FF:11709-123B8: Difference between revisions

Latest revision as of 18:15, 4 June 2020

Name:	Mouse Astrocytes - hippocampus, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12129
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:5772
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004686

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12129		CAGE		DRX008808		DRR009680

Accession ID Mm9

Library id		BAM		CTSS
CNhs12129		DRZ001105		DRZ002490

Accession ID Mm10

Library id		BAM		CTSS
CNhs12129		DRZ012455		DRZ013840

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

CNhs12129

0	0
1	0
10	0
100	0
1000	0.598
1001	-0.0668
1002	0.268
1003	0.502
1004	0
1005	0
1006	0.247
1007	-0.368
1008	0
1009	0.281
101	-0.477
1010	0
1011	0.0299
1012	0
1013	0.172
1014	-0.0083
1015	0.132
1016	0.317
1017	0
1018	0
1019	0
102	0
1020	0.404
1021	0.0871
1022	0.0862
1023	0
1024	0.0941
1025	-0.0611
1026	0
1027	0.0383
1028	0
1029	-0.176
103	0.181
1030	0
1031	0.146
1032	0.583
1033	-0.00544
1034	0
1035	0
1036	-0.223
1037	0
1038	0.0889
1039	0.0561
104	0
1040	0.563
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: CNhs12129

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.707
MA0003.1	MA0003.1	0.243
MA0004.1	MA0004.1	0.89
MA0006.1	MA0006.1	0.285
MA0007.1	MA0007.1	0.078
MA0009.1	MA0009.1	0.601
MA0014.1	MA0014.1	0.543
MA0017.1	MA0017.1	0.13
MA0018.2	MA0018.2	0.369
MA0019.1	MA0019.1	0.382
MA0024.1	MA0024.1	8.68507e-6
MA0025.1	MA0025.1	0.821
MA0027.1	MA0027.1	0.377
MA0028.1	MA0028.1	0.0184
MA0029.1	MA0029.1	0.959
MA0030.1	MA0030.1	0.736
MA0031.1	MA0031.1	0.812
MA0035.2	MA0035.2	0.03
MA0038.1	MA0038.1	0.157
MA0039.2	MA0039.2	0.226
MA0040.1	MA0040.1	0.659
MA0041.1	MA0041.1	0.171
MA0042.1	MA0042.1	0.584
MA0043.1	MA0043.1	0.758
MA0046.1	MA0046.1	4.33986e-4
MA0047.2	MA0047.2	0.596
MA0048.1	MA0048.1	0.649
MA0050.1	MA0050.1	0.139
MA0051.1	MA0051.1	0.708
MA0052.1	MA0052.1	0.453
MA0055.1	MA0055.1	0.272
MA0057.1	MA0057.1	0.854
MA0058.1	MA0058.1	0.936
MA0059.1	MA0059.1	0.874
MA0060.1	MA0060.1	0.444
MA0061.1	MA0061.1	0.973
MA0062.2	MA0062.2	2.09459e-6
MA0065.2	MA0065.2	0.932
MA0066.1	MA0066.1	0.92
MA0067.1	MA0067.1	0.489
MA0068.1	MA0068.1	0.326
MA0069.1	MA0069.1	0.0526
MA0070.1	MA0070.1	0.526
MA0071.1	MA0071.1	0.535
MA0072.1	MA0072.1	0.634
MA0073.1	MA0073.1	0.815
MA0074.1	MA0074.1	0.618
MA0076.1	MA0076.1	0.00269
MA0077.1	MA0077.1	0.515
MA0078.1	MA0078.1	0.836
MA0079.2	MA0079.2	0.0117
MA0080.2	MA0080.2	8.33241e-6
MA0081.1	MA0081.1	0.0944
MA0083.1	MA0083.1	0.734
MA0084.1	MA0084.1	0.131
MA0087.1	MA0087.1	0.201
MA0088.1	MA0088.1	0.812
MA0090.1	MA0090.1	3.69544e-5
MA0091.1	MA0091.1	0.0739
MA0092.1	MA0092.1	0.506
MA0093.1	MA0093.1	0.901
MA0099.2	MA0099.2	2.68476e-4
MA0100.1	MA0100.1	0.778
MA0101.1	MA0101.1	0.175
MA0102.2	MA0102.2	0.247
MA0103.1	MA0103.1	0.0892
MA0104.2	MA0104.2	0.489
MA0105.1	MA0105.1	0.699
MA0106.1	MA0106.1	0.101
MA0107.1	MA0107.1	0.102
MA0108.2	MA0108.2	0.741
MA0111.1	MA0111.1	0.848
MA0112.2	MA0112.2	0.2
MA0113.1	MA0113.1	0.309
MA0114.1	MA0114.1	0.0487
MA0115.1	MA0115.1	0.125
MA0116.1	MA0116.1	0.982
MA0117.1	MA0117.1	0.609
MA0119.1	MA0119.1	0.0832
MA0122.1	MA0122.1	0.765
MA0124.1	MA0124.1	0.497
MA0125.1	MA0125.1	0.922
MA0131.1	MA0131.1	0.0365
MA0135.1	MA0135.1	0.27
MA0136.1	MA0136.1	5.13925e-7
MA0137.2	MA0137.2	0.545
MA0138.2	MA0138.2	0.787
MA0139.1	MA0139.1	0.816
MA0140.1	MA0140.1	5.23638e-5
MA0141.1	MA0141.1	0.899
MA0142.1	MA0142.1	0.93
MA0143.1	MA0143.1	0.54
MA0144.1	MA0144.1	0.788
MA0145.1	MA0145.1	0.0249
MA0146.1	MA0146.1	0.0242
MA0147.1	MA0147.1	0.504
MA0148.1	MA0148.1	0.206
MA0149.1	MA0149.1	0.766
MA0150.1	MA0150.1	0.76
MA0152.1	MA0152.1	0.346
MA0153.1	MA0153.1	0.00105
MA0154.1	MA0154.1	0.722
MA0155.1	MA0155.1	0.221
MA0156.1	MA0156.1	6.54047e-10
MA0157.1	MA0157.1	0.8
MA0159.1	MA0159.1	0.523
MA0160.1	MA0160.1	0.577
MA0162.1	MA0162.1	0.155
MA0163.1	MA0163.1	0.821
MA0164.1	MA0164.1	0.84
MA0258.1	MA0258.1	0.803
MA0259.1	MA0259.1	0.184

