FF:11721-123D2: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Neurons - hippocampal, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12133
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	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	RNAMNh1
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		SAMD00005801

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12133		CAGE		DRX008837		DRR009709

Accession ID Mm9

Library id		BAM		CTSS
CNhs12133		DRZ001134		DRZ002519

Accession ID Mm10

Library id		BAM		CTSS
CNhs12133		DRZ012484		DRZ013869

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

CNhs12133

0	0
1	0.238
10	0
100	0.568
1000	-0.0104
1001	-0.0498
1002	0.202
1003	0.0522
1004	0.0251
1005	-0.184
1006	0.158
1007	0.00165
1008	0
1009	-0.2
101	-0.0723
1010	0
1011	0.1
1012	0.0446
1013	-0.16
1014	0
1015	0.433
1016	0.034
1017	0
1018	0
1019	0
102	0
1020	0.568
1021	0.191
1022	-0.124
1023	0
1024	-0.171
1025	-0.0611
1026	0
1027	0.489
1028	0
1029	-0.148
103	-0.0861
1030	0
1031	-0.529
1032	-0.177
1033	-0.025
1034	0
1035	0
1036	-0.0877
1037	0
1038	0.0726
1039	-0.233
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: CNhs12133

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00226
MA0003.1	MA0003.1	0.126
MA0004.1	MA0004.1	0.882
MA0006.1	MA0006.1	0.0885
MA0007.1	MA0007.1	0.197
MA0009.1	MA0009.1	0.961
MA0014.1	MA0014.1	0.374
MA0017.1	MA0017.1	2.03512e-5
MA0018.2	MA0018.2	0.0114
MA0019.1	MA0019.1	0.263
MA0024.1	MA0024.1	0.015
MA0025.1	MA0025.1	0.299
MA0027.1	MA0027.1	0.647
MA0028.1	MA0028.1	0.878
MA0029.1	MA0029.1	0.513
MA0030.1	MA0030.1	0.383
MA0031.1	MA0031.1	0.06
MA0035.2	MA0035.2	0.11
MA0038.1	MA0038.1	0.0134
MA0039.2	MA0039.2	0.0108
MA0040.1	MA0040.1	0.857
MA0041.1	MA0041.1	0.215
MA0042.1	MA0042.1	0.476
MA0043.1	MA0043.1	0.0162
MA0046.1	MA0046.1	1.8521e-9
MA0047.2	MA0047.2	6.1223e-4
MA0048.1	MA0048.1	0.673
MA0050.1	MA0050.1	1.0469e-8
MA0051.1	MA0051.1	0.00106
MA0052.1	MA0052.1	0.00618
MA0055.1	MA0055.1	0.8
MA0057.1	MA0057.1	0.0552
MA0058.1	MA0058.1	0.819
MA0059.1	MA0059.1	0.757
MA0060.1	MA0060.1	2.36763e-9
MA0061.1	MA0061.1	0.05
MA0062.2	MA0062.2	0.783
MA0065.2	MA0065.2	3.85793e-5
MA0066.1	MA0066.1	0.187
MA0067.1	MA0067.1	0.849
MA0068.1	MA0068.1	0.303
MA0069.1	MA0069.1	0.0814
MA0070.1	MA0070.1	0.552
MA0071.1	MA0071.1	0.23
MA0072.1	MA0072.1	0.238
MA0073.1	MA0073.1	0.921
MA0074.1	MA0074.1	0.337
MA0076.1	MA0076.1	0.289
MA0077.1	MA0077.1	0.00344
MA0078.1	MA0078.1	0.00582
MA0079.2	MA0079.2	0.761
MA0080.2	MA0080.2	9.09905e-11
MA0081.1	MA0081.1	0.448
MA0083.1	MA0083.1	1.07457e-5
MA0084.1	MA0084.1	0.529
MA0087.1	MA0087.1	0.58
MA0088.1	MA0088.1	0.401
MA0090.1	MA0090.1	0.0099
MA0091.1	MA0091.1	0.409
MA0092.1	MA0092.1	0.21
MA0093.1	MA0093.1	0.882
MA0099.2	MA0099.2	8.14343e-5
MA0100.1	MA0100.1	0.651
MA0101.1	MA0101.1	0.136
MA0102.2	MA0102.2	0.731
MA0103.1	MA0103.1	0.0705
MA0104.2	MA0104.2	0.356
MA0105.1	MA0105.1	0.0833
MA0106.1	MA0106.1	0.155
MA0107.1	MA0107.1	0.0761
MA0108.2	MA0108.2	0.00877
MA0111.1	MA0111.1	0.889
MA0112.2	MA0112.2	2.70533e-4
MA0113.1	MA0113.1	0.525
MA0114.1	MA0114.1	1.30914e-4
MA0115.1	MA0115.1	0.0425
MA0116.1	MA0116.1	0.112
MA0117.1	MA0117.1	0.838
MA0119.1	MA0119.1	0.132
MA0122.1	MA0122.1	0.914
MA0124.1	MA0124.1	0.929
MA0125.1	MA0125.1	0.133
MA0131.1	MA0131.1	0.556
MA0135.1	MA0135.1	0.36
MA0136.1	MA0136.1	4.65355e-7
MA0137.2	MA0137.2	0.0521
MA0138.2	MA0138.2	0.741
MA0139.1	MA0139.1	0.224
MA0140.1	MA0140.1	0.00723
MA0141.1	MA0141.1	0.0089
MA0142.1	MA0142.1	0.00167
MA0143.1	MA0143.1	9.53859e-4
MA0144.1	MA0144.1	0.0485
MA0145.1	MA0145.1	0.0261
MA0146.1	MA0146.1	0.0496
MA0147.1	MA0147.1	0.415
MA0148.1	MA0148.1	1.55932e-5
MA0149.1	MA0149.1	0.092
MA0150.1	MA0150.1	0.0658
MA0152.1	MA0152.1	0.381
MA0153.1	MA0153.1	1.94808e-8
MA0154.1	MA0154.1	0.0209
MA0155.1	MA0155.1	0.629
MA0156.1	MA0156.1	2.94742e-4
MA0157.1	MA0157.1	0.0198
MA0159.1	MA0159.1	0.00361
MA0160.1	MA0160.1	0.0914
MA0162.1	MA0162.1	0.277
MA0163.1	MA0163.1	0.00775
MA0164.1	MA0164.1	0.935
MA0258.1	MA0258.1	0.00965
MA0259.1	MA0259.1	0.403

