FF:11299-117B3: Difference between revisions

Latest revision as of 16:31, 3 June 2020

Name:	Mouse Aortic Smooth Muscle cells, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs11297
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	Balb/c
tissue	aorta
dev stage	NA
sex	unknown
age	U
cell type	smooth muscle cell
cell line	NA
company	Cell Applications
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	N/A
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004682

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11297		CAGE		DRX008805		DRR009677

Accession ID Mm9

Library id		BAM		CTSS
CNhs11297		DRZ001102		DRZ002487

Accession ID Mm10

Library id		BAM		CTSS
CNhs11297		DRZ012452		DRZ013837

Download raw sequence, BAM & CTSS

Mm9

Fasta	BAM	CTSS
download	download	donwload

Mm10

BAM	CTSS
download	donwload

RNA-Seq Accession numbers

Method		Sample accession id
sRNA-Seq		SAMD00004682

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
SRhi10002.CGATGT		sRNA-Seq		DRX037375		DRR041741

Accession ID Mm9

Library id		BAM		CTSS
SRhi10002.CGATGT		DRZ007350

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

CNhs11297

0	0
1	0
10	0
100	0
1000	0.00112
1001	0.0559
1002	0.633
1003	0.0979
1004	0
1005	0
1006	-0.214
1007	-0.00561
1008	0
1009	0.702
101	0.0513
1010	0
1011	-0.264
1012	0
1013	0.252
1014	-0.0851
1015	0.0802
1016	0.153
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	-0.0761
1023	0
1024	-0.117
1025	0
1026	0
1027	-0.048
1028	0.634
1029	0.0199
103	0.266
1030	0
1031	0.377
1032	0.0402
1033	0.0606
1034	0
1035	0
1036	0.0563
1037	0
1038	0.0889
1039	-0.0737
104	0
1040	0.585
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: CNhs11297

