FF:11742-123F5: Difference between revisions

Latest revision as of 18:17, 4 June 2020

Name:	Mouse Neurons - cortical, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs11947
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	cortex
dev stage	NA
sex	NA
age	NA
cell type	neuron
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	RNAMNC3
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		SAMD00005136

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11947		CAGE		DRX008832		DRR009704

Accession ID Mm9

Library id		BAM		CTSS
CNhs11947		DRZ001129		DRZ002514

Accession ID Mm10

Library id		BAM		CTSS
CNhs11947		DRZ012479		DRZ013864

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

CNhs11947

0	0
1	0.224
10	0
100	0.833
1000	0
1001	-0.0749
1002	0.536
1003	0.853
1004	0.055
1005	-0.194
1006	0.104
1007	-0.00389
1008	0
1009	-0.19
101	-0.135
1010	0
1011	0.264
1012	0.0498
1013	-0.2
1014	0.055
1015	0.405
1016	0.233
1017	0
1018	0
1019	0
102	0
1020	0.672
1021	0.099
1022	-0.124
1023	0
1024	-0.14
1025	0
1026	0
1027	0.555
1028	0
1029	-0.122
103	-0.0754
1030	0
1031	-0.432
1032	-0.177
1033	0.101
1034	0
1035	0
1036	-0.0795
1037	0
1038	0.0822
1039	-0.219
104	0
1040	-0.216
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: CNhs11947

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00369
MA0003.1	MA0003.1	0.109
MA0004.1	MA0004.1	0.839
MA0006.1	MA0006.1	0.0836
MA0007.1	MA0007.1	0.284
MA0009.1	MA0009.1	0.719
MA0014.1	MA0014.1	0.356
MA0017.1	MA0017.1	5.90785e-6
MA0018.2	MA0018.2	0.128
MA0019.1	MA0019.1	0.316
MA0024.1	MA0024.1	0.108
MA0025.1	MA0025.1	0.209
MA0027.1	MA0027.1	0.692
MA0028.1	MA0028.1	0.788
MA0029.1	MA0029.1	0.614
MA0030.1	MA0030.1	0.293
MA0031.1	MA0031.1	0.0552
MA0035.2	MA0035.2	0.0266
MA0038.1	MA0038.1	0.455
MA0039.2	MA0039.2	0.00321
MA0040.1	MA0040.1	0.648
MA0041.1	MA0041.1	0.398
MA0042.1	MA0042.1	0.939
MA0043.1	MA0043.1	0.123
MA0046.1	MA0046.1	7.96103e-12
MA0047.2	MA0047.2	1.44571e-4
MA0048.1	MA0048.1	0.958
MA0050.1	MA0050.1	3.22891e-9
MA0051.1	MA0051.1	6.34719e-4
MA0052.1	MA0052.1	2.91227e-4
MA0055.1	MA0055.1	0.731
MA0057.1	MA0057.1	0.084
MA0058.1	MA0058.1	0.687
MA0059.1	MA0059.1	0.984
MA0060.1	MA0060.1	4.07196e-4
MA0061.1	MA0061.1	0.0588
MA0062.2	MA0062.2	0.226
MA0065.2	MA0065.2	1.18573e-5
MA0066.1	MA0066.1	0.286
MA0067.1	MA0067.1	0.935
MA0068.1	MA0068.1	0.155
MA0069.1	MA0069.1	0.0718
MA0070.1	MA0070.1	0.477
MA0071.1	MA0071.1	0.25
MA0072.1	MA0072.1	0.113
MA0073.1	MA0073.1	0.825
MA0074.1	MA0074.1	0.404
MA0076.1	MA0076.1	0.642
MA0077.1	MA0077.1	0.00191
MA0078.1	MA0078.1	0.00551
MA0079.2	MA0079.2	0.717
MA0080.2	MA0080.2	3.43002e-11
MA0081.1	MA0081.1	0.376
MA0083.1	MA0083.1	1.15086e-5
MA0084.1	MA0084.1	0.544
MA0087.1	MA0087.1	0.914
MA0088.1	MA0088.1	0.305
MA0090.1	MA0090.1	0.0218
MA0091.1	MA0091.1	0.596
MA0092.1	MA0092.1	0.38
MA0093.1	MA0093.1	0.805
MA0099.2	MA0099.2	1.35285e-5
MA0100.1	MA0100.1	0.827
MA0101.1	MA0101.1	0.13
MA0102.2	MA0102.2	0.745
MA0103.1	MA0103.1	0.0794
MA0104.2	MA0104.2	0.366
MA0105.1	MA0105.1	0.103
MA0106.1	MA0106.1	0.206
MA0107.1	MA0107.1	0.0522
MA0108.2	MA0108.2	1.40306e-4
MA0111.1	MA0111.1	0.78
MA0112.2	MA0112.2	2.2457e-4
MA0113.1	MA0113.1	0.705
MA0114.1	MA0114.1	1.94333e-5
MA0115.1	MA0115.1	0.032
MA0116.1	MA0116.1	0.171
MA0117.1	MA0117.1	0.754
MA0119.1	MA0119.1	0.245
MA0122.1	MA0122.1	0.93
MA0124.1	MA0124.1	0.978
MA0125.1	MA0125.1	0.768
MA0131.1	MA0131.1	0.801
MA0135.1	MA0135.1	0.893
MA0136.1	MA0136.1	3.94315e-9
MA0137.2	MA0137.2	0.0378
MA0138.2	MA0138.2	0.99
MA0139.1	MA0139.1	0.194
MA0140.1	MA0140.1	0.00298
MA0141.1	MA0141.1	0.019
MA0142.1	MA0142.1	0.0116
MA0143.1	MA0143.1	0.00276
MA0144.1	MA0144.1	0.0229
MA0145.1	MA0145.1	0.0235
MA0146.1	MA0146.1	0.0754
MA0147.1	MA0147.1	0.34
MA0148.1	MA0148.1	1.06741e-6
MA0149.1	MA0149.1	0.0693
MA0150.1	MA0150.1	0.0163
MA0152.1	MA0152.1	0.231
MA0153.1	MA0153.1	1.27667e-10
MA0154.1	MA0154.1	0.0281
MA0155.1	MA0155.1	0.721
MA0156.1	MA0156.1	1.41388e-6
MA0157.1	MA0157.1	0.0205
MA0159.1	MA0159.1	0.00406
MA0160.1	MA0160.1	0.077
MA0162.1	MA0162.1	0.391
MA0163.1	MA0163.1	0.0107
MA0164.1	MA0164.1	0.957
MA0258.1	MA0258.1	0.0131
MA0259.1	MA0259.1	0.334

