FF:437-20E7: Difference between revisions

Latest revision as of 19:16, 4 June 2020

Name:	forelimb, embryo E15
Species:	Mouse (Mus musculus)
Library ID:	CNhs11007
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	forelimb
dev stage	15 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		SAMD00005428

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11007		CAGE		DRX008967		DRR009841

Accession ID Mm9

Library id		BAM		CTSS
CNhs11007		DRZ001266		DRZ002649

Accession ID Mm10

Library id		BAM		CTSS
CNhs11007		DRZ012616		DRZ013999

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

CNhs11007

0	0
1	0
10	0
100	0
1000	0
1001	0.0196
1002	0.0533
1003	0.28
1004	0
1005	-0.0202
1006	-0.143
1007	0.161
1008	0
1009	0.135
101	0.0966
1010	0
1011	0.0924
1012	0
1013	-0.142
1014	0.621
1015	0.162
1016	0.304
1017	0.107
1018	0.578
1019	0
102	0
1020	0
1021	-0.0487
1022	-0.0704
1023	0
1024	0.0525
1025	0
1026	0
1027	0
1028	0
1029	0.539
103	0.508
1030	0
1031	0.388
1032	-0.0928
1033	0.0313
1034	0
1035	0
1036	0.16
1037	0
1038	0.0301
1039	-0.203
104	0
1040	0.211
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: CNhs11007

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00714
MA0003.1	MA0003.1	0.0129
MA0004.1	MA0004.1	0.464
MA0006.1	MA0006.1	0.483
MA0007.1	MA0007.1	0.537
MA0009.1	MA0009.1	0.747
MA0014.1	MA0014.1	0.0754
MA0017.1	MA0017.1	6.91858e-12
MA0018.2	MA0018.2	0.00282
MA0019.1	MA0019.1	0.0827
MA0024.1	MA0024.1	0.00219
MA0025.1	MA0025.1	0.0031
MA0027.1	MA0027.1	0.393
MA0028.1	MA0028.1	0.00838
MA0029.1	MA0029.1	0.913
MA0030.1	MA0030.1	0.0964
MA0031.1	MA0031.1	0.00141
MA0035.2	MA0035.2	3.55888e-8
MA0038.1	MA0038.1	0.856
MA0039.2	MA0039.2	0.00276
MA0040.1	MA0040.1	0.145
MA0041.1	MA0041.1	0.137
MA0042.1	MA0042.1	0.268
MA0043.1	MA0043.1	0.232
MA0046.1	MA0046.1	5.81095e-23
MA0047.2	MA0047.2	6.09246e-4
MA0048.1	MA0048.1	0.0373
MA0050.1	MA0050.1	0.00727
MA0051.1	MA0051.1	5.86207e-5
MA0052.1	MA0052.1	0.509
MA0055.1	MA0055.1	0.882
MA0057.1	MA0057.1	0.647
MA0058.1	MA0058.1	0.261
MA0059.1	MA0059.1	0.877
MA0060.1	MA0060.1	0.913
MA0061.1	MA0061.1	0.288
MA0062.2	MA0062.2	8.13679e-7
MA0065.2	MA0065.2	7.77485e-8
MA0066.1	MA0066.1	0.199
MA0067.1	MA0067.1	0.0352
MA0068.1	MA0068.1	0.868
MA0069.1	MA0069.1	0.941
MA0070.1	MA0070.1	0.406
MA0071.1	MA0071.1	6.44416e-5
MA0072.1	MA0072.1	8.62813e-5
MA0073.1	MA0073.1	0.645
MA0074.1	MA0074.1	0.328
MA0076.1	MA0076.1	0.00776
MA0077.1	MA0077.1	0.934
MA0078.1	MA0078.1	0.17
MA0079.2	MA0079.2	0.309
MA0080.2	MA0080.2	2.74538e-10
MA0081.1	MA0081.1	0.0263
MA0083.1	MA0083.1	0.485
MA0084.1	MA0084.1	0.98
MA0087.1	MA0087.1	0.475
MA0088.1	MA0088.1	0.522
MA0090.1	MA0090.1	0.266
MA0091.1	MA0091.1	0.656
MA0092.1	MA0092.1	0.636
MA0093.1	MA0093.1	0.514
MA0099.2	MA0099.2	0.0175
MA0100.1	MA0100.1	0.361
MA0101.1	MA0101.1	0.0831
MA0102.2	MA0102.2	0.672
MA0103.1	MA0103.1	0.00711
MA0104.2	MA0104.2	0.489
MA0105.1	MA0105.1	0.202
MA0106.1	MA0106.1	0.206
MA0107.1	MA0107.1	0.0779
MA0108.2	MA0108.2	0.79
MA0111.1	MA0111.1	0.4
MA0112.2	MA0112.2	0.00779
MA0113.1	MA0113.1	0.201
MA0114.1	MA0114.1	1.79757e-10
MA0115.1	MA0115.1	4.63698e-4
MA0116.1	MA0116.1	0.1
MA0117.1	MA0117.1	0.0183
MA0119.1	MA0119.1	0.28
MA0122.1	MA0122.1	0.646
MA0124.1	MA0124.1	0.439
MA0125.1	MA0125.1	0.838
MA0131.1	MA0131.1	0.563
MA0135.1	MA0135.1	0.175
MA0136.1	MA0136.1	2.51351e-11
MA0137.2	MA0137.2	0.0576
MA0138.2	MA0138.2	2.79001e-5
MA0139.1	MA0139.1	0.0419
MA0140.1	MA0140.1	8.49481e-5
MA0141.1	MA0141.1	3.45545e-8
MA0142.1	MA0142.1	0.895
MA0143.1	MA0143.1	0.518
MA0144.1	MA0144.1	0.061
MA0145.1	MA0145.1	0.14
MA0146.1	MA0146.1	0.0562
MA0147.1	MA0147.1	0.628
MA0148.1	MA0148.1	0.00624
MA0149.1	MA0149.1	0.00437
MA0150.1	MA0150.1	2.60216e-6
MA0152.1	MA0152.1	0.0175
MA0153.1	MA0153.1	8.67678e-16
MA0154.1	MA0154.1	0.0156
MA0155.1	MA0155.1	0.828
MA0156.1	MA0156.1	1.73348e-7
MA0157.1	MA0157.1	0.2
MA0159.1	MA0159.1	4.67319e-4
MA0160.1	MA0160.1	3.31105e-8
MA0162.1	MA0162.1	0.795
MA0163.1	MA0163.1	0.569
MA0164.1	MA0164.1	0.757
MA0258.1	MA0258.1	0.0011
MA0259.1	MA0259.1	0.828

