FF:359-14H2: Difference between revisions

Latest revision as of 19:11, 4 June 2020

Name:	forelimb, embryo E12
Species:	Mouse (Mus musculus)
Library ID:	CNhs10600
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	forelimb
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		SAMD00005383

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10600		CAGE		DRX008964		DRR009838

Accession ID Mm9

Library id		BAM		CTSS
CNhs10600		DRZ001263		DRZ002646

Accession ID Mm10

Library id		BAM		CTSS
CNhs10600		DRZ012613		DRZ013996

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

CNhs10600

0	0
1	0
10	0
100	0.0752
1000	0
1001	0
1002	0.0879
1003	0.0183
1004	0
1005	-0.0651
1006	-0.0491
1007	0.163
1008	0
1009	-0.0572
101	0.142
1010	0
1011	0.00517
1012	0
1013	-0.151
1014	0.152
1015	0.282
1016	0.556
1017	0
1018	0.0752
1019	0
102	0
1020	0
1021	0.139
1022	-0.0922
1023	0
1024	-0.0899
1025	0
1026	0
1027	0
1028	0
1029	0.182
103	0.00715
1030	0
1031	0.15
1032	-0.139
1033	0.0493
1034	0
1035	0
1036	0.0338
1037	0
1038	0.0625
1039	-0.216
104	0
1040	0.146
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: CNhs10600

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	7.30973e-4
MA0003.1	MA0003.1	0.0599
MA0004.1	MA0004.1	0.861
MA0006.1	MA0006.1	0.379
MA0007.1	MA0007.1	0.468
MA0009.1	MA0009.1	0.296
MA0014.1	MA0014.1	0.0947
MA0017.1	MA0017.1	1.5345e-4
MA0018.2	MA0018.2	0.509
MA0019.1	MA0019.1	0.703
MA0024.1	MA0024.1	5.90299e-5
MA0025.1	MA0025.1	0.147
MA0027.1	MA0027.1	0.24
MA0028.1	MA0028.1	0.552
MA0029.1	MA0029.1	0.925
MA0030.1	MA0030.1	0.18
MA0031.1	MA0031.1	0.0311
MA0035.2	MA0035.2	5.06239e-4
MA0038.1	MA0038.1	0.0168
MA0039.2	MA0039.2	0.00984
MA0040.1	MA0040.1	0.0287
MA0041.1	MA0041.1	0.367
MA0042.1	MA0042.1	0.46
MA0043.1	MA0043.1	0.0264
MA0046.1	MA0046.1	4.89279e-10
MA0047.2	MA0047.2	0.013
MA0048.1	MA0048.1	0.203
MA0050.1	MA0050.1	2.75692e-5
MA0051.1	MA0051.1	4.86594e-4
MA0052.1	MA0052.1	0.392
MA0055.1	MA0055.1	0.219
MA0057.1	MA0057.1	0.0873
MA0058.1	MA0058.1	0.767
MA0059.1	MA0059.1	0.842
MA0060.1	MA0060.1	4.66429e-14
MA0061.1	MA0061.1	0.178
MA0062.2	MA0062.2	0.903
MA0065.2	MA0065.2	3.28993e-4
MA0066.1	MA0066.1	0.146
MA0067.1	MA0067.1	0.509
MA0068.1	MA0068.1	0.63
MA0069.1	MA0069.1	0.737
MA0070.1	MA0070.1	0.935
MA0071.1	MA0071.1	0.038
MA0072.1	MA0072.1	0.0467
MA0073.1	MA0073.1	0.554
MA0074.1	MA0074.1	0.66
MA0076.1	MA0076.1	0.354
MA0077.1	MA0077.1	0.07
MA0078.1	MA0078.1	0.898
MA0079.2	MA0079.2	0.714
MA0080.2	MA0080.2	3.99336e-10
MA0081.1	MA0081.1	0.307
MA0083.1	MA0083.1	0.843
MA0084.1	MA0084.1	0.255
MA0087.1	MA0087.1	0.879
MA0088.1	MA0088.1	0.4
MA0090.1	MA0090.1	0.944
MA0091.1	MA0091.1	0.657
MA0092.1	MA0092.1	0.611
MA0093.1	MA0093.1	0.809
MA0099.2	MA0099.2	4.28602e-5
MA0100.1	MA0100.1	0.477
MA0101.1	MA0101.1	0.533
MA0102.2	MA0102.2	0.622
MA0103.1	MA0103.1	0.00378
MA0104.2	MA0104.2	0.585
MA0105.1	MA0105.1	0.05
MA0106.1	MA0106.1	0.203
MA0107.1	MA0107.1	0.346
MA0108.2	MA0108.2	0.905
MA0111.1	MA0111.1	0.329
MA0112.2	MA0112.2	5.14603e-6
MA0113.1	MA0113.1	0.269
MA0114.1	MA0114.1	0.0012
MA0115.1	MA0115.1	0.174
MA0116.1	MA0116.1	0.00279
MA0117.1	MA0117.1	0.239
MA0119.1	MA0119.1	0.0163
MA0122.1	MA0122.1	0.932
MA0124.1	MA0124.1	0.441
MA0125.1	MA0125.1	0.244
MA0131.1	MA0131.1	0.225
MA0135.1	MA0135.1	0.821
MA0136.1	MA0136.1	3.35915e-5
MA0137.2	MA0137.2	0.328
MA0138.2	MA0138.2	2.27713e-5
MA0139.1	MA0139.1	0.0342
MA0140.1	MA0140.1	0.0175
MA0141.1	MA0141.1	0.00109
MA0142.1	MA0142.1	0.903
MA0143.1	MA0143.1	0.0181
MA0144.1	MA0144.1	0.177
MA0145.1	MA0145.1	0.0265
MA0146.1	MA0146.1	0.371
MA0147.1	MA0147.1	0.716
MA0148.1	MA0148.1	4.36245e-4
MA0149.1	MA0149.1	0.00508
MA0150.1	MA0150.1	0.00185
MA0152.1	MA0152.1	0.108
MA0153.1	MA0153.1	9.16701e-11
MA0154.1	MA0154.1	0.00171
MA0155.1	MA0155.1	0.838
MA0156.1	MA0156.1	0.0357
MA0157.1	MA0157.1	0.126
MA0159.1	MA0159.1	0.00145
MA0160.1	MA0160.1	0.0142
MA0162.1	MA0162.1	0.335
MA0163.1	MA0163.1	0.0079
MA0164.1	MA0164.1	0.831
MA0258.1	MA0258.1	9.11974e-4
MA0259.1	MA0259.1	0.65

