FF:376-3I9: Difference between revisions

Latest revision as of 19:14, 4 June 2020

Name:	heart, embryo E13
Species:	Mouse (Mus musculus)
Library ID:	CNhs11013
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	heart
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		SAMD00005990

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11013		CAGE		DRX008973		DRR009847

Accession ID Mm9

Library id		BAM		CTSS
CNhs11013		DRZ001272		DRZ002655

Accession ID Mm10

Library id		BAM		CTSS
CNhs11013		DRZ012622		DRZ014005

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

CNhs11013

0	0
1	0
10	0.134
100	0
1000	0.0719
1001	0.205
1002	0.523
1003	-0.0681
1004	0
1005	-0.0967
1006	0.164
1007	0.0238
1008	0
1009	0.13
101	0.033
1010	0
1011	-0.019
1012	0
1013	-0.236
1014	0.54
1015	0.171
1016	0.089
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0719
1022	0.301
1023	0
1024	0.0719
1025	0
1026	0
1027	-0.048
1028	0
1029	0.171
103	0.0719
1030	0
1031	0.324
1032	0.00398
1033	0.024
1034	0
1035	0.387
1036	0.0388
1037	0
1038	0.0124
1039	0.0898
104	0
1040	0.0667
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: CNhs11013

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00472
MA0003.1	MA0003.1	0.693
MA0004.1	MA0004.1	0.807
MA0006.1	MA0006.1	0.924
MA0007.1	MA0007.1	0.147
MA0009.1	MA0009.1	0.926
MA0014.1	MA0014.1	0.803
MA0017.1	MA0017.1	0.00216
MA0018.2	MA0018.2	0.893
MA0019.1	MA0019.1	0.654
MA0024.1	MA0024.1	9.06794e-5
MA0025.1	MA0025.1	0.151
MA0027.1	MA0027.1	0.0215
MA0028.1	MA0028.1	0.158
MA0029.1	MA0029.1	0.405
MA0030.1	MA0030.1	0.011
MA0031.1	MA0031.1	0.0183
MA0035.2	MA0035.2	0.118
MA0038.1	MA0038.1	0.99
MA0039.2	MA0039.2	0.0214
MA0040.1	MA0040.1	0.0252
MA0041.1	MA0041.1	0.171
MA0042.1	MA0042.1	0.228
MA0043.1	MA0043.1	0.924
MA0046.1	MA0046.1	2.72163e-21
MA0047.2	MA0047.2	0.00336
MA0048.1	MA0048.1	0.0134
MA0050.1	MA0050.1	4.25139e-6
MA0051.1	MA0051.1	0.0021
MA0052.1	MA0052.1	5.87717e-21
MA0055.1	MA0055.1	9.18486e-5
MA0057.1	MA0057.1	0.653