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: CNhs12133

Novel motif	Logo	P-value
1	1	0.179
10	10	0.203
100	100	0.995
101	101	0.955
102	102	0.796
103	103	0.073
104	104	0.933
105	105	0.229
106	106	0.00517
107	107	0.0281
108	108	0.666
109	109	0.00285
11	11	0.0766
110	110	0.146
111	111	0.0265
112	112	0.00372
113	113	0.992
114	114	0.13
115	115	0.279
116	116	0.557
117	117	0.198
118	118	0.474
119	119	0.144
12	12	0.477
120	120	0.963
121	121	0.285
122	122	0.662
123	123	0.584
124	124	0.567
125	125	0.505
126	126	0.205
127	127	0.102
128	128	0.0142
129	129	0.0992
13	13	3.42542e-5
130	130	0.775
131	131	0.532
132	132	0.756
133	133	0.228
134	134	0.488
135	135	0.208
136	136	0.0773
137	137	0.335
138	138	0.579
139	139	0.151
14	14	0.606
140	140	0.398
141	141	0.12
142	142	0.23
143	143	0.812
144	144	0.859
145	145	0.0425
146	146	0.439
147	147	0.965
148	148	0.5
149	149	0.0465
15	15	0.194
150	150	0.199
151	151	0.388
152	152	0.0289
153	153	0.961
154	154	0.989
155	155	0.384
156	156	0.00409
157	157	0.168
158	158	0.301
159	159	0.0178
160	160	0.228
161	161	0.368
162	162	0.752
163	163	0.167
164	164	0.0254
165	165	0.0132
166	166	0.618
167	167	0.572
168	168	0.729
169	169	0.00697
17	17	0.021
18	18	0.772
19	19	0.0375
2	2	0.506
20	20	0.869
21	21	0.546
22	22	0.0664
23	23	0.181
24	24	0.0365
25	25	0.841
26	26	0.00123
27	27	0.671
28	28	0.432
29	29	0.314
3	3	0.0964
30	30	0.519
31	31	0.701
32	32	0.225
33	33	0.283
34	34	0.534
35	35	0.521
36	36	0.917
37	37	0.00977
38	38	0.348
39	39	0.152
4	4	0.569
40	40	0.289
41	41	0.856
42	42	0.355
43	43	0.142
44	44	0.54
45	45	0.38
46	46	0.184
47	47	0.194
48	48	0.161
49	49	0.175
5	5	0.192
50	50	0.226
51	51	0.581
52	52	0.0756
53	53	0.634
54	54	0.579
55	55	0.921
56	56	0.305
57	57	0.717
58	58	0.306
59	59	0.0604
6	6	0.628
60	60	0.00987
61	61	0.267
62	62	0.163
63	63	0.106
64	64	0.927
65	65	0.28
66	66	0.572
67	67	0.711
68	68	0.447
69	69	0.379
7	7	0.0393
70	70	0.013
71	71	0.0394
72	72	0.382
73	73	0.0136
74	74	0.339
75	75	0.131
76	76	0.851
77	77	0.138
78	78	0.0383
79	79	0.611
8	8	0.222
80	80	0.865
81	81	0.374
82	82	0.0302
83	83	0.0992
84	84	0.866
85	85	0.0303
86	86	0.304
87	87	0.338
88	88	0.347
89	89	0.318
9	9	0.315
90	90	0.409
91	91	0.27
92	92	0.117
93	93	0.0364
94	94	0.93
95	95	0.0444
96	96	0.314
97	97	0.876
98	98	0.701
99	99	0.168