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: CNhs10600

Novel motif	Logo	P-value
1	1	0.0577
10	10	0.38
100	100	0.798
101	101	0.614
102	102	0.465
103	103	0.0369
104	104	0.942
105	105	0.292
106	106	0.008
107	107	0.115
108	108	0.736
109	109	0.0692
11	11	0.102
110	110	0.225
111	111	0.0364
112	112	0.0382
113	113	0.7
114	114	0.0128
115	115	0.337
116	116	0.458
117	117	0.305
118	118	0.842
119	119	0.0372
12	12	0.786
120	120	0.356
121	121	0.856
122	122	0.896
123	123	0.0554
124	124	0.143
125	125	0.784
126	126	0.405
127	127	0.113
128	128	0.0411
129	129	0.14
13	13	0.452
130	130	0.569
131	131	0.295
132	132	0.36
133	133	0.267
134	134	0.751
135	135	0.395
136	136	0.919
137	137	0.555
138	138	0.746
139	139	0.0076
14	14	0.36
140	140	0.0451
141	141	0.325
142	142	0.893
143	143	0.239
144	144	0.763
145	145	0.207
146	146	0.539
147	147	0.467
148	148	0.271
149	149	0.195
15	15	0.0729
150	150	0.529
151	151	0.0876
152	152	0.0817
153	153	0.114
154	154	0.973
155	155	0.801
156	156	0.612
157	157	0.793
158	158	0.771
159	159	0.933
160	160	0.69
161	161	0.386
162	162	0.825
163	163	0.081
164	164	0.161
165	165	0.205
166	166	0.309
167	167	0.871
168	168	0.359
169	169	0.00699
17	17	0.0543
18	18	0.278
19	19	0.137
2	2	0.712
20	20	0.718
21	21	0.893
22	22	0.273
23	23	0.113
24	24	0.595
25	25	0.46
26	26	0.34
27	27	0.373
28	28	0.354
29	29	0.373
3	3	0.166
30	30	0.777
31	31	0.324
32	32	0.174
33	33	0.651
34	34	0.632
35	35	0.317
36	36	0.119
37	37	0.0825
38	38	0.306
39	39	0.71
4	4	0.518
40	40	0.183
41	41	0.38
42	42	0.491
43	43	0.141
44	44	0.0051
45	45	0.533
46	46	0.307
47	47	0.0849
48	48	0.0991
49	49	0.124
5	5	0.142
50	50	0.991
51	51	0.528
52	52	0.272
53	53	0.506
54	54	0.382
55	55	0.35
56	56	0.314
57	57	0.502
58	58	0.274
59	59	0.0474
6	6	0.574
60	60	0.124
61	61	0.731
62	62	0.0732
63	63	0.128
64	64	0.35
65	65	0.1
66	66	0.559
67	67	0.996
68	68	0.0427
69	69	0.297
7	7	0.303
70	70	3.09702e-4
71	71	0.196
72	72	0.358
73	73	0.116
74	74	0.315
75	75	0.11
76	76	0.708
77	77	0.121
78	78	0.418
79	79	0.155
8	8	0.146
80	80	0.0997
81	81	0.322
82	82	0.0871
83	83	0.484
84	84	0.778
85	85	0.0204
86	86	0.66
87	87	0.126
88	88	0.781
89	89	0.131
9	9	0.577
90	90	0.11
91	91	0.397
92	92	0.0732
93	93	0.326
94	94	0.757
95	95	0.0943
96	96	0.187
97	97	0.969
98	98	0.22
99	99	0.52