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: CNhs11007

Novel motif	Logo	P-value
1	1	0.187
10	10	0.849
100	100	0.625
101	101	0.851
102	102	0.397
103	103	0.183
104	104	0.379
105	105	0.74
106	106	0.126
107	107	0.772
108	108	0.713
109	109	0.0311
11	11	0.0847
110	110	0.559
111	111	0.0464
112	112	0.0921
113	113	0.696
114	114	0.0137
115	115	0.935
116	116	0.639
117	117	0.423
118	118	0.321
119	119	0.131
12	12	0.516
120	120	0.448
121	121	0.114
122	122	0.995
123	123	0.216
124	124	0.246
125	125	0.661
126	126	0.267
127	127	0.273
128	128	0.375
129	129	0.441
13	13	0.984
130	130	0.155
131	131	0.434
132	132	0.415
133	133	0.0707
134	134	0.835
135	135	0.831
136	136	0.0572
137	137	0.86
138	138	0.423
139	139	0.0405
14	14	0.349
140	140	0.644
141	141	0.737
142	142	0.303
143	143	0.55
144	144	0.282
145	145	0.517
146	146	0.217
147	147	0.256
148	148	0.361
149	149	0.333
15	15	0.0265
150	150	0.899
151	151	0.0101
152	152	0.104
153	153	0.581
154	154	0.415
155	155	0.814
156	156	0.479
157	157	0.763
158	158	0.466
159	159	0.305
160	160	0.243
161	161	0.434
162	162	0.891
163	163	0.121
164	164	0.383
165	165	0.0715
166	166	0.16
167	167	0.701
168	168	0.694
169	169	0.14
17	17	0.24
18	18	0.346
19	19	0.567
2	2	0.891
20	20	0.777
21	21	0.733
22	22	0.413
23	23	0.809
24	24	0.397
25	25	0.145
26	26	0.35
27	27	0.323
28	28	0.213
29	29	0.297
3	3	0.351
30	30	0.979
31	31	0.359
32	32	0.445
33	33	0.392
34	34	0.548
35	35	0.16
36	36	0.0983
37	37	0.103
38	38	0.246
39	39	0.649
4	4	0.769
40	40	0.0293
41	41	0.151
42	42	0.902
43	43	0.278
44	44	0.00959
45	45	0.245
46	46	0.774
47	47	0.159
48	48	0.0898
49	49	0.247
5	5	0.503
50	50	0.696
51	51	0.637
52	52	0.694
53	53	0.883
54	54	0.503
55	55	0.316
56	56	0.57
57	57	0.744
58	58	0.435
59	59	0.108
6	6	0.781
60	60	0.273
61	61	0.596
62	62	0.167
63	63	0.267
64	64	0.399
65	65	0.172
66	66	0.385
67	67	0.457
68	68	0.0345
69	69	0.602
7	7	0.51
70	70	0.0269
71	71	0.832
72	72	0.165
73	73	0.0382
74	74	0.903
75	75	0.0715
76	76	0.91
77	77	0.361
78	78	0.598
79	79	0.879
8	8	0.107
80	80	0.00389
81	81	0.376
82	82	0.166
83	83	0.556
84	84	0.38
85	85	0.0378
86	86	0.884
87	87	7.79746e-6
88	88	0.983
89	89	0.195
9	9	0.966
90	90	0.468
91	91	0.683
92	92	0.92
93	93	0.628
94	94	0.262
95	95	0.00882
96	96	0.698
97	97	0.839
98	98	0.295
99	99	0.547

