FF:11484-119D8: Difference between revisions

Latest revision as of 18:03, 4 June 2020

Name:	Mouse Aortic Smooth Muscle cells - differentiated, biol_rep1
Species:	Mouse (Mus musculus)
Library ID:	CNhs11055
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	NA
dev stage	NA
sex	NA
age	NA
cell type	NA
cell line	NA
company	Cell Applications
collaboration	NA
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	NA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.16

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005370

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11055		CAGE		DRX008803		DRR009675

Accession ID Mm9

Library id		BAM		CTSS
CNhs11055		DRZ001100		DRZ002485

Accession ID Mm10

Library id		BAM		CTSS
CNhs11055		DRZ012450		DRZ013835

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

CNhs11055

0	0
1	0
10	0
100	0
1000	0.0515
1001	-0.0136
1002	0.472
1003	0.259
1004	0
1005	0.0126
1006	-0.143
1007	-0.172
1008	0
1009	0.716
101	0.0536
1010	0
1011	-0.0627
1012	0
1013	0.294
1014	-0.0874
1015	-0.0478
1016	0.23
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	-0.0126
1023	0
1024	-0.21
1025	0
1026	0
1027	-0.048
1028	0.878
1029	-0.0501
103	0.119
1030	0
1031	0.264
1032	0.295
1033	0.0515
1034	0
1035	0
1036	0.0572
1037	0
1038	0.22
1039	-0.0193
104	0
1040	0.828
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: CNhs11055

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.986
MA0003.1	MA0003.1	0.388
MA0004.1	MA0004.1	0.00198
MA0006.1	MA0006.1	0.72
MA0007.1	MA0007.1	0.299
MA0009.1	MA0009.1	0.214
MA0014.1	MA0014.1	0.105
MA0017.1	MA0017.1	0.00101
MA0018.2	MA0018.2	0.114
MA0019.1	MA0019.1	1
MA0024.1	MA0024.1	0.00313
MA0025.1	MA0025.1	0.803
MA0027.1	MA0027.1	0.159
MA0028.1	MA0028.1	0.00123
MA0029.1	MA0029.1	0.477
MA0030.1	MA0030.1	0.329
MA0031.1	MA0031.1	0.331
MA0035.2	MA0035.2	3.05314e-5
MA0038.1	MA0038.1	0.635
MA0039.2	MA0039.2	0.373
MA0040.1	MA0040.1	0.363
MA0041.1	MA0041.1	0.58
MA0042.1	MA0042.1	0.364
MA0043.1	MA0043.1	0.735
MA0046.1	MA0046.1	2.9703e-8
MA0047.2	MA0047.2	0.00692
MA0048.1	MA0048.1	0.00499
MA0050.1	MA0050.1	1.39084e-4
MA0051.1	MA0051.1	0.00375
MA0052.1	MA0052.1	6.60329e-4
MA0055.1	MA0055.1	0.00342
MA0057.1	MA0057.1	0.714
MA0058.1	MA0058.1	1.90164e-4
MA0059.1	MA0059.1	0.2
MA0060.1	MA0060.1	3.98068e-7
MA0061.1	MA0061.1	0.0654
MA0062.2	MA0062.2	0.01
MA0065.2	MA0065.2	0.0886
MA0066.1	MA0066.1	0.746
MA0067.1	MA0067.1	0.995
MA0068.1	MA0068.1	0.0136
MA0069.1	MA0069.1	0.967
MA0070.1	MA0070.1	0.64
MA0071.1	MA0071.1	0.599
MA0072.1	MA0072.1	0.559
MA0073.1	MA0073.1	0.649
MA0074.1	MA0074.1	0.699
MA0076.1	MA0076.1	0.0227
MA0077.1	MA0077.1	0.131
MA0078.1	MA0078.1	0.91
MA0079.2	MA0079.2	0.318
MA0080.2	MA0080.2	0.00272
MA0081.1	MA0081.1	0.597
MA0083.1	MA0083.1	0.0886
MA0084.1	MA0084.1	0.874
MA0087.1	MA0087.1	0.753
MA0088.1	MA0088.1	0.0112
MA0090.1	MA0090.1	3.69655e-4
MA0091.1	MA0091.1	0.724
MA0092.1	MA0092.1	0.288
MA0093.1	MA0093.1	0.0032
MA0099.2	MA0099.2	2.34015e-5
MA0100.1	MA0100.1	0.365
MA0101.1	MA0101.1	0.0145
MA0102.2	MA0102.2	0.851
MA0103.1	MA0103.1	1.29214e-7
MA0104.2	MA0104.2	0.678
MA0105.1	MA0105.1	0.492
MA0106.1	MA0106.1	1.49719e-8
MA0107.1	MA0107.1	0.0786
MA0108.2	MA0108.2	3.60711e-6
MA0111.1	MA0111.1	0.296
MA0112.2	MA0112.2	0.202
MA0113.1	MA0113.1	0.693
MA0114.1	MA0114.1	7.3699e-4
MA0115.1	MA0115.1	0.0504
MA0116.1	MA0116.1	0.733
MA0117.1	MA0117.1	0.661
MA0119.1	MA0119.1	0.152
MA0122.1	MA0122.1	0.706
MA0124.1	MA0124.1	0.951
MA0125.1	MA0125.1	0.0589
MA0131.1	MA0131.1	0.776
MA0135.1	MA0135.1	0.0799
MA0136.1	MA0136.1	0.0532
MA0137.2	MA0137.2	0.021
MA0138.2	MA0138.2	0.00475
MA0139.1	MA0139.1	0.252
MA0140.1	MA0140.1	5.094e-4
MA0141.1	MA0141.1	0.255
MA0142.1	MA0142.1	0.0631
MA0143.1	MA0143.1	0.608
MA0144.1	MA0144.1	0.0574
MA0145.1	MA0145.1	0.106
MA0146.1	MA0146.1	0.0123
MA0147.1	MA0147.1	0.996
MA0148.1	MA0148.1	0.0223
MA0149.1	MA0149.1	0.889
MA0150.1	MA0150.1	0.0116
MA0152.1	MA0152.1	0.0206
MA0153.1	MA0153.1	1.96829e-6
MA0154.1	MA0154.1	0.905
MA0155.1	MA0155.1	0.616
MA0156.1	MA0156.1	0.503
MA0157.1	MA0157.1	0.157
MA0159.1	MA0159.1	0.578
MA0160.1	MA0160.1	0.033
MA0162.1	MA0162.1	0.256
MA0163.1	MA0163.1	0.0635
MA0164.1	MA0164.1	0.852
MA0258.1	MA0258.1	0.608
MA0259.1	MA0259.1	0.357