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: CNhs10600

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011322 mouse forelimb- 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)
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)
0000295 (mouse embryonic day 12 sample)
0011322 (mouse forelimb- 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: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
-|ancestors_in_anatomy_facet=UBERON:0000026,UBERON:0000061,UBERON:0000153,UBERON:0000465,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002101,UBERON:0002102,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0004120,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004710,UBERON:0005423,UBERON:0005732,UBERON:0005733
+|DRA_sample_Accession=CAGE@SAMD00005383
+|accession_numbers=CAGE;DRX008964;DRR009838;DRZ001263;DRZ002646;DRZ012613;DRZ013996
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000295,FF:0011322
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:140739014..140739032,-!p1@Lhx9!2.21!201.21!Lhx9;;chr12:34642510..34642530,+!p1@Twist1!2.03!325.26!Twist1;;chr1:165243591..165243625,-!p2@Prrx1!2.03!160.36!Prrx1;;chr6:52190467..52190500,-!p1@Hoxa10!1.97!92.28!Hoxa10;;chr2:74513125..74513143,+!p1@Hoxd12!1.95!89.07!Hoxd12;;chr8:59799772..59799789,+!p1@Hand2!1.84!189.11!Hand2;;chr3:99057269..99057306,+!p1@Tbx15!1.84!81.69!Tbx15;;chr3:66785857..66785873,-!p1@Shox2!1.76!56.16!Shox2;;chr10:119914001..119914078,-!p4@Hmga2!1.70!66.57!Hmga2;;chr6:52184901..52184959,-!p2@Hoxa10!1.69!48.22!Hoxa10;;chr13:53568104..53568156,-!p1@Msx2!1.65!63.16!Msx2;;chr12:37835120..37835133,+!p2@Meox2!1.65!61.27!Meox2;;chr10:119913546..119913583,-!p3@Hmga2!1.62!82.07!Hmga2;;chr10:119913278..119913298,-!p2@Hmga2!1.60!84.53!Hmga2;;chr12:3891810..3891829,+!p2@Dnmt3a!1.58!56.54!Dnmt3a;;chr6:52176164..52176195,-!p1@Hoxa9!1.58!45.76!Hoxa9;;chr5:38215819..38215823,-!p1@Msx1!1.56!89.64!Msx1;;chr2:74520048..74520064,+!p1@Hoxd11!1.54!33.28!Hoxd11;;chr6:52210774..52210787,-!p1@Hoxa13!1.52!32.15!Hoxa13;;chr12:74147689..74147711,-!p1@Six1!1.50!65.43!Six1;;chr9:87626083..87626108,-!p1@Tbx18!1.48!62.22!Tbx18;;chr10:119913310..119913366,-!p1@Hmga2!1.46!211.42!Hmga2;;chr12:37835141..37835194,+!p1@Meox2!1.44!80.18!Meox2;;chr1:165243379..165243402,-!p3@Prrx1!1.43!38.20!Prrx1;;chr7:53631837..53631850,+!p1@Myod1!1.42!25.34!Myod1;;chr12:28027561..28027591,-!p1@Sox11!1.38!146.75!Sox11;;chr2:38206744..38206766,+!p1@Lhx2!1.38!27.99!Lhx2;;chr17:86087592..86087615,-!p1@Six2!1.38!22.88!Six2;;chr6:52195795..52195825,-!p1@Hoxa11!1.37!22.69!Hoxa11;;chr6:52195763..52195792,-!p2@Hoxa11!1.37!22.31!Hoxa11;;chr2:38206580..38206600,+!p2@Lhx2!1.36!27.23!Lhx2;;chr6:52163319..52163342,-!p1@Hoxa3!1.30!27.23!Hoxa3;;chr1:165243653..165243664,-!p4@Prrx1!1.30!26.47!Prrx1;;chr1:136186574..136186592,+!p1@Myog!1.27!17.59!Myog;;chr6:52190668..52190682,-!p3@Hoxa10!1.25!16.83!Hoxa10;;chr12:57796615..57796687,+!p1@Pax9!1.