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.555
MA0003.1	MA0003.1	0.685
MA0004.1	MA0004.1	0.00299
MA0006.1	MA0006.1	0.786
MA0007.1	MA0007.1	0.354
MA0009.1	MA0009.1	0.0513
MA0014.1	MA0014.1	0.0512
MA0017.1	MA0017.1	0.00277
MA0018.2	MA0018.2	0.898
MA0019.1	MA0019.1	0.707
MA0024.1	MA0024.1	0.0262
MA0025.1	MA0025.1	0.0549
MA0027.1	MA0027.1	0.138
MA0028.1	MA0028.1	9.8713e-5
MA0029.1	MA0029.1	0.699
MA0030.1	MA0030.1	0.608
MA0031.1	MA0031.1	0.281
MA0035.2	MA0035.2	1.47799e-5
MA0038.1	MA0038.1	0.0438
MA0039.2	MA0039.2	0.67
MA0040.1	MA0040.1	0.209
MA0041.1	MA0041.1	0.354
MA0042.1	MA0042.1	0.405
MA0043.1	MA0043.1	0.746
MA0046.1	MA0046.1	2.99033e-9
MA0047.2	MA0047.2	0.00195
MA0048.1	MA0048.1	4.10366e-4
MA0050.1	MA0050.1	0.393
MA0051.1	MA0051.1	0.698
MA0052.1	MA0052.1	0.00468
MA0055.1	MA0055.1	1.16674e-4
MA0057.1	MA0057.1	0.546
MA0058.1	MA0058.1	1.02113e-5
MA0059.1	MA0059.1	0.0771
MA0060.1	MA0060.1	5.02851e-7
MA0061.1	MA0061.1	0.515
MA0062.2	MA0062.2	8.7272e-5
MA0065.2	MA0065.2	0.0211
MA0066.1	MA0066.1	0.587
MA0067.1	MA0067.1	0.522
MA0068.1	MA0068.1	0.0211
MA0069.1	MA0069.1	0.841
MA0070.1	MA0070.1	0.878
MA0071.1	MA0071.1	0.642
MA0072.1	MA0072.1	0.921
MA0073.1	MA0073.1	0.594
MA0074.1	MA0074.1	0.822
MA0076.1	MA0076.1	4.85851e-4
MA0077.1	MA0077.1	0.283
MA0078.1	MA0078.1	0.852
MA0079.2	MA0079.2	0.114
MA0080.2	MA0080.2	8.2785e-4
MA0081.1	MA0081.1	0.506
MA0083.1	MA0083.1	0.0164
MA0084.1	MA0084.1	0.611
MA0087.1	MA0087.1	0.561
MA0088.1	MA0088.1	0.0847
MA0090.1	MA0090.1	0.0244
MA0091.1	MA0091.1	0.586
MA0092.1	MA0092.1	0.416
MA0093.1	MA0093.1	0.00206
MA0099.2	MA0099.2	4.19667e-7
MA0100.1	MA0100.1	0.273
MA0101.1	MA0101.1	0.136
MA0102.2	MA0102.2	0.454
MA0103.1	MA0103.1	2.9454e-7
MA0104.2	MA0104.2	0.415
MA0105.1	MA0105.1	0.647
MA0106.1	MA0106.1	1.6617e-5
MA0107.1	MA0107.1	0.336
MA0108.2	MA0108.2	1.33902e-5
MA0111.1	MA0111.1	0.314
MA0112.2	MA0112.2	0.34
MA0113.1	MA0113.1	0.748
MA0114.1	MA0114.1	0.00127
MA0115.1	MA0115.1	0.321
MA0116.1	MA0116.1	0.835
MA0117.1	MA0117.1	0.411
MA0119.1	MA0119.1	0.996
MA0122.1	MA0122.1	0.705
MA0124.1	MA0124.1	0.602
MA0125.1	MA0125.1	0.129
MA0131.1	MA0131.1	0.473
MA0135.1	MA0135.1	0.0355
MA0136.1	MA0136.1	0.241
MA0137.2	MA0137.2	0.00516
MA0138.2	MA0138.2	2.13263e-4
MA0139.1	MA0139.1	0.813
MA0140.1	MA0140.1	8.22728e-4
MA0141.1	MA0141.1	0.429
MA0142.1	MA0142.1	0.0208
MA0143.1	MA0143.1	0.986
MA0144.1	MA0144.1	0.0656
MA0145.1	MA0145.1	0.339
MA0146.1	MA0146.1	0.0066
MA0147.1	MA0147.1	0.784
MA0148.1	MA0148.1	0.00619
MA0149.1	MA0149.1	0.607
MA0150.1	MA0150.1	0.0102
MA0152.1	MA0152.1	0.451
MA0153.1	MA0153.1	1.83336e-6
MA0154.1	MA0154.1	0.916
MA0155.1	MA0155.1	0.357
MA0156.1	MA0156.1	0.822
MA0157.1	MA0157.1	0.487
MA0159.1	MA0159.1	0.662
MA0160.1	MA0160.1	0.262
MA0162.1	MA0162.1	0.316
MA0163.1	MA0163.1	0.132
MA0164.1	MA0164.1	0.761
MA0258.1	MA0258.1	0.895
MA0259.1	MA0259.1	0.31