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: CNhs11947

Novel motif	Logo	P-value
1	1	0.257
10	10	0.256
100	100	0.897
101	101	0.781
102	102	0.741
103	103	0.183
104	104	0.795
105	105	0.347
106	106	0.00914
107	107	0.0289
108	108	0.44
109	109	0.00412
11	11	0.152
110	110	0.189
111	111	0.0856
112	112	0.0048
113	113	0.865
114	114	0.522
115	115	0.211
116	116	0.657
117	117	0.171
118	118	0.746
119	119	0.171
12	12	0.448
120	120	0.796
121	121	0.132
122	122	0.332
123	123	0.716
124	124	0.519
125	125	0.328
126	126	0.183
127	127	0.109
128	128	0.04
129	129	0.174
13	13	1.04088e-5
130	130	0.746
131	131	0.556
132	132	0.98
133	133	0.49
134	134	0.595
135	135	0.287
136	136	0.103
137	137	0.239
138	138	0.662
139	139	0.313
14	14	0.585
140	140	0.902
141	141	0.0776
142	142	0.086
143	143	0.925
144	144	0.834
145	145	0.0814
146	146	0.281
147	147	0.997
148	148	0.917
149	149	0.0978
15	15	0.244
150	150	0.29
151	151	0.334
152	152	0.0341
153	153	0.689
154	154	0.97
155	155	0.871
156	156	0.00419
157	157	0.121
158	158	0.112
159	159	0.0146
160	160	0.359
161	161	0.26
162	162	0.991
163	163	0.0397
164	164	0.0172
165	165	0.0109
166	166	0.607
167	167	0.647
168	168	0.356
169	169	0.00691
17	17	0.0355
18	18	0.592
19	19	0.0376
2	2	0.489
20	20	0.895
21	21	0.761
22	22	0.0721
23	23	0.262
24	24	0.0346
25	25	0.64
26	26	0.0101
27	27	0.791
28	28	0.282
29	29	0.309
3	3	0.113
30	30	0.396
31	31	0.925
32	32	0.416
33	33	0.239
34	34	0.552
35	35	0.428
36	36	0.732
37	37	0.0058
38	38	0.44
39	39	0.246
4	4	0.533
40	40	0.189
41	41	0.824
42	42	0.369
43	43	0.186
44	44	0.796
45	45	0.411
46	46	0.266
47	47	0.277
48	48	0.233
49	49	0.22
5	5	0.192
50	50	0.313
51	51	0.669
52	52	0.0675
53	53	0.477
54	54	0.654
55	55	0.78
56	56	0.361
57	57	0.914
58	58	0.219
59	59	0.0972
6	6	0.765
60	60	0.00915
61	61	0.339
62	62	0.137
63	63	0.186
64	64	0.94
65	65	0.49
66	66	0.872
67	67	0.715
68	68	0.813
69	69	0.465
7	7	0.0225
70	70	0.0478
71	71	0.0414
72	72	0.334
73	73	0.0137
74	74	0.604
75	75	0.141
76	76	0.85
77	77	0.174
78	78	0.0412
79	79	0.996
8	8	0.367
80	80	0.615
81	81	0.321
82	82	0.0839
83	83	0.115
84	84	0.642
85	85	0.0761
86	86	0.252
87	87	0.248
88	88	0.499
89	89	0.206
9	9	0.351
90	90	0.353
91	91	0.555
92	92	0.119
93	93	0.0169
94	94	0.563
95	95	0.0473
96	96	0.259
97	97	0.85
98	98	0.637
99	99	0.275

