FF:335-25E2: Difference between revisions

Latest revision as of 19:10, 4 June 2020

Name:	forelimb, embryo E11
Species:	Mouse (Mus musculus)
Library ID:	CNhs10596
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	forelimb
dev stage	11 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		SAMD00005527

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10596		CAGE		DRX008963		DRR009837

Accession ID Mm9

Library id		BAM		CTSS
CNhs10596		DRZ001262		DRZ002645

Accession ID Mm10

Library id		BAM		CTSS
CNhs10596		DRZ012612		DRZ013995

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

CNhs10596

0	0
1	0
10	0
100	0
1000	0
1001	-0.0496
1002	-0.0517
1003	-0.102
1004	0
1005	-0.0641
1006	-0.119
1007	0.118
1008	0
1009	-0.0572
101	0.149
1010	0
1011	0
1012	0
1013	-0.217
1014	0
1015	0.374
1016	0.493
1017	0
1018	0.0848
1019	0
102	0
1020	0
1021	0.0361
1022	-0.0855
1023	0
1024	-0.0905
1025	0
1026	0
1027	0
1028	0
1029	-0.0921
103	-0.0446
1030	0
1031	-0.0342
1032	-0.177
1033	0.053
1034	0
1035	0
1036	0.00662
1037	0
1038	-0.065
1039	-0.198
104	0
1040	0.00172
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: CNhs10596

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0062
MA0003.1	MA0003.1	0.0697
MA0004.1	MA0004.1	0.422
MA0006.1	MA0006.1	0.426
MA0007.1	MA0007.1	0.568
MA0009.1	MA0009.1	0.338
MA0014.1	MA0014.1	0.103
MA0017.1	MA0017.1	0.00201
MA0018.2	MA0018.2	0.517
MA0019.1	MA0019.1	0.745
MA0024.1	MA0024.1	9.06651e-7
MA0025.1	MA0025.1	0.305
MA0027.1	MA0027.1	0.128
MA0028.1	MA0028.1	0.0145
MA0029.1	MA0029.1	0.878
MA0030.1	MA0030.1	0.302
MA0031.1	MA0031.1	0.077
MA0035.2	MA0035.2	0.0867
MA0038.1	MA0038.1	0.078
MA0039.2	MA0039.2	0.00705
MA0040.1	MA0040.1	0.485
MA0041.1	MA0041.1	0.176
MA0042.1	MA0042.1	0.992
MA0043.1	MA0043.1	0.00836
MA0046.1	MA0046.1	2.36024e-14
MA0047.2	MA0047.2	0.0705
MA0048.1	MA0048.1	0.0136
MA0050.1	MA0050.1	6.50529e-8
MA0051.1	MA0051.1	6.37755e-5
MA0052.1	MA0052.1	0.00109
MA0055.1	MA0055.1	0.0116
MA0057.1	MA0057.1	0.169
MA0058.1	MA0058.1	0.274
MA0059.1	MA0059.1	0.236
MA0060.1	MA0060.1	7.9107e-22
MA0061.1	MA0061.1	0.199
MA0062.2	MA0062.2	0.0288
MA0065.2	MA0065.2	0.0124
MA0066.1	MA0066.1	0.268
MA0067.1	MA0067.1	0.293
MA0068.1	MA0068.1	0.86
MA0069.1	MA0069.1	0.724
MA0070.1	MA0070.1	0.786
MA0071.1	MA0071.1	0.232
MA0072.1	MA0072.1	0.397
MA0073.1	MA0073.1	0.953
MA0074.1	MA0074.1	0.893
MA0076.1	MA0076.1	0.00922
MA0077.1	MA0077.1	0.00417
MA0078.1	MA0078.1	0.0975
MA0079.2	MA0079.2	0.736
MA0080.2	MA0080.2	3.61812e-7
MA0081.1	MA0081.1	0.552
MA0083.1	MA0083.1	0.258
MA0084.1	MA0084.1	0.617
MA0087.1	MA0087.1	0.851
MA0088.1	MA0088.1	0.704
MA0090.1	MA0090.1	0.334
MA0091.1	MA0091.1	0.971
MA0092.1	MA0092.1	0.572
MA0093.1	MA0093.1	0.397
MA0099.2	MA0099.2	0.00188
MA0100.1	MA0100.1	0.18
MA0101.1	MA0101.1	0.835
MA0102.2	MA0102.2	0.185
MA0103.1	MA0103.1	0.0126
MA0104.2	MA0104.2	0.0576
MA0105.1	MA0105.1	0.107
MA0106.1	MA0106.1	0.463
MA0107.1	MA0107.1	0.639
MA0108.2	MA0108.2	0.0712
MA0111.1	MA0111.1	0.382
MA0112.2	MA0112.2	6.67661e-4
MA0113.1	MA0113.1	0.552
MA0114.1	MA0114.1	0.0132
MA0115.1	MA0115.1	0.802
MA0116.1	MA0116.1	0.0153
MA0117.1	MA0117.1	0.252
MA0119.1	MA0119.1	0.00812
MA0122.1	MA0122.1	0.872
MA0124.1	MA0124.1	0.463
MA0125.1	MA0125.1	0.0369
MA0131.1	MA0131.1	0.128
MA0135.1	MA0135.1	0.956
MA0136.1	MA0136.1	0.212
MA0137.2	MA0137.2	0.69
MA0138.2	MA0138.2	3.43764e-5
MA0139.1	MA0139.1	0.0372
MA0140.1	MA0140.1	0.219
MA0141.1	MA0141.1	0.0303
MA0142.1	MA0142.1	0.678
MA0143.1	MA0143.1	0.00104
MA0144.1	MA0144.1	0.216
MA0145.1	MA0145.1	0.0209
MA0146.1	MA0146.1	0.968
MA0147.1	MA0147.1	0.101
MA0148.1	MA0148.1	5.97186e-4
MA0149.1	MA0149.1	0.318
MA0150.1	MA0150.1	0.00763
MA0152.1	MA0152.1	0.974
MA0153.1	MA0153.1	2.38509e-10
MA0154.1	MA0154.1	0.00158
MA0155.1	MA0155.1	0.873
MA0156.1	MA0156.1	0.609
MA0157.1	MA0157.1	0.211
MA0159.1	MA0159.1	0.0167
MA0160.1	MA0160.1	0.184
MA0162.1	MA0162.1	0.534
MA0163.1	MA0163.1	0.183
MA0164.1	MA0164.1	0.53
MA0258.1	MA0258.1	0.0131
MA0259.1	MA0259.1	0.376