24!16.26!Pax9;;chr15:102087737..102087801,-!p3@Rarg!1.22!25.34!Rarg;;chr13:40829137..40829205,-!p1@Tfap2a!1.22!17.40!Tfap2a;;chr7:144506077..144506128,-!p1@Ebf3!1.21!34.80!Ebf3;;chr3:5218516..5218544,+!p2@Zfhx4!1.20!21.94!Zfhx4;;chr5:120285144..120285160,+!p1@Tbx5!1.20!14.94!Tbx5;;chr6:52190858..52190873,-!p4@Hoxa10!1.20!14.75!Hoxa10;;chr9:71743854..71743909,-!p1@Tcf12!1.18!111.38!Tcf12;;chr7:144505957..144505972,-!p2@Ebf3!1.17!17.21!Ebf3;;chr3:99057256..99057268,+!p3@Tbx15!1.17!13.80!Tbx15;;chr2:30700788..30700824,+!p2@Prrx2!1.16!20.42!Prrx2;;chrX:55283799..55283813,+!p1@Zic3!1.16!13.43!Zic3;;chr2:65683890..65683907,+!p1@Csrnp3!1.15!25.15!Csrnp3;;chr13:55932591..55932622,-!p1@Pitx1!1.14!15.32!Pitx1;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!1.13!21.75!Zfhx3;;chr12:3891753..3891801,+!p4@Dnmt3a!1.13!20.23!Dnmt3a;;chr3:30408674..30408716,-!p2@Mecom!1.12!20.05!Mecom;;chr6:6832076..6832092,-!p1@Dlx5!1.12!14.18!Dlx5;;chr2:74520343..74520383,+!p4@Hoxd11!1.12!12.10!Hoxd11;;chr4:154010409..154010466,-!p2@Prdm16!1.11!27.80!Prdm16;;chr11:101755669..101755686,-!p1@Meox1!1.11!21.37!Meox1;;chr10:119913792..119913820,-!p5@Hmga2!1.11!20.42!Hmga2;;chr13:15555670..15555771,+!p2@Gli3!1.10!29.50!Gli3;;chr7:123182248..123182264,-!p3@Sox6!1.10!13.80!Sox6;;chr9:87625971..87625992,-!p2@Tbx18!1.10!11.54!Tbx18;;chr12:37835248..37835260,+!p4@Meox2!1.09!11.35!Meox2;;chr8:111227518..111227550,+!p@chr8:111227518..111227550,+!1.07!18.72!Zfhx3;;chr1:19199236..19199258,+!p1@Tfap2b!1.07!10.78!Tfap2b;;chr1:165243638..165243649,-!p5@Prrx1!1.05!12.48!Prrx1;;chr2:74529970..74529997,+!p1@Hoxd10!1.05!10.21!Hoxd10;;chr2:33496386..33496410,-!p1@Lmx1b!1.04!10.02!Lmx1b;;chr6:14851440..14851497,+!p2@Foxp2!1.03!24.21!Foxp2;;chr14:56443806..56443848,+!p1@Nfatc4!1.03!20.05!Nfatc4;;chr14:67853457..67853482,+!p2@Ebf2!1.03!13.80!Ebf2;;chr1:165243792..165243808,-!p1@Prrx1!1.02!33.47!Prrx1;;chr18:7004715..7004731,-!p1@Mkx!1.02!22.88!Mkx;;chr2:30700857..30700873,+!p3@Prrx2!1.02!13.24!Prrx2;;chr8:111227354..111227401,+!p@chr8:111227354..111227401,+!1.02!12.86!Zfhx3;;chr3:66785511..66785534,-!p5@Shox2!1.02!9.46!Shox2;;chr4:154010918..154010931,-!p1@Prdm16!1.01!27.80!Prdm16;;chr3:29912271..29912291,-!p16@Mecom!1.01!9.27!Mecom;;chr2:74513064..74513089,+!p2@Hoxd12!1.01!9.27!Hoxd12;;chr12:9581262..9581282,+!p1@Osr1!1.00!111.19!Osr1;;chr15:76287876..76287894,+!p1@Scx!1.00!50.49!Scx;;chr3:5218629..5218684,+!p1@Zfhx4!1.00!30.07!Zfhx4;;chr2:30700881..30700916,+!p1@Prrx2!1.00!17.40!Prrx2;;chr16:25801993..25802014,+!p1@Trp63!1.00!9.08!Trp63;;chr11:85699862..85699920,+!p1@Tbx4!1.00!9.08!Tbx4;;chr1:136186545..136186554,+!p2@Myog!0.99!8.70!Myog;;chr6:52184880..52184893,-!p6@Hoxa10!0.99!8.70!Hoxa10;;chr13:72101178..72101203,-!p1@Irx1!0.98!13.43!Irx1;;chr11:44430877..44430899,+!p6@Ebf1!0.98!10.97!Ebf1;;chr6:52210816..52210831,-!p2@Hoxa13!0.98!8.51!Hoxa13;;chr11:112643496..112643562,+!p1@Sox9!0.97!317.32!Sox9;;chr18:80909801..80909819,-!