FF:11551-120C3: Difference between revisions

Latest revision as of 18:08, 4 June 2020

Name:	Mouse Astrocytes - hippocampus, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12077
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	hippocampus
dev stage	NA
sex	NA
age	NA
cell type	astrocyte
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	lot:3899
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004768

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12077		CAGE		DRX008809		DRR009681

Accession ID Mm9

Library id		BAM		CTSS
CNhs12077		DRZ001106		DRZ002491

Accession ID Mm10

Library id		BAM		CTSS
CNhs12077		DRZ012456		DRZ013841

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

CNhs12077

0	0
1	0
10	0
100	0
1000	0.715
1001	-0.0491
1002	0.44
1003	0.498
1004	0
1005	-0.00897
1006	0.019
1007	-0.315
1008	0
1009	0.333
101	-0.377
1010	0
1011	-0.0304
1012	0
1013	0.333
1014	-0.00795
1015	0.015
1016	0.288
1017	0
1018	0
1019	0
102	0
1020	0.672
1021	0.0772
1022	0.0693
1023	0
1024	-0.0127
1025	-0.0611
1026	0
1027	0.0772
1028	0.143
1029	-0.176
103	0.188
1030	0
1031	0.179
1032	0.531
1033	-0.0385
1034	0
1035	0
1036	-0.219
1037	0
1038	0.137
1039	0.184
104	0
1040	0.51
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: CNhs12077

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.906
MA0003.1	MA0003.1	0.232
MA0004.1	MA0004.1	0.831
MA0006.1	MA0006.1	0.244
MA0007.1	MA0007.1	0.131
MA0009.1	MA0009.1	0.582
MA0014.1	MA0014.1	0.444
MA0017.1	MA0017.1	0.0289
MA0018.2	MA0018.2	0.61
MA0019.1	MA0019.1	0.555
MA0024.1	MA0024.1	4.18849e-5
MA0025.1	MA0025.1	0.633
MA0027.1	MA0027.1	0.35
MA0028.1	MA0028.1	0.148
MA0029.1	MA0029.1	0.996
MA0030.1	MA0030.1	0.652
MA0031.1	MA0031.1	0.876
MA0035.2	MA0035.2	0.00599
MA0038.1	MA0038.1	0.372
MA0039.2	MA0039.2	0.176
MA0040.1	MA0040.1	0.499
MA0041.1	MA0041.1	0.157
MA0042.1	MA0042.1	0.557
MA0043.1	MA0043.1	0.275
MA0046.1	MA0046.1	5.7961e-5
MA0047.2	MA0047.2	0.317
MA0048.1	MA0048.1	0.654
MA0050.1	MA0050.1	0.35
MA0051.1	MA0051.1	0.487
MA0052.1	MA0052.1	0.437
MA0055.1	MA0055.1	0.189
MA0057.1	MA0057.1	0.978
MA0058.1	MA0058.1	0.95
MA0059.1	MA0059.1	0.774
MA0060.1	MA0060.1	0.688
MA0061.1	MA0061.1	0.422
MA0062.2	MA0062.2	8.24389e-4
MA0065.2	MA0065.2	0.319
MA0066.1	MA0066.1	0.501
MA0067.1	MA0067.1	0.792
MA0068.1	MA0068.1	0.373
MA0069.1	MA0069.1	0.0338
MA0070.1	MA0070.1	0.781
MA0071.1	MA0071.1	0.389
MA0072.1	MA0072.1	0.536
MA0073.1	MA0073.1	0.781
MA0074.1	MA0074.1	0.836
MA0076.1	MA0076.1	0.2
MA0077.1	MA0077.1	0.491
MA0078.1	MA0078.1	0.852
MA0079.2	MA0079.2	0.00704
MA0080.2	MA0080.2	9.47975e-7
MA0081.1	MA0081.1	0.421
MA0083.1	MA0083.1	0.918
MA0084.1	MA0084.1	0.151
MA0087.1	MA0087.1	0.214
MA0088.1	MA0088.1	0.923
MA0090.1	MA0090.1	7.88658e-5
MA0091.1	MA0091.1	0.0324
MA0092.1	MA0092.1	0.866
MA0093.1	MA0093.1	0.938
MA0099.2	MA0099.2	0.0297
MA0100.1	MA0100.1	0.649
MA0101.1	MA0101.1	0.0653
MA0102.2	MA0102.2	0.486
MA0103.1	MA0103.1	0.0182
MA0104.2	MA0104.2	0.253
MA0105.1	MA0105.1	0.0781
MA0106.1	MA0106.1	0.146
MA0107.1	MA0107.1	0.0418
MA0108.2	MA0108.2	0.53
MA0111.1	MA0111.1	0.673
MA0112.2	MA0112.2	0.768
MA0113.1	MA0113.1	0.658
MA0114.1	MA0114.1	0.00148
MA0115.1	MA0115.1	0.108
MA0116.1	MA0116.1	0.085
MA0117.1	MA0117.1	0.866
MA0119.1	MA0119.1	0.427
MA0122.1	MA0122.1	0.697
MA0124.1	MA0124.1	0.329
MA0125.1	MA0125.1	0.933
MA0131.1	MA0131.1	0.0481
MA0135.1	MA0135.1	0.119
MA0136.1	MA0136.1	1.20481e-6
MA0137.2	MA0137.2	0.84
MA0138.2	MA0138.2	0.508
MA0139.1	MA0139.1	0.391
MA0140.1	MA0140.1	6.74532e-6
MA0141.1	MA0141.1	0.588
MA0142.1	MA0142.1	0.393
MA0143.1	MA0143.1	0.713
MA0144.1	MA0144.1	0.836
MA0145.1	MA0145.1	0.0475
MA0146.1	MA0146.1	0.0205
MA0147.1	MA0147.1	0.184
MA0148.1	MA0148.1	0.115
MA0149.1	MA0149.1	0.839
MA0150.1	MA0150.1	0.94
MA0152.1	MA0152.1	0.454
MA0153.1	MA0153.1	3.19402e-4
MA0154.1	MA0154.1	0.493
MA0155.1	MA0155.1	0.405
MA0156.1	MA0156.1	2.35917e-7
MA0157.1	MA0157.1	0.747
MA0159.1	MA0159.1	0.233
MA0160.1	MA0160.1	0.492
MA0162.1	MA0162.1	0.239
MA0163.1	MA0163.1	0.564
MA0164.1	MA0164.1	0.755
MA0258.1	MA0258.1	0.293
MA0259.1	MA0259.1	0.174