MA0058.1	MA0058.1	0.788
MA0059.1	MA0059.1	0.266
MA0060.1	MA0060.1	0.135
MA0061.1	MA0061.1	0.197
MA0062.2	MA0062.2	0.327
MA0065.2	MA0065.2	0.081
MA0066.1	MA0066.1	0.637
MA0067.1	MA0067.1	0.59
MA0068.1	MA0068.1	0.386
MA0069.1	MA0069.1	0.274
MA0070.1	MA0070.1	0.793
MA0071.1	MA0071.1	0.909
MA0072.1	MA0072.1	0.109
MA0073.1	MA0073.1	0.984
MA0074.1	MA0074.1	0.605
MA0076.1	MA0076.1	0.868
MA0077.1	MA0077.1	0.917
MA0078.1	MA0078.1	0.228
MA0079.2	MA0079.2	0.527
MA0080.2	MA0080.2	0.00393
MA0081.1	MA0081.1	0.795
MA0083.1	MA0083.1	3.18368e-16
MA0084.1	MA0084.1	0.78
MA0087.1	MA0087.1	0.786
MA0088.1	MA0088.1	0.336
MA0090.1	MA0090.1	0.00285
MA0091.1	MA0091.1	0.946
MA0092.1	MA0092.1	0.907
MA0093.1	MA0093.1	0.858
MA0099.2	MA0099.2	9.25482e-7
MA0100.1	MA0100.1	0.867
MA0101.1	MA0101.1	0.238
MA0102.2	MA0102.2	0.00318
MA0103.1	MA0103.1	5.66736e-6
MA0104.2	MA0104.2	0.669
MA0105.1	MA0105.1	0.439
MA0106.1	MA0106.1	0.883
MA0107.1	MA0107.1	0.102
MA0108.2	MA0108.2	0.613
MA0111.1	MA0111.1	0.333
MA0112.2	MA0112.2	0.57
MA0113.1	MA0113.1	0.893
MA0114.1	MA0114.1	3.0006e-5
MA0115.1	MA0115.1	0.886
MA0116.1	MA0116.1	0.402
MA0117.1	MA0117.1	0.434
MA0119.1	MA0119.1	0.187
MA0122.1	MA0122.1	0.864
MA0124.1	MA0124.1	0.512
MA0125.1	MA0125.1	0.879
MA0131.1	MA0131.1	0.409
MA0135.1	MA0135.1	0.369
MA0136.1	MA0136.1	0.00841
MA0137.2	MA0137.2	0.0541
MA0138.2	MA0138.2	0.0152
MA0139.1	MA0139.1	0.337
MA0140.1	MA0140.1	0.0411
MA0141.1	MA0141.1	0.00914
MA0142.1	MA0142.1	0.21
MA0143.1	MA0143.1	0.715
MA0144.1	MA0144.1	0.28
MA0145.1	MA0145.1	0.174
MA0146.1	MA0146.1	0.927
MA0147.1	MA0147.1	0.643
MA0148.1	MA0148.1	0.0117
MA0149.1	MA0149.1	0.0973
MA0150.1	MA0150.1	0.00486
MA0152.1	MA0152.1	0.947
MA0153.1	MA0153.1	2.9713e-13
MA0154.1	MA0154.1	0.656
MA0155.1	MA0155.1	0.174
MA0156.1	MA0156.1	3.7647e-4
MA0157.1	MA0157.1	0.0654
MA0159.1	MA0159.1	0.0939
MA0160.1	MA0160.1	0.366
MA0162.1	MA0162.1	0.292
MA0163.1	MA0163.1	0.0393
MA0164.1	MA0164.1	0.569
MA0258.1	MA0258.1	0.372
MA0259.1	MA0259.1	0.263