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: CNhs11947

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000204 cortical mouse neuron 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)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002609 (neuron of cerebral cortex)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
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)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000204 (cortical mouse neuron 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:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005136
+|accession_numbers=CAGE;DRX008832;DRR009704;DRZ001129;DRZ002514;DRZ012479;DRZ013864
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,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:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002609
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr6:55631042..55631102,-!p1@Neurod6!2.82!662.47!Neurod6;;chr11:98190918..98190951,-!p1@Neurod2!2.53!336.30!Neurod2;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!2.47!371.27!Pou3f3;;chr1:179374784..179374800,+!p2@Zfp238!2.30!230.59!Zfp238;;chr3:127336052..127336058,+!p1@Neurog2!2.29!192.38!Neurog2;;chr12:28027561..28027591,-!p1@Sox11!2.26!1125.41!Sox11;;chr2:61642631..61642684,+!p1@Tbr1!2.23!169.70!Tbr1;;chr9:118387300..118387317,+!p1@Eomes!2.17!147.83!Eomes;;chr2:38206580..38206600,+!p2@Lhx2!1.98!115.03!Lhx2;;chr8:87297280..87297326,-!p2@Nfix!1.95!199.54!Nfix;;chr2:146047829..146047847,+!p1@Insm1!1.94!152.02!Insm1;;chr2:38206744..38206766,+!p1@Lhx2!1.94!102.06!Lhx2;;chrX:90531838..90531861,+!p1@Arx!1.87!90.72!Arx;;chr12:30213247..30213333,+!p1@Myt1l!1.79!60.89!Myt1l;;chr15:76352832..76352900,-!p1@Scrt1!1.75!55.22!Scrt1;;chr1:57028125..57028149,-!p2@Satb2!1.73!52.11!Satb2;;chr8:87297330..87297365,-!p5@Nfix!1.70!48.87!Nfix;;chr5:98609885..98609900,+!p1@Prdm8!1.69!47.93!Prdm8;;chr2:61642743..61642758,+!p2@Tbr1!1.67!46.31!Tbr1;;chr3:17954233..17954249,+!p1@Bhlhe22!1.67!46.17!Bhlhe22;;chr12:50483639..50483654,+!p1@Foxg1!1.66!45.09!Foxg1;;chrX:58146612..58146615,-!p1@Sox3!1.65!43.74!Sox3;;chr3:95032091..95032183,-!p1@Mllt11!1.64!347.51!Mllt11;;chr1:179374820..179374831,+!p3@Zfp238!1.63!41.72!Zfp238;;chr7:30088977..30089002,+!p2@Dpf1!1.59!52.38!Dpf1;;chr14:13178361..13178386,-!p2@Fezf2!1.58!36.86!Fezf2;;chr14:13178147..13178185,-!p1@Fezf2!1.57!36.18!Fezf2;;chr2:79296783..79296801,-!p1@Neurod1!1.56!35.64!Neurod1;;chr5:24104751..24104773,-!p5@Smarcd3!1.55!34.16!Smarcd3;;chr6:85137520..85137563,+!p1@Emx1!1.54!34.02!Emx1;;chr8:12395603..12395621,+!p1@Sox1!1.54!33.48!Sox1;;chr7:116154364..116154444,+!p1@Tub!1.52!54.68!Tub;;chr7:30092993..30093076,+!p1@Dpf1!1.52!54.27!Dpf1;;chr6:144152648..144152680,-!p5@Sox5!1.52!32.40!Sox5;;chr13:29045321..29045337,-!p2@Sox4!1.49!40.50!Sox4;;chr11:98190955..98190968,-!p2@Neurod2!1.49!29.57!Neurod2;;chr6:144157924..144157955,-!p2@Sox5!1.48!35.91!Sox5;;chr2:61642558..61642595,+!p3@Tbr1!1.48!29.30!Tbr1;;chr1:57028157..57028173,-!p3@Satb2!1.47!28.22!Satb2