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: CNhs12077

Novel motif	Logo	P-value
1	1	0.134
10	10	0.103
100	100	0.468
101	101	0.874
102	102	0.542
103	103	0.106
104	104	0.798
105	105	0.902
106	106	0.234
107	107	0.897
108	108	0.705
109	109	0.0609
11	11	0.606
110	110	0.981
111	111	0.214
112	112	0.217
113	113	0.342
114	114	0.772
115	115	0.689
116	116	0.419
117	117	0.0874
118	118	0.101
119	119	0.279
12	12	0.976
120	120	0.554
121	121	0.653
122	122	0.439
123	123	0.994
124	124	0.578
125	125	0.625
126	126	0.239
127	127	0.913
128	128	0.92
129	129	0.158
13	13	0.187
130	130	0.652
131	131	0.993
132	132	0.247
133	133	0.48
134	134	0.842
135	135	0.387
136	136	0.00965
137	137	0.103
138	138	0.645
139	139	0.487
14	14	0.411
140	140	0.00495
141	141	0.588
142	142	0.0871
143	143	0.536
144	144	0.77
145	145	0.49
146	146	0.926
147	147	0.866
148	148	0.332
149	149	0.478
15	15	0.779
150	150	0.461
151	151	0.785
152	152	0.00323
153	153	0.0606
154	154	0.219
155	155	0.455
156	156	0.0059
157	157	0.662
158	158	0.0256
159	159	0.0832
160	160	0.133
161	161	0.762
162	162	0.949
163	163	0.219
164	164	0.00292
165	165	0.696
166	166	0.793
167	167	0.0785
168	168	0.326
169	169	0.212
17	17	0.958
18	18	0.641
19	19	0.446
2	2	0.049
20	20	0.922
21	21	0.695
22	22	0.122
23	23	0.134
24	24	0.386
25	25	0.288
26	26	0.143
27	27	0.986
28	28	0.526
29	29	0.552
3	3	0.29
30	30	0.246
31	31	0.497
32	32	0.0435
33	33	0.614
34	34	0.334
35	35	0.324
36	36	0.0347
37	37	0.323
38	38	0.772
39	39	0.456
4	4	0.947
40	40	0.586
41	41	0.843
42	42	0.606
43	43	0.335
44	44	0.297
45	45	0.24
46	46	0.0433
47	47	0.958
48	48	0.821
49	49	0.0395
5	5	0.066
50	50	0.194
51	51	0.149
52	52	0.221
53	53	0.885
54	54	0.39
55	55	0.686
56	56	0.818
57	57	0.879
58	58	0.0377
59	59	0.13
6	6	0.859
60	60	0.238
61	61	0.6
62	62	0.12
63	63	0.233
64	64	0.865
65	65	0.261
66	66	0.508
67	67	0.982
68	68	0.465
69	69	0.258
7	7	0.233
70	70	0.582
71	71	0.0403
72	72	0.499
73	73	0.00303
74	74	0.291
75	75	0.229
76	76	0.161
77	77	0.0646
78	78	0.0135
79	79	0.892
8	8	0.407
80	80	0.219
81	81	0.643
82	82	0.778
83	83	0.95
84	84	0.266
85	85	0.338
86	86	0.88
87	87	2.5117e-4
88	88	0.427
89	89	0.597
9	9	0.376
90	90	0.331
91	91	0.842
92	92	0.36
93	93	0.0441
94	94	0.0158
95	95	0.00691
96	96	0.0681
97	97	0.825
98	98	0.27
99	99	0.256