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: CNhs12129

Novel motif	Logo	P-value
1	1	0.33
10	10	0.315
100	100	0.674
101	101	0.975
102	102	0.43
103	103	0.103
104	104	0.822
105	105	0.694
106	106	0.0181
107	107	0.394
108	108	0.488
109	109	0.0211
11	11	0.242
110	110	0.913
111	111	0.555
112	112	0.59
113	113	0.412
114	114	0.528
115	115	0.853
116	116	0.153
117	117	0.252
118	118	0.152
119	119	0.69
12	12	0.861
120	120	0.648
121	121	0.617
122	122	0.564
123	123	0.962
124	124	0.718
125	125	0.766
126	126	0.303
127	127	0.71
128	128	0.214
129	129	0.296
13	13	0.324
130	130	0.764
131	131	0.93
132	132	0.0389
133	133	0.408
134	134	0.756
135	135	0.235
136	136	0.0475
137	137	0.216
138	138	0.875
139	139	0.901
14	14	0.246
140	140	0.0145
141	141	0.903
142	142	0.12
143	143	0.245
144	144	0.77
145	145	0.676
146	146	0.688
147	147	0.896
148	148	0.627
149	149	0.536
15	15	0.936
150	150	0.198
151	151	0.826
152	152	0.00401
153	153	0.052
154	154	0.295
155	155	0.299
156	156	0.0156
157	157	0.436
158	158	0.0231
159	159	0.139
160	160	0.371
161	161	0.747
162	162	0.586
163	163	0.353
164	164	0.00691
165	165	0.809
166	166	0.804
167	167	0.0316
168	168	0.434
169	169	0.142
17	17	0.317
18	18	0.984
19	19	0.27
2	2	0.0763
20	20	0.794
21	21	0.325
22	22	0.0645
23	23	0.0711
24	24	0.236
25	25	0.214
26	26	0.396
27	27	0.738
28	28	0.648
29	29	0.548
3	3	0.884
30	30	0.194
31	31	0.33
32	32	0.00984
33	33	0.774
34	34	0.15
35	35	0.493
36	36	0.129
37	37	0.148
38	38	0.528
39	39	0.262
4	4	0.778
40	40	0.871
41	41	0.819
42	42	0.951
43	43	0.734
44	44	0.209
45	45	0.228
46	46	0.222
47	47	0.656
48	48	0.737
49	49	0.171
5	5	0.176
50	50	0.12
51	51	0.462
52	52	0.0627
53	53	0.814
54	54	0.511
55	55	0.477
56	56	0.406
57	57	0.56
58	58	0.124
59	59	0.079
6	6	0.798
60	60	0.099
61	61	0.705
62	62	0.435
63	63	0.0454
64	64	0.386
65	65	0.0583
66	66	0.313
67	67	0.963
68	68	0.713
69	69	0.257
7	7	0.223
70	70	0.0814
71	71	0.583
72	72	0.708
73	73	0.00507
74	74	0.186
75	75	0.642
76	76	0.114
77	77	0.00442
78	78	0.0129
79	79	0.883
8	8	0.645
80	80	0.327
81	81	0.936
82	82	0.903
83	83	0.8
84	84	0.202
85	85	0.0499
86	86	0.946
87	87	8.85116e-4
88	88	0.421
89	89	0.75
9	9	0.574
90	90	0.487
91	91	0.561
92	92	0.768
93	93	0.148
94	94	0.0428
95	95	0.0276
96	96	0.14
97	97	0.832
98	98	0.105
99	99	0.281