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: CNhs11013

Novel motif	Logo	P-value
1	1	0.573
10	10	0.825
100	100	0.866
101	101	0.949
102	102	0.773
103	103	0.201
104	104	0.871
105	105	0.942
106	106	0.176
107	107	0.571
108	108	0.839
109	109	0.762
11	11	0.388
110	110	0.233
111	111	0.728
112	112	0.378
113	113	0.348
114	114	0.554
115	115	0.892
116	116	0.533
117	117	0.157
118	118	0.521
119	119	0.176
12	12	0.42
120	120	0.204
121	121	0.655
122	122	0.21
123	123	0.0155
124	124	0.564
125	125	0.672
126	126	0.915
127	127	0.285
128	128	0.0376
129	129	0.369
13	13	0.00121
130	130	0.322
131	131	0.671
132	132	0.582
133	133	0.646
134	134	0.682
135	135	0.899
136	136	0.0665
137	137	0.713
138	138	0.0819
139	139	0.821
14	14	0.424
140	140	0.9
141	141	0.191
142	142	0.645
143	143	0.735
144	144	0.0607
145	145	0.2
146	146	0.205
147	147	0.842
148	148	0.545
149	149	0.631
15	15	0.203
150	150	0.511
151	151	0.122
152	152	0.626
153	153	0.438
154	154	0.604
155	155	0.424
156	156	0.207
157	157	0.975
158	158	0.826
159	159	0.274
160	160	0.324
161	161	0.902
162	162	0.947
163	163	0.42
164	164	0.761
165	165	0.19
166	166	0.831
167	167	0.861
168	168	0.75
169	169	0.0989
17	17	0.524
18	18	0.314
19	19	0.58
2	2	0.258
20	20	0.111
21	21	0.69
22	22	0.784
23	23	0.089
24	24	0.451
25	25	0.566
26	26	0.0232
27	27	0.147
28	28	0.339
29	29	0.312
3	3	0.782
30	30	0.0477
31	31	0.613
32	32	0.402
33	33	0.189
34	34	0.784
35	35	0.457
36	36	0.191
37	37	0.243
38	38	0.205
39	39	0.33
4	4	0.808
40	40	0.00386
41	41	0.897
42	42	0.597
43	43	0.534
44	44	0.563
45	45	0.045
46	46	0.878
47	47	0.697
48	48	0.639
49	49	0.58
5	5	0.774
50	50	0.478
51	51	0.875
52	52	0.489
53	53	0.576
54	54	0.626
55	55	0.262
56	56	0.734
57	57	0.413
58	58	0.624
59	59	0.338
6	6	0.193
60	60	0.445
61	61	0.308
62	62	0.423
63	63	0.825
64	64	0.599
65	65	0.151
66	66	0.747
67	67	0.867
68	68	0.42
69	69	0.235
7	7	0.836
70	70	0.0126
71	71	0.0184
72	72	0.101
73	73	0.433
74	74	0.653
75	75	0.534
76	76	0.548
77	77	0.453
78	78	0.876
79	79	0.171
8	8	0.94
80	80	0.0161
81	81	0.5
82	82	0.677
83	83	0.819
84	84	0.593
85	85	0.559
86	86	0.943
87	87	0.00133
88	88	0.267
89	89	0.32
9	9	0.957
90	90	0.943
91	91	0.214
92	92	0.401
93	93	0.261
94	94	0.36
95	95	0.27
96	96	0.419
97	97	0.131
98	98	0.0946
99	99	0.531

