20.83!Tbx15;;chr1:165243591..165243625,-!p2@Prrx1!1.25!25.44!Prrx1;;chr12:74147689..74147711,-!p1@Six1!1.23!34.83!Six1;;chr7:53631837..53631850,+!p1@Myod1!1.23!15.88!Myod1;;chr10:119913278..119913298,-!p2@Hmga2!1.22!34.49!Hmga2;;chr3:101814061..101814094,+!p1@Nhlh2!1.22!15.71!Nhlh2;;chr10:119914001..119914078,-!p4@Hmga2!1.21!20.49!Hmga2;;chr2:28477452..28477483,-!p1@Gfi1b!1.19!17.76!Gfi1b;;chrX:58146612..58146615,-!p1@Sox3!1.19!14.34!Sox3;;chr15:102828658..102828678,+!p1@Hoxc6!1.19!14.34!Hoxc6;;chr13:99124189..99124205,+!p1@Foxd1!1.18!21.34!Foxd1;;chr2:38206580..38206600,+!p2@Lhx2!1.18!17.41!Lhx2;;chr2:79296783..79296801,-!p1@Neurod1!1.17!13.66!Neurod1;;chr2:71384802..71384815,-!p1@Dlx2!1.16!16.56!Dlx2;;chr12:3891810..3891829,+!p2@Dnmt3a!1.15!20.32!Dnmt3a;;chr2:151907546..151907561,+!p1@Scrt2!1.15!12.98!Scrt2;;chr13:55932591..55932622,-!p1@Pitx1!1.13!15.20!Pitx1;;chr8:59799772..59799789,+!p1@Hand2!1.12!35.00!Hand2;;chr10:119913546..119913583,-!p3@Hmga2!1.12!25.61!Hmga2;;chr10:86956396..86956411,-!p1@Ascl1!1.12!18.95!Ascl1;;chr1:165243379..165243402,-!p3@Prrx1!1.12!18.27!Prrx1;;chr12:30213247..30213333,+!p1@Myt1l!1.12!12.29!Myt1l;;chr11:101755669..101755686,-!p1@Meox1!1.11!21.34!Meox1;;chr2:147190749..147190769,+!p1@Pax1!1.11!11.95!Pax1;;chrX:7544943..7545001,-!p1@Gata1!1.11!11.95!Gata1;;chr6:52190467..52190500,-!p1@Hoxa10!1.11!11.78!Hoxa10;;chr10:119913310..119913366,-!p1@Hmga2!1.06!82.64!Hmga2;;chr7:56892217..56892221,-!p1@Dbx1!1.06!10.41!Dbx1;;chrX:108009761..108009788,+!p1@Pou3f4!1.06!10.41!Pou3f4;;chr4:114732112..114732158,+!p1@Tal1!1.05!22.71!Tal1;;chr3:66785857..66785873,-!p1@Shox2!1.05!10.24!Shox2;;chr3:95032091..95032183,-!p1@Mllt11!1.04!86.56!Mllt11;;chr7:144505957..144505972,-!p2@Ebf3!1.04!12.46!Ebf3;;chr2:38206744..38206766,+!p1@Lhx2!1.03!11.95!Lhx2;;chr1:173987720..173987729,-!p1@Nhlh1!1.03!9.73!Nhlh1;;chr14:49287186..49287225,-!p1@Otx2!1.03!9.73!Otx2;;chr2:65683890..65683907,+!p1@Csrnp3!1.02!18.27!Csrnp3;;chr13:72766250..72766273,+!p1@Irx2!1.02!14.85!Irx2;;chr6:52176164..52176195,-!p1@Hoxa9!1.02!11.78!Hoxa9;;chr12:54349410..54349461,+!p1@Npas3!1.02!11.44!Npas3;;chr2:31495237..31495243,+!p1@Prdm12!1.01!9.22!Prdm12;;chr10:12810631..12810649,+!p1@Plagl1!0.99!235.78!Plagl1;;chr9:71743854..71743909,-!p1@Tcf12!0.99!71.20!Tcf12;;chr6:6832076..6832092,-!p1@Dlx5!0.98!10.07!Dlx5;;chr3:34548909..34548927,+!p1@Sox2!0.97!14.51!Sox2;;chr11:98190918..98190951,-!p1@Neurod2!0.97!8.37!Neurod2;;chr4:150503457..150503498,-!p3@Camta1!0.96!9.22!Camta1;;chr2:74513125..74513143,+!p1@Hoxd12!0.96!8.20!Hoxd12;;chrX:55283799..55283813,+!p1