FF:353-12F5: Difference between revisions

Latest revision as of 19:10, 4 June 2020

Name:	heart, embryo E12
Species:	Mouse (Mus musculus)
Library ID:	CNhs11015
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	heart
dev stage	12 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		SAMD00005925

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11015		CAGE		DRX008972		DRR009846

Accession ID Mm9

Library id		BAM		CTSS
CNhs11015		DRZ001271		DRZ002654

Accession ID Mm10

Library id		BAM		CTSS
CNhs11015		DRZ012621		DRZ014004

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

CNhs11015

0	0
1	0
10	0.0915
100	0
1000	0
1001	0.26
1002	0.465
1003	0.00475
1004	0
1005	-0.0389
1006	0.231
1007	0.0156
1008	0
1009	0.00751
101	0.0744
1010	0
1011	-0.0226
1012	0
1013	-0.217
1014	0.539
1015	0.226
1016	0.161
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.137
1023	0
1024	-0.0361
1025	0.0915
1026	0
1027	0
1028	0
1029	0.238
103	0.015
1030	0
1031	0.419
1032	-0.0166
1033	0.00343
1034	0
1035	0.422
1036	-0.0466
1037	0
1038	-0.0129
1039	0.00774
104	0
1040	0.0717
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: CNhs11015

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0217
MA0003.1	MA0003.1	0.523
MA0004.1	MA0004.1	0.95
MA0006.1	MA0006.1	0.81
MA0007.1	MA0007.1	0.071
MA0009.1	MA0009.1	0.855
MA0014.1	MA0014.1	0.563
MA0017.1	MA0017.1	0.0708
MA0018.2	MA0018.2	0.155
MA0019.1	MA0019.1	0.311
MA0024.1	MA0024.1	8.73799e-5
MA0025.1	MA0025.1	0.102
MA0027.1	MA0027.1	0.0265
MA0028.1	MA0028.1	0.853
MA0029.1	MA0029.1	0.295
MA0030.1	MA0030.1	0.0441
MA0031.1	MA0031.1	0.0217
MA0035.2	MA0035.2	0.0671
MA0038.1	MA0038.1	0.831
MA0039.2	MA0039.2	0.0128
MA0040.1	MA0040.1	0.0868
MA0041.1	MA0041.1	0.111
MA0042.1	MA0042.1	0.205
MA0043.1	MA0043.1	0.545
MA0046.1	MA0046.1	8.38694e-13
MA0047.2	MA0047.2	0.0152
MA0048.1	MA0048.1	0.0274
MA0050.1	MA0050.1	2.51774e-6
MA0051.1	MA0051.1	0.00207
MA0052.1	MA0052.1	4.11157e-13
MA0055.1	MA0055.1	0.0158
MA0057.1	MA0057.1	0.614
MA0058.1	MA0058.1	0.645
MA0059.1	MA0059.1	0.101
MA0060.1	MA0060.1	0.316
MA0061.1	MA0061.1	0.651
MA0062.2	MA0062.2	0.00131
MA0065.2	MA0065.2	0.174
MA0066.1	MA0066.1	0.779
MA0067.1	MA0067.1	0.15
MA0068.1	MA0068.1	0.215
MA0069.1	MA0069.1	0.209
MA0070.1	MA0070.1	0.684
MA0071.1	MA0071.1	0.919
MA0072.1	MA0072.1	0.0927
MA0073.1	MA0073.1	0.955
MA0074.1	MA0074.1	0.626
MA0076.1	MA0076.1	0.0798
MA0077.1	MA0077.1	0.748
MA0078.1	MA0078.1	0.22
MA0079.2	MA0079.2	0.285
MA0080.2	MA0080.2	0.00823
MA0081.1	MA0081.1	0.844
MA0083.1	MA0083.1	1.49213e-15
MA0084.1	MA0084.1	0.77
MA0087.1	MA0087.1	0.944
MA0088.1	MA0088.1	0.326
MA0090.1	MA0090.1	0.0119
MA0091.1	MA0091.1	0.747
MA0092.1	MA0092.1	0.71
MA0093.1	MA0093.1	0.872
MA0099.2	MA0099.2	5.48723e-8
MA0100.1	MA0100.1	0.96
MA0101.1	MA0101.1	0.104
MA0102.2	MA0102.2	0.00928
MA0103.1	MA0103.1	9.17424e-7
MA0104.2	MA0104.2	0.262
MA0105.1	MA0105.1	0.0151
MA0106.1	MA0106.1	0.878
MA0107.1	MA0107.1	0.124
MA0108.2	MA0108.2	0.67
MA0111.1	MA0111.1	0.499
MA0112.2	MA0112.2	0.267
MA0113.1	MA0113.1	0.465
MA0114.1	MA0114.1	0.00365
MA0115.1	MA0115.1	0.938
MA0116.1	MA0116.1	0.889
MA0117.1	MA0117.1	0.535
MA0119.1	MA0119.1	0.0699
MA0122.1	MA0122.1	0.924
MA0124.1	MA0124.1	0.258
MA0125.1	MA0125.1	0.826
MA0131.1	MA0131.1	0.687
MA0135.1	MA0135.1	0.23
MA0136.1	MA0136.1	0.00841
MA0137.2	MA0137.2	0.0393
MA0138.2	MA0138.2	0.0411
MA0139.1	MA0139.1	0.585
MA0140.1	MA0140.1	7.87409e-4
MA0141.1	MA0141.1	0.0257
MA0142.1	MA0142.1	0.579
MA0143.1	MA0143.1	0.554
MA0144.1	MA0144.1	0.0707
MA0145.1	MA0145.1	0.293
MA0146.1	MA0146.1	0.559
MA0147.1	MA0147.1	0.259
MA0148.1	MA0148.1	0.0706
MA0149.1	MA0149.1	0.0912
MA0150.1	MA0150.1	0.00181
MA0152.1	MA0152.1	0.658
MA0153.1	MA0153.1	1.10387e-7
MA0154.1	MA0154.1	0.711
MA0155.1	MA0155.1	0.188
MA0156.1	MA0156.1	1.14178e-5
MA0157.1	MA0157.1	0.0442
MA0159.1	MA0159.1	0.394
MA0160.1	MA0160.1	0.846
MA0162.1	MA0162.1	0.293
MA0163.1	MA0163.1	0.0143
MA0164.1	MA0164.1	0.816
MA0258.1	MA0258.1	0.628
MA0259.1	MA0259.1	0.473