p1@Nfatc1!0.97!50.87!Nfatc1;;chr1:93698030..93698064,+!p1@Twist2!0.96!16.83!Twist2;;chr8:90483433..90483457,-!p2@Zfp423!0.96!11.16!Zfp423;;chr6:6831950..6831985,-!p2@Dlx5!0.96!9.08!Dlx5;;chr1:140739042..140739054,-!p2@Lhx9!0.95!7.94!Lhx9;;chr1:38684260..38684312,-!p2@Aff3!0.94!55.60!Aff3;;chr13:15555555..15555574,+!p5@Gli3!0.94!10.40!Gli3;;chr1:120949949..120950000,-!p1@Gli2!0.93!33.85!Gli2;;chr3:30408603..30408668,-!p1@Mecom!0.93!17.78!Mecom;;chr8:111227455..111227464,+!p@chr8:111227455..111227464,+!0.93!9.46!Zfhx3;;chr7:52471143..52471186,+!p1@Tead2!0.92!81.50!Tead2;;chr13:15555496..15555544,+!p1@Gli3!0.92!26.29!Gli3;;chr15:50720601..50720630,-!p2@Trps1!0.92!18.15!Trps1;;chr4:84320893..84320910,-!p1@Bnc2!0.92!16.83!Bnc2;;chr4:135129538..135129558,-!p1@Grhl3!0.92!11.35!Grhl3;;chr6:144157924..144157955,-!p2@Sox5!0.92!9.27!Sox5;;chr6:6831928..6831949,-!p3@Dlx5!0.92!7.38!Dlx5;;chr14:98568971..98569025,-!p1@Dach1!0.91!57.87!Dach1;;chr13:83643159..83643226,+!p3@Mef2c!0.91!7.19!Mef2c;;chr10:119913954..119913972,-!p8@Hmga2!0.91!7.19!Hmga2;;chr10:119913974..119913992,-!p9@Hmga2!0.90!7.00!Hmga2;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.89!18.91!Zfhx3;;chr18:14131045..14131062,-!p3@Zfp521!0.89!10.97!Zfp521;;chr19:25746898..25746910,+!p1@Dmrt2!0.89!10.21!Dmrt2;;chr15:50721942..50721987,-!p13@Trps1!0.89!7.94!Trps1;;chr6:52176144..52176161,-!p2@Hoxa9!0.89!6.81!Hoxa9;;chr18:69504195..69504213,+!p4@Tcf4!0.88!31.77!Tcf4;;chr3:130813200..130813252,+!p1@Lef1!0.88!31.01!Lef1;;chr14:67853425..67853454,+!p1@Ebf2!0.88!9.46!Ebf2;;chr4:154011072..154011095,-!p6@Prdm16!0.88!7.94!Prdm16;;chr3:99044284..99044308,+!p4@Tbx15!0.88!6.62!Tbx15;;chr1:19202352..19202354,+!p2@Tfap2b!0.88!6.62!Tfap2b;;chr14:122874619..122874634,+!p1@Zic2!0.88!6.62!Zic2;;chr1:120950197..120950215,-!p5@Gli2!0.87!8.89!Gli2;;chr7:144505980..144506010,-!p3@Ebf3!0.87!7.94!Ebf3;;chr13:53568191..53568219,-!p2@Msx2!0.87!6.43!Msx2;;chr16:95808192..95808202,-!p2@Erg!0.87!6.43!Erg;;chr10:12810631..12810649,+!p1@Plagl1!0.86!174.17!Plagl1;;chr11:44430812..44430838,+!p1@Ebf1!0.86!64.86!Ebf1;;chrX:45245679..45245702,-!p1@Smarca1!0.86!29.50!Smarca1;;chr15:35225845..35225867,+!p1@Osr2!0.86!16.26!Osr2;;chr13:72101161..72101177,-!p2@Irx1!0.86!8.89!Irx1;;chr2:74506264..74506286,+!p1@Hoxd13!0.86!6.24!Hoxd13;;chr2:167363692..167363710,+!p1@Snai1!0.85!78.29!Snai1;;chr14:56443698..56443726,+!p2@Nfatc4!0.85!11.91!Nfatc4;;chr4:13712168..13712218,+!p4@Runx1t1!0.85!10.40!Runx1t1;;chr2:71384802..71384815,-!p1@Dlx2!0.85!7.56!Dlx2;;chr19:59533595..59533628,+!p6@Emx2!0.85!6.05!Emx2;;chr6:52195747..52195762,-!p3@Hoxa11!0.85!6.05!Hoxa11;;chr5:120285161..120285176,+!p2@Tbx5!0.85!6.05!Tbx5;;chr17:48061584..48061601,-!p2@Foxp4!0.84!40.66!Foxp4;;chr11:99092233..99092273,-!p2@Smarce1!0.84!30.07!Smarce1;;chr16:14705961..14705978,+!p2@Snai2!0.84!29.31!Snai2;;chr10:126778916..126778974,-!p1@Gli1!0.84!13.80!Gli1;;chr11:94981424..94981439,+!p1@Dlx3!0.84!6.81!Dlx