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: CNhs12077

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000197 mouse astrocyte of hippocampus 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)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000128 (oligodendrocyte)
0000126 (macroglial cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0000127 (astrocyte)
0002605 (astrocyte of the cerebral cortex)
0002604 (astrocyte of the hippocampus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte sample)
0000197 (mouse astrocyte of hippocampus 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:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004768
+|accession_numbers=CAGE;DRX008809;DRR009681;DRZ001106;DRZ002491;DRZ012456;DRZ013841
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001954,UBERON:0000956,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0003022,UBERON:0010317,UBERON:0001017,UBERON:0002421,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0000349,UBERON:0002600
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000095,CL:0000243,CL:0000128,CL:0000126,CL:0000125,CL:0000255,CL:0000127,CL:0002605,CL:0002604
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr5:138199361..138199441,+!p2@Tsc22d4!2.10!230.01!Tsc22d4;;chr11:116196664..116196679,-!p1@Foxj1!2.03!161.38!Foxj1;;chrX:90531838..90531861,+!p1@Arx!1.91!99.55!Arx;;chr14:122874619..122874634,+!p1@Zic2!1.89!77.19!Zic2;;chr2:38206744..38206766,+!p1@Lhx2!1.77!69.80!Lhx2;;chr8:87297280..87297326,-!p2@Nfix!1.70!113.16!Nfix;;chrX:55284180..55284195,+!p2@Zic3!1.70!48.80!Zic3;;chr3:34548909..34548927,+!p1@Sox2!1.67!76.22!Sox2;;chr16:91270004..91270023,+!p1@Olig1!1.60!43.75!Olig1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.55!43.75!Pou3f3;;chr16:15887371..15887385,+!p1@Cebpd!1.54!1090.95!Cebpd;;chr14:49287186..49287225,-!p1@Otx2!1.48!28.97!Otx2;;chr12:54349410..54349461,+!p1@Npas3!1.45!32.86!Npas3;;chr4:109650609..109650653,+!p1@Dmrta2!1.41!24.50!Dmrta2;;chr9:91260594..91260612,-!p1@Zic1!1.40!23.91!Zic1;;chr9:91260616..91260653,-!p2@Zic1!1.38!23.14!Zic1;;chr11:21901608..21901634,-!p1@Otx1!1.38!22.94!Otx1;;chr15:79178060..79178074,+!p2@Maff!1.32!25.66!Maff;;chr8:87297330..87297365,-!p5@Nfix!1.32!20.03!Nfix;;chr5:38215819..38215823,-!p1@Msx1!1.31!50.55!Msx1;;chrX:55283799..55283813,+!p1@Zic3!1.31!19.64!Zic3;;chr4:154010409..154010466,-!p2@Prdm16!1.29!43.16!Prdm16;;chr4:135699731..135699747,+!p1@Id3!1.26!1854.86!Id3;;chr13:53568104..53568156,-!p1@Msx2!1.25!24.89!Msx2;;chr3:34548946..34548972,+!p2@Sox2!1.24!18.28!Sox2;;chr10:84218800..84218829,+!p2@Rfx4!1.22!15.75!Rfx4;;chr2:38206580..38206600,+!p2@Lhx2!1.19!17.69!Lhx2;;chr7:25292141..25292158,+!p2@Zfp428!1.18!49.00!Zfp428;;chr19:59533221..59533271,+!p1@Emx2!1.18!17.30!Emx2;;chr17:86020510..86020589,+!p3@Six3!1.18!14.19!Six3;;chr17:86020115..86020128,+!p2@Six3!1.13!12.64!Six3;;chr3:34549096..34549111,+!p3@Sox2!1.13!12.44!Sox2;;chr10:84218895..84218909,+!p1@Rfx4!1.12!12.05!Rfx4;;chr19:28754692..28754757,-!p1@Glis3!1.11!49.39!Glis3;;chr14:122874593..122874610,+!p2@Zic2!1.06!10.50!Zic2;;chr11:96690797..96690813,-!p1@Nfe2l1!1.05!198.90!Nfe2l1;;chr14:122874718..122874729,+!p3@Zic2!1.05!10.30!Zic2;;chr13:48356475..48356492,+!p1@Id4!1.04!219.71!Id4;;chr17:86020156..86020183,+!p1@Six3!1.04!9.92!Six3;;chr12:50483639..50483654,+!p1@Foxg1!1.02!9.53!Foxg1;;chr7:119822957..119822980,+!p2@Tead1!1.01!45.30!Tead1;;chr6:72185232..72185272,-!p1@Atoh8!1.01!27.22!Atoh8;;chr8:87238155..87238187,-!p13@Nfix!1.01!9.33!Nfix;;chr9:91266261..91266282,+!p5@Zic4!1.01!9.33!Zic4;;chr6:72185210..72185228,-!p3@Atoh8!0.99!14.97!Atoh8;;chr19:25685023..25685043,+!p1@Dmrt3!0.99!8.75!Dmrt3;;chr4:154010228..154010244,-!p4@Prdm16!0.98!12.05!Prdm16;;chr11:21901587..21901604,-!p2@Otx1!0.98!8.55!Otx1;;chr1:169619683..169619694,+!p1@Lmx1a!0.98!8.55!Lmx1a;;chr7:91558392..91558434,-!p1@Arnt2!0.97!23.72!Arnt2;;chr9:63869510..63869530,-!p10@Smad6!0.97!8.36!Smad6;;chr8:87297878..87297935,-!p3@Nfix!0.96!18.47!Nfix;;chr13:78339382..78339420,-!p3@Nr2f1!0.96!9.72!Nr2f1;;chr13:78339476..78339515,-!p1@Nr2f1!0.94!12.05!Nr2f1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.93!56.58!Tsc22d3;;chr18:69752912..69752928,+!p9@Tcf4!0.93!11.47!Tcf4;;chr11:5761889..5761969,+!p1@Aebp1!0.92!315.56!Aebp1;;chr12:86814833..86814846,+!p1@Fos!0.91!174.21!Fos;;chr12:34642682..34642753,+!p2@Twist1!0.91!19.44!Twist1;;chr17:56970339..56970428,-!p1@Rfx2!0.89!22.17!Rfx2;;chr11:5761979..5761992,+!p2@Aebp1!0.89!14.19!Aebp1;;chr12:50485973..50486015,+!p2@Foxg1!0.89!6.81!Foxg1;;chr13:78339428..78339466,-!p2@Nr2f1!0.88!9.33!Nr2f1;;chr13:78338076..78338104,-!p4@Nr2f1!0.88!8.36!Nr2f1;;chr11:112643496..112643562,+!p1@Sox9!0.87!254.70!Sox9;;chr5:24108047..24108106,-!p3@Smarcd3!0.87!11.67!Smarcd3;;chr2:105515793..105515808,+!p3@Pax6!0.87!6.42!Pax6;;chr9:106356243..106356264,+!p2@Pcbp4!0.85!28.19!Pcbp4;;chr12:34642510..34642530,+!p1@Twist1!0.85!20.42!Twist1;;chr9:106356278..106356292,+!p3@Pcbp4!0.85!10.69!Pcbp4;;chr19:28754655..28754673,-!p3@Glis3!0.84!9.14!Glis3;;chr8:28087609..28087634,+!p1@Zfp703!0.83!140.38!Zfp703;;chr19:28754622..28754633,-!p4@Glis3!0.83!6.61!Glis3;;chr18:69681575..69681579,+!p41@Tcf4!0.83!5.83!Tcf4;;chr16:43363190..43363242,+!p2@Zbtb20!0.81!17.89!Zbtb20;;chr6:145813905..145813932,-!p2@Bhlhe41!0.81!10.89