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: CNhs11015

Novel motif	Logo	P-value
1	1	0.742
10	10	0.923
100	100	0.905
101	101	0.757
102	102	0.298
103	103	0.329
104	104	0.565
105	105	0.846
106	106	0.775
107	107	0.924
108	108	0.8
109	109	0.984
11	11	0.195
110	110	0.269
111	111	0.607
112	112	0.392
113	113	0.503
114	114	0.938
115	115	0.535
116	116	0.651
117	117	0.396
118	118	0.457
119	119	0.357
12	12	0.388
120	120	0.372
121	121	0.845
122	122	0.289
123	123	0.0681
124	124	0.937
125	125	0.749
126	126	0.732
127	127	0.248
128	128	0.296
129	129	0.355
13	13	0.00201
130	130	0.244
131	131	0.458
132	132	0.315
133	133	0.692
134	134	0.587
135	135	0.721
136	136	0.0227
137	137	0.87
138	138	0.153
139	139	0.932
14	14	0.483
140	140	0.747
141	141	0.209
142	142	0.738
143	143	0.646
144	144	0.0878
145	145	0.0637
146	146	0.183
147	147	0.871
148	148	0.622
149	149	0.989
15	15	0.237
150	150	0.738
151	151	0.172
152	152	0.281
153	153	0.264
154	154	0.742
155	155	0.686
156	156	0.0143
157	157	0.435
158	158	0.431
159	159	0.171
160	160	0.274
161	161	0.66
162	162	0.77
163	163	0.564
164	164	0.394
165	165	0.197
166	166	0.37
167	167	0.765
168	168	0.686
169	169	0.113
17	17	0.234
18	18	0.525
19	19	0.178
2	2	0.526
20	20	0.146
21	21	0.444
22	22	0.634
23	23	0.196
24	24	0.472
25	25	0.328
26	26	0.0253
27	27	0.19
28	28	0.476
29	29	0.207
3	3	0.961
30	30	0.0936
31	31	0.758
32	32	0.482
33	33	0.135
34	34	0.772
35	35	0.91
36	36	0.156
37	37	0.66
38	38	0.173
39	39	0.351
4	4	0.573
40	40	0.00488
41	41	0.871
42	42	0.899
43	43	0.643
44	44	0.468
45	45	0.0729
46	46	0.643
47	47	0.586
48	48	0.414
49	49	0.818
5	5	0.943
50	50	0.485
51	51	0.975
52	52	0.786
53	53	0.552
54	54	0.833
55	55	0.201
56	56	0.999
57	57	0.287
58	58	0.638
59	59	0.4
6	6	0.194
60	60	0.722
61	61	0.415
62	62	0.569
63	63	0.865
64	64	0.469
65	65	0.168
66	66	0.614
67	67	0.607
68	68	0.789
69	69	0.212
7	7	0.56
70	70	0.0224
71	71	0.00663
72	72	0.0651
73	73	0.813
74	74	0.968
75	75	0.785
76	76	0.346
77	77	0.317
78	78	0.647
79	79	0.201
8	8	0.616
80	80	0.0119
81	81	0.771
82	82	0.981
83	83	0.934
84	84	0.968
85	85	0.883
86	86	0.763
87	87	4.15479e-5
88	88	0.315
89	89	0.128
9	9	0.974
90	90	0.706
91	91	0.256
92	92	0.998
93	93	0.636
94	94	0.182
95	95	0.646
96	96	0.394
97	97	0.14
98	98	0.307
99	99	0.663

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: CNhs11015

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011318 mouse heart- embryo E12 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)
0007100 (primary circulatory organ)
0000948 (heart)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0010317 (germ layer / neural crest derived structure)
0004535 (cardiovascular system)
0001009 (circulatory system)