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: CNhs11013

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011327 mouse heart- 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)
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)
0000293 (mouse embryonic day 13 sample)
0011327 (mouse heart- 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
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@SAMD00005990
+|accession_numbers=CAGE;DRX008973;DRR009847;DRZ001272;DRZ002655;DRZ012622;DRZ014005
 |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 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
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38..135129558,-!p1@Grhl3!0.57!4.50!Grhl3;;chr13:73398004..73398017,+!p2@Irx4!0.57!2.70!Irx4;;chr12:28027561..28027591,-!p1@Sox11!0.56!21.07!Sox11;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.56!12.42!Ppp1r13l;;chr14:17407970..17408015,-!p2@Rarb!0.56!8.28!Rarb;;chr2:115891534..115891589,-!p1@Meis2!0.55!45.92!Meis2;;chr4:82151148..82151159,-!p5@Nfib!0.55!8.64!Nfib;;chr8:94881733..94881790,+!p1@Irx5!0.55!5.76!Irx5;;chr5:138187775..138187845,+!p7@Tsc22d4!0.55!3.78!Tsc22d4;;chr1:193007123..193007139,-!p1@Atf3!0.54!17.29!Atf3;;chr4:120624269..120624302,-!p1@Zfp69!0.54!10.62!Zfp69;;chr9:96159147..96159204,+!p2@Tfdp2!0.54!5.22!Tfdp2;;chr13:31898496..31898519,+!p3@Foxc1!0.54!4.50!Foxc1;;chr2:115891409..115891425,-!p2@Meis2!0.53!8.46!Meis2;;chr11:98789140..98789168,+!p5@Rara!0.53!4.32!Rara;;chr5:77524250..77524300,-!p1@Hopx!0.52!61.40!Hopx;;chr12:84828663..84828679,-!p1@Dpf3!0.52!23.05!Dpf3;;chr2:115891381..115891392,-!p5@Meis2!0.52!5.22!Meis2;;chr3:29912058..29912071,-!p6@Mecom!0.52!2.70!Mecom;;chr10:12844757..12844771,+!p2@Plagl1!0.52!2.34!Plagl1;;chr10:30562939..30562969,-!p5@Hey2!0.52!2.34!Hey2;;chr4:135840573..135840601,+!p1@Zfp46!0.51!22.69!Zfp46;;chr18:65741358..65741415,+!p1@Zfp532!0.51!12.24!Zfp532;;chr9:63869834..63869849,-!p5@Smad6!0.51!4.32!Smad6;;chr11:70043257..70043263,-!p1@Bcl6b!0.50!4.32!Bcl6b;;chr10:62327990..62328025,-!p2@Tet1!0.50!3.78!Tet1;;chr13:72101161..72101177,-!p2@Irx1!0.50!3.24!Irx1;;chr13:72101141..72101158,-!p3@Irx1!0.50!2.88!Irx1;;chr13:73397958..73397994,+!p1@Irx4!0.50!2.16!Irx4;;chr9:87625998..87626007,-!p4@Tbx18!0.50!2.16!Tbx18;;chr4:133109285..133109308,+!p1@Nr0b2!0.50!2.16!Nr0b2;;chr2:104966933..104966966,+!p3@Wt1!0.50!2.16!Wt1;;chr10:92773591..92773623,-!p1@Elk3!0.49!62.30!Elk3;;chr2:168415815..168415872,-!p1@Nfatc2!0.49!14.77!Nfatc2;;chr4:148178529..148178548,+!p3@Casz1!0.49!5.94!Casz1;;chr7:119822915..119822936,+!p5@Tead1!0.49!3.96!Tead1;;chr8:94325814..94325839,-!p2@Irx3!0.48!5.04!Irx3;;chr8:87225702..87225726,+!p3@Lyl1!0.48!4.86!Lyl1;;chr15:103085660..103085681,-!p1@Nfe2!0.48!3.42!Nfe2;;chr13:83663902..83663927,+!p1@Mef2c!0.47!64.46!Mef2c;;chr4:3865501..3865548,-!p1@Plag1!0.47!13.14!Plag1;;chr8:94325847..94325869,-!p3@Irx3!0.47!3.60!Irx3;;chr2:30700830..30700843,+!p4@Prrx2!0.47!1.98!Prrx2;;chr