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: CNhs11055

Novel motif	Logo	P-value
1	1	0.669
10	10	0.159
100	100	0.518
101	101	0.209
102	102	0.162
103	103	0.894
104	104	0.843
105	105	0.774
106	106	0.975
107	107	0.735
108	108	0.908
109	109	0.0119
11	11	0.247
110	110	0.0222
111	111	0.19
112	112	0.383
113	113	0.175
114	114	0.0728
115	115	0.865
116	116	0.308
117	117	0.227
118	118	0.948
119	119	0.541
12	12	0.4
120	120	0.539
121	121	0.312
122	122	0.588
123	123	0.289
124	124	0.796
125	125	0.67
126	126	0.336
127	127	0.256
128	128	0.407
129	129	0.72
13	13	0.0424
130	130	0.963
131	131	0.236
132	132	0.55
133	133	0.0203
134	134	0.832
135	135	0.218
136	136	0.206
137	137	0.608
138	138	0.931
139	139	0.0618
14	14	0.903
140	140	0.082
141	141	0.729
142	142	0.129
143	143	0.652
144	144	0.322
145	145	0.814
146	146	0.856
147	147	0.932
148	148	0.434
149	149	0.165
15	15	0.935
150	150	0.049
151	151	0.787
152	152	0.109
153	153	0.446
154	154	0.836
155	155	0.447
156	156	0.00155
157	157	0.572
158	158	0.0248
159	159	0.0172
160	160	0.337
161	161	0.473
162	162	0.604
163	163	0.897
164	164	0.0402
165	165	0.463
166	166	0.865
167	167	0.489
168	168	0.313
169	169	0.0118
17	17	0.728
18	18	0.604
19	19	0.188
2	2	0.884
20	20	0.433
21	21	0.283
22	22	0.0974
23	23	0.997
24	24	0.564
25	25	0.564
26	26	0.0673
27	27	0.311
28	28	0.921
29	29	0.221
3	3	0.182
30	30	0.214
31	31	0.441
32	32	0.224
33	33	0.832
34	34	0.296
35	35	0.0969
36	36	0.458
37	37	0.0342
38	38	0.929
39	39	0.301
4	4	0.171
40	40	0.0732
41	41	0.867
42	42	0.459
43	43	0.398
44	44	0.76
45	45	0.832
46	46	0.928
47	47	0.578
48	48	0.77
49	49	0.445
5	5	0.746
50	50	0.38
51	51	0.652
52	52	0.886
53	53	0.906
54	54	0.315
55	55	0.964
56	56	0.88
57	57	0.716
58	58	0.237
59	59	0.767
6	6	0.77
60	60	0.453
61	61	0.631
62	62	0.666
63	63	0.801
64	64	0.644
65	65	0.75
66	66	0.442
67	67	0.728
68	68	0.0397
69	69	0.0541
7	7	0.864
70	70	0.0596
71	71	0.227
72	72	0.907
73	73	0.0099
74	74	0.921
75	75	0.102
76	76	0.104
77	77	0.755
78	78	0.0697
79	79	0.423
8	8	0.252
80	80	0.00324
81	81	0.344
82	82	0.16
83	83	0.271
84	84	0.34
85	85	0.186
86	86	0.283
87	87	0.00422
88	88	0.72
89	89	0.207
9	9	0.766
90	90	0.255
91	91	0.346
92	92	0.636
93	93	0.329
94	94	0.451
95	95	0.00639
96	96	0.295
97	97	0.146
98	98	0.027
99	99	0.646