@Zic3!0.96!8.20!Zic3;;chr11:84339016..84339044,-!p1@Lhx1!0.96!8.02!Lhx1;;chr6:52184901..52184959,-!p2@Hoxa10!0.96!8.02!Hoxa10;;chr13:117099847..117099907,-!p1@Isl1!0.95!15.02!Isl1;;chr13:53568104..53568156,-!p1@Msx2!0.95!11.78!Msx2;;chr1:19199236..19199258,+!p1@Tfap2b!0.95!7.85!Tfap2b;;chr17:86087592..86087615,-!p1@Six2!0.95!7.85!Six2;;chr2:146047829..146047847,+!p1@Insm1!0.94!14.17!Insm1;;chr6:52163319..52163342,-!p1@Hoxa3!0.94!11.27!Hoxa3;;chr6:52167459..52167492,-!p1@Hoxa7!0.94!9.39!Hoxa7;;chr12:57796615..57796687,+!p1@Pax9!0.94!7.68!Pax9;;chr7:144506077..144506128,-!p1@Ebf3!0.93!17.93!Ebf3;;chr13:48758276..48758291,+!p1@Barx1!0.93!7.51!Barx1;;chr15:102087737..102087801,-!p3@Rarg!0.92!12.29!Rarg;;chr19:25746898..25746910,+!p1@Dmrt2!0.92!11.10!Dmrt2;;chr13:56353536..56353542,-!p1@Neurog1!0.92!7.34!Neurog1;;chr14:67853425..67853454,+!p1@Ebf2!0.90!10.07!Ebf2;;chrX:90531838..90531861,+!p1@Arx!0.90!8.88!Arx;;chr2:147190725..147190747,+!p2@Pax1!0.90!7.00!Pax1;;chr12:37835120..37835133,+!p2@Meox2!0.89!9.90!Meox2;;chr11:11584970..11585030,+!p2@Ikzf1!0.89!9.90!Ikzf1;;chr13:83643159..83643226,+!p3@Mef2c!0.89!6.83!Mef2c;;chr9:24578720..24578735,-!p1@Tbx20!0.89!6.83!Tbx20;;chr14:104867201..104867258,-!p1@Pou4f1!0.88!9.39!Pou4f1;;chr15:102797288..102797302,+!p1@Hoxc10!0.88!6.66!Hoxc10;;chr9:118387300..118387317,+!p1@Eomes!0.88!6.66!Eomes;;chr1:179374784..179374800,+!p2@Zfp238!0.87!7.68!Zfp238;;chr13:40829137..40829205,-!p1@Tfap2a!0.87!7.34!Tfap2a;;chr4:87452200..87452229,-!p2@Mllt3!0.86!13.83!Mllt3;;chr4:87452180..87452196,-!p3@Mllt3!0.86!12.81!Mllt3;;chr19:59533221..59533271,+!p1@Emx2!0.86!7.85!Emx2;;chr1:78193687..78193692,-!p1@Pax3!0.86!6.32!Pax3;;chr4:13670499..13670526,+!p2@Runx1t1!0.85!14.17!Runx1t1;;chr7:116154364..116154444,+!p1@Tub!0.85!10.76!Tub;;chr14:67853457..67853482,+!p2@Ebf2!0.85!8.88!Ebf2;;chr7:122989632..122989668,-!p2@Sox6!0.85!6.15!Sox6;;chr12:109242266..109242295,-!p1@Bcl11b!0.84!53.44!Bcl11b;;chr7:6649134..6649167,-!p1@Zim1!0.84!33.98!Zim1;;chr10:126778916..126778974,-!p1@Gli1!0.84!13.83!Gli1;;chr4:53792566..53792578,+!p1@Tal2!0.84!5.98!Tal2;;chr14:56443806..56443848,+!p1@Nfatc4!0.83!12.12!Nfatc4;;chr2:120365588..120365602,-!p2@Zfp106!0.83!9.90!Zfp106;;chr17:44951553..44951586,-!p2@Runx2!0.83!6.49!Runx2;;chr14:122874619..122874634,+!p1@Zic2!0.83!5.80!Zic2;;chr11:96132637..96132652,+!p1@Hoxb9!0.83!5.80!Hoxb9;;chr12:3891753..3891801,+!p4@Dnmt3a!0.82!9.39!Dnmt3a;;chr13:72101178..72101203,-!p1@Irx1!0.82!9.05!Irx1;;chr15:103082088..103082136,-!p2@Nfe2!0.82!5.63!Nfe2;;chr10:102491405..102491416,-!p1@Alx1!0.82!5.63!Alx1;