1:189821700..189821713,+!p4@Esrrg!0.47!1.98!Esrrg;;chr2:104966874..104966907,+!p2@Wt1!0.47!1.98!Wt1;;chr2:180069423..180069434,-!p2@Gata5!0.47!1.98!Gata5;;chr1:170362040..170362113,-!p2@Pbx1!0.46!19.99!Pbx1;;chr17:37139472..37139514,+!p1@Zfp57!0.46!17.29!Zfp57;;chr2:152223441..152223465,-!p2@Sox12!0.46!10.26!Sox12;;chr4:114732112..114732158,+!p1@Tal1!0.46!5.04!Tal1;;chr13:72101178..72101203,-!p1@Irx1!0.46!3.42!Irx1;;chr10:119914001..119914078,-!p4@Hmga2!0.46!2.88!Hmga2;;chr9:106356243..106356264,+!p2@Pcbp4!0.45!10.62!Pcbp4;;chr2:115891454..115891471,-!p3@Meis2!0.45!7.20!Meis2;;chr18:55152179..55152194,-!p5@Zfp608!0.45!6.66!Zfp608;;chr18:14130694..14130697,-!p2@Zfp521!0.45!5.22!Zfp521;;chr5:77524304..77524315,-!p5@Hopx!0.45!4.68!Hopx;;chr7:119822940..119822945,+!p6@Tead1!0.45!2.52!Tead1;;chr7:123174606..123174636,-!p5@Sox6!0.45!2.52!Sox6;;chr15:40486854..40486867,+!p7@Zfpm2!0.45!2.34!Zfpm2;;chr17:46693107..46693137,-!p1@Srf!0.44!24.13!Srf;;chr16:95680889..95680991,-!p1@Erg!0.44!19.81!Erg;;chr18:3281034..3281104,-!p1@Crem!0.44!17.29!Crem;;chr13:31898637..31898653,+!p2@Foxc1!0.44!3.78!Foxc1;;chr2:115890469..115890485,-!p7@Meis2!0.44!3.24!Meis2;;chr2:152223586..152223604,-!p5@Sox12!0.44!2.88!Sox12;;chr7:123174485..123174514,-!p6@Sox6!0.44!2.34!Sox6;;chr8:94881872..94881887,+!p2@Irx5!0.44!1.98!Irx5;;chr12:39506873..39506913,+!p1@Etv1!0.43!24.49!Etv1;;chr5:20387850..20387869,-!p1@Phtf2!0.43!24.31!Phtf2;;chr9:71743854..71743909,-!p1@Tcf12!0.43!18.91!Tcf12;;chr8:92872242..92872285,-!p1@Tox3!0.43!5.58!Tox3;;chr2:152223783..152223812,-!p4@Sox12!0.43!4.86!Sox12;;chr15:40486754..40486771,+!p2@Zfpm2!0.43!3.60!Zfpm2;;chr7:17642053..17642066,-!p2@Hif3a!0.43!2.70!Hif3a;;chr3:30408384..30408431,-!p4@Mecom!0.43!2.34!Mecom;;chr4:148275237..148275311,+!p2@Casz1!0.42!9.18!Casz1;;chr7:108966820..108966835,+!p1@Phox2a!0.42!1.62!Phox2a;;chr1:189432881..189432903,+!p2@Esrrg!0.42!1.62!Esrrg;;chr18:11052516..11052525,+!p5@Gata6!0.42!1.62!Gata6;;chr9:87626109..87626120,-!p3@Tbx18!0.42!1.62!Tbx18;;chr6:37392095..37392154,-!p1@Creb3l2!0.41!72.93!Creb3l2;;chr17:35031460..35031518,+!p1@Zbtb12!0.41!11.16!Zbtb12;;chr11:98789099..98789124,+!p3@Rara!0.41!6.66!Rara;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.41!5.04!Hmga1;;chr7:30954700..30954715,-!p2@LOC677248,p2@Zfp146!0.41!4.86!Zfp146;;chr16:43503493..43503570,+!p9@Zbtb20!0.41!3.24!Zbtb20;;chr18:14131020..14131033,-!p4@Zfp521!0.41!2.34!Zfp521;;chr5:138187341..138187406,+!p3@Tsc22d4!0.40!23.77!Tsc22d4;;chr8:124806048..124806094,+!p1@Zfpm1!0.40!20.17!Zfpm1;;chr4:13712228..13712267,+!p3@Runx1t1!0.40!3.24!Runx1t1;;chr15:40486615..40486628,+!p3@Zfpm2!0.40!2.88!Zfpm2;;chr15:40486883..40486903,+!p4@Zfpm2!0.40!2.34!Zfpm2;;chr3:29912079..29912096,-!p10@Mecom!0.40!1.80!Mecom;;c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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011327
 |is_obsolete=
+|library_id=CNhs11013
+|library_id_phase_based=2:CNhs11013