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)
0000295 (mouse embryonic day 12 sample)
0011318 (mouse heart- embryo E12 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0004140 (primary heart field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008835
+|DRA_sample_Accession=CAGE@SAMD00005925
+|accession_numbers=CAGE;DRX008972;DRR009846;DRZ001271;DRZ002654;DRZ012621;DRZ014004
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0007100,UBERON:0000948,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0010317,UBERON:0004535,UBERON:0001009
 |ancestors_in_cell_lineage_facet=
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr9:24578720..24578735,-!p1@Tbx20!2.44!276.98!Tbx20;;chr8:59799772..59799789,+!p1@Hand2!1.88!205.44!Hand2;;chr14:63864056..63864102,-!p1@Gata4!1.75!94.51!Gata4;;chr17:26978409..26978442,-!p1@Nkx2-5!1.75!55.11!Nkx2-5;;chr11:57645506..57645523,-!p1@Hand1!1.56!34.94!Hand1;;chr2:180069370..180069409,-!p1@Gata5!1.54!38.93!Gata5;;chr12:34642510..34642530,+!p1@Twist1!1.47!87.01!Twist1;;chr11:101755669..101755686,-!p1@Meox1!1.43!45.73!Meox1;;chr5:77543897..77543911,-!p2@Hopx!1.42!47.14!Hopx;;chr6:97879817..97879857,+!p2@Mitf!1.42!25.56!Mitf;;chr1:189821714..189821761,+!p1@Esrrg!1.40!43.86!Esrrg;;chr10:22539932..22539956,-!p1@Tcf21!1.32!52.53!Tcf21;;chr17:26978521..26978536,-!p2@Nkx2-5!1.28!18.06!Nkx2-5;;chr10:119913278..119913298,-!p2@Hmga2!1.21!34.24!Hmga2;;chrX:58146612..58146615,-!p1@Sox3!1.18!14.07!Sox3;;chr7:119885539..119885574,+!p3@Tead1!1.17!13.84!Tead1;;chr4:87452180..87452196,-!p3@Mllt3!1.13!24.63!Mllt3;;chr14:63890491..63890516,-!p2@Gata4!1.12!12.20!Gata4;;chr8:87425854..87425891,+!p1@Klf1!1.11!11.96!Klf1;;chr10:12810631..12810649,+!p1@Plagl1!1.10!305.35!Plagl1;;chr12:3891810..3891829,+!p2@Dnmt3a!1.10!18.29!Dnmt3a;;chr5:77544170..77544181,-!p6@Hopx!1.10!11.49!Hopx;;chr14:63890459..63890484,-!p4@Gata4!1.09!11.26!Gata4;;chr5:120285144..120285160,+!p1@Tbx5!1.08!11.02!Tbx5;;chr9:87626083..87626108,-!p1@Tbx18!1.06!22.98!Tbx18;;chr10:119913310..119913366,-!p1@Hmga2!1.05!80.44!Hmga2;;chr10:30562571..30562597,-!p1@Hey2!1.04!23.92!Hey2;;chr14:63890519..63890539,-!p3@Gata4!1.03!9.62!Gata4;;chr9:87625971..87625992,-!p2@Tbx18!1.02!9.38!Tbx18;;chr10:119913546..119913583,-!p3@Hmga2!1.00!19.23!Hmga2;;chr18:11052642..11052659,+!p1@Gata6!0.99!44.79!Gata6;;chr2:30700788..30700824,+!p2@Prrx2!0.99!13.60!Prrx2;;chr14:63890660..63890687,-!p7@Gata4!0.98!8.44!Gata4;;chr5:24107779..24107825,-!p1@Smarcd3!0.95!55.35!Smarcd3;;chr18:80909801..80909819,-!p1@Nfatc1!0.93!46.44!Nfatc1;;chr4:87452200..87452229,-!p2@Mllt3!0.93!16.65!Mllt3;;chr5:77544108..77544119,-!p7@Hopx!0.93!7.50!Hopx;;chr7:6649134..6649167,-!p1@Zim1!0.91!40.34!Zim1;;chr18:11052456..11052477,+!p3@Gata6!0.91!22.75!Gata6;;chr15:103085660..103085681,-!p1@Nfe2!0.88!10.08!Nfe2;;chr10:119914001..119914078,-!p4@Hmga2!0.87!8.91!Hmga2;;chr3:128917187..128917223,+!p2@Pitx2!0.87!7.50!Pitx2;;chr13:53568104..53568156,-!p1@Msx2!0.86!9.62!Msx2;;chr4:114732112..114732158,+!p1@Tal1!0.85!13.84!Tal1;;chr2:104966766..104966786,+!p1@Wt1!0.85!9.85!Wt1;;chr14:63864337..63864381,-!p6@Gata4!0.84!5.86!Gata4;;chr18:11052485..11052508,+!p2@Gata6!0.83!17.12!Gata6;;chr11:18918434..18918489,-!p3@Meis1!0.83!9.38!Meis1;;chr2:17976799..17976829,+!p5@Mllt10!0.82!7.04!Mllt10;;chr5:77543935..77543947,-!p4@Hopx!0.81!5.39!Hopx;;chr3:29911808..29911833,-!p8@Mecom!0.81!5.39!Mecom;;chr18:11052606..11052633,+!p4@Gata6!0.80!14.07!Gata6;;chrX:137135036..137135064,-!p4@Tsc22d3!0.79!10.55!Tsc22