!Bhlhe41;;chr7:52071956..52071978,-!p1@Atf5!0.79!184.13!Atf5;;chr7:17647736..17647772,-!p1@Hif3a!0.79!19.83!Hif3a;;chr9:48644037..48644067,-!p2@Zbtb16!0.79!13.61!Zbtb16;;chr9:106356265..106356276,+!p4@Pcbp4!0.79!8.75!Pcbp4;;chr15:81633203..81633215,+!p3@Tef!0.79!8.36!Tef;;chr11:60023912..60023930,-!p1@Srebf1!0.78!132.99!Srebf1;;chr11:96690779..96690790,-!p3@Nfe2l1!0.78!13.03!Nfe2l1;;chr1:9690398..9690410,-!p2@Mybl1!0.78!6.22!Mybl1;;chr8:87298020..87298041,-!p9@Nfix!0.78!5.06!Nfix;;chr19:55816546..55816556,+!p3@Tcf7l2!0.77!20.03!Tcf7l2;;chr5:125538737..125538781,-!p2@Ncor2!0.77!18.86!Ncor2;;chr19:28754600..28754612,-!p2@Glis3!0.77!8.17!Glis3;;chr17:86020468..86020504,+!p6@Six3!0.77!4.86!Six3;;chr14:49287107..49287125,-!p3@Otx2!0.77!4.86!Otx2;;chr9:106356211..106356242,+!p1@Pcbp4!0.75!100.71!Pcbp4;;chr7:52960700..52960719,+!p2@Dbp!0.75!5.83!Dbp;;chr15:79178029..79178044,+!p4@Maff!0.75!5.83!Maff;;chr17:86012772..86012825,+!p4@Six3!0.75!4.67!Six3;;chr16:91270091..91270143,+!p2@Olig1!0.75!4.67!Olig1;;chrX:55283827..55283838,+!p3@Zic3!0.75!4.67!Zic3;;chr10:42303385..42303401,-!p1@Nr2e1!0.75!4.67!Nr2e1;;chr2:38207200..38207210,+!p13@Lhx2!0.74!4.47!Lhx2;;chr5:77524250..77524300,-!p1@Hopx!0.73!98.38!Hopx;;chr8:87324243..87324277,-!p1@Nfix!0.72!115.49!Nfix;;chr11:98636531..98636559,-!p1@Nr1d1!0.72!27.03!Nr1d1;;chr7:25292076..25292114,+!p4@Zfp428!0.72!12.83!Zfp428;;chr1:169619239..169619257,+!p4@Lmx1a!0.72!4.28!Lmx1a;;chr7:52960555..52960662,+!p1@Dbp!0.71!39.27!Dbp;;chr15:79177964..79177986,+!p1@Maff!0.71!15.55!Maff;;chr15:79178013..79178028,+!p3@Maff!0.71!5.64!Maff;;chr2:105509045..105509071,+!p1@Pax6!0.71!4.08!Pax6;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!0.71!4.08!Eno1;;chr16:4594740..4594759,+!p1@Glis2!0.70!51.72!Glis2;;chrX:137077653..137077669,-!p3@Tsc22d3!0.70!20.42!Tsc22d3;;chr5:65194853..65194866,+!p5@Klf3!0.69!12.64!Klf3;;chr5:138199339..138199346,+!p18@Tsc22d4!0.69!3.89!Tsc22d4;;chr9:91256933..91256954,+!p4@Zic4!0.69!3.89!Zic4;;chr16:91225808..91225824,+!p1@Olig2!0.69!3.89!Olig2;;chr10:42303452..42303470,-!p2@Nr2e1!0.69!3.89!Nr2e1;;chr14:13178361..13178386,-!p2@Fezf2!0.69!3.89!Fezf2;;chr2:152561980..152561997,+!p1@Id1!0.68!128.13!Id1;;chr8:87502608..87502623,-!p1@Junb!0.68!71.74!Junb;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.68!12.05!Tfcp2l1;;chr6:145814003..145814056,-!p1@Bhlhe41!0.68!12.05!Bhlhe41;;chr5:125538703..125538715,-!p5@Ncor2!0.68!4.67!Ncor2;;chr7:25292160..25292213,+!p3@Zfp428!0.67!10.11!Zfp428;;chr15:81633224..81633235,+!p5@Tef!0.67!4.67!Tef;;chr5:138199481..138199491,+!p16@Tsc22d4!0.67!3.69!Tsc22d4;;chr14:118636238..118636257,-!p2@Sox21!0.67!3.69!Sox21;;chr