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: CNhs10596

Novel motif	Logo	P-value
1	1	0.0994
10	10	0.818
100	100	0.534
101	101	0.517
102	102	0.691
103	103	0.0145
104	104	0.746
105	105	0.227
106	106	0.00707
107	107	0.0371
108	108	0.658
109	109	0.314
11	11	0.321
110	110	0.616
111	111	0.0612
112	112	0.0826
113	113	0.515
114	114	0.0782
115	115	0.245
116	116	0.868
117	117	0.45
118	118	0.771
119	119	0.0308
12	12	0.865
120	120	0.828
121	121	0.327
122	122	0.572
123	123	0.0383
124	124	0.248
125	125	0.695
126	126	0.793
127	127	0.0509
128	128	0.0592
129	129	0.206
13	13	0.887
130	130	0.735
131	131	0.189
132	132	0.311
133	133	0.778
134	134	0.862
135	135	0.219
136	136	0.479
137	137	0.363
138	138	0.739
139	139	0.0134
14	14	0.297
140	140	0.00542
141	141	0.164
142	142	0.238
143	143	0.986
144	144	0.98
145	145	0.391
146	146	0.664
147	147	0.383
148	148	0.547
149	149	0.186
15	15	0.146
150	150	0.729
151	151	0.144
152	152	0.151
153	153	0.0572
154	154	0.91
155	155	0.283
156	156	0.00253
157	157	0.52
158	158	0.868
159	159	0.15
160	160	0.739
161	161	0.656
162	162	0.72
163	163	0.0431
164	164	0.516
165	165	0.476
166	166	0.978
167	167	0.811
168	168	0.164
169	169	0.0799
17	17	0.076
18	18	0.586
19	19	0.0878
2	2	0.486
20	20	0.271
21	21	0.773
22	22	0.342
23	23	0.0211
24	24	0.815
25	25	0.572
26	26	0.626
27	27	0.374
28	28	0.403
29	29	0.776
3	3	0.298
30	30	0.661
31	31	0.423
32	32	0.214
33	33	0.8
34	34	0.676
35	35	0.367
36	36	0.53
37	37	0.193
38	38	0.33
39	39	0.791
4	4	0.638
40	40	0.592
41	41	0.883
42	42	0.742
43	43	0.179
44	44	0.151
45	45	0.445
46	46	0.463
47	47	0.138
48	48	0.241
49	49	0.165
5	5	0.139
50	50	0.943
51	51	0.446
52	52	0.19
53	53	0.347
54	54	0.279
55	55	0.61
56	56	0.366
57	57	0.716
58	58	0.225
59	59	0.0928
6	6	0.535
60	60	0.104
61	61	0.473
62	62	0.0841
63	63	0.2
64	64	0.488
65	65	0.155
66	66	0.281
67	67	0.542
68	68	0.401
69	69	0.248
7	7	0.369
70	70	0.00254
71	71	0.467
72	72	0.537
73	73	0.353
74	74	0.247
75	75	0.659
76	76	0.488
77	77	0.152
78	78	0.448
79	79	0.32
8	8	0.463
80	80	0.151
81	81	0.297
82	82	0.0285
83	83	0.49
84	84	0.894
85	85	0.0241
86	86	0.802
87	87	0.889
88	88	0.457
89	89	0.0652
9	9	0.407
90	90	0.0923
91	91	0.532
92	92	0.0256
93	93	0.512
94	94	0.77
95	95	0.563
96	96	0.262
97	97	0.875
98	98	0.379
99	99	0.644