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: CNhs11297

Novel motif	Logo	P-value
1	1	0.898
10	10	0.242
100	100	0.666
101	101	0.141
102	102	0.523
103	103	0.761
104	104	0.548
105	105	0.834
106	106	0.66
107	107	0.401
108	108	0.726
109	109	0.0768
11	11	0.363
110	110	0.0867
111	111	0.259
112	112	0.674
113	113	0.242
114	114	0.296
115	115	0.483
116	116	0.278
117	117	0.0468
118	118	0.881
119	119	0.599
12	12	0.135
120	120	0.428
121	121	0.26
122	122	0.517
123	123	0.225
124	124	0.456
125	125	0.759
126	126	0.949
127	127	0.307
128	128	0.236
129	129	0.861
13	13	0.281
130	130	0.971
131	131	0.989
132	132	0.542
133	133	0.0177
134	134	0.758
135	135	0.0323
136	136	0.333
137	137	0.7
138	138	0.857
139	139	0.0599
14	14	0.69
140	140	0.0729
141	141	0.523
142	142	0.246
143	143	0.745
144	144	0.62
145	145	0.648
146	146	0.305
147	147	0.949
148	148	0.591
149	149	0.845
15	15	0.503
150	150	0.0898
151	151	0.617
152	152	0.156
153	153	0.819
154	154	0.54
155	155	0.799
156	156	0.00355
157	157	0.967
158	158	0.324
159	159	0.0361
160	160	0.195
161	161	0.6
162	162	0.667
163	163	0.815
164	164	0.0729
165	165	0.384
166	166	0.728
167	167	0.542
168	168	0.154
169	169	0.0417
17	17	0.989
18	18	0.87
19	19	0.551
2	2	0.31
20	20	0.0705
21	21	0.339
22	22	0.298
23	23	0.894
24	24	0.632
25	25	0.415
26	26	0.0667
27	27	0.111
28	28	0.947
29	29	0.109
3	3	0.303
30	30	0.221
31	31	0.434
32	32	0.504
33	33	0.764
34	34	0.311
35	35	0.141
36	36	0.328
37	37	0.0805
38	38	0.715
39	39	0.346
4	4	0.0999
40	40	0.0669
41	41	0.997
42	42	0.737
43	43	0.849
44	44	0.74
45	45	0.427
46	46	0.922
47	47	0.608
48	48	0.846
49	49	0.355
5	5	0.453
50	50	0.337
51	51	0.69
52	52	0.695
53	53	0.655
54	54	0.554
55	55	0.463
56	56	0.862
57	57	0.598
58	58	0.539
59	59	0.805
6	6	0.764
60	60	0.951
61	61	0.593
62	62	0.97
63	63	0.965
64	64	0.889
65	65	0.558
66	66	0.635
67	67	0.619
68	68	0.116
69	69	0.0823
7	7	0.688
70	70	0.0194
71	71	0.504
72	72	0.732
73	73	0.0219
74	74	0.441
75	75	0.071
76	76	0.0215
77	77	0.888
78	78	0.269
79	79	0.803
8	8	0.283
80	80	0.00375
81	81	0.993
82	82	0.299
83	83	0.298
84	84	0.175
85	85	0.86
86	86	0.369
87	87	0.0796
88	88	0.763
89	89	0.184
9	9	0.742
90	90	0.273
91	91	0.452
92	92	0.679
93	93	0.293
94	94	0.659
95	95	0.2
96	96	0.498
97	97	0.0962
98	98	0.0235
99	99	0.652