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: CNhs11007

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011351 mouse forelimb- embryo E15 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)
0000298 (mouse embryonic day 15 sample)
0011351 (mouse forelimb- embryo E15 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@DRS008830
+|DRA_sample_Accession=CAGE@SAMD00005428
-|accession_numbers=CAGE;DRX008967;DRR009841;DRZ001266;DRZ002649
+|accession_numbers=CAGE;DRX008967;DRR009841;DRZ001266;DRZ002649;DRZ012616;DRZ013999
 |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 9: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr12:34642510..34642530,+!p1@Twist1!1.97!283.33!Twist1;;chr1:165243591..165243625,-!p2@Prrx1!1.81!94.81!Prrx1;;chr6:52190467..52190500,-!p1@Hoxa10!1.80!62.28!Hoxa10;;chr2:74513125..74513143,+!p1@Hoxd12!1.74!54.22!Hoxd12;;chr11:121380640..121380655,-!p1@Zfp750!1.62!66.73!Zfp750;;chr4:135129538..135129558,-!p1@Grhl3!1.61!59.50!Grhl3;;chr1:140739014..140739032,-!p1@Lhx9!1.57!45.88!Lhx9;;chr16:25801993..25802014,+!p1@Trp63!1.56!35.31!Trp63;;chr3:99057269..99057306,+!p1@Tbx15!1.53!40.04!Tbx15;;chr12:37835120..37835133,+!p2@Meox2!1.47!40.32!Meox2;;chr13:40829137..40829205,-!p1@Tfap2a!1.47!32.25!Tfap2a;;chr8:59799772..59799789,+!p1@Hand2!1.46!78.13!Hand2;;chr9:87626083..87626108,-!p1@Tbx18!1.43!55.33!Tbx18;;chr12:37835141..37835194,+!p1@Meox2!1.39!72.01!Meox2;;chr1:165243379..165243402,-!p3@Prrx1!1.35!31.98!Prrx1;;chr5:120285144..120285160,+!p1@Tbx5!1.35!21.13!Tbx5;;chr13:53568104..53568156,-!p1@Msx2!1.33!30.03!Msx2;;chr6:52195795..52195825,-!p1@Hoxa11!1.33!20.58!Hoxa11;;chr15:102087737..102087801,-!p3@Rarg!1.29!30.31!Rarg;;chr6:52176164..52176195,-!p1@Hoxa9!1.27!21.97!Hoxa9;;chr18:7004715..7004731,-!p1@Mkx!1.26!40.32!Mkx;;chr18:80909801..80909819,-!p1@Nfatc1!1.25!96.48!Nfatc1;;chr5:38215819..38215823,-!p1@Msx1!1.25!43.38!Msx1;;chr11:121380594..121380609,-!p2@Zfp750!1.25!28.92!Zfp750;;chr6:52184901..52184959,-!p2@Hoxa10!1.23!16.13!Hoxa10;;chr12:37835248..37835260,+!p4@Meox2!1.23!16.13!Meox2;;chr12:74147689..74147711,-!p1@Six1!1.22!34.20!Six1;;chr10:126778916..126778974,-!p1@Gli1!1.21!33.64!Gli1;;chr1:93698030..93698064,+!p1@Twist2!1.19!29.19!Twist2;;chr11:121380611..121380625,-!p3@Zfp750!1.19!17.52!Zfp750;;chr6:6832076..6832092,-!p1@Dlx5!1.19!16.96!Dlx5;;chr9:31720843..31720888,-!p1@Barx2!1.17!15.29!Barx2;;chr2:74520048..74520064,+!p1@Hoxd11!1.17!13.90!Hoxd11;;chr7:53631837..53631850,+!p1@Myod1!1.17!13.62!Myod1;;chr6:52195763..52195792,-!p2@Hoxa11!1.17!13.62!Hoxa