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: CNhs10596

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011314 mouse forelimb- embryo E11 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)
0002102 (forelimb)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0000153 (anterior region of body)
0010708 (pectoral complex)

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)
0000294 (mouse embryonic day 11 sample)
0011314 (mouse forelimb- embryo E11 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:0005417 (forelimb bud)
UBERON:0005733 (limb field)
UBERON:0005732 (limb/fin field)
UBERON:0005729 (forelimb/pectoral fin field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005527
+|accession_numbers=CAGE;DRX008963;DRR009837;DRZ001262;DRZ002645;DRZ012612;DRZ013995
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002102,UBERON:0000479,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0004708,UBERON:0002101,UBERON:0004710,UBERON:0010317,UBERON:0010707,UBERON:0000153,UBERON:0010708
 |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=chr1:140739014..140739032,-!p1@Lhx9!2.37!294.25!Lhx9;;chr2:74513125..74513143,+!p1@Hoxd12!2.16!142.49!Hoxd12;;chr1:165243591..165243625,-!p2@Prrx1!2.14!206.95!Prrx1;;chr12:34642510..34642530,+!p1@Twist1!2.12!395.14!Twist1;;chr8:59799772..59799789,+!p1@Hand2!2.06!315.38!Hand2;;chr6:52190467..52190500,-!p1@Hoxa10!1.91!79.76!Hoxa10;;chr3:99057269..99057306,+!p1@Tbx15!1.83!80.62!Tbx15;;chr2:74520048..74520064,+!p1@Hoxd11!1.81!62.95!Hoxd11;;chr12:3891810..3891829,+!p2@Dnmt3a!1.80!95.50!Dnmt3a;;chr6:52210774..52210787,-!p1@Hoxa13!1.74!53.68!Hoxa13;;chr6:52184901..52184959,-!p2@Hoxa10!1.72!51.31!Hoxa10;;chr2:38206744..38206766,+!p1@Lhx2!1.69!56.91!Lhx2;;chr5:38215819..38215823,-!p1@Msx1!1.66!112.53!Msx1;;chr13:53568104..53568156,-!p1@Msx2!1.63!60.79!Msx2;;chr3:66785857..66785873,-!p1@Shox2!1.63!42.04!Shox2;;chr6:52195795..52195825,-!p1@Hoxa11!1.62!40.96!Hoxa11;;chr12:37835120..37835133,+!p2@Meox2!1.60!54.54!Meox2;;chr6:52195763..52195792,-!p2@Hoxa11!1.60!38.59!Hoxa11;;chr6:52176164..52176195,-!p1@Hoxa9!1.59!46.56!Hoxa9;;chr10:119913546..119913583,-!p3@Hmga2!1.56!71.57!Hmga2;;chr2:38206580..38206600,+!p2@Lhx2!1.56!43.76!Lhx2;;chr6:52190668..52190682,-!p3@Hoxa10!1.55!34.71!Hoxa10;;chr10:119913310..119913366,-!p1@Hmga2!1.50!230.23!Hmga2;;chr10:119913278..119913298,-!p2@Hmga2!1.50!67.47!Hmga2;;chr2:30700788..30700824,+!p2@Prrx2!1.46!41.60!Prrx2;;chr12:28027561..28027591,-!p1@Sox11!1.45!173.53!Sox11;;chrX:55283799..55283813,+!p1@Zic3!1.45!27.16!Zic3;;chr10:119914001..119914078,-!p4@Hmga2!1.41!33.63!Hmga2;;chr1:165243653..165243664,-!p4@Prrx1!1.40!33.84!Prrx1;;chr1:165243379..165243402,-!p3@Prrx1!1.37!32.98!Prrx1;;chr12:37835141..37835194,+!p1@Meox2!1.35!64.89!Meox2;;chr2:30700881..30700916,+!p1@Prrx2!1.31!36.43!Prrx2;;chr13:40829137..40829205,-!p1@Tfap2a!1.31!21.77!Tfap2a;;chr14:122874619..122874634,+!p1@Zic2!1.30!18.75