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: CNhs11297

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000104 mouse aortic smooth muscle cell 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0000359 (vascular associated smooth muscle cell)
0002539 (aortic smooth muscle cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001135 (smooth muscle tissue)
0000947 (aorta)
0001637 (artery)
0000483 (epithelium)
0000479 (tissue)
0000055 (vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0004573 (systemic artery)
0002385 (muscle tissue)
0003509 (arterial blood vessel)
0007500 (epithelial tube open at both ends)
0001981 (blood vessel)
0004237 (blood vessel smooth muscle)
0004695 (arterial system smooth muscle)
0002049 (vasculature)
0010317 (germ layer / neural crest derived structure)
0002111 (artery smooth muscle tissue)
0007798 (vascular system)
0001015 (musculature)
0004178 (aorta smooth muscle tissue)
0002204 (musculoskeletal system)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0010191 (aortic system)
0000383 (musculature of body)
0004572 (arterial system)
0004537 (blood vasculature)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000104 (mouse aortic smooth muscle cell 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
CL:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)
CL:0000514 (smooth muscle myoblast)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008695
+|DRA_sample_Accession=CAGE@SAMD00004682
-|accession_numbers=CAGE;DRX008805;DRR009677;DRZ001102;DRZ002487
+|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00004682
+|accession_numbers=CAGE;DRX008805;DRR009677;DRZ001102;DRZ002487;DRZ012452;DRZ013837
+|accession_numbers_RNASeq=sRNA-Seq;DRX037375;DRR041741;DRZ007350
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001135,UBERON:0000947,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0004573,UBERON:0002385,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0004237,UBERON:0004695,UBERON:0002049,UBERON:0010317,UBERON:0002111,UBERON:0007798,UBERON:0001015,UBERON:0004178,UBERON:0002204,UBERON:0004535,UBERON:0004571,UBERON:0010191,UBERON:0000383,UBERON:0004572,UBERON:0004537,UBERON:0001009
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000255,CL:0000359,CL:0002539
@@ Line 9: / Line 11: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:5761979..5761992,+!p2@Aebp1!1.80!123.71!Aebp1;;chr11:5761889..5761969,+!p1@Aebp1!1.65!1718.55!Aebp1;;chr1:165243792..165243808,-!p1@Prrx1!1.63!140.78!Prrx1;;chr9:8900459..8900489,+!p1@Pgr!1.57!36.16!Pgr;;chr10:119913278..119913298,-!p2@Hmga2!1.49!65.89!Hmga2;;chr1:165243379..165243402,-!p3@Prrx1!1.48!43.13!Prrx1;;chr1:165243591..165243625,-!p2@Prrx1!1.45!41.30!Prrx1;;chr19:59533221..59533271,+!p1@Emx2!1.44!32.30!Emx2;;chr7:51787434..51787448,-!p1@Spib!1.38!33.04!Spib;;chr1:165243653..165243664,-!p4@Prrx1!1.33!28.27!Prrx1;;chr9:96632