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: CNhs11055

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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0001134,UBERON:0001135,UBERON:0000947,UBERON:0001637,UBERON:0002100,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0003914,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0003509,UBERON:0004573,UBERON:0002036,UBERON:0002385,UBERON:0001981,UBERON:0002049,UBERON:0000486,UBERON:0007500,UBERON:0003104,UBERON:0004237,UBERON:0004695,UBERON:0000914,UBERON:0005256,UBERON:0006598,UBERON:0002111,UBERON:0007798,UBERON:0001015,UBERON:0002532,UBERON:0004178,UBERON:0002329,UBERON:0002204,UBERON:0004535,UBERON:0004571,UBERON:0010191,UBERON:0000383,UBERON:0004572,UBERON:0004537,UBERON:0003077,UBERON:0004290,UBERON:0009142,UBERON:0003081,UBERON:0001009,UBERON:0006603,UBERON:0003082,UBERON:0004872,UBERON:0006965,UBERON:0003059,UBERON:0007282,UBERON:0009618,UBERON:0007285
+|DRA_sample_Accession=CAGE@SAMD00005370
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000055,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0000680,CL:0002321,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000220,CL:0000004,CL:0000192,CL:0000211,CL:0000056,CL:0000255,CL:0000359,CL:0000222,CL:0002539,CL:0000355,CL:0000514
+|accession_numbers=CAGE;DRX008803;DRR009675;DRZ001100;DRZ002485;DRZ012450;DRZ013835
+|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
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000104
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:5761979..5761992,+!p2@Aebp1!1.79!120.36!Aebp1;;chr11:5761889..5761969,+!p1@Aebp1!1.58!1445.80!Aebp1;;chr10:119913278..119913298,-!p2@Hmga2!1.55!74.66!Hmga2;;chr1:165243792..165243808,-!p1@Prrx1!1.54!113.06!Prrx1;;chr19:5447886..5447905,+!p1@Fosl1!1.45!27.45!Fosl1;;chr6:83661226..83661282,+!p1@Vax2!1.38!22.79!Vax2;;chr1:140739014..140739032,-!p1@Lhx9!1.22!20.02!Lhx9;;chr10:126727842..126727859,+!p1@Ddit3!1.20!423.14!Ddit3;;chr1:165243591..165243625,-!p2@Prrx1!1.20!22.41!Prrx1;;chr10:67599319..67599360,-!p2@Arid5b!1.19!156.87!Arid5b;;chr16:15887371..15887385,+!p1@Cebpd!1.18!470.60!Cebpd;;chr2:152758901..152758925,-!p1@Foxs1!1.18!62.07!Foxs1;;chr10:67375146..67375208,-!p2@Zfp365!1.16!20.65!Zfp365;;chr1:165243653..165243664,-!p4@Prrx1!1.16!19.14!Prrx1;;chr10:119913546..119913583,-!p3@Hmga2!1.12!25.43!Hmga2;;chr1:165243272..165243283,-!p6@Prrx1!1.12!14.60!Prrx1;;chr11:96147952..96147967,+!p1@Hoxb7!1.11!14.73!Hoxb7;;chr1:93698030..93698064,+!p1@Twist2!1.09!22.91!Twist2;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!1.09!21.02!Zbtb38;;chr11:98636531..98636559,-!p1@Nr1d1!1.08!62.57!Nr1d1;;chr12:34642510..34642530,+!p1@Twist1!1.08!35.38!Twist1;;chr1:165243379..165243402,-!p3@Prrx1!1.08!16.49!Prrx1;;chr19:5447692..5447711,+!p2@Fosl1!1.04!9.95!Fosl1;;chr9:96632719..96632745,-!p7@Zbtb38!1.04!9.95!Zbtb38;;chr10:67599375..67599386,-!p3@Arid5b!1.03!17.75!Arid5b;;chr7:52071956..52071978,-!p1@Atf5!1.02!309.71!Atf5;;chr13:72766250..72766273,+!p1@Irx2!1.02!14.86!Irx2;;chr10:119913310..119913366,-!p1@Hmga2!1.00!71.64!Hmga2