!Zic2;;chr3:99057256..99057268,+!p3@Tbx15!1.29!18.54!Tbx15;;chr9:87626083..87626108,-!p1@Tbx18!1.26!37.29!Tbx18;;chr2:74529970..74529997,+!p1@Hoxd10!1.26!17.03!Hoxd10;;chr2:74520343..74520383,+!p4@Hoxd11!1.25!16.60!Hoxd11;;chr9:71743854..71743909,-!p1@Tcf12!1.23!122.87!Tcf12;;chr2:30700857..30700873,+!p3@Prrx2!1.23!21.99!Prrx2;;chr1:165243638..165243649,-!p5@Prrx1!1.23!19.19!Prrx1;;chr12:74147689..74147711,-!p1@Six1!1.19!31.90!Six1;;chr12:3891753..3891801,+!p4@Dnmt3a!1.17!22.42!Dnmt3a;;chr2:33496386..33496410,-!p1@Lmx1b!1.16!13.37!Lmx1b;;chr6:52190858..52190873,-!p4@Hoxa10!1.16!13.37!Hoxa10;;chr2:74513064..74513089,+!p2@Hoxd12!1.14!12.72!Hoxd12;;chr4:154010409..154010466,-!p2@Prdm16!1.13!29.32!Prdm16;;chr7:52471143..52471186,+!p1@Tead2!1.12!128.05!Tead2;;chr1:140739042..140739054,-!p2@Lhx9!1.12!12.07!Lhx9;;chr6:52163319..52163342,-!p1@Hoxa3!1.11!17.46!Hoxa3;;chr2:74506264..74506286,+!p1@Hoxd13!1.11!11.86!Hoxd13;;chr1:19199236..19199258,+!p1@Tfap2b!1.11!11.86!Tfap2b;;chr10:119913792..119913820,-!p5@Hmga2!1.10!19.83!Hmga2;;chr16:25801993..25802014,+!p1@Trp63!1.10!11.64!Trp63;;chr19:7342725..7342784,+!p1@Rcor2!1.08!45.48!Rcor2;;chr6:52176144..52176161,-!p2@Hoxa9!1.07!10.78!Hoxa9;;chr2:71384802..71384815,-!p1@Dlx2!1.06!12.93!Dlx2;;chr12:57796615..57796687,+!p1@Pax9!1.06!10.56!Pax9;;chr3:130813200..130813252,+!p1@Lef1!1.05!45.70!Lef1;;chr5:120285144..120285160,+!p1@Tbx5!1.05!10.35!Tbx5;;chr6:52195747..52195762,-!p3@Hoxa11!1.05!10.35!Hoxa11;;chr6:52210816..52210831,-!p2@Hoxa13!1.04!9.92!Hoxa13;;chr6:52184880..52184893,-!p6@Hoxa10!1.04!9.92!Hoxa10;;chr15:35225845..35225867,+!p1@Osr2!1.03!25.01!Osr2;;chr8:90483433..90483457,-!p2@Zfp423!1.03!13.15!Zfp423;;chr1:19202352..19202354,+!p2@Tfap2b!1.03!9.70!Tfap2b;;chr17:86087592..86087615,-!p1@Six2!1.03!9.70!Six2;;chr11:99092233..99092273,-!p2@Smarce1!1.02!46.35!Smarce1;;chr3:66785511..66785534,-!p5@Shox2!1.02!9.48!Shox2;;chr2:74520075..74520087,+!p6@Hoxd11!1.01!9.27!Hoxd11;;chr13:40826150..40826167,-!p3@Tfap2a!1.00!9.92!Tfap2a;;chr1:165243792..165243808,-!p1@Prrx1!0.99!31.26!Prrx1;;chr4:154010918..154010931,-!p1@Prdm16!0.99!26.08!Prdm16;;chr13:15555670..15555771,+!p2@Gli3!0.99!22.42!Gli3;;chr11:99092280..99092302,-!p3@Smarce1!0.99!13.80!Smarce1;;chr4:154010228..154010244,-!p4@Prdm16!0.98!12.07!Prdm16;;chr2:30700830..30700843,+!p4@Prrx2!0.98!8.62!Prrx2;;chr15:76287876..76287894,+!p1@Scx!0.97!46.56!Scx;;chr3:29912271..29912291,-!p16@Mecom!0.97!8.41!Mecom;;chr14:122874593..122874610,+!p2@Zic2!0.96!8.19!Zic2;;chr7:53631837..53631850,+!p1@Myod1!0.96!8.19!Myod1;;chr2:167363692..167363710,+!p1@Snai1!0.94!96.36!Snai1;;chr12:37835248..37835260,+!p4@Meox2!0.94!7.76!Meox2;;chr3:99044284..99044308,+!p4@Tbx15!0.94!7.76!Tbx15;;chr7:144506077..144506128,-!p1@Ebf3!0.93!17.89!Ebf3;;chr3:5218516..5218544,+!p2@Zfhx4!0.93!11.43!Zfhx4;;chr15:102087737..102087801,-!p3@Rarg!0.92!12.29!Rarg;;chr11:23978022..23978076,+!p1@Bcl11a!0.91!161.46!Bcl11a;;chr12