;;chr2:71384802..71384815,-!p1@Dlx2!1.45!33.35!Dlx2;;chr17:48015839..48015915,-!p3@Foxp4!1.44!31.19!Foxp4;;chr1:179374862..179374873,+!p6@Zfp238!1.43!26.19!Zfp238;;chr13:56353536..56353542,-!p1@Neurog1!1.43!25.92!Neurog1;;chr12:109242266..109242295,-!p1@Bcl11b!1.42!205.75!Bcl11b;;chr4:22415443..22415506,-!p1@Pou3f2!1.42!25.11!Pou3f2;;chr11:23978111..23978134,+!p3@Bcl11a!1.41!50.63!Bcl11a;;chr4:109650609..109650653,+!p1@Dmrta2!1.40!23.90!Dmrta2;;chr3:17954392..17954407,+!p2@Bhlhe22!1.39!23.76!Bhlhe22;;chr1:57028606..57028625,-!p4@Satb2!1.39!23.76!Satb2;;chr2:151907546..151907561,+!p1@Scrt2!1.38!22.82!Scrt2;;chr2:172375081..172375105,+!p1@Tfap2c!1.38!22.82!Tfap2c;;chr1:179374764..179374776,+!p5@Zfp238!1.37!22.68!Zfp238;;chr4:154335024..154335039,+!p1@Hes5!1.35!25.79!Hes5;;chr19:59533221..59533271,+!p1@Emx2!1.34!25.38!Emx2;;chr11:21901608..21901634,-!p1@Otx1!1.34!21.06!Otx1;;chr12:50483663..50483678,+!p3@Foxg1!1.34!20.79!Foxg1;;chr1:173987720..173987729,-!p1@Nhlh1!1.34!20.79!Nhlh1;;chr3:101814061..101814094,+!p1@Nhlh2!1.34!20.66!Nhlh2;;chr4:124334894..124334899,+!p1@Pou3f1!1.33!26.60!Pou3f1;;chr12:50485973..50486015,+!p2@Foxg1!1.33!20.39!Foxg1;;chr14:13178323..13178347,-!p3@Fezf2!1.31!19.44!Fezf2;;chr19:7342725..7342784,+!p1@Rcor2!1.29!74.39!Rcor2;;chr7:25292160..25292213,+!p3@Zfp428!1.28!44.55!Zfp428;;chr6:55631251..55631265,-!p2@Neurod6!1.28!18.09!Neurod6;;chr4:119960301..119960359,-!p1@Foxo6!1.27!55.62!Foxo6;;chr1:57029281..57029326,-!p1@Satb2!1.27!27.27!Satb2;;chr18:69680960..69681007,+!p10@Tcf4!1.27!22.95!Tcf4;;chr11:23977742..23977794,+!p6@Bcl11a!1.27!22.14!Bcl11a;;chr10:42303385..42303401,-!p1@Nr2e1!1.27!17.69!Nr2e1;;chr10:86956396..86956411,-!p1@Ascl1!1.25!25.92!Ascl1;;chr4:22415290..22415307,-!p2@Pou3f2!1.24!16.20!Pou3f2;;chr2:105515635..105515661,+!p5@Pax6!1.24!16.20!Pax6;;chr8:87297878..87297935,-!p3@Nfix!1.23!35.10!Nfix;;chr4:54957886..54957907,+!p3@Zfp462!1.23!27.14!Zfp462;;chr9:118387969..118387984,+!p2@Eomes!1.23!16.07!Eomes;;chr2:151906844..151906873,+!p3@Scrt2!1.23!15.93!Scrt2;;chr5:24104540..24104584,-!p7@Smarcd3!1.22!15.66!Smarcd3;;chr7:25292141..25292158,+!p2@Zfp428!1.18!49.41!Zfp428;;chr7:91558472..91558512,-!p2@Arnt2!1.18!19.98!Arnt2;;chr8:87298020..87298041,-!p9@Nfix!1.18!14.04!Nfix;;chr3:34548909..34548927,+!p1@Sox2!1.17!23.36!Sox2;;chr11:23978229..23978268,+!p8@Bcl11a!1.17!15.66!Bcl11a;;chr14:118636238..118636257,-!p2@Sox21!1.17!13.91!Sox21;;chr2:151907338..151907360,+!p2@Scrt2!1.17!13.77!Scrt2;;chr2:181501745..181501778,+!p1@Myt1!1.17!13.64!Myt1;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!1.16!13.50!Pou3f3;;chr17:37140628..37140631,+!p2@Zfp57!1.15!26.06!Zfp57;;chr4:82145196..82145229,-!p7@Nfib!1.15!13.23!Nfib;;chrX:108009761..108009788,+!p1@Pou3f4!1.15!13.10!Pou3f4;;chr2:115891534..115891589,-!p1@Meis2!1.14!180.50!Meis2;;chr12:12948633..12948651,-!p1@Mycn!1.14!123.40!Mycn;;chr4:122673278..122673336,+!p1@Mycl1!1.13!39.15!Mycl1;;chr13:78338076..78338104,-!p4@Nr2f1!1.13!15.53!Nr2f1;;chr3:34549144..34549155,+!p5@Sox2!1.13!12.42!Sox2;;