;;chr3:32264565..32264613,-!p1@Zmat3!0.99!99.46!Zmat3;;chr5:120121169..120121171,+!p4@Tbx3!0.98!15.49!Tbx3;;chr14:22807216..22807231,-!p3@Zfp503!0.98!14.86!Zfp503;;chr10:5636374..5636421,-!p1@Esr1!0.97!10.58!Esr1;;chr14:22807083..22807104,-!p1@Zfp503!0.95!144.03!Zfp503;;chr12:34642682..34642753,+!p2@Twist1!0.94!21.28!Twist1;;chr11:96160426..96160443,+!p2@Hoxb6!0.94!7.81!Hoxb6;;chr10:67375223..67375240,-!p4@Zfp365!0.93!8.56!Zfp365;;chr10:107769168..107769215,+!p1@Pawr!0.92!77.93!Pawr;;chr9:96653072..96653154,-!p1@Zbtb38!0.92!20.14!Zbtb38;;chr7:89137163..89137200,-!p1@Bnc1!0.92!8.94!Bnc1;;chr11:5761871..5761882,+!p3@Aebp1!0.91!19.14!Aebp1;;chr10:119913792..119913820,-!p5@Hmga2!0.91!12.59!Hmga2;;chr10:67599361..67599372,-!p5@Arid5b!0.91!11.33!Arid5b;;chr10:119913266..119913277,-!p6@Hmga2!0.91!7.05!Hmga2;;chr4:13712228..13712267,+!p3@Runx1t1!0.90!12.34!Runx1t1;;chr10:67599432..67599444,-!p4@Arid5b!0.90!11.46!Arid5b;;chr2:152758938..152758954,-!p2@Foxs1!0.90!9.69!Foxs1;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.90!9.32!Hoxb2;;chr15:81633165..81633188,+!p2@Tef!0.88!57.03!Tef;;chr6:72185232..72185272,-!p1@Atoh8!0.88!19.64!Atoh8;;chr19:59533221..59533271,+!p1@Emx2!0.88!8.31!Emx2;;chr10:67375368..67375433,-!p1@Zfp365!0.87!11.58!Zfp365;;chr11:96180045..96180059,+!p1@Hoxb4!0.87!9.32!Hoxb4;;chr11:96684043..96684069,-!p9@Nfe2l1!0.87!6.42!Nfe2l1;;chr4:124805061..124805087,-!p1@Zc3h12a!0.86!20.40!Zc3h12a;;chr8:123608252..123608268,+!p1@Foxf1a!0.86!9.57!Foxf1a;;chr1:122498955..122498968,+!p1@En1!0.86!6.29!En1;;chr19:59534008..59534046,+!p7@Emx2!0.86!6.29!Emx2;;chr10:107769229..107769238,+!p3@Pawr!0.85!8.81!Pawr;;chr14:22806778..22806795,-!p5@Zfp503!0.85!6.67!Zfp503;;chr19:55816546..55816556,+!p3@Tcf7l2!0.84!24.17!Tcf7l2;;chr17:37140628..37140631,+!p2@Zfp57!0.84!12.34!Zfp57;;chrX:7341077..7341091,+!p5@Tfe3!0.83!10.07!Tfe3;;chr11:96143666..96143725,+!p1@Hoxb8!0.83!6.67!Hoxb8;;chr7:52960555..52960662,+!p1@Dbp!0.82!50.74!Dbp;;chr17:84586544..84586592,-!p3@Zfp36l2!0.82!8.06!Zfp36l2;;chr12:50484072..50484092,+!p4@Foxg1!0.82!5.67!Foxg1;;chr3:99057677..99057730,+!p2@Tbx15!0.82!5.54!Tbx15;;chr16:43363152..43363186,+!p3@Zbtb20!0.81!13.09!Zbtb20;;chr13:72101178..72101203,-!p1@Irx1!0.81!8.69!Irx1;;chr1:165243638..165243649,-!p5@Prrx1!0.81!6.67!Prrx1;;chr8:87297280..87297326,-!p2@Nfix!0.80!13.35!Nfix;;chr3:32264530..32264544,-!p2@Zmat3!0.80!8.56!Zmat3;;chr6:52133827..52133854,-!p2@Hoxa3!0.80!5.29!Hoxa3;;chr19:10315179..10315241,-!p1@Gm98!0.79!58.92!Gm98;;chr18:14131126..14131211,-!p1@Zfp521!0.78!116.83!Zfp521;;chr15:40486566..40486600,+!p1@Zfpm2!0.78!31.98!Zfpm2;;chr7:20214704..20214800,-!p1@Relb!0.78!17.75!Relb;;chr18:11052606..11052633,+!p4@Gata6!0.78!13.47!Gata6;;chr15:40486754..40486771,+!p2@Zfpm2!0.78!9.32!Zfpm2;;chr6:72185210..72185228,-!p3@Atoh8!0.78!8.94!Atoh8;;chr10:5734525..5734569,-!p3@Esr1!0.78!8.56!Esr1;;chr1:93698068..93698085,+!p2@Twist2!0.78!6.04!Twist2;;chr2:74542918..74542971,+!p1@Hoxd8!0.77!7.68!Hoxd8;;chr10:119914001..119914078,-!p4@Hmga2!0.77!6.92!Hmga2;;chr11:96690797..96690813,-!p1@Nfe2l1!0.76!101.10!Nfe2l1;;chr16:43363190