:12948633..12948651,-!p1@Mycn!0.91!70.92!Mycn;;chr11:99092312..99092333,-!p4@Smarce1!0.91!10.78!Smarce1;;chrX:98449898..98449913,+!p2@Foxo4!0.90!23.28!Foxo4;;chrX:55283827..55283838,+!p3@Zic3!0.90!6.90!Zic3;;chr3:107398056..107398082,+!p1@Alx3!0.90!6.90!Alx3;;chr3:29911926..29911942,-!p13@Mecom!0.89!6.68!Mecom;;chr9:106356211..106356242,+!p1@Pcbp4!0.88!133.65!Pcbp4;;chr3:30408674..30408716,-!p2@Mecom!0.88!10.99!Mecom;;chr4:154011072..154011095,-!p6@Prdm16!0.88!7.98!Prdm16;;chr6:6832076..6832092,-!p1@Dlx5!0.88!7.76!Dlx5;;chr2:74536026..74536039,+!p1@Hoxd9!0.87!6.47!Hoxd9;;chr13:53568081..53568094,-!p3@Msx2!0.87!6.47!Msx2;;chr14:56443698..56443726,+!p2@Nfatc4!0.86!12.07!Nfatc4;;chr11:94981424..94981439,+!p1@Dlx3!0.86!7.11!Dlx3;;chr3:29912249..29912262,-!p26@Mecom!0.86!6.25!Mecom;;chr10:126778916..126778974,-!p1@Gli1!0.85!14.23!Gli1;;chr11:23978111..23978134,+!p3@Bcl11a!0.85!13.15!Bcl11a;;chr14:56443806..56443848,+!p1@Nfatc4!0.85!12.72!Nfatc4;;chr13:53568191..53568219,-!p2@Msx2!0.85!6.04!Msx2;;chr10:119913266..119913277,-!p6@Hmga2!0.85!6.04!Hmga2;;chr1:19199221..19199234,+!p6@Tfap2b!0.85!6.04!Tfap2b;;chr9:87625971..87625992,-!p2@Tbx18!0.85!6.04!Tbx18;;chr11:112643496..112643562,+!p1@Sox9!0.84!236.26!Sox9;;chr3:29912154..29912168,-!p11@Mecom!0.84!6.68!Mecom;;chr14:98568971..98569025,-!p1@Dach1!0.83!47.21!Dach1;;chr1:93698030..93698064,+!p1@Twist2!0.83!12.07!Twist2;;chr2:65683890..65683907,+!p1@Csrnp3!0.83!11.64!Csrnp3;;chr19:7342786..7342803,+!p2@Rcor2!0.83!7.98!Rcor2;;chr8:90483459..90483475,-!p1@Zfp423!0.82!16.38!Zfp423;;chr2:152223783..152223812,-!p4@Sox12!0.82!13.58!Sox12;;chr3:30408603..30408668,-!p1@Mecom!0.82!13.58!Mecom;;chr12:34642682..34642753,+!p2@Twist1!0.81!15.31!Twist1;;chr7:135019147..135019187,-!p3@Zfp668!0.81!12.50!Zfp668;;chr18:14131045..14131062,-!p3@Zfp521!0.81!9.05!Zfp521;;chr4:135129538..135129558,-!p1@Grhl3!0.81!8.62!Grhl3;;chr11:23978353..23978379,+!p10@Bcl11a!0.81!6.68!Bcl11a;;chr6:6831950..6831985,-!p2@Dlx5!0.81!6.04!Dlx5;;chr15:102087880..102087927,-!p2@Rarg!0.80!12.93!Rarg;;chr14:98568761..98568814,-!p2@Dach1!0.79!38.59!Dach1;;chr11:101646566..101646603,-!p1@Etv4!0.79!18.11!Etv4;;chr10:119913954..119913972,-!p8@Hmga2!0.79!5.17!Hmga2;;chrX:55284180..55284195,+!p2@Zic3!0.79!5.17!Zic3;;chr1:38684260..38684312,-!p2@Aff3!0.78!38.37!Aff3;;chr10:119913839..119913869,-!p7@Hmga2!0.78!6.47!Hmga2;;chr11:76485958..76485963,+!p1@Bhlha9!0.78!4.96!Bhlha9;;chr3:29912169..29912182,-!p12@Mecom!0.78!4.96!Mecom;;chr2:74550015..74550057,+!p2@Hoxd3!0.78!4.96!Hoxd3;;chr3:29911947..29911958,-!p14@Mecom!0.78!4.96!Mecom;;chr6:72739185..72739232,-!p1@Tcf7l1!0.77!54.75!Tcf7l1;;chr7:134169741..134169760,-!p10@Maz!0.77!15.95!Maz;;chr18:69504195..69504213,+!p4@Tcf4!0.76!23.93!Tcf4;;chr2:74549968..74549996,+!p1@Hoxd3!0.76!6.04!Hoxd3;;chr3:29911808..29911833,-!p8@Mecom!0.76!4.74!Mecom;;chr6:52190656..52190667,-!p7@Hoxa10!0.76!4.74!Hoxa10;;chr11:44430812..44430838,+!p1@Ebf1!0