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: CNhs12129

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@SAMD00004686
+|accession_numbers=CAGE;DRX008808;DRR009680;DRZ001105;DRZ002490;DRZ012455;DRZ013840
 |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=chr11:116196664..116196679,-!p1@Foxj1!2.16!214.19!Foxj1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.11!234.62!Tsc22d4;;chrX:90531838..90531861,+!p1@Arx!1.91!100.18!Arx;;chr8:87297280..87297326,-!p2@Nfix!1.86!161.91!Nfix;;chr2:38206744..38206766,+!p1@Lhx2!1.81!76.23!Lhx2;;chr16:91270004..91270023,+!p1@Olig1!1.81!72.94!Olig1;;chr3:34548909..34548927,+!p1@Sox2!1.80!102.37!Sox2;;chr14:122874619..122874634,+!p1@Zic2!1.79!60.85!Zic2;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.65!54.48!Pou3f3;;chrX:55284180..55284195,+!p2@Zic3!1.65!43.50!Zic3;;chr11:21901608..21901634,-!p1@Otx1!1.49!29.66!Otx1;;chr16:15887371..15887385,+!p1@Cebpd!1.47!915.87!Cebpd;;chr4:109650609..109650653,+!p1@Dmrta2!1.47!28.56!Dmrta2;;chr13:53568104..53568156,-!p1@Msx2!1.42!36.91!Msx2;;chr5:38215819..38215823,-!p1@Msx1!1.40!61.29!Msx1;;chr3:34548946..34548972,+!p2@Sox2!1.38!25.26!Sox2;;chr8:87297330..87297365,-!p5@Nfix!1.38!22.85!Nfix;;chr19:59533221..59533271,+!p1@Emx2!1.35!26.14!Emx2;;chr14:49287186..49287225,-!p1@Otx2!1.33!20.21!Otx2;;chr12:54349410..54349461,+!p1@Npas3!1.27!21.31!Npas3;;chr2:38206580..38206600,+!p2@Lhx2!1.26!21.31!Lhx2;;chrX:137077716..137077734,-!p1@Tsc22d3!1.24!116.21!Tsc22d3;;chr7:25292141..25292158,+!p2@Zfp428!1.24!56.02!Zfp428;;chr15:79178060..79178074,+!p2@Maff!1.21!19.77!Maff;;chr6:72185232..72185272,-!p1@Atoh8!1.20!42.18!Atoh8;;chr4:135699731..135699747,+!p1@Id3!1.14!1430.82!Id3;;chr4:154010409..154010466,-!p2@Prdm16!1.14!29.88!Prdm16;;chr19:25685023..25685043,+!p1@Dmrt3!1.14!12.74!Dmrt3;;chr10:84218895..84218909,+!p1@Rfx4!1.11!11.86!Rfx4;;chr1:169619683..169619694,+!p1@Lmx1a!1.09!11.42!Lmx1a;;chr9:91260616..91260653,-!p2@Zic1!1.06!10.54!Zic1;;chr13:78338076..78338104,-!p4@Nr2f1!1.05!12.96!Nr2f1;;chr3:34549096..34549111,+!p3@Sox2!1.05!10.33!Sox2;;chr9:91260594..91260612,-!p1@Zic1!1.05!10.11!Zic1;;chr17:86020510..86020589,+!p3@Six3!1.05!10.11!Six3;;chr12:50485973..50486015,+!p2@Foxg1!1.05!10.11!Foxg1;;chrX:55283799..55283813,+!p1@Zic3!1.05!10.11!Zic3;;chr13:78339428..78339466,-!p2@Nr2f1!1.02!12.96!Nr2f1;;chr6:72185210..72185228,-!p3@Atoh8!1.01!16.04!Atoh8;;chr11:21901587..21901604,-!p2@Otx1!1.00!9.01!Otx1;;chr9:48644037..