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;376
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;376
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm9.nobarcode.rdna.fa.gz
 |name=heart, embryo E13
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11013,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.105831544265488,0,0,0,0,0.0593982918581375,1.14237980914199,0,0.0336824287726504,0,0,1.03174218770919,0,0,0,0,0,0,0.226500517039064,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.0345714314890375,0,0,0,0,0,0.0855687931927616,-0.00195702629799732,0.00032378925394716,0.208496191917837,0.0482724388882005,0,0,0,0,0,0,0,0,0,0,0,0.0719048481885784,0.381248733648294,0,0,0,0,0.137119823382151,0,0.102741695720705,0,0.18757322340964,0,0.101830187666827,-0.075059533675561,0.341698380763026,0.165150770995376,0,0,0,-0.0136084362032114,0,0,0.00797067663465989,-0.116646606270874,0.0836314122736936,0.0547469484129233,0,0,0,0,0,0,0.141508525764343,0.276007168127841,0.0467052166139591,0.00167684854110606,0,0,0,0
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
 |top_motifs=HOX{A5,B5}:3.36655691012;EVI1:2.72021129395;GATA4:2.67123721896;MEF2{A,B,C,D}:2.27226993398;SRF:2.14779826461;IKZF2:1.96852718092;NR5A1,2:1.75590111224;RXR{A,B,G}:1.67903283237;NANOG{mouse}:1.66122108762;HIF1A:1.63637485267;UFEwm:1.61032703559;FOXL1:1.58870089454;NR3C1:1.5042712896;ALX1:1.43574508871;NFE2L1:1.4144306577;TEAD1:1.41014404363;POU3F1..4:1.35756025296;NKX2-1,4:1.24647068368;PRDM1:1.22586502833;SOX5:1.19379331722;CDC5L:1.15996747253;HMGA1,2:1.08591340512;NKX3-1:1.02939643503;PAX4:0.990755830658;GATA6:0.953743705234;KLF4:0.849639589062;NKX2-2,8:0.835340770846;E2F1..5:0.814232530841;MYBL2:0.783605340395;ZNF143:0.761457234896;IKZF1:0.743574483184;TGIF1:0.735635229226;SOX{8,9,10}:0.734072881912;CDX1,2,4:0.724445085075;GFI1:0.708441169787;T:0.605430871945;ZNF384:0.587013125702;MZF1:0.58569007463;FOXP1:0.577211706094;NFATC1..3:0.559377987589;TOPORS:0.507588594369;PITX1..3:0.471677315578;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.466301708988;NFY{A,B,C}:0.461424041492;PATZ1:0.455365082608;NRF1:0.42774690286;SOX17:0.412752254162;TLX1..3_NFIC{dimer}:0.412597703752;EN1,2:0.408116110478;AR:0.399183463024;RREB1:0.386301252682;CUX2:0.376715383243;ZBTB16:0.370107582438;EBF1:0.367363078422;GCM1,2:0.352847523784;ARID5B:0.340364820443;FOX{I1,J2}:0.325898280915;NKX6-1,2:0.291889723826;MAZ:0.273366205983;NR6A1:0.258171507692;ZIC1..3:0.229885808882;ESRRA:0.229503132678;TEF:0.227881452119;CRX:0.216419480198;SPIB:0.192568713449;ATF2:0.19033473418;EP300:0.164046710479;GFI1B:0.151967467186;XCPE1{core}:0.137854851596;SOX2:0.119290147033;YY1:0.118432048337;ELF1,2,4:0.113093684992;MAFB:0.109782456961;BREu{core}:0.0968496377331;FOXP3:0.0522063884155;CREB1:0.0488094761132;ELK1,4_GABP{A,B1}:0.0239392678534;TFAP4:0.015772741147;HOXA9_MEIS1:0.00728827165413;GTF2A1,2:-0.00515942035311;SMAD1..7,9:-0.00749173470625;VSX1,2:-0.0112169534191;STAT1,3