;chr2:71367871..71367898,+!p1@Dlx1!0.82!5.63!Dlx1;;chr17:37139472..37139514,+!p1@Zfp57!0.81!39.44!Zfp57;;chr7:30088977..30089002,+!p2@Dpf1!0.81!7.68!Dpf1;;chr7:144505980..144506010,-!p3@Ebf3!0.81!6.66!Ebf3;;chr2:74550015..74550057,+!p2@Hoxd3!0.81!5.46!Hoxd3;;chr19:55968967..55968991,+!p7@Tcf7l2!0.81!5.46!Tcf7l2;;chr1:6720216..6720232,+!p1@St18!0.81!5.46!St18;;chr5:38215819..38215823,-!p1@Msx1!0.80!14.68!Msx1;;chr6:14851440..14851497,+!p2@Foxp2!0.80!13.83!Foxp2;;chr2:74549968..74549996,+!p1@Hoxd3!0.80!6.83!Hoxd3;;chr2:71367142..71367167,+!p2@Dlx1!0.80!5.29!Dlx1;;chr1:136186545..136186554,+!p2@Myog!0.80!5.29!Myog;;chr3:128916868..128916890,+!p1@Pitx2!0.79!7.34!Pitx2;;chr14:67853632..67853674,+!p3@Ebf2!0.79!6.32!Ebf2;;chr6:6831950..6831985,-!p2@Dlx5!0.79!5.80!Dlx5;;chr7:122989594..122989626,-!p1@Sox6!0.79!5.12!Sox6;;chr10:84218895..84218909,+!p1@Rfx4!0.79!5.12!Rfx4;;chr12:37835141..37835194,+!p1@Meox2!0.78!16.73!Meox2;;chr13:15555670..15555771,+!p2@Gli3!0.78!13.66!Gli3;;chr9:87626083..87626108,-!p1@Tbx18!0.78!11.78!Tbx18;;chr2:61642631..61642684,+!p1@Tbr1!0.77!4.95!Tbr1;;chr16:25801993..25802014,+!p1@Trp63!0.77!4.95!Trp63;;chr11:96132767..96132796,+!p2@Hoxb9!0.77!4.95!Hoxb9;;chr5:98609885..98609900,+!p1@Prdm8!0.77!4.95!Prdm8;;chr1:93698030..93698064,+!p1@Twist2!0.76!10.07!Twist2;;chr13:31717548..31717596,+!p1@Foxf2!0.76!10.07!Foxf2;;chr2:30700788..30700824,+!p2@Prrx2!0.76!7.68!Prrx2;;chr13:72766279..72766296,+!p2@Irx2!0.76!7.34!Irx2;;chr13:44936126..44936164,+!p6@Jarid2!0.76!5.63!Jarid2;;chr11:33103563..33103583,-!p1@Tlx3!0.76!4.78!Tlx3;;chr12:9581262..9581282,+!p1@Osr1!0.75!61.63!Osr1;;chr5:24107676..24107722,-!p4@Smarcd3!0.75!6.49!Smarcd3;;chr2:115891534..115891589,-!p1@Meis2!0.74!71.03!Meis2;;chr15:76287876..76287894,+!p1@Scx!0.74!27.15!Scx;;chr6:52154414..52154462,-!p1@Hoxa5!0.74!6.49!Hoxa5;;chr1:169528823..169528860,+!p5@Rxrg!0.74!4.44!Rxrg;;chr8:12395603..12395621,+!p1@Sox1!0.74!4.44!Sox1;;chr11:85699862..85699920,+!p1@Tbx4!0.74!4.44!Tbx4;;chr9:96159147..96159204,+!p2@Tfdp2!0.73!8.71!Tfdp2;;chr11:96153767..96153822,+!p1@Hoxb6!0.73!7.17!Hoxb6;;chr15:103085690..103085710,-!p3@Nfe2!0.73!4.78!Nfe2;;chr3:5218516..5218544,+!p2@Zfhx4!0.72!6.66!Zfhx4;;chr1:93698068..93698085,+!p2@Twist2!0.72!5.12!Twist2;;chr1:169528720..169528749,+!p6@Rxrg!0.72!4.27!Rxrg;;chr2:74529970..74529997,+!p1@Hoxd10!0.72!4.27!Hoxd10;;chr6:52195795..52195825,-!p1@Hoxa11!0.72!4.27!Hoxa11;;chr4:84320893..84320910,-!p1@Bnc2!0.71!9.90!Bnc2;;chr11:18918434..18918489,-!p3@Meis1!0.71!6.83!Meis1;;chr7:91558472..91558512,-!p2@Arnt2!0.71!6.15!Arnt2;;chr8:111227354..111