48644067,-!p2@Zbtb16!0.99!22.19!Zbtb16;;chr13:48356475..48356492,+!p1@Id4!0.98!188.71!Id4;;chr9:106356278..106356292,+!p3@Pcbp4!0.98!14.94!Pcbp4;;chr13:78339476..78339515,-!p1@Nr2f1!0.98!13.40!Nr2f1;;chr12:34642510..34642530,+!p1@Twist1!0.97!27.02!Twist1;;chr8:87297878..87297935,-!p3@Nfix!0.97!18.89!Nfix;;chr14:122874593..122874610,+!p2@Zic2!0.96!8.13!Zic2;;chr5:77524250..77524300,-!p1@Hopx!0.95!163.89!Hopx;;chr8:87238155..87238187,-!p13@Nfix!0.95!7.91!Nfix;;chr7:25292160..25292213,+!p3@Zfp428!0.94!19.55!Zfp428;;chr2:172375081..172375105,+!p1@Tfap2c!0.94!7.69!Tfap2c;;chr14:122874718..122874729,+!p3@Zic2!0.94!7.69!Zic2;;chr11:60023912..60023930,-!p1@Srebf1!0.93!190.91!Srebf1;;chr13:78339382..78339420,-!p3@Nr2f1!0.93!9.01!Nr2f1;;chr11:112643496..112643562,+!p1@Sox9!0.92!283.40!Sox9;;chr15:76287876..76287894,+!p1@Scx!0.91!40.86!Scx;;chr8:28087609..28087634,+!p1@Zfp703!0.90!165.42!Zfp703;;chr19:28754692..28754757,-!p1@Glis3!0.89!29.66!Glis3;;chr12:50483639..50483654,+!p1@Foxg1!0.89!6.81!Foxg1;;chr10:84218800..84218829,+!p2@Rfx4!0.89!6.81!Rfx4;;chr9:63869510..63869530,-!p10@Smad6!0.89!6.81!Smad6;;chr9:106356243..106356264,+!p2@Pcbp4!0.88!29.88!Pcbp4;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!0.88!6.59!Eno1;;chr11:96690797..96690813,-!p1@Nfe2l1!0.87!131.37!Nfe2l1;;chr6:72185553..72185612,-!p2@Atoh8!0.87!12.74!Atoh8;;chr9:91266261..91266282,+!p5@Zic4!0.87!6.37!Zic4;;chr16:91225808..91225824,+!p1@Olig2!0.87!6.37!Olig2;;chr7:91558392..91558434,-!p1@Arnt2!0.86!18.23!Arnt2;;chrX:137135036..137135064,-!p4@Tsc22d3!0.86!12.74!Tsc22d3;;chr17:86020156..86020183,+!p1@Six3!0.85!6.15!Six3;;chr12:120085700..120085711,+!p1@Sp8!0.85!6.15!Sp8;;chr7:119822957..119822980,+!p2@Tead1!0.84!30.32!Tead1;;chr15:79178029..79178044,+!p4@Maff!0.84!7.47!Maff;;chr17:86020115..86020128,+!p2@Six3!0.84!5.93!Six3;;chr14:118636238..118636257,-!p2@Sox21!0.84!5.93!Sox21;;chr17:56970339..56970428,-!p1@Rfx2!0.83!19.33!Rfx2;;chr18:69752912..69752928,+!p9@Tcf4!0.83!9.01!Tcf4;;chr14:49287107..49287125,-!p3@Otx2!0.83!5.71!Otx2;;chr5:125538737..125538781,-!p2@Ncor2!0.82!21.31!Ncor2;;chr9:106356265..106356276,+!p4@Pcbp4!0.82!9.45!Pcbp4;;chr9:106356211..106356242,+!p1@Pcbp4!0.81!113.58!Pcbp4;;chr16:91270091..91270143,+!p2@Olig1!0.78!5.05!Olig1;;chr8:87324243..87324277,-!p1@Nfix!0.77!130.27!Nfix;;chr12:34642682..34642753,+!p2@Twist1!0.77!13.84!Twist1;;chr2:105509045..105509071,+!p1@Pax6!0.77!4.83!Pax6;;chr11:5761889..5761969,+!p1@Aebp1!0