6:72185553..72185612,-!p2@Atoh8!0.66!7.58!Atoh8;;chr10:67375368..67375433,-!p1@Zfp365!0.66!6.81!Zfp365;;chrX:137077608..137077619,-!p6@Tsc22d3!0.66!5.06!Tsc22d3;;chr10:67599432..67599444,-!p4@Arid5b!0.65!6.03!Arid5b;;chrX:137077682..137077692,-!p5@Tsc22d3!0.65!5.83!Tsc22d3;;chr9:106355684..106355744,+!p5@Pcbp4!0.65!5.64!Pcbp4;;chr18:69753168..69753186,+!p12@Tcf4!0.65!4.86!Tcf4;;chr14:118636214..118636235,-!p1@Sox21!0.65!4.28!Sox21;;chr14:49282415..49282426,-!p4@Otx2!0.65!3.50!Otx2;;chr14:118635860..118635885,-!p3@Sox21!0.65!3.50!Sox21;;chr8:12395603..12395621,+!p1@Sox1!0.65!3.50!Sox1;;chr2:24331085..24331100,-!p1@Pax8!0.65!3.50!Pax8;;chr11:80196900..80196917,+!p3@Zfp207!0.64!12.83!Zfp207;;chr5:34530277..34530292,-!p3@Mxd4!0.63!9.33!Mxd4;;chr12:57636034..57636087,-!p1@Nkx2-1!0.63!3.31!Nkx2-1;;chr9:96653072..96653154,-!p1@Zbtb38!0.62!9.72!Zbtb38;;chr6:90412608..90412630,+!p2@Klf15!0.62!7.39!Klf15;;chrX:137135036..137135064,-!p4@Tsc22d3!0.62!6.81!Tsc22d3;;chr17:87153240..87153254,+!p1@Epas1!0.61!71.74!Epas1;;chr15:76287876..76287894,+!p1@Scx!0.61!20.03!Scx;;chr6:108610766..108610781,+!p2@Bhlhe40!0.61!6.03!Bhlhe40;;chr10:42303410..42303422,-!p3@Nr2e1!0.61!3.11!Nr2e1;;chr19:59533139..59533152,+!p2@Emx2!0.61!3.11!Emx2;;chr15:81977766..81977789,+!p3@Srebf2!0.60!22.17!Srebf2;;chr12:74147689..74147711,-!p1@Six1!0.60!7.39!Six1;;chrX:137077699..137077705,-!p8@Tsc22d3!0.60!4.08!Tsc22d3;;chr11:72990738..72990763,+!p2@LOC100047518,p2@Tax1bp3!0.59!19.05!Tax1bp3;;chr17:87153440..87153451,+!p4@Epas1!0.59!6.61!Epas1;;chr7:119822940..119822945,+!p6@Tead1!0.59!3.89!Tead1;;chr4:154010313..154010324,-!p9@Prdm16!0.59!2.92!Prdm16;;chr13:78338057..78338069,-!p11@Nr2f1!0.59!2.92!Nr2f1;;chr18:35020854..35020869,+!p1@Egr1!0.58!133.57!Egr1;;chr17:34784132..34784161,+!p1@Atf6b!0.58!19.64!Atf6b;;chr17:87153462..87153473,+!p3@Epas1!0.58!12.64!Epas1;;chr11:5761871..5761882,+!p3@Aebp1!0.58!8.36!Aebp1;;chr3:32264565..32264613,-!p1@Zmat3!0.57!37.33!Zmat3;;chr2:30700881..30700916,+!p1@Prrx2!0.57!5.83!Prrx2;;chr6:72185179..72185196,-!p4@Atoh8!0.57!3.89!Atoh8;;chr5:28492230..28492257,+!p1@En2!0.57!2.72!En2;;chr16:43508231..43508271,+!p21@Zbtb20!0.57!2.72!Zbtb20;;chr13:53568081..53568094,-!p3@Msx2!0.57!2.72!Msx2;;chr17:87153028..87153049,+!p2@Epas1!0.56!67.47!Epas1;;chr4:154010918..154010931,-!p1@Prdm16!0.56!9.14!Prdm16;;chr3:8666997..8667012,-!p2@Hey1!0.56!7.00!Hey1;;chr6:90412556..90412581,+!p3@Klf15!0.56!6.61!Klf15;;chr7:119822915..119822936,+!p5@Tead1!0.56!4.86!Tead1;;chr11:100800671..100800770,-!p1@Stat3!0.55!104.41!Stat3;;chr16:22439681..22439698,-!p1@Etv5!0.55!56.00!Etv5;;chr8:72356532..72356611,+!p1@Pbx4!0.55!12.83!Pbx4;;chr9:48