11;;chr19:5560600..5560617,-!p1@Ovol1!1.16!16.40!Ovol1;;chr13:72766250..72766273,+!p1@Irx2!1.14!20.02!Irx2;;chr1:19199236..19199258,+!p1@Tfap2b!1.14!12.79!Tfap2b;;chr3:66785857..66785873,-!p1@Shox2!1.11!11.96!Shox2;;chr1:136186574..136186592,+!p1@Myog!1.10!11.68!Myog;;chr11:94981424..94981439,+!p1@Dlx3!1.09!12.79!Dlx3;;chr2:38206744..38206766,+!p1@Lhx2!1.08!13.35!Lhx2;;chr3:99057256..99057268,+!p3@Tbx15!1.08!11.12!Tbx15;;chr15:102751603..102751630,+!p1@Hoxc13!1.08!11.12!Hoxc13;;chr9:43013917..43013968,-!p1@Pou2f3!1.08!11.12!Pou2f3;;chr6:52210774..52210787,-!p1@Hoxa13!1.07!10.84!Hoxa13;;chr1:165243653..165243664,-!p4@Prrx1!1.06!15.01!Prrx1;;chr7:123182248..123182264,-!p3@Sox6!1.06!12.51!Sox6;;chr12:37835203..37835218,+!p3@Meox2!1.06!12.51!Meox2;;chr3:30408603..30408668,-!p1@Mecom!1.05!23.63!Mecom;;chr1:165243272..165243283,-!p6@Prrx1!1.05!12.51!Prrx1;;chr12:28027561..28027591,-!p1@Sox11!1.04!65.90!Sox11;;chr15:35225845..35225867,+!p1@Osr2!1.04!25.30!Osr2;;chr19:59533221..59533271,+!p1@Emx2!1.04!12.23!Emx2;;chr13:40825465..40825469,-!p2@Tfap2a!1.04!10.01!Tfap2a;;chr13:72101178..72101203,-!p1@Irx1!1.03!15.29!Irx1;;chr7:144506077..144506128,-!p1@Ebf3!1.02!22.24!Ebf3;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!1.02!16.96!Zfhx3;;chr3:30408674..30408716,-!p2@Mecom!1.02!15.57!Mecom;;chr2:30700857..30700873,+!p3@Prrx2!1.02!13.07!Prrx2;;chr7:144505957..144505972,-!p2@Ebf3!1.02!11.68!Ebf3;;chr6:6831950..6831985,-!p2@Dlx5!1.02!10.57!Dlx5;;chr19:25746898..25746910,+!p1@Dmrt2!1.01!13.90!Dmrt2;;chr5:77543897..77543911,-!p2@Hopx!1.00!17.52!Hopx;;chr7:144505980..144506010,-!p3@Ebf3!1.00!10.84!Ebf3;;chr10:12810631..12810649,+!p1@Plagl1!0.99!233.84!Plagl1;;chr12:9581262..9581282,+!p1@Osr1!0.98!105.66!Osr1;;chr9:71743854..71743909,-!p1@Tcf12!0.98!68.96!Tcf12;;chr2:30700788..30700824,+!p2@Prrx2!0.98!13.35!Prrx2;;chr10:119914001..119914078,-!p4@Hmga2!0.98!11.68!Hmga2;;chr17:44951553..44951586,-!p2@Runx2!0.98!9.45!Runx2;;chr2:74520343..74520383,+!p4@Hoxd11!0.98!8.62!Hoxd11;;chr12:57796615..57796687,+!p1@Pax9!0.98!8.62!Pax9;;chr8:94881733..94881790,+!p1@Irx5!0.97!16.68!Irx5;;chr15:76287876..76287894,+!p1@Scx!0.96!45.88!Scx;;chr3:5218629..5218684,+!p1@Zfhx4!0.96!27.25!Zfhx4;;chr6:14851287..14851342,+!p1@Foxp2!0.96!27.25!Foxp2;;chr2:9800207..9800234,-!p1@Gata3!0.96!25.30!Gata3;;chr6:14851440..14851497,+!p2@Foxp2!0.96!20.30!Foxp2;;chr8:111227518..111227550,+!p@chr8:111227518..111227550,+!0.96!14.46!Zfhx3;;chr15:50721942..50721987,-!p13@Trps1!0.96!9.45!Trps1;;chr14:56443806..56443848,+!p1@Nfatc4!0.95!16.40!Nfatc4;;chr1:93698068..93698085,+!p2@Twist2!0.94!9.18!Twist2;;chr15:50720601..50720630,-!p2@Trps1!0.93!18.63!Trps1;;chr13:72766279..72766296,+!p2@Irx2!0.93!11.40!Irx2;;chr1:19202352..19202354,+!p2@Tfap2b!0.93!7.51!Tfap2b;;chr13:15555670..15555771,+!p2@Gli3!0.92!19.19!Gli3;;chr8:87297280..87297326,-!p2@Nfix!0.92!17.80!Nfix;;chr9:87625971..87625992,-!p2@Tbx18!0.92!7.23!Tbx18;;chr2:172375081..172375105,+!p1@Tfap2c!0.92!7.23!Tfap2c;;chr12:109242266..109242295,-!p1@Bcl11b!0.91!63.12!Bcl11b;;chrX:45245644..45245666,-!p2@Smarca1!0.91!23.91!Smarca1;;chr10:119913546..119913583,-!p3@Hmga2!0.91!15.29!Hmga2;;chr2:30700881..30700916,+!p1@Prrx2!0.90!13.35!Prrx2;;chr13:40826150..40826167,-!p3@Tfap2a!0.90!7.79!Tfap2a;;chr1:19199095..19199114,+!p5@Tfap2b!0.90!6.95!Tfap2b;;chr11:96880072..96880079,+!p1@Sp6!0.90!6.95!Sp6;;chr2:74506264..74506286,+!p1@Hoxd13!0.90!6.95!Hoxd13;;chr3:130813736..130813752,+!p3@Lef1!0.89!9.73!Lef1;;chr13:31717548..31717596,+!p1@Foxf2!0.88!13.35!Foxf2;;chr4:13712228..13712267,+!p3@Runx1t1!0.88!11.68!Runx1t1;;chr1:19199221..19199234,+!p6@Tfap2b!0.88!6.67!Tfap2b;;chr1:19199079..19199092,+!p7@Tfap2b!0.88!6.67!Tfap2b;;chr19:59533429..59533470,+!p4@Emx2!0.88!6.67!Emx2;;chr5:120285161..120285176,+!p2@Tbx5!0.88!6.67!Tbx5;;chr6:52190668..52190682,-!p3@Hoxa10!0.88!6.67!Hoxa10;;chr7:17647736..17647772,-!p1@Hif3a!0.87!23.91!Hif3a;;chr2:65683890..65683907,+!p1@Csrnp3!0.87!12.79!Csrnp3;;chr3:107398056..107398082,+!p1@Alx3!0.87!6.40!Alx3;;chr3:99044284..99044308,+!p4@Tbx15!0.87!6.40!Tbx15;;chr18:14131126..14131211,-!p1@Zfp521!0.86!138.47!Zfp521;;chrX:45245679..45245702,-!p1@Smarca1!0.86!29.75!Smarca1;;chr7:6649134..6649167,-!p1@Zim1!0.84!33.92!Zim1;;chr2:38206580..38206600,+!p2@Lhx2!0.84!7.51!Lhx2;;chr6:144157924..144157955,-!p2@Sox5!0.84!7.51!Sox5;;chr1:165243638..165243649,-!p5@Prrx1!0.84!7.23!Prrx1;;chr4:82151274..82151290,-!p3@Nfib!0.83!100.93!Nfib;;chr2:120365588..120365602,-!p2@Zfp106!0.83!10.01!Zfp106;;chr1:19199151..19199170,+!p3@Tfap2b!0.83!5.84!Tfap2b;;chr2:74529970..74529997,+!p1@Hoxd10!0.83!5.84!Hoxd10;;chr11:44431687..44431706,+!p2@Ebf1!0.82!27.80!Ebf1;;chr1:120949949..120950000,-!p1@Gli2!0.82!25.86!Gli2;;chr13:15555496..15555544,+!p1@Gli3!0.82!20.85!Gli3;;chr1:120950098..120950132,-!p2@Gli2!0.82!13.35!Gli2;;chr6:52163319..52163342,-!p1@Hoxa3!0.82!8.34!Hoxa3;;chr14:67853632..67853674,+!p3@Ebf2!0.82!6.95!Ebf2;;chr4:84321300..84321315,-!p2@Bnc2!0.82!6.95!Bnc2;;chr2:74517742..74517758,+!p2@Hoxd11!0.82!5.56!Hoxd11;;chr2:74517609..74517621,+!p3@Hoxd11!0.82!5.56!Hoxd11;;chr5:120285130..120285141