FF:11809-124D9: Difference between revisions

Latest revision as of 18:21, 4 June 2020

Name:	neurospheres - parasympathetic neuron derived, biol_rep3
Species:	Mouse (Mus musculus)
Library ID:	CNhs13086
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	ANATOMICAL SYSTEM
dev stage	NA
sex	NA
age	NA
cell type	NA
cell line	NA
company	NA
collaboration	Hideki Enomoto (RIKEN CDB)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	para3
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005235

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13086		CAGE		DRX008867		DRR009739

Accession ID Mm9

Library id		BAM		CTSS
CNhs13086		DRZ001164		DRZ002549

Accession ID Mm10

Library id		BAM		CTSS
CNhs13086		DRZ012514		DRZ013899

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

CNhs13086

0	0
1	0
10	0
100	0
1000	0
1001	-0.0749
1002	-0.116
1003	-0.118
1004	0
1005	-0.101
1006	-0.0376
1007	0.121
1008	0
1009	0.00729
101	-0.0159
1010	0
1011	-0.108
1012	0
1013	-0.123
1014	-0.0851
1015	0.213
1016	0.442
1017	0
1018	0
1019	0
102	0
1020	0.431
1021	0.198
1022	-0.14
1023	0
1024	-0.0313
1025	-0.0525
1026	0
1027	0.267
1028	0
1029	-0.115
103	-0.0848
1030	0
1031	0.383
1032	0.0944
1033	0.148
1034	0
1035	0
1036	-0.0746
1037	0
1038	0.0604
1039	-0.17
104	0
1040	0.103
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: CNhs13086

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00263
MA0003.1	MA0003.1	0.053
MA0004.1	MA0004.1	0.982
MA0006.1	MA0006.1	0.347
MA0007.1	MA0007.1	0.617
MA0009.1	MA0009.1	0.0363
MA0014.1	MA0014.1	0.761
MA0017.1	MA0017.1	7.01846e-4
MA0018.2	MA0018.2	6.51267e-5
MA0019.1	MA0019.1	0.944
MA0024.1	MA0024.1	0.0374
MA0025.1	MA0025.1	0.634
MA0027.1	MA0027.1	0.961
MA0028.1	MA0028.1	0.611
MA0029.1	MA0029.1	0.572
MA0030.1	MA0030.1	0.608
MA0031.1	MA0031.1	0.579
MA0035.2	MA0035.2	0.006
MA0038.1	MA0038.1	0.441
MA0039.2	MA0039.2	0.386
MA0040.1	MA0040.1	0.943
MA0041.1	MA0041.1	0.124
MA0042.1	MA0042.1	0.509
MA0043.1	MA0043.1	0.0101
MA0046.1	MA0046.1	1.03915e-6
MA0047.2	MA0047.2	0.0452
MA0048.1	MA0048.1	0.883
MA0050.1	MA0050.1	0.00316