3;;chr10:106923133..106923146,-!p1@Myf5!0.84!5.86!Myf5;;chr11:23978022..23978076,+!p1@Bcl11a!0.83!134.27!Bcl11a;;chr14:98568761..98568814,-!p2@Dach1!0.83!41.79!Dach1;;chrX:98449898..98449913,+!p2@Foxo4!0.83!19.86!Foxo4;;chr11:44430989..44431015,+!p4@Ebf1!0.83!10.59!Ebf1;;chr4:13712228..13712267,+!p3@Runx1t1!0.83!10.40!Runx1t1;;chr12:37835203..37835218,+!p3@Meox2!0.83!7.00!Meox2;;chr17:44951553..44951586,-!p2@Runx2!0.83!6.43!Runx2;;chr4:154010940..154010962,-!p3@Prdm16!0.82!13.05!Prdm16;;chr19:59533221..59533271,+!p1@Emx2!0.82!7.00!Emx2;;chr15:102828658..102828678,+!p1@Hoxc6!0.82!5.67!Hoxc6;;chr14:56443742..56443756,+!p6@Nfatc4!0.82!5.67!Nfatc4;;chr11:23977965..23977974,+!p11@Bcl11a!0.82!5.67!Bcl11a;;chr7:53631818..53631829,+!p2@Myod1!0.82!5.67!Myod1;;chr7:123182318..123182332,-!p11@Sox6!0.82!5.67!Sox6;;chr18:84256138..84256150,-!p7@Tshz1!0.82!5.67!Tshz1;;chr13:15555035..15555073,+!p4@Gli3!0.81!15.51!Gli3;;chr13:15555428..15555440,+!p7@Gli3!0.81!6.43!Gli3;;chr13:53568081..53568094,-!p3@Msx2!0.81!5.48!Msx2;;chr3:107398056..107398082,+!p1@Alx3!0.81!5.48!Alx3;;chr16:14705925..14705951,+!p1@Snai2!0.80!40.47!Snai2;;chr19:7342725..7342784,+!p1@Rcor2!0.80!23.26!Rcor2;;chr11:23978111..23978134,+!p3@Bcl11a!0.80!11.72!Bcl11a;;chr10:119913839..119913869,-!p7@Hmga2!0.80!6.81!Hmga2;;chr12:105711446..105711464,-!p1@Gsc!0.80!5.29!Gsc;;chr2:30700830..30700843,+!p4@Prrx2!0.80!5.29!Prrx2;;chr2:74499300..74499309,-!p@chr2:74499300..74499309,-!0.80!5.29!Evx2;;chr5:120285130..120285141,+!p3@Tbx5!0.80!5.29!Tbx5;;chr18:69505797..69505852,+!p2@Tcf4!0.79!66.00!Tcf4;;chr7:6649134..6649167,-!p1@Zim1!0.79!30.26!Zim1;;chr3:5218546..5218561,+!p4@Zfhx4!0.79!8.32!Zfhx4;;chr1:165243272..165243283,-!p6@Prrx1!0.79!6.43!Prrx1;;chr13:31898767..31898785,+!p4@Foxc1!0.79!6.43!Foxc1;;chr2:74517742..74517758,+!p2@Hoxd11!0.79!5.11!Hoxd11;;chr1:19199221..19199234,+!p6@Tfap2b!0.79!5.11!Tfap2b;;chr1:169528823..169528860,+!p5@Rxrg!0.79!5.11!Rxrg;;chr6:72739185..72739232,-!p1@Tcf7l1!0.78!56.54!Tcf7l1;;chr18:69504157..69504184,+!p3@Tcf4!0.78!34.04!Tcf4;;chr12:34642682..34642753,+!p2@Twist1!0.78!14.18!Twist1;;chr13:22036953..22037009,+!p1@Zfp184!0.78!14.18!Zfp184;;chr13:72766250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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0005417,UBERON:0005733,UBERON:0005732,UBERON:0005729,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:359-14H2
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011322
+|is_a=EFO:0002091;;FF:0011322
+|is_obsolete=
+|library_id=CNhs10600
+|library_id_phase_based=2:CNhs10600
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;359
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;359
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E12.CNhs10600.359-14H2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E12.CNhs10600.359-14H2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E12.CNhs10600.359-14H2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E12.CNhs10600.359-14H2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/forelimb%252c%2520embryo%2520E12.CNhs10600.359-14H2.mm9.nobarcode.rdna.fa.gz