chr12:109242296..109242307,-!p3@Bcl11b!1.12!17.69!Bcl11b;;chr13:29045559..29045574,-!p1@Sox4!1.11!983.65!Sox4;;chr4:82151274..82151290,-!p3@Nfib!1.11!191.98!Nfib;;chr13:78339382..78339420,-!p3@Nr2f1!1.11!13.91!Nr2f1;;chr12:30219426..30219506,+!p2@Myt1l!1.11!11.88!Myt1l;;chr11:23980664..23980706,+!p2@Bcl11a!1.10!50.36!Bcl11a;;chr13:78339428..78339466,-!p2@Nr2f1!1.08!15.26!Nr2f1;;chr14:118636214..118636235,-!p1@Sox21!1.08!13.23!Sox21;;chr2:152223783..152223812,-!p4@Sox12!1.07!24.98!Sox12;;chr7:30089006..30089022,+!p3@Dpf1!1.06!10.40!Dpf1;;chr11:21901587..21901604,-!p2@Otx1!1.06!10.40!Otx1;;chr9:21420744..21420755,+!p3@Smarca4!1.05!30.11!Smarca4;;chr19:19185671..19185693,-!p1@Rorb!1.05!24.44!Rorb;;chr4:150503457..150503498,-!p3@Camta1!1.05!11.61!Camta1;;chr2:38194778..38194798,+!p3@Lhx2!1.05!10.26!Lhx2;;chr4:48058129..48058179,+!p2@Nr4a3!1.04!18.90!Nr4a3;;chr18:69753168..69753186,+!p12@Tcf4!1.04!13.37!Tcf4;;chr6:38204274..38204327,-!p3@D630045J12Rik!1.03!19.71!D630045J12Rik;;chr6:6832076..6832092,-!p1@Dlx5!1.03!11.34!Dlx5;;chr17:37139472..37139514,+!p1@Zfp57!1.02!64.94!Zfp57;;chr10:13685585..13685645,+!p2@Hivep2!1.02!33.48!Hivep2;;chr13:78339476..78339515,-!p1@Nr2f1!1.02!14.58!Nr2f1;;chr6:144157968..144157989,-!p7@Sox5!1.02!9.45!Sox5;;chr19:7342786..7342803,+!p2@Rcor2!1.01!12.56!Rcor2;;chr13:29045252..29045271,-!p5@Sox4!1.01!11.61!Sox4;;chr12:54349410..54349461,+!p1@Npas3!1.01!11.21!Npas3;;chr14:13178241..13178254,-!p4@Fezf2!1.01!9.18!Fezf2;;chr6:144157893..144157905,-!p14@Sox5!1.01!9.18!Sox5;;chr4:87678709..87678726,-!p4@Mllt3!1.00!28.35!Mllt3;;chr4:48058016..48058032,+!p3@Nr4a3!1.00!15.53!Nr4a3;;chr1:179372625..179372654,+!p4@Zfp238!1.00!13.91!Zfp238;;chr18:69753145..69753159,+!p14@Tcf4!1.00!12.42!Tcf4;;chr4:82145232..82145259,-!p9@Nfib!1.00!8.91!Nfib;;chr2:35960919..35960954,-!p1@Lhx6!0.98!16.20!Lhx6;;chr3:34549096..34549111,+!p3@Sox2!0.98!8.64!Sox2;;chr11:23978270..23978290,+!p9@Bcl11a!0.98!8.51!Bcl11a;;chr10:42303452..42303470,-!p2@Nr2e1!0.97!8.37!Nr2e1;;chr13:29045274..29045293,-!p6@Sox4!0.96!9.86!Sox4;;chr1:57028111..57028122,-!p9@Satb2!0.96!8.10!Satb2;;chr2:151907110..151907126,+!p6@Scrt2!0.95!7.97!Scrt2;;chr2:105515586..105515606,+!p4@Pax6!0.95!7.83!Pax6;;chr12:28027256..28027282,-!p2@Sox11!0.95!7.83!Sox11;;chr2:71367142..71367167,+!p2@Dlx1!0.95!7.83!Dlx1;;chr13:29044875..29044928,-!p4@Sox4!0.94!10.40!Sox4;;chr11:23978291..23978323,+!p7@Bcl11a!0.94!7.70!Bcl11a;;chr6:144158267..144158282,-!p16@Sox5!0.94!7.70!Sox5;;chr2:73109983..73109996,+!p1@Sp9!0.94!7.70!Sp9;;chr15:76352740..76352781,-!p5@Scrt1!0.93!7.43!Scrt1;;chr1:179372543..179372557,+!p9@Zfp238!0.93!7.43!Zfp238;;chr2:105509045..105509071,+!p1@Pax6!0.93!7.43!Pax6;;chr4:13670499..13670526,+!p2@Runx1t1!0.92!16.88!Runx1t1;;chr4:22415600..22415616,-!p3@Pou3f2!0.92!7.29!Pou3f2;;chr8:87238155..87238187,-!p13@Nfix!0.92!7.29!Nfix;;chr9:18278055..18278126,-!p1@Zfp558!0.91!21.33!Zfp558;;chr1:170361991..170362015,-!p6@Pbx1!0.91!16.34!Pbx1;;chr7:37483231..37483263,+!p2@Tshz3!0.91!11.07!Tshz3;;chr7:25292331..25292421