d3;;chr13:72766279..72766296,+!p2@Irx2!0.79!7.97!Irx2;;chr10:30562617..30562637,-!p2@Hey2!0.79!6.57!Hey2;;chr7:17647736..17647772,-!p1@Hif3a!0.78!19.00!Hif3a;;chr14:17407878..17407926,-!p1@Rarb!0.78!11.96!Rarb;;chr2:120365588..120365602,-!p2@Zfp106!0.78!8.91!Zfp106;;chr2:30700881..30700916,+!p1@Prrx2!0.77!9.62!Prrx2;;chr9:87625998..87626007,-!p4@Tbx18!0.77!4.93!Tbx18;;chr2:28477452..28477483,-!p1@Gfi1b!0.76!6.10!Gfi1b;;chr2:104966874..104966907,+!p2@Wt1!0.76!4.69!Wt1;;chrX:7544943..7545001,-!p1@Gata1!0.76!4.69!Gata1;;chr8:87225670..87225697,+!p2@Lyl1!0.75!14.78!Lyl1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.75!7.97!Dnmt3a;;chr4:150482563..150482655,-!p2@Camta1!0.74!17.35!Camta1;;chr9:63869751..63869767,-!p1@Smad6!0.73!12.66!Smad6;;chr9:71743854..71743909,-!p1@Tcf12!0.72!37.76!Tcf12;;chr4:148178559..148178603,+!p1@Casz1!0.72!13.37!Casz1;;chr17:26978449..26978458,-!p3@Nkx2-5!0.72!4.22!Nkx2-5;;chr14:63890691..63890718,-!p8@Gata4!0.72!4.22!Gata4;;chr3:128916868..128916890,+!p1@Pitx2!0.71!5.86!Pitx2;;chrX:45245679..45245702,-!p1@Smarca1!0.70!19.93!Smarca1;;chr8:94881733..94881790,+!p1@Irx5!0.70!8.44!Irx5;;chr14:63890545..63890560,-!p5@Gata4!0.70!3.99!Gata4;;chr1:189821700..189821713,+!p4@Esrrg!0.70!3.99!Esrrg;;chr12:28027561..28027591,-!p1@Sox11!0.69!29.32!Sox11;;chr8:123640063..123640077,+!p1@Foxc2!0.69!7.50!Foxc2;;chr13:31898767..31898785,+!p4@Foxc1!0.69!4.93!Foxc1;;chr1:92895299..92895373,+!p2@Lrrfip1!0.68!89.82!Lrrfip1;;chr14:17407970..17408015,-!p2@Rarb!0.68!11.26!Rarb;;chr17:26978464..26978469,-!p4@Nkx2-5!0.68!3.75!Nkx2-5;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.67!16.18!Ppp1r13l;;chr15:40486883..40486903,+!p4@Zfpm2!0.67!5.16!Zfpm2;;chr13:31898729..31898761,+!p1@Foxc1!0.66!9.85!Foxc1;;chr2:30700857..30700873,+!p3@Prrx2!0.66!5.16!Prrx2;;chr6:53523358..53523388,+!p1@Creb5!0.65!48.31!Creb5;;chr19:10315179..10315241,-!p1@Gm98!0.65!42.45!Gm98;;chr8:94325321..94325366,-!p1@Irx3!0.65!9.38!Irx3;;chr3:66785857..66785873,-!p1@Shox2!0.65!3.52!Shox2;;chr14:64562503..64562524,+!p1@Sox7!0.63!22.28!Sox7;;chr1:193007123..193007139,-!p1@Atf3!0.63!21.34!Atf3;;chrX:45245644..45245666,-!p2@Smarca1!0.63!11.96!Smarca1;;chr13:73397958..73397994,+!p1@Irx4!0.63!3.28!Irx4;;chr12:84828663..84828679,-!p1@Dpf3!0.62!29.32!Dpf3;;chr1:191994550..191994623,-!p1@Prox1!0.61!25.09!Prox1;;chr2:115891409..115891425,-!p2@Meis2!0.61!10.32!Meis2;;chr2:115891381..115891392,-!p5@Meis2!0.61!6.80!Meis2;;chr8:94325847..94325869,-!p3@Irx3!0.61!5.39!Irx3;;chr1:189432907..189432926,+!p3@Esrrg!0.61!3.05!Esrrg;;chr2:105003277..105003280,+!p5@Wt1!0.61!3.05!Wt1;;chr2:180069423..180069434,-!p2@Gata5!0.61!3.05!Gata5;;chr5:120285130..120285141,+!p3@Tbx5!0.61!3.05!Tbx5;;chr2:152223441..152223465,-!p2@Sox12!0.60!14.54!Sox12;;chr4:13670499..13670526,+!p2@Runx1t1!0.60!7.50!Runx1t1;;chr7:89137163..89137200,-!p1@Bnc1!0.60!3.75!Bnc1;;chr15:103085690..103085710,-!p3@Nfe2!0.60!3.28!Nfe2;;chr4:82151148..82151159,-!p5@Nfib!0.59!9.62!Nfib;;chr10:92773591..92773623,-!p1@Elk3!0.58!76.69!Elk3;;chr7:52471143..52471186,+!p1@Tead2!0.58!36.35!Tead2;;chr7:119822957..119822980,+!p2@Tead1!0.58!16.42!Tead1;;chr18:65741358..65741415,+!p1@Zfp532!0.58!14.31!Zfp532;;chr6:14851440..14851497,+!p2@Foxp2!0.58!7.97!Foxp2;;chr15:40486754..40486771,+!p2@Zfpm2!0.58!5.39!Zfpm2;;chr13:72766250..72766273,+!p1@Irx2!0.58!4.69!Irx2;;chr5:120285161..120285176,+!p2@Tbx5!0.58!2.81!Tbx5;;chr4:87452167..87452178,-!p8@Mllt3!0.58!2.81!Mllt3;;chr12:12948633..12948651,-!p1@Mycn!0.57!31.90!Mycn;;chr2:152