644306..48644364,-!p1@Zbtb16!0.55!12.44!Zbtb16;;chr7:91558631..91558652,-!p3@Arnt2!0.55!4.08!Arnt2;;chr7:52960663..52960677,+!p6@Dbp!0.55!2.53!Dbp;;chr2:105515635..105515661,+!p5@Pax6!0.55!2.53!Pax6;;chr2:38194778..38194798,+!p3@Lhx2!0.55!2.53!Lhx2;;chr16:43510380..43510393,+!p39@Zbtb20!0.55!2.53!Zbtb20;;chr14:122874356..122874371,+!p4@Zic2!0.55!2.53!Zic2;;chr12:50483778..50483789,+!p6@Foxg1!0.55!2.53!Foxg1;;chr13:78338032..78338049,-!p8@Nr2f1!0.55!2.53!Nr2f1;;chr2:166888107..166888224,-!p1@Znfx1!0.53!44.33!Znfx1;;chr10:67599319..67599360,-!p2@Arid5b!0.53!33.44!Arid5b;;chr10:67599375..67599386,-!p3@Arid5b!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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000197
 |is_obsolete=
+|library_id=CNhs12077
+|library_id_phase_based=2:CNhs12077
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11551
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11551
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor2.CNhs12077.11551-120C3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor2.CNhs12077.11551-120C3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor2.CNhs12077.11551-120C3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor2.CNhs12077.11551-120C3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor2.CNhs12077.11551-120C3.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Astrocytes - hippocampus, donor2
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12077,LSID838,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.52790269293833,0,0,0,0,0.0583191666343674,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.468032912198399,-0.558422792324031,0,0.0771606661507038,0,0.0771606661507038,0,-0.209322725495826,0,-0.0863167842992827,-0.984211366477826,0.0250711947824934,0.373097696573221,0,0,0,0,0,0,0,0,0,0,0.142658407030909,-0.0660055475634404,0,0,0,0,0,0,0.0167733509456356,0,0,-0.0160932186452332,-0.243225778194271,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0250893989567433,0,0,0,0,-0.0729766207869965,0.51985047648542,-0.0788315948399074,0,0,0,0,0,0,0.141632979299592,-0.0328717596743719,0.117740311777205,0,0,0.249863259792521,0.289122511557198,0
 |rna_box=120
 |rna_catalog_number=custom
@@ Line 61: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=N/A
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11551-120C3;search_select_hide=table117:11551-120C3
 }}

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FF:11551-120C3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:08, 4 June 2020

CNhs12077

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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