,+!p1@Zfp428!0.90!52.38!Zfp428;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.90!13.37!D630045J12Rik;;chr1:57028556..57028583,-!p5@Satb2!0.90!7.02!Satb2;;chr3:95032184..95032195,-!p4@Mllt11!0.89!8.51!Mllt11;;chr15:100430414..100430470,-!p1@Pou6f1!0.88!21.33!Pou6f1;;chr2:71367871..71367898,+!p1@Dlx1!0.88!6.62!Dlx1;;chr9:106356278..106356292,+!p3@Pcbp4!0.87!11.48!Pcbp4;;chr4:87678639..87678653,-!p11@Mllt3!0.87!8.10!Mllt3;;chr13:29045174..29045188,-!p7@Sox4!0.87!7.70!Sox4;;chr9:91260616..91260653,-!p2@Zic1!0.87!6.48!Zic1;;chr15:76353005..76353021,-!p2@Scrt1!0.87!6.35!Scrt1;;chr17:35031460..35031518,+!p1@Zbtb12!0.86!33.48!Zbtb12;;chr15:100325682..100325698,-!p1@Csrnp2!0.86!30.92!Csrnp2;;chr11:23978078..23978096,+!p4@Bcl11a!0.86!20.12!Bcl11a;;chr2:56967334..56967366,-!p1@Nr4a2!0.86!13.23!Nr4a2;;chr5:122499831..122499891,-!p1@Cux2!0.86!9.99!Cux2;;chr2:152223762..152223777,-!p8@Sox12!0.86!7.16!Sox12;;chr3:34548946..34548972,+!p2@Sox2!0.86!7.02!Sox2;;chr18:69681020..69681032,+!p23@Tcf4!0.86!6.21!Tcf4;;chr11:98603185..98603208,+!p1@Thra!0.85!393.00!Thra;;chr15:75447105..75447159,+!p1@Zfp41!0.84!24.98!Zfp41;;chr7:25292076..25292114,+!p4@Zfp428!0.84!16.88!Zfp428;;chr7:135019147..135019187,-!p3@Zfp668!0.84!13.50!Zfp668;;chr4:87678673..87678706,-!p6@Mllt3!0.84!13.37!Mllt3;;chr2:65683890..65683907,+!p1@Csrnp3!0.84!11.88!Csrnp3;;chr6:144157991..144158007,-!p9@Sox5!0.84!5.94!Sox5;;chr1:38684260..38684312,-!p2@Aff3!0.83!43.07!Aff3;;chr11:98603160..98603171,+!p3@Thra!0.83!28.76!Thra;;chr4:150482563..150482655,-!p2@Camta1!0.83!21.87!Camta1;;chr2:152223881..152223933,-!p3@Sox12!0.83!20.66!Sox12;;chr7:25292118..25292129,+!p8@Zfp428!0.83!7.02!Zfp428;;chr2:151906968..151906988,+!p5@Scrt2!0.83!5.81!Scrt2;;chr6:85137491..85137504,+!p3@Emx1!0.83!5.81!Emx1;;chr10:82226649..82226694,-!p2@Nfyb!0.82!38.34!Nfyb;;ch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bpl1!0.35!48.60!Tbpl1;;chr19:5424768..5424811,-!p2@Drap1!0.35!37.94!Drap1;;chr12:84828663..84828679,-!p1@Dpf3!0.35!14.99!Dpf3;;chr17:34169016..34169068,+!p2@Rxrb!0.35!14.18!Rxrb;;chr2:164860321..164860359,-!p2@Ncoa5!0.35!13.50!Ncoa5;;chr3:8666963..8666978,-!p1@Hey1!0.35!12.42!Hey1;;chr5:31754800..31754825,+!p2@Zfp512!0.35!9.59!Zfp512;;chr14:52634412..52634500,-!p2@Zfp219!0.35!8.64!Zfp219;;chr18:79306158..79306249,-!p1@Setbp1!0.35!6.08!Setbp1;;chr13:15555079..15555136,+!p3@Gli3!0.35!5.81!Gli3;;chr7:30857891..30857943,-!p1@LOC100505067,p3@Zfp82!0.35!4.73!Zfp82;;chr7:35841581..35841605,-!p2@Cebpg!0.35!4.46!Cebpg;;chr5:24107903..24107917,-!p6@Smarcd3!0.35!1.76!Smarcd3;;chr16:43503720..43503739,+!p18@Zbtb20!0.35!1.49!Zbtb20;;chr17:51951383..51951409,-!p19@Satb1!0.35!1.22!Satb1;;chr9:96632719..96632745,-!p7@Zbtb38!0.35!1.22!Zbtb38;;chr7:38554684..38554696,-!p10@Zfp536!0.35!1.22!Zfp536;;chr2:71368815..71368836,+!p4@Dlx1!0.35!1.22!Dlx1;;chr4:150503544..150503561,-!p8@Camta1!0.35!1.22!Camta1;;chr4:32325928..32325939,+!p11@Bach2!0.35!1.22!Bach2;;chr2:81893535..81893548,+!p1@Zfp804a!0.35!1.22!Zfp804a;;chr1:6720216..6720232,+!p1@St18!0.