..43363242,+!p2@Zbtb20!0.75!15.61!Zbtb20;;chr18:11052485..11052508,+!p2@Gata6!0.75!13.97!Gata6;;chr10:13686815..13686846,+!p3@Hivep2!0.75!11.20!Hivep2;;chr11:96164821..96164865,+!p1@Hoxb5!0.75!4.66!Hoxb5;;chr1:93698095..93698113,+!p3@Twist2!0.74!5.54!Twist2;;chr17:37139472..37139514,+!p1@Zfp57!0.73!32.73!Zfp57;;chr5:65194853..65194866,+!p5@Klf3!0.73!13.85!Klf3;;chr15:102087737..102087801,-!p3@Rarg!0.73!7.55!Rarg;;chr6:52161666..52161711,-!p1@Hoxa6!0.73!4.41!Hoxa6;;chr14:19071466..19071550,-!p1@Nr1d2!0.72!32.48!Nr1d2;;chr2:30700881..30700916,+!p1@Prrx2!0.72!8.56!Prrx2;;chr6:52167513..52167549,-!p2@Hoxa7!0.72!6.29!Hoxa7;;chr4:55545051..55545110,-!p2@Klf4!0.72!5.54!Klf4;;chr10:5636354..5636373,-!p2@Esr1!0.72!4.28!Esr1;;chr19:46379199..46379301,+!p1@Nfkb2!0.71!26.56!Nfkb2;;chr17:34784073..34784118,+!p2@Atf6b!0.71!18.63!Atf6b;;chr19:59534052..59534083,+!p8@Emx2!0.71!4.15!Emx2;;chr15:81977802..81977828,+!p2@Srebf2!0.70!38.90!Srebf2;;chr1:92895299..92895373,+!p2@Lrrfip1!0.69!91.65!Lrrfip1;;chrX:7339938..7339963,+!p1@Tfe3!0.69!22.54!Tfe3;;chr2:71384802..71384815,-!p1@Dlx2!0.69!5.04!Dlx2;;chr5:32438831..32438878,+!p1@Fosl2!0.68!45.07!Fosl2;;chr2:167514456..167514473,+!p1@Cebpb!0.67!188.09!Cebpb;;chr14:22807107..22807119,-!p2@Zfp503!0.67!18.26!Zfp503;;chr18:11052456..11052477,+!p3@Gata6!0.67!12.72!Gata6;;chr18:7004715..7004731,-!p1@Mkx!0.67!9.69!Mkx;;chr11:96145450..96145517,+!p2@Hoxb7!0.67!5.92!Hoxb7;;chr7:51787434..51787448,-!p1@Spib!0.67!5.54!Spib;;chr7:52960700..52960719,+!p2@Dbp!0.67!4.66!Dbp;;chr10:80889867..80889924,-!p1@Nfic!0.66!117.71!Nfic;;chr10:5734677..5734702,-!p4@Esr1!0.66!3.53!Esr1;;chr11:96160360..96160397,+!p3@Hoxb6!0.66!3.53!Hoxb6;;chr4:124805092..124805135,-!p2@Zc3h12a!0.65!17.00!Zc3h12a;;chr15:102087880..102087927,-!p2@Rarg!0.65!8.81!Rarg;;chr12:74147689..74147711,-!p1@Six1!0.65!8.31!Six1;;chr10:13686783..13686814,+!p4@Hivep2!0.65!7.81!Hivep2;;chr8:123640063..123640077,+!p1@Foxc2!0.65!6.92!Foxc2;;chr11:98636508..98636524,-!p3@Nr1d1!0.65!4.41!Nr1d1;;chr11:53583544..53583559,+!p1@Irf1!0.64!66.47!Irf1;;chr7:119822957..119822980,+!p2@Tead1!0.64!18.76!Tead1;;chr16:43236133..43236154,+!p17@Zbtb20!0.64!4.03!Zbtb20;;chr10:127080230..127080241,+!p6@Stat6!0.64!3.90!Stat6;;chr17:84587167..84587239,-!p2@Zfp36l2!0.63!12.84!Zfp36l2;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.63!9.06!Hmga1;;chr17:44872561..44872615,-!p1@Runx2!0.63!8.31!Runx2;;chr3:32264814..32264835,-!p5@Zmat3!0.63!3.27!Zmat3;;chr4:82151274..82151290,-!p3@Nfib!0.62!60.43!Nfib;;chr10:107769750..107769799,+!p2@Pawr!0.62!7.55!Pawr;;chr15:79178013..79178028,+!p3@Maff!0.62!4.41!Maff;;chr12:50485973..50486015,+!p2@Foxg1!0.62!3.15!Foxg1;;chr13:72766234..72766243,+!p3@Irx2!0.62!3.15!Irx2;;chr10:67599450..67599456,-!p8@Arid5b!0.61!3.78!Arid5b;;chr13:31898729..31898761,+!p1@Foxc1!0.60!8.31!Foxc1;;chr10:26093876..26093894,-!p2@L3mbtl3!0.60!7.93!L3mbtl3;;chr19:46380235..46380277,+!p3@Nfkb2!0.60!7.30!Nfkb2;;chr5:65203599..65203617,+!p8@Klf3!0.60!5.41!Klf3;;chr5:32438395..32438406,+!p3@Fosl2!0.60!4.91!Fosl2;;chr10:67599461..67599470,-!p6@Arid5b!0.60!3.65!Arid5b;;chr11:96143962..96144035,+!p2@Hoxb8!0.60!3.02!Hoxb8;;chr1:165244244..165244254,-!p8@Prrx1!0.60!3.02!Prrx1;;chr9:96632636..96632649,-!p16@Zbtb38!0.60!3.02!Zbtb38;;chr19:5637528..5637548,+!p2@Rela!0.59!20.52!Rela;;chr13:67552527..67552574,-!p1@Zfp874a!0.59!15.23!Zfp874a;;chr4:55545152..55545194,-!p3@Klf4!0.59!3.53!Klf4;;chr11:96160403..96160416,+!p4@Hoxb6!0.59!2.90!Hoxb6;;chr1:170362273..170362317,-!p1@Pbx1!0.58!99.33!Pbx1;;chr5:38215819..38215823,-!p1@Msx1!0.58!8.44!Msx1;;chr10:67000609..67000625,+!p1@Egr2!0.58!7.43!Egr2;;chr12:9581284..9581303,+!p2@Osr1!0.58!6.04!Osr1;;chr4:124799704..124799713,-!p4@Zc3h12a!0.58!2.77!Zc3h12a;;chr9:96632690..96632703,-!p20@Zbtb38!0.58!2.77!Zbtb38;;chr17:84587279..84587294,-!p1@Zfp36l2!0.57!359.44!Zfp36l2;;chr19:26822880..26822964,+!p2@Smarca2!0.57!28.45!Smarca2;;chr13:31717548..31717596,+!p1@Foxf2!0.57!6.17!Foxf2;;chr15:79178029..79178044,+!p4@Maff!0.57!3.53!Maff;;chr2:152561980..152561997,+!p1@Id1!0.56!95.30!Id1;;chr8:87324243..87324277,-!p1@Nfix!0.56!79.69!Nfix;;chr1:193007123..193007139,-!p1@Atf3!0.56!17.88!Atf3;;chr18:11052642..11052659,+!p1@Gata6!0.56!16.11!Gata6;;chr19:28754692..28754757,-!p1@Glis3!0.56!13.35!Glis3;;chr15:79177964..79177986,+!p1@Maff!0.56!10.70!Maff;;chr18:75979866..75979890,+!p3@Zbtb7c!0.56!6.29!Zbtb7c;;chr5:53981592..53981616,+!p3@Rbpj!0.56!5.67!Rbpj;;chr4:13712168..13712218,+!p4@Runx1t1!0.56!4.91!Runx1t1;;chr2:30700857..30700873,+!p3@Prrx2!0.56!3.90!Prrx2;;chr17:84587077..84587097,-!p4@Zfp36l2!0.56!3.65!Zfp36l2;;chr10:107769219..107769226,+!p5@Pawr!0.56!3.40!Pawr;;chr2:74543397..74543435,+!p2@Hoxd8!0.56!2.64!Hoxd8;;chr2:167363692..167363710,+!p1@Snai1!0.55!39.41!Snai1;;chr16:14705925..14705951,+!p1@Snai2!0.55!22.28!Snai2;;chr11:72990738..72990763,+!p2@LOC100047518,p2@Tax1bp3!0.55!17.37!Tax1bp3;;chr17:45692642..45692663,+!p1@Nfkbie!0.55!9.69!Nfkbie;;chr13:99124189..99124205,+!p1@Foxd1!0.55!4.28!Foxd1;;chr11:16952347..16952366,-!p2@Plek!0.55!4.15!Plek;;chr19:46380346..46380360,+!p6@Nfkb2!0.55!2.52!Nfkb2;;chr9:8900459..8900489,+!p1@Pgr!0.55!2.52!Pgr;;chr12:56593574..56593592,-!p1@Nfkbia!0.54!162.91!Nfkbia;;chr12:86940338..86940357,+!p1@Jdp2!0.54!30.72!Jdp2;;chr9:121668850..121668885,+!p2@Zfp651!0.54!5.29!Zfp651;;chr19:28754600..28754612,-!p2@Glis3!0.54!4.41!Glis3;;chr6:72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Atf4!0.31!211.63!Atf4;;chr1:64167972..64168026,-!p1@Klf7!0.31!43.94!Klf7;;chr11:60034052..60034134,-!p2@Srebf1!0.31!43.56!Srebf1;;chr17:28487692..28487765,-!p1@Tead3!0.31!35.75!Tead3;;chr14:52640373..52640412,-!p1@Zfp219!0.31!10.32!Zfp219;;chr3:135354476..135354528,-!p2@Nfkb1!0.31!9.57!Nfkb1;;chrX:108810678..108810736,-!p1@Hdx!0.31!5.54!Hdx;;chr5:110539087..110539133,+!p1@Zfp605!0.31!4.91!Zfp605;;chr7:91558392..91558434,-!p1@Arnt2!0.31!4.41!Arnt2;;chr1:170362322..170362333,-!p8@Pbx1!0.31!4.15!Pbx1;;chr11:59285966..59285990,-!p2@Zfp867!0.31!4.03!Zfp867;;chr3:135354452..135354475,-!p5@Nfkb1!0.31!3.90!Nfkb1;;chr7:148008023..148008092,-!p1@Zfp941!0.31!3.78!Zfp941;;chr10:92773708..92773734,-!p3@Elk3!0.31!2.90!Elk3;;chr9:63869802..63869815,-!p3@Smad6!0.31!2.