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: CNhs12133

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000202 mouse hippocampal 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)
0002608 (hippocampal neuron)

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)
0000201 (hippocampal neuron sample)
0000203 (mouse neuron samples)
0000202 (mouse hippocampal 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
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+|DRA_sample_Accession=CAGE@SAMD00005801
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002371,CL:0002319,CL:0000221,CL:0000117,CL:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0002608,CL:0002609,CL:0000133,CL:0000337
+|accession_numbers=CAGE;DRX008837;DRR009709;DRZ001134;DRZ002519;DRZ012484;DRZ013869
+|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:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002609,CL:0002608
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000201,FF:0000203,FF:0000202
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:71384802..71384815,-!p1@Dlx2!2.37!283.32!Dlx2;;chr6:55631042..55631102,-!p1@Neurod6!2.35!220.48!Neurod6;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!2.28!234.81!Pou3f3;;chrX:90531838..90531861,+!p1@Arx!2.27!227.47!Arx;;chr11:98190918..98190951,-!p1@Neurod2!2.14!136.82!Neurod2;;chr12:28027561..28027591,-!p1@Sox11!2.05!685.34!Sox11;;chr8:12395603..12395621,+!p1@Sox1!1.98!94.20!Sox1;;chr1:179374784..179374800,+!p2@Zfp238!1.96!106.08!Zfp238;;chr2:61642631..61642684,+!p1@Tbr1!1.91!80.35!Tbr1;;chr10:86956396..86956411,-!p1@Ascl1!1.85!105.95!Ascl1;;chr6:6832076..6832092,-!p1@Dlx5!1.83!78.03!Dlx5;;chrX:108009761..108009788,+!p1@Pou3f4!1.81!64.19!Pou3f4;;chr3:34548909..34548927,+!p1@Sox2!1.80!101.91!Sox2;;chr2:146047829..146047847,+!p1@Insm1!1.75!96.52!Insm1;;chr15:76352832..76352900,-!p1@Scrt1!1.70!49.00!Scrt1;;chr2:71367871..71367898,+!p1@Dlx1!1.69!48.02!Dlx1;;chr2:73109983..73109996,+!p1@Sp9!1.69!47.89!Sp9;;chr2:71367142..71367167,+!p2@Dlx1!1.68!46.79!Dlx1;;chr12:109242266..109242295,-!p1@Bcl11b!1.63!335.38!Bcl11b;;chr7:30088977..30089002,+!p2@Dpf1!1.62!55.24!Dpf1;;chr3:95032091..95032183,-!p1@Mllt11!1.61!319.33!Mllt11;;chr12:30213247..30213333,+!p1@Myt1l!1.59!37.85!Myt1l;;chr4:154335024..154335039,+!p1@Hes5!1.58!43.97!Hes5;;chr3:127336052..127336058,+!p1@Neurog2!1.56!35.40!Neurog2;;chr2:71384458..71384526,-!p2@Dlx2!1.56!35.40!Dlx2;;chr2:71366660..71366702,+!p3@Dlx1!1.53!32.95!Dlx1;;chr5:98609885..98609900,+!p1@Prdm8!1.50!30.62!Prdm8;;chr13:117099847..117099907,-!p1@Isl1!1.46!50.47!Isl1;;chr7:116154364..116154444,+!p1@Tub!1.44!45.44!Tub;;chr2:73110004..73110016,+!p2@Sp9!1.44!26.58!Sp9;;chr2:61642743..61642758,+!p2@Tbr1!1.44!26.46!Tbr1;;chr2:38206744..38206766,+!p1@Lhx2!1.43!31.48!Lhx2;;chrX:58146612..58146615,-!p1@Sox3!1.43!26.09!Sox3;;chr7:30092993..30093076,+!p1@Dpf1!1.41!42.26!Dpf1;;chr3:34548946..34548972,+!p2@Sox2!1.40!26.46!Sox2;;chr12:50483639..50483654,+!p1@Foxg1!1.40!24.38!Foxg1;;chr12:54349410..54349461,+!p1@Npas3!1.39