.75!49.58!Ebf1;;chr13:15555496..15555544,+!p1@Gli3!0.75!17.46!Gli3;;chr18:65741935..65741964,+!p2@Zfp532!0.75!13.80!Zfp532;;chr2:152561980..152561997,+!p1@Id1!0.74!147.45!Id1;;chr17:35031460..35031518,+!p1@Zbtb12!0.74!25.01!Zbtb12;;chr15:50720601..50720630,-!p2@Trps1!0.74!11.64!Trps1;;chr1:93698068..93698085,+!p2@Twist2!0.74!5.39!Twist2;;chr14:22807083..22807104,-!p1@Zfp503!0.73!85.15!Zfp503;;chr1:120949949..120950000,-!p1@Gli2!0.73!21.13!Gli2;;chr2:17976799..17976829,+!p5@Mllt10!0.73!5.60!Mllt10;;chr1:19199151..19199170,+!p3@Tfap2b!0.73!4.31!Tfap2b;;chr2:71367871..71367898,+!p1@Dlx1!0.73!4.31!Dlx1;;chr6:6831928..6831949,-!p3@Dlx5!0.73!4.31!Dlx5;;chr13:30077847..30077906,-!p1@E2f3!0.72!37.29!E2f3;;chrX:66613481..66613562,+!p1@Aff2!0.72!20.48!Aff2;;chr18:65741358..65741415,+!p1@Zfp532!0.72!20.26!Zfp532;;chr3:29912058..29912071,-!p6@Mecom!0.72!4.96!Mecom;;chr16:4559608..4559681,-!p1@Tfap4!0.71!38.16!Tfap4;;chr4:154010940..154010962,-!p3@Prdm16!0.71!9.92!Prdm16;;chr2:156666727..156666753,+!p2@Tgif2!0.71!6.47!Tgif2;;chr19:59533221..59533271,+!p1@Emx2!0.71!5.17!Emx2;;chr14:56443742..56443756,+!p6@Nfatc4!0.71!4.10!Nfatc4;;chr15:102076870..102076941,-!p1@Rarg!0.70!50.23!Rarg;;chr11:23978078..23978096,+!p4@Bcl11a!0.70!13.58!Bcl11a;;chr3:5218546..5218561,+!p4@Zfhx4!0.70!6.47!Zfhx4;;chr7:19895354..19895369,-!p1@Fosb!0.70!5.82!Fosb;;chr13:15555555..15555574,+!p5@Gli3!0.70!5.60!Gli3;;chr12:37835203..37835218,+!p3@Meox2!0.70!4.96!Meox2;;chr4:154010334..154010347,-!p8@Prdm16!0.70!4.96!Prdm16;;chr1:93698095..93698113,+!p3@Twist2!0.70!4.96!Twist2;;chr14:22807107..22807119,-!p2@Zfp503!0.69!19.19!Zfp503;;chr14:52634234..52634281,-!p3@Zfp219!0.69!11.86!Zfp219;;chr15:102751603..102751630,+!p1@Hoxc13!0.69!3.88!Hoxc13;;chr1:136186574..136186592,+!p1@Myog!0.69!3.88!Myog;;chr11:96880072..96880079,+!p1@Sp6!0.69!3.88!Sp6;;chr2:84877369..84877459,+!p1@Ssrp1!0.68!90.75!Ssrp1;;chr10:79896347..79896358,-!p2@Tcf3!0.68!15.31!Tcf3;;chr10:79896328..79896339,-!p3@Tcf3!0.68!14.44!Tcf3;;chr3:5218629..5218684,+!p1@Zfhx4!0.68!13.80!Zfhx4;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.68!11.21!Zfhx3;;chr18:14130694..14130697,-!p2@Zfp521!0.68!9.70!Zfp521;;chr15:50721942..50721987,-!p13@Trps1!0.68!4.53!Trps1;;chr2:152223441..152223465,-!p2@Sox12!0.67!17.25!Sox12;;chr15:75447105..754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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011314
 |is_obsolete=
+|library_id=CNhs10596
+|library_id_phase_based=2:CNhs10596
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;335
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;335
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E11.CNhs10596.335-25E2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E11.CNhs10596.335-25E2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E11.CNhs10596.335-25E2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E11.CNhs10596.335-25E2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E11.CNhs10596.335-25E2.mm9.nobarcode.rdna.fa.gz