90!Smad6;;chr13:67229127..67229153,+!p2@Zfp759!0.31!2.90!Zfp759;;chr1:69732511..69732540,-!p2@Ikzf2!0.31!1.64!Ikzf2;;chr18:14131020..14131033,-!p4@Zfp521!0.31!1.64!Zfp521;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.31!1.51!Hoxb2;;chr17:37139519..37139531,+!p5@Zfp57!0.31!1.38!Zfp57;;chr15:40486458..40486467,+!p9@Zfpm2!0.31!1.38!Zfpm2;;chr8:109817400..109817417,+!p1@Nfat5!0.30!37.52!Nfat5;;chr12:36219645..36219730,-!p1@Ahr!0.30!17.00!Ahr;;chr3:94758041..94758142,+!p1@Rfx5!0.30!15.86!Rfx5;;chr10:93610727..93610754,+!p2@Nr2c1!0.30!3.78!Nr2c1;;chr1:170361730..170361769,-!p7@Pbx1!0.30!3.40!Pbx1;;chr5:107125778..107125803,-!p4@Zfp644!0.30!3.27!Zfp644;;chr10:80812991..80813004,-!p3@Hmg20b!0.30!3.02!Hmg20b;;chr13:55206625..55206636,+!p2@Zfp346!0.30!2.77!Zfp346;;chr15:61818965..61819046,+!p3@Myc!0.30!2.39!Myc;;chr17:44873393..44873418,-!p4@Runx2!0.30!2.39!Runx2;;chr18:83079981..83080037,+!p6@Zfp516!0.30!2.39!Zfp516;;chr2:120996813..120996829,-!p2@Zscan29!0.30!2.27!Zscan29;;chr16:4594853..4594884,+!p3@Glis2!0.30!2.14!Glis2;;chr10:119913839..119913869,-!p7@Hmga2!0.30!1.51!Hmga2;;chr7:119822940..119822945,+!p6@Tead1!0.30!1.51!Tead1;;chr9:56266504..56266516,+!p5@Hmg20a!0.30!1.26!Hmg20a;;chr9:8899828..8899855,+!p3@Pgr!0.30!1.01!Pgr;;chr19:59533429..59533470,+!p4@Emx2!0.30!1.01!Emx2;;chr1:140739042..140739054,-!p2@Lhx9!0.30!1.01!Lhx9;;chr2:71367871..71367898,+!p1@Dlx1!0.30!1.01!Dlx1;;chr2:74549915..74549930,+!p6@Hoxd3!0.30!1.01!Hoxd3;;chr11:96143843..96143868,+!p3@Hoxb8!0.30!1.01!Hoxb8;;chr10:5734582..5734595,-!p10@Esr1!0.30!1.01!Esr1;;chr11:96132637..96132652,+!p1@Hoxb9!0.30!1.01!Hoxb9;;chr16:14705668..14705683,+!p3@Snai2!0.30!1.01!Snai2;;chr17:44872524..44872537,-!p9@Runx2!0.30!1.01!Runx2;;chr11:100800671..100800770,-!p1@Stat3!0.29!57.16!Stat3;;chr15:38230448..38230470,-!p1@Klf10!0.29!36.26!Klf10;;chr10:33670996..33671069,-!p1@Zufsp!0.29!34.24!Zufsp;;chr17:71200529..71200556,-!p1@Tgif1!0.29!27.82!Tgif1;;chr1:181476358..181476391,-!p1@Tfb2m!0.29!26.94!Tfb2m;;chr9:71743854..71743909,-!p1@Tcf12!0.29!13.47!Tcf12;;chr14:18493386..18493464,+!p1@Thrb!0.29!6.04!Thrb;;chr7:19679964..19679982,+!p1@Six5!0.29!4.28!Six5;;chr15:100058289..100058300,+!p3@Atf1!0.29!4.03!Atf1;;chr9:63605691..63605705,-!p3@Smad3!0.29!3.78!Smad3;;chr17:37139432..37139444,+!p4@Zfp57!0.29!1.64!Zfp57;;chr7:134565516..134565573,-!p1@Zfp688!0.28!19.64!Zfp688;;chr17:35372700..35372762,-!p1@Nfkbil1!0.28!18.13!Nfkbil1;;chr13:21622953..21622972,-!p2@Zfp192!0.28!9.57!Zfp192;;chr9:63869751..63869767,-!p1@Smad6!0.28!3.78!Smad6;;chr11:50745114..50745144,-!p1@Zfp354b!0.28!3.65!Zfp354b;;chr5:140267510..140267555,+!p2@Mafk!0.28!3.27!Mafk;;chrX:70587989..70588000,+!p3@Zfp275!0.28!2.64!Zfp275;;chr17:37139455..37139469,+!p3@Zfp57!0.28!1.89!Zfp57;;chr19:5423800..5423821,-!p5@Drap1!0.28!1.76!Drap1;;chr13:53568104..53568156,-!p1@Msx2!0.28!1.76!Msx2;;chr5:65203575..65203589,+!p11@Klf3!0.28!1.26!Klf3;;chr9:71743910..71743915,-!p7@Tcf12!0.28!1.13!Tcf12;;chr11:100800771..100800798,-!p2@Stat3!0.27!10.58!Stat3;;chr5:34530293..34530318,-!p2@Mxd4!0.27!8.81!Mxd4;;chr10:127984472..127984504,-!p2@