.76!218.37!Aebp1;;chr8:87324171..87324182,-!p6@Nfix!0.76!8.57!Nfix;;chr5:77543897..77543911,-!p2@Hopx!0.75!9.45!Hopx;;chr5:24108047..24108106,-!p3@Smarcd3!0.75!8.57!Smarcd3;;chr10:42303385..42303401,-!p1@Nr2e1!0.75!4.61!Nr2e1;;chr2:38194778..38194798,+!p3@Lhx2!0.75!4.61!Lhx2;;chr17:86012772..86012825,+!p4@Six3!0.75!4.61!Six3;;chr13:78338032..78338049,-!p8@Nr2f1!0.75!4.61!Nr2f1;;chr16:22439681..22439698,-!p1@Etv5!0.73!84.58!Etv5;;chr2:30700881..30700916,+!p1@Prrx2!0.73!8.79!Prrx2;;chr2:105515793..105515808,+!p3@Pax6!0.73!4.39!Pax6;;chr15:81633203..81633215,+!p3@Tef!0.72!7.03!Tef;;chr6:145814003..145814056,-!p1@Bhlhe41!0.71!13.18!Bhlhe41;;chrX:137077608..137077619,-!p6@Tsc22d3!0.71!5.71!Tsc22d3;;chr8:87298020..87298041,-!p9@Nfix!0.71!4.17!Nfix;;chr19:59533139..59533152,+!p2@Emx2!0.71!4.17!Emx2;;chr2:152561980..152561997,+!p1@Id1!0.70!132.91!Id1;;chr7:17647736..17647772,-!p1@Hif3a!0.70!15.82!Hif3a;;chr15:79178013..79178028,+!p3@Maff!0.70!5.49!Maff;;chr11:96690779..96690790,-!p3@Nfe2l1!0.69!10.33!Nfe2l1;;chr19:5447886..5447905,+!p1@Fosl1!0.69!3.95!Fosl1;;chr19:25684746..25684751,+!p2@Dmrt3!0.69!3.95!Dmrt3;;chr8:12395603..12395621,+!p1@Sox1!0.69!3.95!Sox1;;chr10:42303410..42303422,-!p3@Nr2e1!0.68!3.73!Nr2e1;;chr19:59532915..59532940,+!p5@Emx2!0.68!3.73!Emx2;;chr1:42752559..42752566,+!p@chr1:42752559..42752566,+!0.68!3.73!Pou3f3;;chr19:28754600..28754612,-!p2@Glis3!0.67!6.37!Glis3;;chr2:30700857..30700873,+!p3@Prrx2!0.67!5.27!Prrx2;;chr7:25292076..25292114,+!p4@Zfp428!0.66!10.98!Zfp428;;chr7:30092993..30093076,+!p1@Dpf1!0.66!6.59!Dpf1;;chr8:72356384..72356434,+!p2@Pbx4!0.66!5.93!Pbx4;;chr1:9690398..9690410,-!p2@Mybl1!0.66!4.39!Mybl1;;chr19:28754622..28754633,-!p4@Glis3!0.66!4.17!Glis3;;chr16:4594740..4594759,+!p1@Glis2!0.65!46.57!Glis2;;chr11:52096804..52096896,-!p1@Tcf7!0.65!32.95!Tcf7;;chr6:90412556..90412581,+!p3@Klf15!0.65!8.35!Klf15;;chr6:72185179..72185196,-!p4@Atoh8!0.65!4.83!Atoh8;;chr10:42303452..42303470,-!p2@Nr2e1!0.65!3.51!Nr2e1;;chr1:169619239..169619257,+!p4@Lmx1a!0.65!3.51!Lmx1a;;chr17:86020468..86020504,+!p6@Six3!0.65!3.51!Six3;;chr19:44831390..44831414,+!p1@Pax2!0.65!3.51!Pax2;;chr12:50483778..50483789,+!p6@Foxg1!0.65!3.51!Foxg1;;chr14:13178361..13178386,-!p2@Fezf2!0.65!3.51!Fezf2;;chr4:149611803..149611814,+!p6@LOC100045967,p6@LOC100503183,p7@Eno1,p8@Gm5506!0.65!3.51!Eno1;;chr9:48644306..48644364,-!p1@Zbtb16!0.64!15.60!Zbtb16;;chr4:154010918..154010931,-!p1@Prdm16!0.64!11.20!Prdm16;;chr