!28.54!Npas3;;chr2:115891534..115891589,-!p1@Meis2!1.37!308.80!Meis2;;chr2:65683890..65683907,+!p1@Csrnp3!1.36!41.52!Csrnp3;;chr17:86020156..86020183,+!p1@Six3!1.36!22.17!Six3;;chr2:35959541..35959548,-!p2@Lhx6!1.35!21.56!Lhx6;;chr4:124334894..124334899,+!p1@Pou3f1!1.34!26.83!Pou3f1;;chr1:57028125..57028149,-!p2@Satb2!1.34!21.07!Satb2;;chr9:118387300..118387317,+!p1@Eomes!1.34!21.07!Eomes;;chr2:79296783..79296801,-!p1@Neurod1!1.34!20.70!Neurod1;;chr17:25707623..25707639,-!p1@Sox8!1.33!84.40!Sox8;;chr16:91225808..91225824,+!p1@Olig2!1.33!20.58!Olig2;;chr2:61642558..61642595,+!p3@Tbr1!1.33!20.46!Tbr1;;chr17:48015839..48015915,-!p3@Foxp4!1.30!22.05!Foxp4;;chr2:38206580..38206600,+!p2@Lhx2!1.29!22.54!Lhx2;;chr7:91558472..91558512,-!p2@Arnt2!1.26!24.50!Arnt2;;chr1:169528457..169528482,+!p3@Rxrg!1.26!17.15!Rxrg;;chr16:91270004..91270023,+!p1@Olig1!1.25!18.99!Olig1;;chr7:25292160..25292213,+!p3@Zfp428!1.24!40.18!Zfp428;;chr15:76352740..76352781,-!p5@Scrt1!1.24!16.41!Scrt1;;chr6:6831950..6831985,-!p2@Dlx5!1.22!17.39!Dlx5;;chr2:151907546..151907561,+!p1@Scrt2!1.21!15.31!Scrt2;;chr3:17954233..17954249,+!p1@Bhlhe22!1.21!15.07!Bhlhe22;;chr10:42303385..42303401,-!p1@Nr2e1!1.21!15.07!Nr2e1;;chr8:12395500..12395511,+!p5@Sox1!1.20!14.82!Sox1;;chr7:25292141..25292158,+!p2@Zfp428!1.19!50.22!Zfp428;;chr6:6831928..6831949,-!p3@Dlx5!1.19!14.45!Dlx5;;chr17:86020510..86020589,+!p3@Six3!1.19!14.33!Six3;;chr11:23977742..23977794,+!p6@Bcl11a!1.17!17.15!Bcl11a;;chr4:150503457..150503498,-!p3@Camta1!1.16!15.07!Camta1;;chrX:108009734..108009752,+!p2@Pou3f4!1.16!13.60!Pou3f4;;chr1:179374820..179374831,+!p3@Zfp238!1.14!12.86!Zfp238;;chr14:118636238..118636257,-!p2@Sox21!1.14!12.74!Sox21;;chr4:22415443..22415506,-!p1@Pou3f2!1.14!12.74!Pou3f2;;chr5:75471615..75471622,+!p1@Gsx2!1.13!12.62!Gsx2;;chr12:30219426..30219506,+!p2@Myt1l!1.13!12.62!Myt1l;;chr11:23980664..23980706,+!p2@Bcl11a!1.12!52.67!Bcl11a;;chr2:115890953..115890974,-!p6@Meis2!1.12!18.62!Meis2;;chr11:98190955..98190968,-!p2@Neurod2!1.12!12.25!Neurod2;;chr19:19185671..19185693,-!p1@Rorb!1.11!28.30!Rorb;;chr11:23978229..23978268,+!p8@Bcl11a!1.11!13.60!Bcl11a;;chr13:78338076..78338104,-!p4@Nr2f1!1.10!14.58!Nr2f1;;chr2:181501745..181501778,+!p1@Myt1!1.10!11.51!Myt1;;chr11:23978270..23978290,+!p9@Bcl11a!1.09!11.39!Bcl11a;;chr11:23978291..23978323,+!p7@Bcl11a!1.09!11.27!Bcl11a;;chr2:71367979..71367993,+!p7@Dlx1!1.09!11.27!Dlx1;;chr13:29045559..29045574,-!p1@Sox4!1.08!903.12!Sox4;;chr2:71368815..71368836,+!p4@Dlx1!1.08!10.90!Dlx1;;chr2:151907338..151907360,+!p2@Scrt2!1.07!10.66!Scrt2;;chr19:7342725..7342784,+!p1@Rcor2!1.05!42.01!Rcor2;;chr11:23978111..23978134,+!p3@Bcl11a!1.05!21.44!Bcl11a;;chr7:25292331..25292421,+!p1@Zfp428!1.04!71.66!Zfp428;;chr7:30089006..30089022,+!p3@Dpf1!1.04!10.04!Dpf1;;chr1:169528520..169528542,+!p2@Rxrg!1.04!10.04!Rxrg;;chr6:6813269..6813272,+!p2@Dlx6!1.04!10.04!Dlx6;;chr1:179374764..179374776,+!p5@Zfp238!1.03!9.80!Zfp238;;chr2:71368786..71368813,+!p5@Dlx1!1.03!9.80!Dlx1;;chr12:109242296..109242307,-!p3@Bcl11b!1.02!14.09!Bcl