 |name=forelimb, embryo E11
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10596,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0172259571264161,0,0,0,0,0,-0.392654596147399,0,0,0,0,0.0713416617805424,0,0,0,0,0,0,-0.10711409471295,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.240810697197058,0,0,0,0,0,-0.0319115439442175,-0.0348569411945362,0.0840246560464222,-0.357509761545558,0.229224309639939,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,0,0,0,0,0.186561353169033,-0.0406075504057947,-0.0733117866014577,-0.0262545231818975,0,-0.0780086007519514,0,-0.0217377740957516,0,0,0,-0.199937815161395,-0.127551015487084,0.00594766132971743,0,0,0,0,0,0,-0.154201558792817,-0.291016808028243,-0.0923918206797908,0,0,0,0,0
 |rna_box=25
 |rna_catalog_number=
@@ Line 58: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=25E2
+|rna_tube_id=2.50E+03
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
 |top_motifs=NFY{A,B,C}:2.37057364123;ZNF143:1.8072188306;LEF1_TCF7_TCF7L1,2:1.73831279723;ZNF384:1.6533180509;NANOG{mouse}:1.63857803123;PAX8:1.59804168032;SOX2:1.58047584289;E2F1..5:1.5192183303;TFDP1:1.42511551784;PDX1:1.42428358263;STAT5{A,B}:1.32739106131;GFI1:1.31155766895;SOX17:1.22933597421;YY1:1.22472446691;VSX1,2:1.17516164283;NRF1:1.15872301309;CDC5L:1.10854491723;FOXP3:1.07236251156;ELK1,4_GABP{A,B1}:1.05469737661;EN1,2:1.03312397962;ZNF238:0.987303819232;TOPORS:0.976704110758;RXR{A,B,G}:0.955558356819;BREu{core}:0.894270320281;SOX{8,9,10}:0.887711436615;SOX5:0.881373533875;CDX1,2,4:0.849802362545;HMX1:0.835308092679;ZBTB16:0.769568621552;POU1F1:0.737891069938;PAX6:0.734233623751;HES1:0.714783186434;LHX3,4:0.713292468687;RREB1:0.712883618678;MZF1:0.707608378721;POU2F1..3:0.652756091354;NANOG:0.649735865034;TEF:0.624264479541;HSF1,2:0.60512123326;PATZ1:0.599737839421;PAX5:0.587984259342;MED-1{core}:0.576438413672;TFAP2{A,C}:0.566418366744;FOXQ1:0.556163127241;UFEwm:0.540423004919;MYB:0.521842541924;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.511770284322;CUX2:0.506138894232;MAZ:0.490051959978;PAX1,9:0.451246798318;GATA4:0.446980834021;ALX1:0.446597930056;ONECUT1,2:0.437115489373;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.40521222367;GTF2A1,2:0.39857973837;PRRX1,2:0.396885361411;IKZF2:0.395302506608;STAT1,3:0.390421634049;HIC1:0.343769826706;EP300:0.306298955054;ALX4:0.296516839845;PITX1..3:0.280382082516;MTE{core}:0.272293862892;KLF4:0.266272185467;NKX2-3_NKX2-5:0.266256111539;NKX3-1:0.248763266553;HMGA1,2:0.248114668127;MYBL2:0.234055464011;RFX1:0.230505358242;HIF1A:0.22043898189;PBX1:0.192775602427;GTF2I:0.159132666345;RORA:0.146041121237;FOX{I1,J2}:0.145086244608;SPZ1:0.138296337938;ZFP161:0.137455340245;ATF2:0.136973954791;RBPJ:0.136047054294;AHR_ARNT_ARNT2:0.13502952177;RFX2..5_RFXANK_RFXAP:0.0927598110427;FOXD3:0.0866386671969;NKX6-1,2:0.066585