 |name=forelimb, embryo E12
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10600,LSID654,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.082287568726025,0,0,0,0,0.0482429709156081,0.170679547437887,0,0,0,0,0.643969067707464,0,0,0,0,0,0,0.137430576377934,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0663545255643774,0,0,0,0,0,0.0575110062497738,0.0710493375317471,0.112709245581563,0.393856339726259,0.373969742043964,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0.538872590703816,0,0,0,-0.0428469550828748,0,0,0,0,0,0.112523642024868,0.121027409640128,-0.0828704430081453,-0.00113174879782779,0,0,0.0436268660171595,0,0,0,0.0748788621623314,0.0839450447436028,-0.033921351606117,-0.00361099507697024,0,0,0,0,0,0,-0.131529267619585,-0.358292995966912,-0.200144963485248,0,0,0,0,0
 |rna_box=14
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=forelimb
 |top_motifs=ZNF384:1.995379037;ZNF143:1.95797029733;NFY{A,B,C}:1.91337864104;SOX2:1.75352535626;GFI1:1.7214458372;SOX5:1.71916511406;ZNF238:1.68921804276;NANOG{mouse}:1.61837266309;LEF1_TCF7_TCF7L1,2:1.51461632693;MZF1:1.43263651231;PDX1:1.3963389508;NKX2-1,4:1.37596830743;RREB1:1.37488145118;TFDP1:1.3482003417;NRF1:1.26246540658;E2F1..5:1.25965114848;PAX6:1.16581468798;MYBL2:1.14692007316;PATZ1:1.14279802752;GFI1B:1.10069588918;SOX17:1.07900152946;TOPORS:1.07853214466;CDX1,2,4:0.96127251752;BREu{core}:0.949082300429;MAZ:0.940665562447;GATA4:0.937384605598;FOXP3:0.933633708622;SOX{8,9,10}:0.893098154983;HMX1:0.881247454206;HMGA1,2:0.874286152608;STAT5{A,B}:0.870600062847;FOXD3:0.845046477457;HIC1:0.827708229825;CDC5L:0.824624077437;EN1,2:0.819777055925;PITX1..3:0.80025163842;VSX1,2:0.753797639433;RXR{A,B,G}:0.74956699392;HBP1_HMGB_SSRP1_UBTF:0.747977990258;PAX8:0.738916914641;PAX1,9:0.725467390787;NKX2-3_NKX2-5:0.719416299562;FOX{I1,J2}:0.702202243421;ZBTB16:0.661831099747;MED-1{core}:0.657246134822;GTF2I:0.645906803067;HES1:0.642172716404;GTF2A1,2:0.634319619734;KLF4:0.629848719059;PRRX1,2:0.607914147752;NKX3-1:0.590695161922;TEAD1:0.590679658162;CUX2:0.589470231541;RBPJ:0.557451083777;NANOG:0.539303031076;NR6A1:0.52857919454;IKZF2:0.525762167939;MTE{core}:0.518995412109;AIRE:0.515692102936;PRDM1:0.504875965397;HSF1,2:0.500460926937;TFAP2{A,C}:0.488046963719;IKZF1:0.479519449146;FOXP1:0.466651881508;LHX3,4:0.464397425124;NKX6-1,2:0.453363500582;STAT1,3:0.451752616326;ELK1,4_GABP{A,B1}:0.438510004237;EP300:0.436024195516;ZFP161:0.432515099985;HIF1A:0.399979048412;XCPE1{core}:0.395920833397;ATF2:0.395355911188;EGR1..3:0.38769886298;DBP:0.375579517225;NHLH1,2:0.336990374879;PAX5:0.329821275754;UFEwm:0.326395358696;HOXA9_MEIS1:0.316691244202;DMAP1_NCOR{1,2}_SMARC:0.314084583582;ONECUT1,2:0.304302706455;TFAP2B:0.287130526398;TGIF1:0.283515129747;BPTF:0.262267922648;MYB:0.244511185787;YY1:0.24443284052;PBX1:0.238997657244;AHR_ARNT_ARNT2:0.203634905534;POU1F1:0.186255574139;NFATC1..3:0.120135257965;ATF6:0.116534728953;RFX2..5_RFXANK_RFXAP:0.112458824558;POU2F1..3:0.106976564843;T:0.104915628307;FOXL1:0.0902368979223;ATF4:0.0838079467377;ALX4:0.0755238559481;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0690396270352;POU3F1..4:0.0663788823436;RFX1:0.0534579491371;TEF:0.0315156735959;POU5F1:0.0198933347546;GCM1,2:0.0153867959655;TFCP2:0.0153212606022;MEF2{A,B,C,D}:-0.00976160909684;RORA:-0.0297054035604;SPZ1:-0.0300113344734;SRF:-0.0437564062177;CRX:-0.0468187758002;GZF1:-0.0472938993545;TFAP4:-0.0640207309131;CREB1:-0.0847106040875;SP1:-0.0956917333947;ELF1,2,4:-0.100516957415;ADNP_IRX_SIX_ZHX:-0.102955914856;MTF1:-0.115283816093;TBX4,5:-0.120175206906;GLI1..3:-0.135883023579;ZBTB6:-0.153730456287;TAL1_TCF{3,4,12}:-0.162822553618;ESR1:-0.180360191776;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.188037399469;ALX1:-0.21400787324;REST:-0.224552646338;SPIB:-0.232165313092;RUNX1..3:-0.24505471924;SPI1:-0.304859418667;TLX1..3_NFIC{dimer}:-0.320527097882;HOX{A4,D4}:-0.321017305951;FOXO1,3,4:-0.323584938491;EVI1:-0.325694715782;MYFfamily:-0.331358240305;NR3C1:-0.333305379915;TBP:-0.339349070955;ZIC1..3:-0.350060137917;SREBF1,2:-0.353979813116;FOXA2:-0.357086760764;OCT4_SOX2{dimer}:-0.358762095756;FOSL2:-0.366905483354;PAX4:-0.381824478014;HNF4A_NR2F1,2:-0.384674812247;HNF1A:-0.40598594878;JUN:-0.410309732131;TLX2:-0.414570429104;ATF5_CREB3:-0.430992426604;PAX2:-0.454965487322;NFKB1_REL_RELA:-0.455190605346;bHLH_family:-0.465652212205;NKX3-2:-0.471116043686;TP53:-0.484762305023;FOXN1:-0.528972488582;POU6F1:-0.540230851315;ZNF423:-0.555005566798;MAFB:-0.567982854369;HAND1,2:-0.571012935845;ETS1,2:-0.577645533852;SMAD1..7,9:-0.598008564458;GATA6:-0.604293518029;NFE2L1:-0.608781441836;HOX{A5,B5}:-0.610267141502;HLF:-0.616733091936;SNAI1..3:-0.626288366025;IRF7:-0.629174445957;NFIX:-0.630401321375;ZNF148:-0.653200757348;FOXQ1:-0.669048205789;MYOD1:-0.684389835352;RXRA_VDR{dimer}:-0.711556114903;FOS_FOS{B,L1}_JUN{B,D}:-0.772712590906;FOX{D1,D2}:-0.78275770876;NFIL3:-0.832368600004;ESRRA:-0.8649276824;FOX{F1,F2,J1}:-0.892945352519;ZEB1:-0.901653508793;IRF1,2:-0.938060855679;ARID5B:-0.956136197032;AR:-1.00529253317;BACH2:-1.0103515281;NR1H4:-1.02927390184;PPARG:-1.11093617247;NKX2-2,8:-1.12147442735;NR5A1,2:-1.22840931949;FOXM1:-1.24345107514;EBF1:-1.29180401788;LMO2:-1.378607571;NFE2L2:-1.38248430703;STAT2,4,6:-1.48628637246;NFE2:-1.48800814072;CEBPA,B_DDIT3:-1.60184995248
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:359-14H2;search_select_hide=table117:359-14H2
 }}

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FF:359-14H2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:11, 4 June 2020

CNhs10600

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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