35!1.22!St18;;chr14:118635860..118635885,-!p3@Sox21!0.35!1.22!Sox21;;chr13:78335738..78335747,-!p24@Nr2f1!0.35!1.22!Nr2f1;;chr14:118636183..118636192,-!p4@Sox21!0.35!1.22!Sox21;;chr13:31717597..31717613,+!p2@Foxf2!0.35!1.22!Foxf2;;chr5:24104452..24104472,-!p11@Smarcd3!0.35!1.22!Smarcd3;;chr11:98614697..98614707,+!p15@Thra!0.35!1.22!Thra;;chr13:53076396..53076452,-!p1@Nfil3!0.34!34.97!Nfil3;;chr18:69753015..69753104,+!p1@Tcf4!0.34!26.19!Tcf4;;chr6:86476190..86476201,-!p3@Pcbp1!0.34!24.98!Pcbp1;;chr10:22451142..22451191,-!p2@Tbpl1!0.34!19.17!Tbpl1;;chr13:55431084..55431137,-!p1@Mxd3!0.34!14.85!Mxd3;;chr7:5003117..5003159,+!p1@Zfp580!0.34!14.31!Zfp580;;chr2:154439063..154439105,+!p1@Zfp341!0.34!11.75!Zfp341;;chr7:17200019..17200060,-!p4@Grlf1!0.34!8.10!Grlf1;;chr2:152223441..152223465,-!p2@Sox12!0.34!7.56!Sox12;;chr13:15555035..15555073,+!p4@Gli3!0.34!4.59!Gli3;;chr15:57526316..57526332,+!p4@Zhx2!0.34!3.92!Zhx2;;chr14:76814883..76814898,+!p9@Tsc22d1!0.34!3.24!Tsc22d1;;chr18:69839537..69839544,+!p13@Tcf4!0.34!2.70!Tcf4;;chr7:134169648..134169657,-!p14@Maz!0.34!2.03!Maz;;chr1:170361678..170361689,-!p13@Pbx1!0.34!1.62!Pbx1;;chr1:120950149..120950160,-!p7@Gli2!0.34!1.35!Gli2;;chr10:12810631..12810649,+!p1@Plagl1!0.33!50.22!Plagl1;;chr1:64167972..64168026,-!p1@Klf7!0.33!45.23!Klf7;;chr5:143996822..143996930,+!p1@Zfp12!0.33!39.42!Zfp12;;chr17:28314075..28314159,+!p1@Zfp523!0.33!22.68!Zfp523;;chr2:72818459..72818528,-!p3@Sp3!0.33!13.64!Sp3;;chr2:156665817..156665877,+!p1@Tgif2!0.33!11.75!Tgif2;;chr2:44968737..44968758,-!p2@Zeb2!0.33!10.40!Zeb2;;chr7:148513599..148513636,-!p3@Deaf1!0.33!6.89!Deaf1;;chr18:69504123..69504155,+!p5@Tcf4!0.33!6.35!Tcf4;;chr15:57526469..57526534,+!p1@Zhx2!0.33!6.21!Zhx2;;chr12:77470461..77470504,-!p3@Zbtb25!0.33!5.13!Zbtb25;;chr7:4947724..4947743,-!p3@Zfp579!0.33!3.65!Zfp579;;chr2:126501253..126501268,-!p3@Gabpb1!0.33!3.51!Gabpb1;;chr2:44972821..44972865,-!p10@Zeb2!0.33!3.11!Zeb2;;chr7:17199962..17199972,-!p7@Grlf1!0.33!2.16!Grlf1;;chr3:94668075..94668087,+!p6@Pogz!0.33!2.03!Pogz;;chr8:87324203..87324206,-!p10@Nfix!0.33!1.89!Nfix;;chr17:51971932..51971958,-!p2@Satb1!0.33!1.89!Satb1;;chr5:107003725..107003746,-!p5@Zfp644!0.33!1.76!Zfp644;;chr11:121121297..121121369,+!p1@Foxk2!0.32!111.24!Foxk2;;chr5:125343044..125343141,+!p1@Zfp664!0.32!81.68!Zfp664;;chr9:110034519..110034606,+!p1@Smarcc1!0.32!81.41!Smarcc1;;chr17:57074836..57074927,-!p1@Mllt1!0.32!51.57!Mllt1;;chr16:23988711..23988727,-!p1@Bcl6!0.32!21.74!Bcl6;;chr11:120494853..120494905,-!p1@Mafg!0.32!17.69!Mafg;;chr7:24919167..24919203,+!p1@Zfp235!0.32!13.10!Zfp235;;chr18:65741358..65741415,+!p1@Zfp532!0.32!7.56!Zfp532;;chr7:30836380..30836430,-!p1@Zfp14!0.32!6.62!Zfp14;;chr8:81923412..81923431,-!p2@Smad1!0.32!6.21!Smad1;;chr18:55150011..55150059,-!p3@Zfp608!0.32!5.54!Zfp608;;chr7:148513548..148513560,-!p7@Deaf1!0.32!2.16!Deaf1;;chr2:156666727..156666753,+!p2@Tgif2!0.32!2.03!Tgif2;;chr17:51971960..51971979,-!p1@Satb1!0.32!1.76!Satb1;;chr1:170361695..170361722,-!p12@Pbx1!0.32!1.62!Pbx1;;chr15:40