18:69753168..69753186,+!p12@Tcf4!0.64!4.83!Tcf4;;chr5:125538703..125538715,-!p5@Ncor2!0.64!4.17!Ncor2;;chr7:52960555..52960662,+!p1@Dbp!0.63!32.95!Dbp;;chr6:90412582..90412601,+!p1@Klf15!0.63!17.79!Klf15;;chrX:137077653..137077669,-!p3@Tsc22d3!0.63!17.14!Tsc22d3;;chr11:5761979..5761992,+!p2@Aebp1!0.63!7.25!Aebp1;;chr9:106355684..106355744,+!p5@Pcbp4!0.63!5.27!Pcbp4;;chr5:138199339..138199346,+!p18@Tsc22d4!0.63!3.30!Tsc22d4;;chr12:57636034..57636087,-!p1@Nkx2-1!0.63!3.30!Nkx2-1;;chr14:118636214..118636235,-!p1@Sox21!0.62!3.95!Sox21;;chr10:76424613..76424689,-!p1@Pcbp3!0.61!78.65!Pcbp3;;chr15:81977802..81977828,+!p2@Srebf2!0.61!31.63!Srebf2;;chrX:137077699..137077705,-!p8@Tsc22d3!0.61!4.17!Tsc22d3;;chrX:108009761..108009788,+!p1@Pou3f4!0.61!3.08!Pou3f4;;chr14:118635860..118635885,-!p3@Sox21!0.61!3.08!Sox21;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.61!3.08!Pou3f3;;chr2:38207200..38207210,+!p13@Lhx2!0.61!3.08!Lhx2;;chr8:87502608..87502623,-!p1@Junb!0.60!58.66!Junb;;chr15:81977766..81977789,+!p3@Srebf2!0.60!22.41!Srebf2;;chr19:55816546..55816556,+!p3@Tcf7l2!0.59!12.96!Tcf7l2;;chrX:55283827..55283838,+!p3@Zic3!0.59!2.86!Zic3;;chr7:52071956..52071978,-!p1@Atf5!0.58!112.04!Atf5;;chr2:167363692..167363710,+!p1@Snai1!0.58!41.74!Snai1;;chr14:76814784..76814803,+!p7@Tsc22d1!0.58!5.93!Tsc22d1;;chr19:28754655..28754673,-!p3@Glis3!0.58!4.61!Glis3;;chr17:87153240..87153254,+!p1@Epas1!0.57!65.47!Epas1;;chr11:52096750..52096772,-!p4@Tcf7!0.57!4.61!Tcf7;;chr19:5424768..5424811,-!p2@Drap1!0.56!63.27!Drap1;;chr10:107769168..107769215,+!p1@Pawr!0.56!33.39!Pawr;;chr5:24107993..24108036,-!p2@Smarcd3!0.56!7.25!Smarcd3;;chr12:74147689..74147711,-!p1@Six1!0.56!6.59!Six1;;chr6:108610766..108610781,+!p2@Bhlhe40!0.56!5.27!Bhlhe40;;chr2:30700788..30700824,+!p2@Prrx2!0.56!4.39!Prrx2;;chr3:8667033..8667046,-!p3@Hey1!0.56!3.95!Hey1;;chr6:145813964..145813994,-!p3@Bhlhe41!0.56!3.51!Bhlhe41;;chr12:50486176..50486186,+!p8@Foxg1!0.56!2.64!Foxg1;;chr13:53568191..53568219,-!p2@Msx2!0.56!2.64!Msx2;;chr5:34530277..34530292,-!p3@Mxd4!0.55!7.69!Mxd4;;chr6:145813905..145813932,-!p2@Bhlhe41!0.55!5.49!Bhlhe41;;chr3:32264530..32264544,-!p2@Zmat3!0.55!4.39!Zmat3;;chr7:52960700..52960719,+!p2@Dbp!0.55!3.30!Dbp;;chrX:137077682..137077692,-!p5@Tsc22d3!0.54!4.39!Tsc22d3;;chr10:67599432..67599444,-!p4@Arid5b!0.54!4.39!Arid5b;;chr7:25292118..25292129,+!p8@Zfp428!0.54!3.08!Zfp428;;chr11:100800671..100800770,-!p1@Stat3!0.53!99.30!Stat3;;chr7