636..96632649,-!p16@Zbtb38!1.33!20.37!Zbtb38;;chr6:83661226..83661282,+!p1@Vax2!1.32!19.82!Vax2;;chr19:5447886..5447905,+!p1@Fosl1!1.31!19.27!Fosl1;;chr1:165243272..165243283,-!p6@Prrx1!1.24!20.01!Prrx1;;chr11:96132767..96132796,+!p2@Hoxb9!1.20!14.68!Hoxb9;;chr9:96653072..96653154,-!p1@Zbtb38!1.16!36.16!Zbtb38;;chr10:67599319..67599360,-!p2@Arid5b!1.15!145.00!Arid5b;;chr8:123608252..123608268,+!p1@Foxf1a!1.15!19.27!Foxf1a;;chr1:93698030..93698064,+!p1@Twist2!1.12!24.60!Twist2;;chr19:59532915..59532940,+!p5@Emx2!1.12!12.30!Emx2;;chr2:152758901..152758925,-!p1@Foxs1!1.10!51.76!Foxs1;;chr5:32438395..32438406,+!p3@Fosl2!1.08!16.89!Fosl2;;chr9:8900409..8900425,+!p2@Pgr!1.08!11.01!Pgr;;chr11:96160426..96160443,+!p2@Hoxb6!1.07!10.83!Hoxb6;;chr9:96632593..96632620,-!p12@Zbtb38!1.07!10.65!Zbtb38;;chr19:59534052..59534083,+!p8@Emx2!1.06!10.46!Emx2;;chr10:119913546..119913583,-!p3@Hmga2!1.04!21.11!Hmga2;;chr11:96147952..96147967,+!p1@Hoxb7!1.03!12.30!Hoxb7;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!1.01!17.62!Zbtb38;;chr11:96690797..96690813,-!p1@Nfe2l1!1.00!176.94!Nfe2l1;;chr1:165243638..165243649,-!p5@Prrx1!1.00!11.01!Prrx1;;chr19:59534008..59534046,+!p7@Emx2!1.00!8.99!Emx2;;chr16:15887371..15887385,+!p1@Cebpd!0.99!305.97!Cebpd;;chr10:119913310..119913366,-!p1@Hmga2!0.99!69.38!Hmga2;;chr17:37140628..37140631,+!p2@Zfp57!0.96!16.70!Zfp57;;chr11:18918434..18918489,-!p3@Meis1!0.95!12.85!Meis1;;chr9:96632719..96632745,-!p7@Zbtb38!0.95!7.89!Zbtb38;;chr12:50484072..50484092,+!p4@Foxg1!0.94!7.71!Foxg1;;chr5:53981592..53981616,+!p3@Rbpj!0.93!14.68!Rbpj;;chr10:107769168..107769215,+!p1@Pawr!0.91!74.89!Pawr;;chr11:5761871..5761882,+!p3@Aebp1!0.91!19.27!Aebp1;;chr10:67375146..67375208,-!p2@Zfp365!0.91!11.01!Zfp365;;chr6:52133827..52133854,-!p2@Hoxa3!0.91!7.16!Hoxa3;;chr15:40486566..40486600,+!p1@Zfpm2!0.90!42.95!Zfpm2;;chr19:5447692..5447711,+!p2@Fosl1!0.89!6.79!Fosl1;;chr9:8899828..8899855,+!p3@Pgr!0.87!6.42!Pgr;;chr5:32438831..32438878,+!p1@Fosl2!0.86!68.65!Fosl2;;chr10:67375368..67375433,-!p1@Zfp365!0.86!11.56!Zfp365;;chr11:96143666..96143725,+!p1@Hoxb8!0.86!7.16!Hoxb8;;chr14:22807216..22807231,-!p3@Zfp503!0.85!10.83!Zfp503;;chr19:59533139..59533152,+!p2@Emx2!0.85!6.06!Emx2;;chr1:165243978..165243992,-!p9@Prrx1!0.85!6.06!Prrx1;;chr9:96632690..96632703,-!p20@Zbtb38!0.85!6.06!Zbtb38;;chr13:31898637..31898653,+!p2@Foxc1!0.84!11.01!Foxc1;;chr10:107769229..107769238,+!p3@Pawr!0.84!8.63!Pawr;;chr19:28754692..28754757,-!p1@Glis3!0.83!25.51!Glis3;;chr19:59533163..59533185,+!p3@Emx2!0.83!5.69!Emx2;;chr3:32264565..32264613,-!p1@Zmat3!0.82!66.44!Zmat3;;chr13:99124189..99124205,+!p1@Foxd1!0.81!8.63!Foxd1;;chr2:74542918..74542971,+!p1@Hoxd8!0.81!8.44!Hoxd8;;chr14:22807107..22807119,-!p2@Zfp503!0.80!25.15!Zfp503;;chr8:87297280..87297326,-!p2@Nfix!0.80!13.22!Nfix;;chr8:123640063..123640077,+!p1@Foxc2!0.80!10.10!Foxc2;;chr11:96143962..96144035,