486854..40486867,+!p7@Zfpm2!0.32!1.49!Zfpm2;;chr13:31717614..31717628,+!p3@Foxf2!0.32!1.08!Foxf2;;chr15:76352799..76352809,-!p7@Scrt1!0.32!1.08!Scrt1;;chr2:156665757..156665768,+!p7@Tgif2!0.32!1.08!Tgif2;;chr2:163051181..163051205,+!p2@Tox2!0.32!1.08!Tox2;;chr2:172376261..172376267,+!p4@Tfap2c!0.32!1.08!Tfap2c;;chr7:147235047..147235079,-!p2@Msx3!0.32!1.08!Msx3;;chr6:6813269..6813272,+!p2@Dlx6!0.32!1.08!Dlx6;;chr7:123182318..123182332,-!p11@Sox6!0.32!1.08!Sox6;;chr4:48058196..48058205,+!p4@Nr4a3!0.32!1.08!Nr4a3;;chr3:101814037..101814046,+!p2@Nhlh2!0.32!1.08!Nhlh2;;chr2:71384541..71384555,-!p6@Dlx2!0.32!1.08!Dlx2;;chr4:97248389..97248402,+!p21@Nfia!0.32!1.08!Nfia;;chr2:71384401..71384424,-!p3@Dlx2!0.32!1.08!Dlx2;;chr10:84218931..84218942,+!p4@Rfx4!0.32!1.08!Rfx4;;chrX:98624993..98625047,+!p1@Nono!0.31!316.99!Nono;;chr8:13869673..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+|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000204
 |is_obsolete=
+|library_id=CNhs11947
+|library_id_phase_based=2:CNhs11947
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11742
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11742
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520cortical%252c%2520donor2.CNhs11947.11742-123F5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520cortical%252c%2520donor2.CNhs11947.11742-123F5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520cortical%252c%2520donor2.CNhs11947.11742-123F5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520cortical%252c%2520donor2.CNhs11947.11742-123F5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520cortical%252c%2520donor2.CNhs11947.11742-123F5.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - cortical, donor2
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11947,LSID836,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.079873308133669,0,0,0,0,0,-0.185895480115689,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0657937730229687,0,0,0,0,0,0,0,0,0,0,0,0,0.579719609956359,-0.558422792324031,0,0,0,0,0,-0.0234705551451111,0.103807782330171,-0.00108419689905936,-0.206406262331573,0.554273435086359,0.0549981337564001,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0,-0.0811796440958188,-0.206842875009215,-0.0542832604409114,-0.0213292688003332,0,-0.0230104669955513,0.0835915849691429,0,0,0,0.0326928470057874,-0.00801812562191595,0.406052261792375,-0.0238334610835073,0,0,0,0,0,0,0.215128282687886,0.238888272223523,0.0800745526910252,0,0,0,0.518467531314141,0
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 60: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=N/A
 |sample_cell_line=
@@ Line 80: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11742-123F5;search_select_hide=table117:11742-123F5
 }}

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FF:11742-123F5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:17, 4 June 2020

CNhs11947

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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