11b;;chr6:144157924..144157955,-!p2@Sox5!1.02!12.00!Sox5;;chr6:144152648..144152680,-!p5@Sox5!1.02!9.55!Sox5;;chr17:86020115..86020128,+!p2@Six3!1.02!9.55!Six3;;chr12:50485973..50486015,+!p2@Foxg1!1.02!9.43!Foxg1;;chr17:37139472..37139514,+!p1@Zfp57!1.01!62.96!Zfp57;;chr9:18278055..18278126,-!p1@Zfp558!1.01!26.95!Zfp558;;chr5:24104751..24104773,-!p5@Smarcd3!1.01!9.19!Smarcd3;;chr12:12948633..12948651,-!p1@Mycn!1.00!89.17!Mycn;;chr4:122673278..122673336,+!p1@Mycl1!1.00!29.03!Mycl1;;chr13:78339382..78339420,-!p3@Nr2f1!1.00!10.78!Nr2f1;;chr8:12395670..12395682,+!p3@Sox1!1.00!9.06!Sox1;;chr8:12395629..12395644,+!p6@Sox1!1.00!9.06!Sox1;;chr15:76352677..76352737,-!p3@Scrt1!1.00!8.94!Scrt1;;chr4:22415290..22415307,-!p2@Pou3f2!1.00!8.94!Pou3f2;;chr1:57028157..57028173,-!p3@Satb2!1.00!8.94!Satb2;;chr1:189821714..189821761,+!p1@Esrrg!0.99!16.54!Esrrg;;chr13:29045321..29045337,-!p2@Sox4!0.99!11.88!Sox4;;chr13:44936126..44936164,+!p6@Jarid2!0.99!10.17!Jarid2;;chr12:109241728..109241781,-!p2@Bcl11b!0.99!9.43!Bcl11b;;chr2:71384401..71384424,-!p3@Dlx2!0.99!8.82!Dlx2;;chr6:38204274..38204327,-!p3@D630045J12Rik!0.98!17.39!D630045J12Rik;;chr3:101814061..101814094,+!p1@Nhlh2!0.98!8.57!Nhlh2;;chr10:42303452..42303470,-!p2@Nr2e1!0.98!8.45!Nr2e1;;chr2:181501710..181501742,+!p2@Myt1!0.98!8.45!Myt1;;chr19:59244875..59244895,-!p2@Vax1!0.98!8.45!Vax1;;chr7:91558392..91558434,-!p1@Arnt2!0.97!23.52!Arnt2;;chr4:13670499..13670526,+!p2@Runx1t1!0.97!18.99!Runx1t1;;chr4:54957886..54957907,+!p3@Zfp462!0.97!14.70!Zfp462;;chr14:118636214..118636235,-!p1@Sox21!0.97!10.17!Sox21;;chr15:76353005..76353021,-!p2@Scrt1!0.97!8.33!Scrt1;;chr3:34549096..34549111,+!p3@Sox2!0.96!8.21!Sox2;;chr2:71384425..71384456,-!p4@Dlx2!0.96!8.08!Dlx2;;chr12:50483663..50483678,+!p3@Foxg1!0.96!8.08!Foxg1;;chrX:108009798..108009815,+!p3@Pou3f4!0.96!8.08!Pou3f4;;chr4:150482563..150482655,-!p2@Camta1!0.95!28.79!Camta1;;chr4:13670571..13670625,+!p1@Runx1t1!0.95!22.17!Runx1t1;;chr19:59533221..59533271,+!p1@Emx2!0.95!9.80!Emx2;;chr6:6812962..6812979,+!p1@Dlx6!0.95!7.96!Dlx6;;chr4:119960301..119960359,-!p1@Foxo6!0.94!25.48!Foxo6;;chr2:35960919..35960954,-!p1@Lhx6!0.94!14.94!Lhx6;;chr2:152223783..152223812,-!p4@Sox12!0.93!17.64!Sox12;;chr2:56967334..56967366,-!p1@Nr4a2!0.93!15.68!Nr4a2;;chr2:181498020..181498040,+!p5@Myt1!0.93!7.59!Myt1;;chr2:71366574..71366587,+!p8@Dlx1!0.93!7.59!Dlx1;;chr14:13178147..13178185,-!p1@Fezf2!0.93!7.47!Fezf2;;chr12:3891753..3891801,+!p4@Dnmt3a!0.92!12.25!Dnmt3a;;chr1:179374862..179374873,+!p6@Zfp238!0.92!7.23!Zfp238;;chr6:6812988..6813002,+!p3@Dlx6!0.92!7.23!Dlx6;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.91!19.60!Zfhx3;;chr17:37140628..37140631,+!p2@Zfp57!0.91!14.58!Zfp57;;chr1:57029281..57029326,-!p1@Satb2!0.90!11.02!Satb2;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.89!6.74!Pou3f3;;chr14:13178361..13178386,-!p2@Fezf2!0.89!6.74!Fezf2;;chr9:106356278..106356292,+!p3@Pcbp4!0.88!11.51!Pcbp4;;chr2:65683842..65683856,+!p3@Csrnp3!0.88!6.61!Csrnp3;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