569186;AIRE:0.0542975742653;ELF1,2,4:0.0484659858;ESR1:0.0342172926112;HAND1,2:0.0310947673304;ADNP_IRX_SIX_ZHX:0.0238411536581;EGR1..3:0.0211044490872;XCPE1{core}:0.0206760729447;NR6A1:0.0200385990015;TEAD1:0.0121000856565;GCM1,2:0.0114421440666;HOXA9_MEIS1:-0.000389289383433;GFI1B:-0.00288666291827;ATF4:-0.00737807459224;IKZF1:-0.0200575167799;TFAP2B:-0.0500804592461;NKX2-1,4:-0.0579875653192;HOX{A4,D4}:-0.0697160517125;ZIC1..3:-0.0703687983801;OCT4_SOX2{dimer}:-0.0923937427078;NFE2L1:-0.0975257068483;DBP:-0.100119355008;POU5F1:-0.110248958453;T:-0.128723150844;CRX:-0.12978599004;CREB1:-0.13180714187;SREBF1,2:-0.132269202932;TP53:-0.144113939204;GZF1:-0.144297993864;TBX4,5:-0.183326330292;SPIB:-0.186292454523;POU3F1..4:-0.188652149094;NHLH1,2:-0.189912823906;DMAP1_NCOR{1,2}_SMARC:-0.21481624735;PAX4:-0.226078742046;BPTF:-0.233345327908;RUNX1..3:-0.247195059012;bHLH_family:-0.256285781093;ATF6:-0.259859063499;FOXO1,3,4:-0.269298366417;HBP1_HMGB_SSRP1_UBTF:-0.293903753432;NFKB1_REL_RELA:-0.309921622635;FOXP1:-0.31919091967;ZNF423:-0.327201204139;REST:-0.331678941044;SPI1:-0.341515632028;HNF4A_NR2F1,2:-0.344794272739;TFCP2:-0.351678245389;SRF:-0.362584500433;PRDM1:-0.378826018144;GATA6:-0.401886643996;ATF5_CREB3:-0.407951482959;MEF2{A,B,C,D}:-0.407980814056;ETS1,2:-0.408290633298;ZBTB6:-0.427277085033;HLF:-0.441473858733;NR3C1:-0.443165106904;NR1H4:-0.453703311451;EVI1:-0.487199614771;JUN:-0.507460343156;HNF1A:-0.513504852617;TLX2:-0.547726224146;SP1:-0.55645470879;SNAI1..3:-0.573209217169;TBP:-0.574542328684;FOXL1:-0.58054564818;TFAP4:-0.587055125149;TAL1_TCF{3,4,12}:-0.588583304976;ZEB1:-0.590029005842;MTF1:-0.595654099503;NFATC1..3:-0.609496564935;NFIL3:-0.63221561504;BACH2:-0.648495953534;FOX{D1,D2}:-0.663372188166;GLI1..3:-0.67202261956;NKX2-2,8:-0.69793454484;TGIF1:-0.705675756185;FOS_FOS{B,L1}_JUN{B,D}:-0.709290943483;NR5A1,2:-0.744255704636;PPARG:-0.752401393374;FOSL2:-0.77279825109;ESRRA:-0.783566372896;FOXM1:-0.807468183154;MYOD1:-0.815267589656;MYFfamily:-0.820057434102;POU6F1:-0.827974905081;FOXA2:-0.831247442056;TLX1..3_NFIC{dimer}:-0.832791383434;PAX2:-0.842651525081;SMAD1..7,9:-0.855552277364;RXRA_VDR{dimer}:-0.873447904129;ARID5B:-0.876842508221;NFIX:-0.891957784214;HOX{A5,B5}:-0.899001998859;FOX{F1,F2,J1}:-0.9044551636;NFE2:-0.913377779652;AR:-0.913840403693;ZNF148:-0.941100022352;FOXN1:-0.947108127035;MAFB:-0.952636868991;NFE2L2:-1.05525290526;IRF1,2:-1.06124285994;IRF7:-1.09002168467;NKX3-2:-1.13355456949;CEBPA,B_DDIT3:-1.25882771535;EBF1:-1.32561039424;LMO2:-1.59440815601;STAT2,4,6:-1.60253731176
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:335-25E2;search_select_hide=table117:335-25E2
 }}

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FF:335-25E2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:10, 4 June 2020

CNhs10596

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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