223586..152223604,-!p5@Sox12!0.57!4.22!Sox12;;chr17:37139472..37139514,+!p1@Zfp57!0.56!21.81!Zfp57;;chr4:114730254..114730276,+!p2@Tal1!0.56!3.52!Tal1;;chr9:106356211..106356242,+!p1@Pcbp4!0.55!62.15!Pcbp4;;chr8:124806048..124806094,+!p1@Zfpm1!0.55!29.55!Zfpm1;;chr4:120624269..120624302,-!p1@Zfp69!0.55!11.02!Zfp69;;chr2:115891427..115891441,-!p4@Meis2!0.55!6.33!Meis2;;chr8:87225702..87225726,+!p3@Lyl1!0.55!5.86!Lyl1;;chr13:31898637..31898653,+!p2@Foxc1!0.55!5.16!Foxc1;;chrX:103070746..103070764,-!p5@Atrx!0.55!4.22!Atrx;;chr6:53523332..53523343,+!p2@Creb5!0.55!3.99!Creb5;;chr11:18918406..18918431,-!p6@Meis1!0.55!3.75!Meis1;;chr7:19895354..19895369,-!p1@Fosb!0.55!3.75!Fosb;;chr7:17642018..17642045,-!p4@Hif3a!0.55!3.05!Hif3a;;chr12:87702062..87702081,+!p4@Esrrb!0.55!2.58!Esrrb;;chr15:103082088..103082136,-!p2@Nfe2!0.55!2.58!Nfe2;;chr13:78339382..78339420,-!p3@Nr2f1!0.54!3.05!Nr2f1;;chr17:48061584..48061601,-!p2@Foxp4!0.53!19.47!Foxp4;;chr4:120488308..120488366,-!p1@Nfyc!0.53!17.35!Nfyc;;chr2:115890469..115890485,-!p7@Meis2!0.53!4.22!Meis2;;chr2:115890953..115890974,-!p6@Meis2!0.53!3.99!Meis2;;chr5:138187775..138187845,+!p7@Tsc22d4!0.53!3.52!Tsc22d4;;chr2:115891534..115891589,-!p1@Meis2!0.52!42.92!Meis2;;chr5:138187341..138187406,+!p3@Tsc22d4!0.52!31.90!Tsc22d4;;chr4:126700722..126700753,+!p4@Sfpq!0.52!6.80!Sfpq;;chr13:72101178..72101203,-!p1@Irx1!0.52!3.99!Irx1;;chr10:62327990..62328025,-!p2@Tet1!0.52!3.99!Tet1;;chr4:154010228..154010244,-!p4@Prdm16!0.52!3.52!Prdm16;;chr3:130813736..130813752,+!p3@Lef1!0.52!3.52!Lef1;;chr10:30562939..30562969,-!p5@Hey2!0.52!2.35!Hey2;;chr6:97879802..97879816,+!p5@Mitf!0.52!2.35!Mitf;;chr9:87626109..87626120,-!p3@Tbx18!0.52!2.35!Tbx18;;chr2:168415815..168415872,-!p1@Nfatc2!0.51!15.71!Nfatc2;;chr4:13670571..13670625,+!p1@Runx1t1!0.51!7.50!Runx1t1;;chr7:19946535..19946550,+!p3@Ppp1r13l!0.51!3.75!Ppp1r13l;;chr4:3865501..3865548,-!p1@Plag1!0.50!14.31!Plag1;;chr17:35031460..35031518,+!p1@Zbtb12!0.50!13.84!Zbtb12;;chr2:133377954..133377973,+!p1@Bmp2!0.50!8.68!Bmp2;;chr4:148178529..148178548,+!p3@Casz1!0.50!6.10!Casz1;;chr13:72101161..72101177,-!p2@Irx1!0.50!3.28!Irx1;;chr3:29912058..29912071,-!p6@Mecom!0.50!2.58!Mecom;;chr2:152223469..152223512,-!p1@Sox12!0.49!14.31!Sox12;;chr17:46693078..46693097,-!p3@Srf!0.49!10.79!Srf;;chr6:14851287..14851342,+!p1@Foxp2!0.49!8.68!Foxp2;;chr8:81552216..81552249,+!p3@Zfp827!0.49!7.27!Zfp827;;chr9:96653072..96653154,-!p1@Zbtb38!0.49!6.80!Zbtb38;;chr13:22036953..22037009,+!p1@Zfp184!0.49!6.80!Zfp184;;chr9:63869729..63869749,-!p4@Smad6!0.49!4.93!Smad6;;chr8:123608252..123608268,+!p1@Foxf1a!0.49!3.52!Foxf1a;;chr4:135129538..135129558,-!p1@Grhl3!0.49!3.52!Grhl3;;chr3:30408384..30408431,-!p4@Mecom!0.49!2.81!Mecom;;chr10:119913266..119913277,-!p6@Hmga2!0.49!2.11!Hmga2;;chr12:77278238..77278252,-!p1@Esr2!0.49!2.11!Esr2;;chr4:133276801..133276891,-!p3@Arid1a!0.48!28.38!Arid1a;;chrX:48558950..48559016,-!p1@Mbnl3!0.48!8.21!Mbnl3;;chr13:117099847..117099907,-!p1@Isl1!0.48!4.46!Isl1;;chr13:78339428..78339466,-!p2@Nr2f1!0.48!3.05!Nr2f1;;chr6:52154414..52154462,-!p1@Hoxa5!0.48!3.05!Hoxa5;;chr15:40486566..40486600,+!p1@Zfpm2!0.47!15.48!Zfpm2;;chr9:63869850..63869873,-!p2@Smad6!0.47!7.27!Smad6;;chr5:77524304..77524315,-!p5@Hopx!0.47!4.93!Hopx;;chr11:23978111..23978134,+!p3@Bcl11a!0.47!4.93!Bcl11a;;chr9:63869802..63869815,-!p3@Smad6!0.47!4.69!Smad6;;chr7:17642053..17642066,-!p2@Hif3a!0.47!3.05!Hif3a;;chr10:119913792..119913820,-!p5@Hmga2!0.46!3.75!Hmga2;;chr1:165243591..165243625,-