.87!12.62!D630045J12Rik;;chr12:3891810..3891829,+!p2@Dnmt3a!0.87!10.17!Dnmt3a;;chr13:78339428..78339466,-!p2@Nr2f1!0.87!9.06!Nr2f1;;chr19:7342786..7342803,+!p2@Rcor2!0.87!8.70!Rcor2;;chr1:6720216..6720232,+!p1@St18!0.87!6.49!St18;;chr11:21901608..21901634,-!p1@Otx1!0.87!6.49!Otx1;;chr2:115890864..115890869,-!p14@Meis2!0.87!6.37!Meis2;;chr1:169528491..169528505,+!p4@Rxrg!0.87!6.37!Rxrg;;chr13:48356475..48356492,+!p1@Id4!0.86!145.76!Id4;;chr9:21420744..21420755,+!p3@Smarca4!0.86!18.86!Smarca4;;chr6:55631251..55631265,-!p2@Neurod6!0.86!6.25!Neurod6;;chr5:122345353..122345358,-!p5@Cux2!0.86!6.25!Cux2;;chr2:151906844..151906873,+!p3@Scrt2!0.86!6.25!Scrt2;;chr8:87297280..87297326,-!p2@Nfix!0.85!14.82!Nfix;;chr5:148000254..148000260,+!p1@Gsx1!0.85!6.12!Gsx1;;chr2:172375081..172375105,+!p1@Tfap2c!0.85!6.00!Tfap2c;;chr4:82145196..82145229,-!p7@Nfib!0.85!6.00!Nfib;;chr3:51144477..51144506,-!p6@Elf2!0.84!9.31!Elf2;;chr5:122499831..122499891,-!p1@Cux2!0.84!9.31!Cux2;;chr7:130644017..130644092,-!p1@Zkscan2!0.83!11.76!Zkscan2;;chr18:69753168..69753186,+!p12@Tcf4!0.83!7.96!Tcf4;;chr5:24104540..24104584,-!p7@Smarcd3!0.83!5.76!Smarcd3;;chr8:12395874..12395885,+!p2@Sox1!0.83!5.76!Sox1;;chr15:75447105..75447159,+!p1@Zfp41!0.82!24.13!Zfp41;;chr7:135019147..135019187,-!p3@Zfp668!0.82!12.98!Zfp668;;chr6:144157968..144157989,-!p7@Sox5!0.82!5.63!Sox5;;chr8:47379946..47379955,-!p1@Helt!0.82!5.63!Helt;;chr6:14851440..14851497,+!p2@Foxp2!0.81!14.09!Foxp2;;chr1:170361730..170361769,-!p7@Pbx1!0.81!12.98!Pbx1;;chr1:57028606..57028625,-!p4@Satb2!0.81!5.51!Satb2;;chr2:65768174..65768247,+!p2@Csrnp3!0.81!5.39!Csrnp3;;chr1:173987720..173987729,-!p1@Nhlh1!0.81!5.39!Nhlh1;;chr13:44936077..44936096,+!p9@Jarid2!0.81!5.39!Jarid2;;chr12:28027256..28027282,-!p2@Sox11!0.81!5.39!Sox11;;chr12:30220074..30220102,+!p3@Myt1l!0.81!5.39!Myt1l;;chr11:23978078..23978096,+!p4@Bcl11a!0.80!17.27!Bcl11a;;chr4:22415600..22415616,-!p3@Pou3f2!0.80!5.27!Pou3f2;;chr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kna;;chr18:69753145..69753159,+!p14@Tcf4!0.63!4.65!Tcf4;;chr16:43503594..43503634,+!p15@Zbtb20!0.63!4.04!Zbtb20;;chr12:109241852..109241873,-!p4@Bcl11b!0.63!4.04!Bcl11b;;chr11:23978206..23978219,+!p12@Bcl11a!0.63!3.31!Bcl11a;;chr4:82145232..82145259,-!p9@Nfib!0.63!3.31!Nfib;;chr3:34548845..34548856,+!p4@Sox2!0.63!3.31!Sox2;;chr14:13178323..13178347,-!p3@Fezf2!0.63!3.31!Fezf2;;chr7:38557887..38557910,-!p5@Zfp536!0.63!3.31!Zfp536;;chr4:82151274..82151290,-!p3@Nfib!0.62!60.63!Nfib;;chr3:5218629..5218684,+!p1@Zfhx4!0.62!11.76!Zfhx4;;chr4:54957910..54957954,+!p2@Zfp462!0.62!11.02!Zfp462;;chr11:44430989..44431015,+!p4@Ebf1!0.62!6.25!Ebf1;;chr11:18918434..18918489,-!p3@Meis1!0.62!5.39!Meis1;;chr12:72149359..72149406,+!p4@Arid4a!0.62!4.41!Arid4a;;chr19:19185697..19185711,-!p2@Rorb!0.62!4.29!Rorb;;chr15:76352799..76352809,-!p7@Scrt1!0.62!3.18!Scrt1;;chr8:112229478..112229536,+!p1@Zfp821!0.61!32.46!Zfp821;;chr18:55149735..55149776,-!p4@Zfp608!0.61!8.45!Zfp608;;chr4:63071739..63071760,-!p5@Akna!0.61!4.78!Akna;;chr7:25292223..25