+!p2@Hoxb8!0.80!5.32!Hoxb8;;chr4:84320893..84320910,-!p1@Bnc2!0.79!12.30!Bnc2;;chr11:96132637..96132652,+!p1@Hoxb9!0.79!5.14!Hoxb9;;chr16:14705961..14705978,+!p2@Snai2!0.78!25.51!Snai2;;chr5:120121169..120121171,+!p4@Tbx3!0.78!9.36!Tbx3;;chr1:57029281..57029326,-!p1@Satb2!0.78!8.08!Satb2;;chr2:167514456..167514473,+!p1@Cebpb!0.77!238.61!Cebpb;;chr12:34642682..34642753,+!p2@Twist1!0.77!13.95!Twist1;;chr10:5636374..5636421,-!p1@Esr1!0.77!6.24!Esr1;;chr9:8900490..8900502,+!p4@Pgr!0.77!4.96!Pgr;;chr9:8900563..8900574,+!p5@Pgr!0.77!4.96!Pgr;;chr18:11052485..11052508,+!p2@Gata6!0.76!14.50!Gata6;;chr19:46380235..46380277,+!p3@Nfkb2!0.76!10.83!Nfkb2;;chr11:96180045..96180059,+!p1@Hoxb4!0.76!6.97!Hoxb4;;chr11:96164821..96164865,+!p1@Hoxb5!0.76!4.77!Hoxb5;;chr10:126727842..126727859,+!p1@Ddit3!0.75!146.65!Ddit3;;chr14:22807083..22807104,-!p1@Zfp503!0.75!89.75!Zfp503;;chr11:96690779..96690790,-!p3@Nfe2l1!0.75!11.93!Nfe2l1;;chr10:67599361..67599372,-!p5@Arid5b!0.75!7.53!Arid5b;;chr2:152758938..152758954,-!p2@Foxs1!0.75!6.61!Foxs1;;chr10:67375223..67375240,-!p4@Zfp365!0.75!5.32!Zfp365;;chr1:165244244..165244254,-!p8@Prrx1!0.75!4.59!Prrx1;;chr13:29045559..29045574,-!p1@Sox4!0.74!412.61!Sox4;;chr16:14705925..14705951,+!p1@Snai2!0.74!35.42!Snai2;;chr15:102076652..102076679,-!p4@Rarg!0.74!8.44!Rarg;;chr2:71384802..71384815,-!p1@Dlx2!0.74!5.69!Dlx2;;chr17:37139472..37139514,+!p1@Zfp57!0.73!32.85!Zfp57;;chr18:11052642..11052659,+!p1@Gata6!0.73!24.60!Gata6;;chr17:34784073..34784118,+!p2@Atf6b!0.73!19.46!Atf6b;;chr16:43363190..43363242,+!p2@Zbtb20!0.73!14.87!Zbtb20;;chr6:72185232..72185272,-!p1@Atoh8!0.73!13.58!Atoh8;;chr15:102087737..102087801,-!p3@Rarg!0.73!7.53!Rarg;;chr19:28754600..28754612,-!p2@Glis3!0.73!7.34!Glis3;;chr19:46379199..46379301,+!p1@Nfkb2!0.72!27.16!Nfkb2;;chr13:31717548..31717596,+!p1@Foxf2!0.72!8.99!Foxf2;;chr1:93698095..93698113,+!p3@Twist2!0.72!5.32!Twist2;;chr3:99057677..99057730,+!p2@Tbx15!0.72!4.22!Tbx15;;chr6:15135215..15135244,+!p11@Foxp2!0.72!4.22!Foxp2;;chr7:52071956..52071978,-!p1@Atf5!0.71!153.26!Atf5;;chr19:10315179..10315241,-!p1@Gm98!0.71!48.46!Gm98;;chr16:43363152..43363186,+!p3@Zbtb20!0.71!10.28!Zbtb20;;chr10:67599375..67599386,-!p3@Arid5b!0.71!8.08!Arid5b;;chr4:13712228..13712267,+!p3@Runx1t1!0.71!7.53!Runx1t1;;chr10:119914001..119914078,-!p4@Hmga2!0.71!5.87!Hmga2;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.71!5.69!Hoxb2;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.70!7.34!Hoxb2;;chr15:79178013..79178028,+!p3@Maff!0.70!5.51!Maff;;chr19:46380399..46380417,+!p4@Nfkb2!0.70!4.04!Nfkb2;;chr2:30700881..30700916,+!p1@Prrx2!0.69!7.89!Prrx2;;chr3:32264530..32264544,-!p2@Zmat3!0.69!6.42!Zmat3;;chr11:96160360..96160397,+!p3@Hoxb6!0.69!3.85!Hoxb6;;chr10:67375342..67375365,-!p3@Zfp365!0.69!3.85!Zfp365;;chr5:46247735..46247746,-!p13@Lcorl!0.69!3.85!Lcorl;;chr10:119913792..119913820,-!p5@Hmga2!0.68!6.97!