MA0051.1	MA0051.1	0.00936
MA0052.1	MA0052.1	0.0712
MA0055.1	MA0055.1	0.75
MA0057.1	MA0057.1	0.263
MA0058.1	MA0058.1	0.737
MA0059.1	MA0059.1	0.172
MA0060.1	MA0060.1	3.74419e-4
MA0061.1	MA0061.1	0.0486
MA0062.2	MA0062.2	0.767
MA0065.2	MA0065.2	2.67924e-4
MA0066.1	MA0066.1	0.213
MA0067.1	MA0067.1	0.257
MA0068.1	MA0068.1	0.338
MA0069.1	MA0069.1	0.448
MA0070.1	MA0070.1	0.0269
MA0071.1	MA0071.1	0.279
MA0072.1	MA0072.1	0.6
MA0073.1	MA0073.1	0.941
MA0074.1	MA0074.1	0.625
MA0076.1	MA0076.1	0.244
MA0077.1	MA0077.1	0.0264
MA0078.1	MA0078.1	0.059
MA0079.2	MA0079.2	0.244
MA0080.2	MA0080.2	1.4951e-7
MA0081.1	MA0081.1	0.747
MA0083.1	MA0083.1	0.4
MA0084.1	MA0084.1	0.72
MA0087.1	MA0087.1	0.579
MA0088.1	MA0088.1	0.837
MA0090.1	MA0090.1	0.728
MA0091.1	MA0091.1	0.911
MA0092.1	MA0092.1	0.749
MA0093.1	MA0093.1	0.936
MA0099.2	MA0099.2	0.351
MA0100.1	MA0100.1	0.554
MA0101.1	MA0101.1	0.326
MA0102.2	MA0102.2	0.759
MA0103.1	MA0103.1	3.05695e-4
MA0104.2	MA0104.2	0.834
MA0105.1	MA0105.1	3.2462e-5
MA0106.1	MA0106.1	0.671
MA0107.1	MA0107.1	0.136
MA0108.2	MA0108.2	0.116
MA0111.1	MA0111.1	0.985
MA0112.2	MA0112.2	4.1254e-5
MA0113.1	MA0113.1	0.443
MA0114.1	MA0114.1	4.37954e-4
MA0115.1	MA0115.1	0.27
MA0116.1	MA0116.1	7.7378e-4
MA0117.1	MA0117.1	0.831
MA0119.1	MA0119.1	0.11
MA0122.1	MA0122.1	0.866
MA0124.1	MA0124.1	0.877
MA0125.1	MA0125.1	0.0803
MA0131.1	MA0131.1	0.587
MA0135.1	MA0135.1	0.332
MA0136.1	MA0136.1	3.39243e-5
MA0137.2	MA0137.2	0.467
MA0138.2	MA0138.2	0.0827
MA0139.1	MA0139.1	0.0245
MA0140.1	MA0140.1	0.00695
MA0141.1	MA0141.1	0.00632
MA0142.1	MA0142.1	0.19
MA0143.1	MA0143.1	0.0316
MA0144.1	MA0144.1	0.667
MA0145.1	MA0145.1	0.123
MA0146.1	MA0146.1	0.641
MA0147.1	MA0147.1	0.608
MA0148.1	MA0148.1	0.0558
MA0149.1	MA0149.1	0.741
MA0150.1	MA0150.1	0.276
MA0152.1	MA0152.1	0.796
MA0153.1	MA0153.1	4.01314e-5
MA0154.1	MA0154.1	0.00529
MA0155.1	MA0155.1	0.554
MA0156.1	MA0156.1	0.00762
MA0157.1	MA0157.1	0.0657
MA0159.1	MA0159.1	0.193
MA0160.1	MA0160.1	0.158
MA0162.1	MA0162.1	0.172
MA0163.1	MA0163.1	0.00127
MA0164.1	MA0164.1	0.886
MA0258.1	MA0258.1	0.0292
MA0259.1	MA0259.1	0.992