292234,+!p7@Zfp428!0.61!4.04!Zfp428;;chr8:12395843..12395852,+!p7@Sox1!0.61!3.06!Sox1;;chr2:81893535..81893548,+!p1@Zfp804a!0.61!3.06!Zfp804a;;chr4:109650609..109650653,+!p1@Dmrta2!0.61!3.06!Dmrta2;;chr13:56353536..56353542,-!p1@Neurog1!0.61!3.06!Neurog1;;chr9:55785981..55786009,-!p2@Scaper!0.60!9.31!Scaper;;chr1:38684383..38684394,-!p4@Aff3!0.60!4.29!Aff3;;chr17:37139519..37139531,+!p5@Zfp57!0.60!3.67!Zfp57;;chr7:123182248..123182264,-!p3@Sox6!0.60!3.67!Sox6;;chr17:86020468..86020504,+!p6@Six3!0.60!2.94!Six3;;chr14:118635860..118635885,-!p3@Sox21!0.60!2.94!Sox21;;chr1:6724908..6724955,+!p2@St18!0.60!2.94!St18;;chr9:91260594..91260612,-!p1@Zic1!0.60!2.94!Zic1;;chr1:173341474..173341513,+!p2@Usf1!0.59!47.65!Usf1;;chr10:127896315..127896333,+!p2@Smarcc2!0.59!9.06!Smarcc2;;chr8:92872177..92872201,-!p2@Tox3!0.59!5.63!Tox3;;chr9:21420812..21420815,+!p6@Smarca4!0.59!4.78!Smarca4;;chr7:25292246..25292259,+!p6@Zfp428!0.59!3.80!Zfp428;;chr11:98603119..98603130,+!p2@Thra!0.58!28.79!Thra;;chr10:13685585..13685645,+!p2@Hivep2!0.58!11.39!Hivep2;;chr1:38684431..38684450,-!p3@Aff3!0.58!5.02!Aff3;;chr18:69752912..69752928,+!p9@Tcf4!0.58!4.65!Tcf4;;chr7:37483231..37483263,+!p2@Tshz3!0.58!4.65!Tshz3;;chr12:30220046..30220070,+!p6@Myt1l!0.58!2.82!Myt1l;;chr4:97248473..97248496,+!p16@Nfia!0.58!2.82!Nfia;;chr4:13678723..13678739,+!p10@Runx1t1!0.58!2.82!Runx1t1;;chr12:109241804..109241823,-!p5@Bcl11b!0.58!2.82!Bcl11b;;chr17:48061584..48061601,-!p2@Foxp4!0.57!21.31!Foxp4;;chr17:35031524..35031539,+!p4@Zbtb12!0.57!3.80!Zbtb12;;chr7:25292118..25292129,+!p8@Zfp428!0.57!3.43!Zfp428;;chr7:91558537..91558558,-!p4@Arnt2!0.57!3.43!Arnt2;;chr3:95032213..95032226,-!p6@Mllt11!0.57!3.43!Mllt11;;chr17:86020137..86020149,+!p5@Six3!0.57!2.69!Six3;;chr5:122500227..122500240,-!p6@Cux2!0.57!2.69!Cux2;;chr6:144157991..144158007,-!p9@Sox5!0.57!2.69!Sox5;;chr2:105509045..105509071,+!p1@Pax6!0.57!2.69!Pax6;;chr2:65768149..65768173,+!p4@Csrnp3!0.57!2.69!Csrnp3;;chr10:42303434..42303445,-!p4@Nr2e1!0.57!2.69!Nr2e1;;chr10:79862089..79862129,-!p2@Mbd3!0.56!36.01!Mbd3;;chr8:112229540..112229566,+!p2@Zfp821!0.56!6.61!Zfp821;;chr7:25292310..25292329,+!p5@Zfp428!0.56!4.04!Zfp428;;chr2:152223852..152223872,-!p7@Sox12!0.56!3.67!Sox12;;chr1:38684414..38684427,-!p7@Aff3!0.56!3.31!Aff3;;chr1:170362273..170362317,-!p1@Pbx1!0.55!93.22!Pbx1;;chr1:93309740..93309811,-!p1@Hes6!0.55!64.55!Hes6;;chr8:108939219..108939296,+!p1@Zfp90!0.55!34.30!Zfp90;;chr1:170362040..170362113,-!p2@Pbx1!0.55!24.99!Pbx1;;chr1:170362242..170362256,-!p3@Pbx1!0.55!22.91!Pbx1;;chr17:48061605..48061629,-!p6@Foxp4!0.55!12.49!Foxp4;;chr2:163028808..163028869,+!p1@Tox2!0.55!11.02!Tox2;;chr13:15555670..15555771,+!p2@Gli3!0.55!7.59!Gli3;;chr18:55149986..55150009,-!p7@Zfp608!0.55!5.63!Zfp608;;chr13:29044875..29044928,-!p4@Sox4!0.55!3.67!Sox4;;chr3:153991607..153991627,-!p2@Lhx8!0.55!2.57!Lhx8;;chr19:59245978..59245982,-!p1@Vax1!0.55!2.57!Vax1;;chr2:151907110..151907126,+!p6@Scrt2!0.55!2.57!Scrt2;;chr1:179375791..179375803,+!p10@Zfp238!0.55!2.57!Zfp238;;chr10:84218895..