!p2@Prrx1!0.46!3.28!Prrx1;;chr1:140739014..140739032,-!p1@Lhx9!0.46!2.58!Lhx9;;chr2:152223734..152223756,-!p6@Sox12!0.46!2.35!Sox12;;chr2:30700830..30700843,+!p4@Prrx2!0.46!1.88!Prrx2;;chr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fp26!0.14!22.05!Zfp26;;chr18:24179250..24179314,-!p1@Zfp191!0.14!19.70!Zfp191;;chr11:69393868..69393884,+!p2@Trp53!0.14!16.42!Trp53;;chr7:17199897..17199955,-!p1@Grlf1!0.14!13.60!Grlf1;;chr8:108939219..108939296,+!p1@Zfp90!0.14!12.43!Zfp90;;chr12:25336211..25336274,+!p1@Klf11!0.14!12.43!Klf11;;chr3:54611674..54611690,-!p2@Rfxap!0.14!8.44!Rfxap;;chr5:39075982..39076052,-!p1@Zfp518b!0.14!8.21!Zfp518b;;chr7:6238191..6238224,+!p1@Zfp667!0.14!6.80!Zfp667;;chr10:62328186..62328219,-!p1@Tet1!0.14!6.80!Tet1;;chr10:79389784..79389833,+!p1@Arid3a!0.14!5.86!Arid3a;;chr6:131338483..131338494,-!p5@Csda!0.14!5.86!Csda;;chr18:83084030..83084056,+!p1@Zfp516!0.14!5.63!Zfp516;;chr6:65728988..65729056,+!p1@Prdm5!0.14!5.39!Prdm5;;chr3:51081199..51081228,-!p3@Elf2!0.14!3.75!Elf2;;chr15:79177964..79177986,+!p1@Maff!0.14!3.52!Maff;;chr4:131817511..131817537,-!p2@Gmeb1!0.14!3.28!Gmeb1;;chrX:71330995..71331011,-!p2@Mecp2!0.14!3.05!Mecp2;;chr16:43363190..43363242,+!p2@Zbtb20!0.14!3.05!Zbtb20;;chr7:37483021..37483078,+!p1@Tshz3!0.14!3.05!Tshz3;;chr2:91864300..91864379,-!p2@Creb3l1!0.14!2.81!Creb3l1;;chr13:67830046..67830082,-!p2@Zfp71-rs1!0.14!2.81!Zfp71-rs1;;chr17:71202822..71202877,-!p3@Tgif1!0.14!2.81!Tgif1;;chr8:81923398..81923409,-!p4@Smad1!0.14!2.35!Smad1;;chr7:30954700..30954715,-!p2@LOC677248,p2@Zfp146!0.14!2.11!Zfp146;;chr4:97444280..97444291,+!p10@Nfia!0.14!2.11!Nfia;;chr1:95651346..95651383,-!p3@Thap4!0.14!2.11!Thap4;;chr12:74147689..74147711,-!p1@Six1!0.14!1.88!Six1;;chr6:128250471..128250519,-!p1@Tead4!0.14!1.64!Tead4;;chr10:92773708..92773734,-!p3@Elk3!0.14!1.64!Elk3;;chr11:44430989..44431015,+!p4@Ebf1!0.14!1.41!Ebf1;;chr15:98701606..98701618,-!p1@Mll2!0.14!1.41!Mll2;;chr4:118954858..118954885,-!p5@Ybx1!0.14!1.41!Ybx1;;chr12:85559762..85559778,-!p5@C130039O16Rik!0.14!1.17!C130039O16Rik;;chr8:81552528..81552553,+!p6@Zfp827!0.14!1.17!Zfp827;;chr7:56136974..56136989,-!p4@E2f8!0.14!1.17!E2f8;;chr11:102178005..102178022,-!p8@Ubtf!0.14!1.17!Ubtf;;chr2:153067138..153067147,-!p3@Plagl2!0.14!1.17!Plagl2;;chr2:162880306..162880319,+!p3@Mybl2!0.14!0.94!Mybl2;;chr2:38206580..38206600,+!p2@Lhx2!0.14!0.70!Lhx2;;chr7:56136349..56136360,-!p5@E2f8!0.14!0.70!E2f8;;chr3:30995296..30995300,+!p6@Skil!0.14!0.70!Skil;;chr10:107769219..107769226,+!p5@Pawr!0.14!0.70!Pawr;;chr11:102177974..102177992,-!p17@Ubtf!0.14!0.70!Ubtf;;chr7:123177377..123177409,-!p7@Sox6!0.14!0.70!Sox6;;chr7:144505957..144505972,-!p2@Ebf3!0.14!0.70!Ebf3;;chr5:31262543..31262555,-!p3@Preb!0.14!0.70!Preb;;chrX:137077134..137077143,-!p10@Tsc22d3!0.14!0.47!Tsc22d3;;chr8:94325446..94325459,-!p8@Irx3!0.14!0.47!Irx3;;chr2:27532912..27532923,+!p9@Rxra!0.14!0.47!Rxra;;chr2:34227273..34227292,-!p4@Pbx3!0.14!0.47!Pbx3;;chr18:35721854..35721914,+!p1@Matr3!0.13!90.53!Matr3;;chr7:133839456..133839523,+!p1@Bola2!0.13!60.51!Bola2;;chr4:149611320..149611348,+!p1@Eno1,p1@Gm5506,p1@LOC100045967,p1@LOC100503183!0.13!52.53!Eno1;;chr19:5912771..5912822,-!p1@Dpf2!0.13!51.60!Dpf2;;chr8:77517558..77517597,+!p1@Hmgxb4!0.13!26.03!Hmgxb4;;chr11:23978022..23978076,+!p1@Bcl11a!0.13!26.03!Bcl11a;;chrX:45947560..45947670,-!p1@Zfp280c!0.13!22.05!Zfp280c;;chr13:44826722..44826742,+!p1@Jarid2!0.13!19.23!Jarid2;;chr5:34163344..34163484,+!p1@Whsc1!0.13!18.76!Whsc1;;chrX:70587953..70587968,+!p1@Zfp275!0.13!12.43!Zfp275;;chr7:24993112..24993158,-!p1@Zfp111!0.13!11.96!Zfp111;;chr1:167932744..167932778,-!p1@Pou2f1!0.13!10.08!Pou2f1;;chr8:112229478..112229536,+!p1@Zfp821!0.13!9.85!Zfp821;;chr9:122832168..122832210,+!p1@Zfp105!0.13!8.68!Zfp105;;chr4:97444590..97444607,+!p6@Nfia!0.13!8.21!Nfia;;chr7:88005795..88005858,+!p1@Zscan2!0.13!7.97!Zscan2;;chr14:55711198..55711258,-!p1@Zfhx2!0.13!6.33!Zfhx2;;chr19:12870598..12870636,-!p1@U05342,p1@Zfp91!0.13!5.39!Zfp91;;