Zc3h10!0.27!4.66!Zc3h10;;chr19:9016975..9017004,+!p2@Mta2!0.27!4.28!Mta2;;chr5:34530277..34530292,-!p3@Mxd4!0.27!3.53!Mxd4;;chr11:100683839..100683890,-!p2@Stat5b!0.27!3.15!Stat5b;;chr5:65213356..65213412,+!p6@Klf3!0.27!2.77!Klf3;;chr8:4613211..4613224,+!p3@Zfp958!0.27!2.77!Zfp958;;chrX:131543765..131543775,-!p2@Zmat1!0.27!2.77!Zmat1;;chr6:146744595..146744613,+!p2@Arntl2!0.27!2.01!Arntl2;;chr19:55817629..55817652,+!p14@Tcf7l2!0.27!1.51!Tcf7l2;;chr10:88996336..88996380,-!p2@Nr1h4!0.27!1.26!Nr1h4;;chr10:5636678..5636725,-!p6@Esr1!0.27!0.88!Esr1;;chr10:5734473..5734489,-!p5@Esr1!0.27!0.88!Esr1;;chr19:46380374..46380397,+!p7@Nfkb2!0.27!0.88!Nfkb2;;chr9:32349051..32349061,-!p5@Fli1!0.27!0.88!Fli1;;chr8:87298020..87298041,-!p9@Nfix!0.27!0.88!Nfix;;chr5:120130377..120130432,+!p10@Tbx3!0.27!0.88!Tbx3;;chr1:92950128..92950139,+!p4@Lrrfip1!0.27!0.88!Lrrfip1;;chr1:57029076..57029098,-!p8@Satb2!0.27!0.88!Satb2;;chr1:122499088..122499099,+!p2@En1!0.27!0.88!En1;;chr12:50483639..50483654,+!p1@Foxg1!0.27!0.88!Foxg1;;chr2:74543202..74543213,+!p3@Hoxd8!0.27!0.88!Hoxd8;;chr4:82145196..82145229,-!p7@Nfib!0.27!0.88!Nfib;;chr11:74644437..74644507,+!p1@Mnt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+|ffid_belonging_in_development=CL:0000355,CL:0000222,CL:0000514
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000104
 |is_obsolete=
+|library_id=CNhs11055
+|library_id_phase_based=2:CNhs11055
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11484
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11484
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Aortic%2520Smooth%2520Muscle%2520cells%2520-%2520differentiated%252c%2520biol_rep1.CNhs11055.11484-119D8.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Aortic Smooth Muscle cells - differentiated, biol_rep1
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11055,LSID722,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.00439008891219311,0,0,0,0,0,0.0376981684905899,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.137112034106908,0,0,0,0,0,0.0514985917256918,0,0,0,0,0,0,0,-0.204512678913103,0,0,0,0,0,-0.0463469728754285,-0.0224317450492065,-0.0781397259425183,-0.984211366477826,0.291689847811126,0,0,0,0,0,0,0,0,0,0,0,0.0975327392940296,-0.0660055475634404,0,0,0,0,0.00865163664281703,0,0.216740279009006,0.0514985917256918,0.177128640687699,0,-0.0288254825644768,-0.259152065613694,-0.158091042771083,0.00193008793622582,0,0,-0.0644614201728004,-0.151395207110669,0,0,-0.0725188018741778,-0.0417856855323068,0.116279666836118,0.0187011444541221,0,0,0,0,0,0,0.0844700624147315,0.150183924444153,0.0834315900436999,0,0,0.0514985917256918,0,0
 |rna_box=119
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=0.335
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11484-119D8;search_select_hide=table117:11484-119D8
 }}

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FF:11484-119D8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:03, 4 June 2020

CNhs11055

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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