227401,+!p@chr8:111227354..111227401,+!0.71!5.80!Zfhx3;;chr1:19199151..19199170,+!p3@Tfap2b!0.71!4.10!Tfap2b;;chr6:144152648..144152680,-!p5@Sox5!0.71!4.10!Sox5;;chrX:55284180..55284195,+!p2@Zic3!0.71!4.10!Zic3;;chr13:72101141..72101158,-!p3@Irx1!0.70!5.12!Irx1;;chr4:13670571..13670625,+!p1@Runx1t1!0.69!11.78!Runx1t1;;chr4:109650609..109650653,+!p1@Dmrta2!0.69!3.93!Dmrta2;;chr4:139388835..139388867,-!p1@Pax7!0.69!3.93!Pax7;;chr15:102820964..102821006,+!p1@Hoxc8!0.69!3.93!Hoxc8;;chr19:55969923..55969944,+!p6@Tcf7l2!0.69!3.93!Tcf7l2;;chr1:91827728..91827743,-!p2@Gbx2!0.69!3.93!Gbx2;;chr8:87225670..87225697,+!p2@Lyl1!0.68!12.29!Lyl1;;chr15:35225845..35225867,+!p1@Osr2!0.68!10.59!Osr2;;chr13:31898767..31898785,+!p4@Foxc1!0.68!4.78!Foxc1;;chr4:84321300..84321315,-!p2@Bnc2!0.68!4.78!Bnc2;;chr2:93482464..93482491,+!p1@Alx4!0.68!3.76!Alx4;;chr14:67853682..67853702,+!p4@Ebf2!0.68!3.76!Ebf2;;chr2:181501988..181502026,+!p3@Myt1!0.68!3.76!Myt1;;chr7:108966820..108966835,+!p1@Phox2a!0.68!3.76!Phox2a;;chr6:85137520..85137563,+!p1@Emx1!0.68!3.76!Emx1;;chr5:28492230..28492257,+!p1@En2!0.68!3.76!En2;;chr11:96160360..96160397,+!p3@Hoxb6!0.68!3.76!Hoxb6;;chrX:45245679..45245702,-!p1@Smarca1!0.67!18.78!Smarca1;;chr11:23980664..23980706,+!p2@Bcl11a!0.67!18.27!Bcl11a;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.67!7.00!Zfhx3;;chr8:123608252..123608268,+!p1@Foxf1a!0.67!5.80!Foxf1a;;chr13:72101161..72101177,-!p2@Irx1!0.67!5.29!Irx1;;chr19:7342786..7342803,+!p2@Rcor2!0.67!5.12!Rc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+|ffid_belonging_in_development=FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:372-23H2
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011326
+|is_a=EFO:0002091;;FF:0011326
+|is_obsolete=
+|library_id=CNhs10512
+|library_id_phase_based=2:CNhs10512
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;372
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;372
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm9.nobarcode.rdna.fa.gz
 |name=whole body, embryo E13
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10512,LSID649,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0353527433052081,0,0,0,0,0,0.165140531048985,0,0.0160021988646997,0,0,0.423454163230103,0,0,0,0,0,0,0.114403328408601,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.125880624888478,0,0,0,0,0.0397547224753756,-0.00648439445216505,0.0434749980250053,-0.165600634294475,0.570031266887888,0.528971272900276,0,0,0,0,0,0,0,0,0,0,0,0.0684580848992459,0.00245253733580557,0,0,0,0,0,0,0,0,0,0.0293216757670706,0.05879287862843,-0.042618697855713,0.393481429263671,0.139913529060692,0,0.128608867799195,0.0564643643879859,0,0.127580061998599,0,0.0357320247268346,-0.0142380219422279,-0.221924215268137,0.0487484671586915,0,0,0,0,0,0,-0.110954269430899,-0.242604836358064,-0.101557980039939,0,0,0,0,0