@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011318
 |is_obsolete=
-|library_ids=CNhs11015
+|library_id=CNhs11015
+|library_id_phase_based=2:CNhs11015
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;353
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;353
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E12.CNhs11015.353-12F5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E12.CNhs11015.353-12F5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E12.CNhs11015.353-12F5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E12.CNhs11015.353-12F5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E12.CNhs11015.353-12F5.mm9.nobarcode.rdna.fa.gz
 |name=heart, embryo E12
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11015,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.050697319656798,0,0,0,0,0.0457501310086346,1.30246751905958,0,0.0126432881548696,0,0,0.951094281105133,0,0,0,0,0,0,-0.0248561466440979,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0733622750997791,0,0,0,0,0,-0.117822463478557,-0.00909028292942954,-0.0178031846774569,0.428413163073311,0.0175084936344772,0,0,0,0,0,0,0,0,0,0,0,0,0.315498753775328,0,0,0,0,0.0253325036432612,0,0.151074083839566,0,0,0,0.215791235851563,-0.0232735256945578,0.473694024652728,0.204002761083699,0,0.0915002620172692,-0.013928657263616,-0.117716914593033,0.287377131644828,0,0,-0.194015533628832,0.0358701866832409,0.0126686671773617,0,0,0,0,0,0.0915002620172692,0.0437264914184948,0.281917055907157,0.00446775055722315,0,0,0,0,0
@@ Line 85: / Line 97: @@
 |top_motifs=HOX{A5,B5}:3.71065490525;GATA4:3.14312851544;EVI1:2.67523938171;IKZF2:2.32138653622;SRF:2.17496995833;MEF2{A,B,C,D}:1.96264023617;NR3C1:1.73944018761;ALX1:1.67873384698;GATA6:1.65732888735;UFEwm:1.60408363884;NR5A1,2:1.46452788795;PITX1..3:1.43401050173;POU3F1..4:1.41037805444;NKX2-1,4:1.38029846185;PRDM1:1.35617653943;HIF1A:1.34154541339;NKX2-2,8:1.31386375613;FOXL1:1.29542239316;RXR{A,B,G}:1.28167986672;TEAD1:1.24558140414;T:1.03260323945;KLF4:1.0124313107;GFI1:0.974244210768;NKX3-1:0.922304743858;NFE2L1:0.916231347174;MZF1:0.866983660604;FOXP1:0.803757117472;HMGA1,2:0.76933438401;NR6A1:0.752147054589;CDC5L:0.750085042591;ZNF384:0.738360766586;PATZ1:0.724954349408;E2F1..5:0.72125110107;ZBTB16:0.704879708503;TOPORS:0.676745899332;CDX1,2,4:0.67156780241;MYBL2:0.656805890839;NFATC1..3:0.655808353158;RREB1:0.646786467264;NANOG{mouse}:0.637412998907;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.637321549414;ZNF143:0.634327316638;CUX2:0.607669116816;NKX6-1,2:0.582489930733;SOX5:0.559986631719;NFY{A,B,C}:0.549136269762;TEF:0.544216181023;GCM1,2:0.542582148311;IKZF1:0.534383946958;SOX{8,9,10}:0.513735494708;SOX17:0.510650077829;EN1,2:0.452074484168;PAX4:0.421439400047;MAZ:0.359984760749;GFI1B:0.338121929751;ESRRA:0.32771081304;EBF1:0.324662242848;TGIF1:0.323568299788;SOX2:0.314814834072;TFAP4:0.310602362821;TLX1..3_NFIC{dimer}:0.23935295886;NRF1:0.166712025884;POU1F1:0.164392581377;PDX1:0.160326595447;FOX{I1,J2}:0