,+!p3@Tbx5!0.82!5.56!Tbx5;;chr6:6831928..6831949,-!p3@Dlx5!0.82!5.56!Dlx5;;chr11:21901608..21901634,-!p1@Otx1!0.82!5.56!Otx1;;chr13:83643159..83643226,+!p3@Mef2c!0.82!5.56!Mef2c;;chr1:122498955..122498968,+!p1@En1!0.82!5.56!En1;;chr14:67853425..67853454,+!p1@Ebf2!0.81!8.06!Ebf2;;chr8:111227354..111227401,+!p@chr8:111227354..111227401,+!0.81!7.51!Zfhx3;;chr11:101755669..101755686,-!p1@Meox1!0.80!10.01!Meox1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.80!8.90!Dnmt3a;;chr12:34642682..34642753,+!p2@Twist1!0.79!14.74!Twist1;;chr10:119913278..119913298,-!p2@Hmga2!0.79!12.23!Hmga2;;chr12:37835219..37835230,+!p5@Meox2!0.78!5.00!Meox2;;chr6:52190858..52190873,-!p4@Hoxa10!0.78!5.00!Hoxa10;;chr6:52210816..52210831,-!p2@Hoxa13!0.78!5.00!Hoxa13;;chr4:84321317..84321332,-!p4@Bnc2!0.78!5.00!Bnc2;;chr1:19199119..19199134,+!p4@Tfap2b!0.78!5.00!Tfap2b;;chr14:99697871..99697934,+!p1@Klf5!0.77!106.21!Klf5;;chr3:5218516..5218544,+!p2@Zfhx4!0.77!7.51!Zfhx4;;chr13:72101161..72101177,-!p2@Irx1!0.77!6.95!Irx1;;chr4:3865501..3865548,-!p1@Plag1!0.76!26.41!Plag1;;chr8:94325814..94325839,-!p2@Irx3!0.76!10.57!Irx3;;chr18:14131020..14131033,-!p4@Zfp521!0.76!6.40!Zfp521;;chr3:30408384..30408431,-!p4@Mecom!0.76!6.12!Mecom;;chr4:135129447..135129467,-!p2@Grhl3!0.76!5.84!Grhl3;;chr1:19199021..19199048,+!p8@Tfap2b!0.76!4.73!Tfap2b;;chr17:44951431..44951445,-!p3@Runx2!0.76!4.73!Runx2;;chrX:55283799..55283813,+!p1@Zic3!0.76!4.73!Zic3;;chr16:14705925..14705951,+!p1@Snai2!0.75!35.59!Snai2;;chr3:130813200..130813252,+!p1@Lef1!0.75!22.52!Lef1;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.75!19.74!Ppp1r13l;;chr1:165243792..165243808,-!p1@Prrx1!0.75!17.52!Prrx1;;chr12:3891810..3891829,+!p2@Dnmt3a!0.75!7.51!Dnmt3a;;chr8:94881872..94881887,+!p2@Irx5!0.75!5.00!Irx5;;chr4:82151178..82151262,-!p1@Nfib!0.74!200.75!Nfib;;chr13:31898729..31898761,+!p1@Foxc1!0.74!11.96!Foxc1;;chr15:102087880..102087927,-!p2@Rarg!0.74!11.12!Rarg;;chr17:44872561..44872615,-!p1@Runx2!0.74!10.84!Runx2;;chr12:25257141..25257173,+!p1@Grhl1!0.74!10.01!Grhl1;;chr11:23978111..23978134,+!p3@Bcl11a!0.74!10.01!Bcl11a;;chr15:102197405..102197454,-!p1@Sp7!0.74!4.45!Sp7;;chr15:95485240..95485257,-!p1@Dbx2!0.74!4.45!Dbx2;;chr2:74499300..74499309,-!p@chr2:74499300..74499309,-!0.74!4.45!Evx2;;chr18:69752912..69752928,+!p9@Tcf4!0.73!6.95!Tcf4;;chr10:119913310..119913366,-!p1@Hmga2!0.72!36.98!Hmga2;;chr4:134708451..134708469,+!p1@Runx3!0.72!8.06!Runx3;;chr1:57029281..57029326,-!p1@Satb2!0.72!6.95!Satb2;;chrX:66613481..66613562,+!p1@Aff2!0.71!19.74!Aff2;;chr8:90483