 |rna_box=23
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=whole body
 |top_motifs=SOX{8,9,10}:1.87341066433;PRRX1,2:1.78567327886;SOX2:1.77622876165;VSX1,2:1.77061130574;MZF1:1.67079686944;NFY{A,B,C}:1.62935997949;GFI1:1.5613625676;RREB1:1.53827669919;SOX5:1.53671083952;LEF1_TCF7_TCF7L1,2:1.42382631219;GATA6:1.35773003942;PAX1,9:1.33742711969;NANOG:1.33266050279;HOXA9_MEIS1:1.308598835;PATZ1:1.25170996912;ZNF143:1.24594311435;NKX2-3_NKX2-5:1.1704543275;MYBL2:1.16966355141;ZNF384:1.14442998238;OCT4_SOX2{dimer}:1.13468610769;SOX17:1.13157436477;TFDP1:1.08835306976;MAZ:1.06594410348;ADNP_IRX_SIX_ZHX:1.03438384521;PRDM1:1.03314992038;HOX{A5,B5}:1.02555576382;GZF1:0.998499642292;NKX2-1,4:0.987634269635;ZNF238:0.94886216682;POU5F1:0.929961181982;BREu{core}:0.921485790824;GFI1B:0.920075593194;PAX6:0.919360934456;GTF2I:0.918177719352;TGIF1:0.916432840697;CUX2:0.914474251876;FOXD3:0.90225596939;NRF1:0.88925884068;LHX3,4:0.871317935591;HOX{A4,D4}:0.818271252213;NKX3-2:0.817868378792;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.811664465457;DBP:0.811135958971;NHLH1,2:0.805706135973;POU3F1..4:0.799537010965;AHR_ARNT_ARNT2:0.795633613694;STAT5{A,B}:0.785936325932;MED-1{core}:0.778332008411;NANOG{mouse}:0.776825928872;E2F1..5:0.773779143242;MTE{core}:0.763900522494;PBX1:0.762292683698;EN1,2:0.757359767227;HSF1,2:0.748031208646;ONECUT1,2:0.744117348488;GATA4:0.718746066421;FOXP1:0.698531198895;XCPE1{core}:0.68641054229;PITX1..3:0.680735716397;HIC1:0.651271663245;NKX3-1:0.636689586329;EP300:0.626358976811;KLF4:0.616980533806;HBP1_HMGB_SSRP1_UBTF:0.552434398581;ATF2:0.543964573733;GTF2A1,2:0.530698951742;EGR1..3:0.527605034657;MYFfamily:0.520968059588;ZFP161:0.504762911371;TFAP2B:0.488892432237;CDC5L:0.472535894401;SMAD1..7,9:0.472366300512;YY1:0.470662731438;TFAP4:0.444237532056;NKX6-1,2:0.441678889493;TAL1_TCF{3,4,12}:0.428809909721;FOX{I1,J2}:0.428769596927;CDX1,2,4:0.399824143832;ZNF423:0.375399910929;FOXP3:0.372796369338;HIF1A:0.360689364221;TBP:0.359138545255;TBX4,5:0.351837263926;POU2F1..3:0.333140571184;IKZF1:0.331355248786;RBPJ:0.326274692102;SP1:0.319615744153;PAX5:0.316466581372;TLX2:0.315039117813;MTF1:0.314747406507;PAX4:0.307093227222;POU6F1:0.305631541715;MAFB:0.304660875222;TEAD1:0.300781397927;ZBTB6:0.298147783809;ZNF148:0.291024773752;TOPORS:0.281621256553;CRX:0.280171468917;RFX1:0.264742012256;FOXN1:0.264329993785;REST:0.259217983045;IKZF2:0.256912240385;HMX1:0.253634719355;HES1:0.244596937792;ZIC1..3:0.232410588594;SRF:0.23053265093;HMGA1,2:0.164013695389;UFEwm:0.15599126576;FOXL1:0.15072477768;JUN:0.137433844696;FOXA2:0.130238719813;RXR{A,B,G}:0.127552878334;ATF6:0.122254638779;TLX1..3_NFIC{dimer}:0.112928923044;MEF2{A,B,C,D}:0.081821921288;ZBTB16:0.0805812952105;GLI1..3:0.0758550687602;ELK1,4_GABP{A,B1}:0.0728310195173;FOX{F1,F2,J1}:0.0464797157336;NR6A1:0.0255686601686;GCM1,2:0.00814128106226;RFX2..5_RFXANK_RFXAP:-0.0140061313849;TFAP2{A,C}:-0.0243239649644;STAT1,3:-0.0353547922451;PAX8:-0.040733398979;MYB:-0.0478540751881;HNF1A:-0.0991320523284;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.118262316619;TFCP2:-0.136778447857;ATF5_CREB3:-0.151638814127;LMO2:-0.152606032239;SPZ1:-0.156181964551;POU1F1:-0.200577163644;PDX1:-0.202989228795;T:-0.216082441105;EVI1:-0.226308879095;ATF4:-0.242070275688;PAX2:-0.247032817946;NR3C1:-0.266330640722;SNAI1..3:-0.292638785652;ELF1,2,4:-0.300489523558;NFATC1..3:-0.331796376277;NFE2:-0.334911071805;SPIB:-0.341422589391;TEF:-0.356411473852;ARID5B:-0.363928609535;RORA:-0.365033106364;HNF4A_NR2F1,2:-0.374991927497;MYOD1:-0.378821607514;RUNX1..3:-0.396438620406;NFIX:-0.399298673098;CREB1:-0.401762127983;SPI1:-0.404060315131;BPTF:-0.437225294853;ESR1:-0.437312967374;AIRE:-0.467813369088;NFE2L2:-0.50595701835;FOXM1:-0.509742825693;NFKB1_REL_RELA:-0.584573055399;NFIL3:-0.608460119344;bHLH_family:-0.609698221229;NFE2L1:-0.618988843964;PPARG:-0.630586225819;RXRA_VDR{dimer}:-0.639015579145;DMAP1_NCOR{1,2}_SMARC:-0.64700225312;TP53:-0.66489223693;ALX1:-0.674802401646;NR5A1,2:-0.677033658313;ZEB1:-0.681325745586;ETS1,2:-0.692229719632;SREBF1,2:-0.701385496414;HLF:-0.719765379442;FOS_FOS{B,L1}_JUN{B,D}:-0.771083468888;CEBPA,B_DDIT3:-0.89388834527;FOSL2:-0.898439026506;EBF1:-0.907737243602;BACH2:-0.953965752483;ESRRA:-0.963378136565;IRF7:-0.971665978204;AR:-0.985967470151;FOXQ1:-0.992153458359;IRF1,2:-1.0226722961;HAND1,2:-1.08512848032;NKX2-2,8:-1.09915295977;FOX{D1,D2}:-1.11924854473;STAT2,4,6:-1.12244739896;ALX4:-1.15284783267;FOXO1,3,4:-1.47584990636;NR1H4:-1.5813512996
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:372-23H2;search_select_hide=table117:372-23H2
 }}

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FF:372-23H2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:13, 4 June 2020

CNhs10512

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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