Hmga2;;chr10:5734525..5734569,-!p3@Esr1!0.68!6.61!Esr1;;chr1:93698068..93698085,+!p2@Twist2!0.68!4.59!Twist2;;chr10:67741461..67741483,-!p1@Arid5b!0.67!114.72!Arid5b;;chr10:107769219..107769226,+!p5@Pawr!0.67!4.77!Pawr;;chr19:59533595..59533628,+!p6@Emx2!0.67!3.67!Emx2;;chr7:119822957..119822980,+!p2@Tead1!0.66!20.01!Tead1;;chr10:107769750..107769799,+!p2@Pawr!0.66!8.44!Pawr;;chr5:32438894..32438908,+!p2@Fosl2!0.66!8.26!Fosl2;;chrX:7341077..7341091,+!p5@Tfe3!0.66!6.61!Tfe3;;chr13:72766250..72766273,+!p1@Irx2!0.66!5.87!Irx2;;chr15:79178029..79178044,+!p4@Maff!0.66!4.59!Maff;;chr14:22806778..22806795,-!p5@Zfp503!0.66!4.04!Zfp503;;chr1:92895299..92895373,+!p2@Lrrfip1!0.65!84.62!Lrrfip1;;chr17:44872561..44872615,-!p1@Runx2!0.65!8.81!Runx2;;chr11:96145450..96145517,+!p2@Hoxb7!0.65!5.51!Hoxb7;;chr15:79178060..79178074,+!p2@Maff!0.65!4.77!Maff;;chr3:99057269..99057306,+!p1@Tbx15!0.65!4.41!Tbx15;;chr6:52161666..52161711,-!p1@Hoxa6!0.65!3.49!Hoxa6;;chr11:96164905..96164919,+!p2@Hoxb5!0.65!3.49!Hoxb5;;chr6:72185553..72185612,-!p2@Atoh8!0.64!7.16!Atoh8;;chr12:74147689..74147711,-!p1@Six1!0.63!7.89!Six1;;chr12:75002389..75002406,+!p4@Hif1a!0.63!3.30!Hif1a;;chr19:59533429..59533470,+!p4@Emx2!0.63!3.30!Emx2;;chr11:96160403..96160416,+!p4@Hoxb6!0.63!3.30!Hoxb6;;chr10:119913266..119913277,-!p6@Hmga2!0.63!3.30!Hmga2;;chr3:152058408..152058453,+!p5@Gm8261,p5@Zzz3!0.62!7.89!Zzz3;;chr8:87297878..87297935,-!p3@Nfix!0.62!7.89!Nfix;;chr6:128250380..128250442,-!p2@Tead4!0.62!4.22!Tead4;;chr15:102076870..102076941,-!p1@Rarg!0.60!39.28!Rarg;;chr10:92773818..92773906,-!p2@Elk3!0.60!16.89!Elk3;;chr2:72818978..72818997,-!p4@Sp3!0.60!15.23!Sp3;;chr18:11052606..11052633,+!p4@Gata6!0.60!8.63!Gata6;;chr2:74543397..74543435,+!p2@Hoxd8!0.60!2.94!Hoxd8;;chr11:53164378..53164392,+!p2@Aff4!0.59!30.65!Aff4;;chr15:40486754..40486771,+!p2@Zfpm2!0.58!5.51!Zfpm2;;chr11:18918406..18918431,-!p6@Meis1!0.58!4.04!Meis1;;chr1:170362242..170362256,-!p3@Pbx1!0.57!24.23!Pbx1;;chrX:7339938..7339963,+!p1@Tfe3!0.57!16.89!Tfe3;;chr6:72185210..72185228,-!p3@Atoh8!0.57!5.14!Atoh8;;chr6:52114821..52114828,-!p1@Hoxa2!0.57!4.41!Hoxa2;;chr15:40486458..40486467,+!p9@Zfpm2!0.57!3.30!Zfpm2;;chr12:50485973..50486015,+!p2@Foxg1!0.57!2.75!Foxg1;;chr15:101097270..101097290,+!p1@Nr4a1!0.56!33.77!Nr4a1;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.56!7.53!Hmga1;;chr6:52167513..52167549,-!p2@Hoxa7!0.56!4.04!Hoxa7;;chr7:89137163..89137200,-!p1@Bnc1!0.56!3.30!Bnc1;;chr9:63605740..63605771,-!p1@Smad3!0.55!46.99!Smad3;;chr11:18918917..18918944,-!p1@Meis1!0.55!41.11!Meis1;;chr19:46380172..46380231,+!p2@Nfkb2!0.55!21.66!Nfkb2;;chr18:83079981..83080037,+!p6@Zfp516!0.55!4.96!Zfp516;;chr19:28754655..28754673,-!p3@Glis3!0.55!4.22!Glis3;;chr1:140739014..140739032,-!p1@Lhx9!0.55!3.49!Lhx9;;chr11:96180069..96180089,+!p3@Hoxb4!0.55!2.57!Hoxb4;;chr12:86940338..86940357,+!p1@Jdp2!0.54!31.02!Jdp2;;chr18