.156323387034;ATF2:0.155297169657;ZIC1..3:0.150728502066;SPIB:0.141110043425;NANOG:0.10995434874;BREu{core}:0.108970668489;GTF2A1,2:0.10454848297;FOXD3:0.0822833696887;HOX{A4,D4}:0.0454822339103;EP300:0.0342209437013;ARID5B:0.0316184872051;STAT1,3:0.00754494894442;CRX:-0.00331952973318;TFDP1:-0.0096008692651;HOXA9_MEIS1:-0.0204695806407;XCPE1{core}:-0.039746690988;FOXO1,3,4:-0.0482887240511;FOSL2:-0.0522491800461;MYB:-0.080901971018;SPI1:-0.0894888277786;TBP:-0.0934537963821;AIRE:-0.102360101523;ZFP161:-0.113661373409;GTF2I:-0.114146597353;NHLH1,2:-0.117297973573;NKX3-2:-0.119593464361;ELF1,2,4:-0.123697291109;HBP1_HMGB_SSRP1_UBTF:-0.123725401866;NFE2L2:-0.138729704236;ONECUT1,2:-0.157993611943;HIC1:-0.158835703558;YY1:-0.165908116384;FOXP3:-0.184549965351;HES1:-0.189928030851;PAX8:-0.203106013872;MAFB:-0.204989466956;PAX5:-0.205312095507;HSF1,2:-0.212541093329;PAX2:-0.213910489121;OCT4_SOX2{dimer}:-0.217388162363;ZNF238:-0.226327267041;GLI1..3:-0.227446466686;TFCP2:-0.228290764478;FOXA2:-0.253285980137;EGR1..3:-0.273082947313;ELK1,4_GABP{A,B1}:-0.273856268044;SMAD1..7,9:-0.277457889993;HAND1,2:-0.288594057147;RFX2..5_RFXANK_RFXAP:-0.299820086203;NKX2-3_NKX2-5:-0.30501464909;CREB1:-0.317529687539;ETS1,2:-0.318667748111;TFAP2{A,C}:-0.321398593633;TFAP2B:-0.332266188728;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.332375937063;FOX{F1,F2,J1}:-0.336961667665;DBP:-0.339997942536;SP1:-0.36805098369;MTE{core}:-0.370010889276;VSX1,2:-0.376818125563;AHR_ARNT_ARNT2:-0.377741269678;ATF4:-0.39932249139;NR1H4:-0.410414366368;JUN:-0.413827729895;TBX4,5:-0.416067823859;RFX1:-0.429891850446;RORA:-0.443949363157;LEF1_TCF7_TCF7L1,2:-0.449782017106;BPTF:-0.45601954788;AR:-0.459698837579;HNF1A:-0.464829671078;bHLH_family:-0.48896373056;ZBTB6:-0.491745783386;MTF1:-0.501733966286;ESR1:-0.523239173215;MED-1{core}:-0.529000603364;ZNF148:-0.533778569229;PAX1,9:-0.580774867765;HNF4A_NR2F1,2:-0.580800989118;MYFfamily:-0.583193292088;IRF1,2:-0.591073701468;NFE2:-0.592052095027;TP53:-0.610399509787;RUNX1..3:-0.619694315225;GZF1:-0.628758249634;FOX{D1,D2}:-0.632234377667;REST:-0.697384766013;PAX6:-0.702047974932;IRF7:-0.703493358433;FOXQ1:-0.726021196453;POU5F1:-0.740420084425;HLF:-0.751945253448;ATF5_CREB3:-0.756350928774;BACH2:-0.762026876259;NFKB1_REL_RELA:-0.763284112252;RXRA_VDR{dimer}:-0.772917255312;PBX1:-0.777811574041;ALX4:-0.780342489883;PRRX1,2:-0.788505594483;ZNF423:-0.822136525588;SREBF1,2:-0.840411204501;NFIL3:-0.848996408343;POU2F1..3:-0.88249428614;POU6F1:-0.945317607076;STAT5{A,B}:-0.951097726493;HMX1:-0.97905762416;ZEB1:-0.984291782866;LHX3,4:-0.998342099945;SNAI1..3:-1.03747183138;TLX2:-1.05398451469;FOS_FOS{B,L1}_JUN{B,D}:-1.07287464552;DMAP1_NCOR{1,2}_SMARC:-1.11462057806;FOXN1:-1.14501359091;ADNP_IRX_SIX_ZHX:-1.16581234109;PPARG:-1.16951894152;RBPJ:-1.18259732325;CEBPA,B_DDIT3:-1.20301082084;NFIX:-1.23847722456;LMO2:-1.24203084429;MYOD1:-1.2658994222;ATF6:-1.43814584297;TAL1_TCF{3,4,12}:-1.44827590843;FOXM1:-1.50536560395;STAT2,4,6:-1.53132582689;SPZ1:-1.57569635422
 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:353-12F5;search_select_hide=table117:353-12F5
-|DRA_sample_Accession=CAGE@DRS008835
-|accession_numbers=DRX008972;DRR009846;DRZ001271;DRZ002654;CAGE
-|library_id=CNhs11015
 }}

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From FANTOM5_SSTAR

Latest revision as of 19:10, 4 June 2020

CNhs11015

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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