:26067619..26067702,+!p2@Cic!0.53!17.14!Cic;;chr10:67375368..67375433,-!p1@Zfp365!0.53!4.83!Zfp365;;chr11:116196714..116196729,-!p2@Foxj1!0.53!2.42!Foxj1;;chr2:24331085..24331100,-!p1@Pax8!0.53!2.42!Pax8;;chr13:53568081..53568094,-!p3@Msx2!0.53!2.42!Msx2;;chr13:53076396..53076452,-!p1@Nfil3!0.52!53.82!Nfil3;;chr11:98636531..98636559,-!p1@Nr1d1!0.52!16.48!Nr1d1;;chr3:94819136..94819168,-!p2@Zfp687!0.52!14.50!Zfp687;;chr15:79177964..79177986,+!p1@Maff!0.52!9.8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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000197
 |is_obsolete=
+|library_id=CNhs12129
+|library_id_phase_based=2:CNhs12129
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11709
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11709
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor1.CNhs12129.11709-123B8.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor1.CNhs12129.11709-123B8.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor1.CNhs12129.11709-123B8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor1.CNhs12129.11709-123B8.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Astrocytes%2520-%2520hippocampus%252c%2520donor1.CNhs12129.11709-123B8.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Astrocytes - hippocampus, donor1
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12129,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.566246598068875,0,0,0,0,0.00190886352542928,0,0,0,0,0.0431240519609854,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.273867775589477,-0.558422792324031,0,0,0,0.0862481039219708,0,-0.123074621573855,0.00365369938596144,-0.0372991337250912,-0.897963262555856,-0.0500069254561529,0.321894675570492,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.0302507723344594,0,0,-0.0348329706539777,-0.20244242069718,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0260669842735262,0,0.0862481039219708,0,0,-0.101525405360172,0.505947887207281,-0.0788315948399074,0,0,0,0,0,0,0.337344292791396,0.256645158316561,0.219461159462403,0,0,0,0.25462426926745,0
@@ Line 83: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11709-123B8;search_select_hide=table117:11709-123B8
 }}

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FF:11709-123B8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:15, 4 June 2020

CNhs12129

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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