:11052456..11052477,+!p3@Gata6!0.54!9.18!Gata6;;chr10:13686815..13686846,+!p3@Hivep2!0.54!6.42!Hivep2;;chr12:9581284..9581303,+!p2@Osr1!0.54!5.51!Osr1;;chr19:55816546..55816556,+!p3@Tcf7l2!0.53!11.20!Tcf7l2;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!0.53!9.73!Atf1;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!0.53!2.39!Eno1;;chr3:17954392..17954407,+!p2@Bhlhe22!0.53!2.39!Bhlhe22;;chr1:122498955..122498968,+!p1@En1!0.53!2.39!En1;;chr10:5636354..5636373,-!p2@Esr1!0.53!2.39!Esr1;;chr11:96160451..96160462,+!p5@Hoxb6!0.53!2.39!Hoxb6;;chr11:96143843..96143868,+!p3@Hoxb8!0.53!2.39!Hoxb8;;chr11:100800671..100800770,-!p1@Stat3!0.52!96.91!Stat3;;chr12:34642510..34642530,+!p1@Twist1!0.52!8.99!Twist1;;chr16:43619101..43619151,+!p6@Zbtb20!0.52!6.61!Zbtb20;;ch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@@ Line 44: / Line 47: @@
 |is_obsolete=
 |library_id=CNhs11297
-|library_ids=CNhs11297
+|library_id_phase_based=2:CNhs11297
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11299
+|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#srna;sample;SRhi10002.CGATGT.11299
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11299
+|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#srna;sample;SRhi10002.CGATGT.11299
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%252c%2520donor1.CNhs11297.11299-117B3.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Aortic Smooth Muscle cells, donor1
 |namespace=FANTOM5
@@ Line 50: / Line 64: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11297,LSID905,release009,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=SRhi10002,,,
 |repeat_enrich_byfamily=-0.0225400690470547,0,0,0,0,0,0.291204194074583,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.00138229629592471,0,0,0,0,0,0.135798219778432,0,0,0,0,0,0,0,-0.199569419706231,0,0,0,0,0,-2.94586725000032e-05,-0.0313118376967838,0.00293295298544205,-0.984211366477826,0.0129196758578684,0,0,0,0,0,0,0,0,0,0,0,0.135798219778432,-0.0660055475634404,0,0,0,0,0,0,0.240872055492449,0,0,0,0.0731212516783237,-0.310650657339386,-0.158091042771083,0.0459865599001164,0,0,-0.051027501757499,-0.062306191396817,0,0,-0.0697248542115851,-0.102938412379939,-0.116049714385712,0.0569666249385247,0,0,0,0,0.0365927089968535,0,-0.0465987003515363,-0.0975170544988644,-0.106648365048858,0,0,0.135798219778432,0,0
@@ Line 65: / Line 79: @@
 |rna_tube_id=117B3
 |rna_weight_ug=56.6
+|rnaseq_library_id=SRhi10002.CGATGT
 |sample_age=U
 |sample_category=primary cells
@@ Line 87: / Line 102: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11299-117B3;search_select_hide=table117:11299-117B3
 }}

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FF:11299-117B3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 16:31, 3 June 2020

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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