433..90483457,-!p2@Zfp423!0.71!5.84!Zfp423;;chr14:56443781..56443800,+!p3@Nfatc4!0.71!5.56!Nfatc4;;chr8:111227455..111227464,+!p@chr8:111227455..111227464,+!0.71!5.28!Zfhx3;;chr13:53568191..53568219,-!p2@Msx2!0.71!4.17!Msx2;;chr5:42155788..42155800,-!p1@Nkx3-2!0.71!4.17!Nkx3-2;;chr6:52176144..52176161,-!p2@Hoxa9!0.71!4.17!Hoxa9;;chr2:103264245..103264268,+!p2@Elf5!0.71!4.17!Elf5;;chr19:59533139..59533152,+!p2@Emx2!0.71!4.17!Emx2;;chr10:126778639..126778670,-!p3@Gli1!0.71!4.17!Gli1;;chr2: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@@ Line 44: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11007
+|library_id_phase_based=2:CNhs11007
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;437
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;437
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E15.CNhs11007.437-20E7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E15.CNhs11007.437-20E7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E15.CNhs11007.437-20E7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E15.CNhs11007.437-20E7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E15.CNhs11007.437-20E7.mm9.nobarcode.rdna.fa.gz
 |name=forelimb, embryo E15
 |namespace=FANTOM5
@@ Line 49: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11007,LSID730,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.207662295784855,0,0,0,0,0.096017983637161,0.63824095356942,0,0,0,0,1.16321265297152,0,0,0,0,0,0,0.316552597573357,0,0,0,0,0,0,0,0,0,0,0,0,0,0.293876582830625,0,0,0,0,0.0310542486345914,-0.0600312868963652,0.0383106086477096,-0.108738109438398,1.13439774750764,0.108572189849578,0,0,0,0,0,0,0,0,0,0,0,0,0.0405413623611589,0.192035967274322,0,0,0,0,0,0,0,0.106546909924599,0.0792542767630628,0.231376464148791,0.0677901705205431,0.166641733135889,0.389685694399469,0,0.106546909924599,0.000920474200029997,0,0.263432896140446,0,0.0536754064966632,-0.0506522447523175,0.239077229814095,0.113204372434415,0,0,0,0,0,0,0.102401757979965,0.412159679710612,-0.0848130991988764,0.0278791940031317,0,0,0,0
@@ Line 62: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=20E7
+|rna_tube_id=2.00E+08
 |rna_weight_ug=
 |sample_age=
@@ Line 86: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:437-20E7;search_select_hide=table117:437-20E7
 }}

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FF:437-20E7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:16, 4 June 2020

CNhs11007

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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