84218909,+!p1@Rfx4!0.55!2.57!Rfx4;;chr7:17199897..17199955,-!p1@Grlf1!0.54!35.15!Grlf1;;chr7:88005795..88005858,+!p1@Zscan2!0.54!21.93!Zscan2;;chr18:65741935..65741964,+!p2@Zfp532!0.54!8.08!Zfp532;;chr8:87297878..87297935,-!p3@Nfix!0.54!6.37!Nfix;;chr11:98602203..98602266,+!p4@Thra!0.54!4.29!Thra;;chr14:65568567..65568588,-!p3@Hmbox1!0.54!4.16!Hmbox1;;chr12:72149325..72149343,+!p2@Arid4a!0.54!3.80!Arid4a;;chrX:34442872..34442899,-!p1@Nkrf!0.54!3.43!Nkrf;;chr2:152223734..152223756,-!p6@Sox12!0.54!3.06!Sox12;;chr11:44431191..44431205,+!p11@Ebf1!0.54!2.82!Ebf1;;chr2:151907604..151907629,+!p4@Scrt2!0.54!2.45!Scrt2;;chr12:57636220..57636236,-!p3@Nkx2-1!0.54!2.45!Nkx2-1;;chr13:78338057..78338069,-!p11@Nr2f1!0.54!2.45!Nr2f1;;chr2:71367605..71367621,+!p9@Dlx1!0.54!2.45!Dlx1;;chr6:55631324..55631335,-!p3@Neurod6!0.54!2.45!Neurod6;;chr7:5003165..5003203,+!p2@Zfp580!0.53!16.78!Zfp580;;chr6:51382677..51382783,+!p1@Nfe2l3!0.53!7.23!Nfe2l3;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+|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000202
 |is_obsolete=
+|library_id=CNhs12133
+|library_id_phase_based=2:CNhs12133
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11721
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11721
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor1.CNhs12133.11721-123D2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor1.CNhs12133.11721-123D2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor1.CNhs12133.11721-123D2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor1.CNhs12133.11721-123D2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520hippocampal%252c%2520donor1.CNhs12133.11721-123D2.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Neurons - hippocampal, donor1
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12133,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0312078257577653,0,0,0,0,0,-0.339854334228546,0,0,0,0,-0.0341564505132085,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.413213384236133,-0.558422792324031,0,0,0,0,0,-0.141363441053972,0.207487332897458,-0.241867663276521,-0.251040691946138,0.964870936656776,0.392677539788484,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.00733583480045826,0,0,0,0,0,-0.134483136255326,-0.310650657339386,-0.0221724738873744,-0.0540618988688149,0,-0.0780086007519514,0.0928467529945367,0.0822222204770975,0,0,0.0575275453134798,0.0490228837767129,0.183834724112744,-0.0286488049565744,0,0,0,0,0,0,0.0582646737991566,-0.13226655490807,0.0129784022177023,0,0,0,0.413698727548783,0
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 59: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=N/A
 |sample_cell_line=
@@ Line 79: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11721-123D2;search_select_hide=table117:11721-123D2
 }}

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FF:11721-123D2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12133

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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