:-0.0217439834292;FOSL2:-0.0301120567754;PAX2:-0.0385293304208;HAND1,2:-0.0429943750333;ZFP161:-0.0462081700876;PDX1:-0.0531994631681;MYB:-0.0741279467327;ATF4:-0.0815518284338;HBP1_HMGB_SSRP1_UBTF:-0.101713409599;PAX5:-0.105045559726;HOX{A4,D4}:-0.106013380876;FOXD3:-0.114915025393;TBX4,5:-0.118694990867;DBP:-0.139863915789;TBP:-0.148466526733;HSF1,2:-0.150262828943;SPI1:-0.151940452815;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.164363768755;NANOG:-0.172856677089;ZNF238:-0.178114885706;PAX8:-0.179236074826;EGR1..3:-0.186536065624;TFAP2B:-0.189412005455;GTF2I:-0.198966980708;HIC1:-0.212425301577;NFE2L2:-0.220371923423;SP1:-0.221496390639;POU1F1:-0.241087543937;TFDP1:-0.24151803929;TFCP2:-0.241723562309;GLI1..3:-0.248822093334;PAX1,9:-0.266103944844;HES1:-0.277610527628;NKX2-3_NKX2-5:-0.28520002975;RFX2..5_RFXANK_RFXAP:-0.307500485115;ETS1,2:-0.316212995873;AIRE:-0.320989805764;TFAP2{A,C}:-0.335681807933;ZBTB6:-0.346718854019;JUN:-0.368527698718;ALX4:-0.371821436667;MTE{core}:-0.378067411885;ONECUT1,2:-0.38460655808;NHLH1,2:-0.38510671329;STAT5{A,B}:-0.387647251471;RORA:-0.395304371973;FOXO1,3,4:-0.411225834329;RFX1:-0.41366676306;TP53:-0.424633263711;POU5F1:-0.457565490725;MED-1{core}:-0.488532818983;ESR1:-0.497634153656;NKX3-2:-0.528159722673;bHLH_family:-0.530491724132;OCT4_SOX2{dimer}:-0.544393943347;ZNF423:-0.563507432127;ATF5_CREB3:-0.570974213945;GZF1:-0.571021225628;TLX2:-0.57241728843;IRF1,2:-0.578960400157;ZNF148:-0.587983612428;MTF1:-0.589578298887;IRF7:-0.595058231803;BACH2:-0.596376183954;LHX3,4:-0.602777119694;RUNX1..3:-0.624409565201;HNF4A_NR2F1,2:-0.687596066821;LEF1_TCF7_TCF7L1,2:-0.693611736074;AHR_ARNT_ARNT2:-0.698124283618;SREBF1,2:-0.71712684767;HNF1A:-0.719431032803;REST:-0.725903247504;NFKB1_REL_RELA:-0.734530035285;FOX{D1,D2}:-0.743707678586;RXRA_VDR{dimer}:-0.792525548771;BPTF:-0.802426003338;PAX6:-0.808620303448;RBPJ:-0.808761363551;NR1H4:-0.809050830134;PBX1:-0.812791774784;FOXA2:-0.813829041435;NFIL3:-0.827131259274;MYFfamily:-0.840645489949;ADNP_IRX_SIX_ZHX:-0.850661018992;NFE2:-0.872997553466;HLF:-0.901165890065;ZEB1:-0.924905170611;FOXQ1:-0.942854266846;PRRX1,2:-0.944019804619;POU2F1..3:-0.950807263565;NFIX:-0.95297711124;FOS_FOS{B,L1}_JUN{B,D}:-1.01645543552;POU6F1:-1.01741761563;DMAP1_NCOR{1,2}_SMARC:-1.06201546011;HMX1:-1.07393566195;LMO2:-1.07525617178;SNAI1..3:-1.08542919466;FOX{F1,F2,J1}:-1.12202270557;FOXN1:-1.17850796794;CEBPA,B_DDIT3:-1.25828369;PPARG:-1.27926937279;ATF6:-1.30090276829;TAL1_TCF{3,4,12}:-1.30099711825;MYOD1:-1.36099459388;FOXM1:-1.74646230256;SPZ1:-1.76845995915;STAT2,4,6:-1.89175236185
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:376-3I9;search_select_hide=table117:376-3I9
 }}

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FF:376-3I9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:14, 4 June 2020

CNhs11013

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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