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: CNhs13086

Novel motif	Logo	P-value
1	1	0.103
10	10	0.0603
100	100	0.911
101	101	0.709
102	102	0.836
103	103	0.0161
104	104	0.859
105	105	0.307
106	106	0.0392
107	107	0.114
108	108	0.744
109	109	0.0254
11	11	0.0643
110	110	0.149
111	111	0.00398
112	112	0.0567
113	113	0.647
114	114	0.0424
115	115	0.324
116	116	0.484
117	117	0.239
118	118	0.522
119	119	0.0343
12	12	0.704
120	120	0.437
121	121	0.177
122	122	0.328
123	123	0.617
124	124	0.774
125	125	0.907
126	126	0.35
127	127	0.5
128	128	0.0701
129	129	0.0866
13	13	0.0306
130	130	0.65
131	131	0.975
132	132	0.378
133	133	0.673
134	134	0.598
135	135	0.585
136	136	0.793
137	137	0.415
138	138	0.71
139	139	0.17
14	14	0.536
140	140	0.0402
141	141	0.112
142	142	0.589
143	143	0.867
144	144	0.645
145	145	0.233
146	146	0.582
147	147	0.753
148	148	0.536
149	149	0.118
15	15	0.0851
150	150	0.489
151	151	0.441
152	152	0.127
153	153	0.605
154	154	0.711
155	155	0.716
156	156	0.00188
157	157	0.254
158	158	0.676
159	159	0.0549
160	160	0.164
161	161	0.412
162	162	0.898
163	163	0.404
164	164	0.118
165	165	0.173
166	166	0.642
167	167	0.892
168	168	0.716
169	169	0.0131
17	17	0.0401
18	18	0.745
19	19	0.117
2	2	0.506
20	20	0.828
21	21	0.489
22	22	0.416
23	23	0.325
24	24	0.257
25	25	0.365
26	26	0.0447
27	27	0.245
28	28	0.582
29	29	0.274
3	3	0.0723
30	30	0.763
31	31	0.854
32	32	0.104
33	33	0.382
34	34	0.495
35	35	0.551
36	36	0.196
37	37	0.0706
38	38	0.253
39	39	0.457
4	4	0.739
40	40	0.341
41	41	0.912
42	42	0.246
43	43	0.173
44	44	0.11
45	45	0.521
46	46	0.158
47	47	0.118
48	48	0.161
49	49	0.164
5	5	0.174
50	50	0.739
51	51	0.465
52	52	0.319
53	53	0.489
54	54	0.545
55	55	0.554
56	56	0.517
57	57	0.251
58	58	0.0951
59	59	0.0461
6	6	0.799
60	60	0.12
61	61	0.329
62	62	0.0275
63	63	0.164
64	64	0.368
65	65	0.141
66	66	0.352
67	67	0.957
68	68	0.484
69	69	0.915
7	7	0.103
70	70	0.00924
71	71	0.0751
72	72	0.474
73	73	0.153
74	74	0.177
75	75	0.118
76	76	0.96
77	77	0.213
78	78	0.0536
79	79	0.108
8	8	0.097
80	80	0.703
81	81	0.451
82	82	0.0313
83	83	0.236
84	84	0.901
85	85	0.0246
86	86	0.345
87	87	0.408
88	88	0.519
89	89	0.0625
9	9	0.509
90	90	0.183
91	91	0.222
92	92	0.0568
93	93	0.292
94	94	0.218
95	95	0.124
96	96	0.33
97	97	0.939
98	98	0.163
99	99	0.157

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: CNhs13086

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011143 mouse neurospheres - parasympathetic neuron derived sample

part_of relathionship
UBERON:0000011 parasympathetic nervous system

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)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0000011 (parasympathetic nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0011143 (mouse neurospheres - parasympathetic neuron derived 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:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005235
+|accession_numbers=CAGE;DRX008867;DRR009739;DRZ001164;DRZ002549;DRZ012514;DRZ013899
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0000011,UBERON:0001016
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0000107
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:59799772..59799789,+!p1@Hand2!2.28!516.90!Hand2;;chr16:91270004..91270023,+!p1@Olig1!2.25!202.68!Olig1;;chr10:86956396..86956411,-!p1@Ascl1!2.18!226.18!Ascl1;;chr15:78994907..78994926,-!p1@Sox10!2.09!298.36!Sox10;;chr4:99322820..99322845,+!p1@Foxd3!1.99!121.44!Foxd3;;chr7:108966820..108966835,+!p1@Phox2a!1.80!61.99!Phox2a;;chr5:67490284..67490302,-!p1@Phox2b!1.72!52.09!Phox2b;;chr1:193007123..193007139,-!p1@Atf3!1.54!182.02!Atf3;;chr3:34548909..34548927,+!p1@Sox2!1.50!51.52!Sox2;;chr5:67490474..67490494,-!p2@Phox2b!1.50!30.29!Phox2b;;chr1:193041811..193041838,-!p2@Atf3!1.48!28.87!Atf3;;chr2:146047829..146047847,+!p1@Insm1!1.45!47.84!Insm1;;chr7:38557887..38557910,-!p5@Zfp536!1.45!27.46!Zfp536;;chr5:138199361..138199441,+!p2@Tsc22d4!1.42!46.42!Tsc22d4;;chr2:71384802..71384815,-!p1@Dlx2!1.41!30.29!Dlx2;;chr14:34791937..34791977,-!p1@Zfp488!1.39!23.78!Zfp488;;chr2:71367871..71367898,+!p1@Dlx1!1.37!22.36!Dlx1;;chr6:83020355..83020371,-!p1@Tlx2!1.30!18.97!Tlx2;;chr5:67490391..67490404,-!p3@Phox2b!1.28!18.12!Phox2b;;chr18:69752912..69752928,+!p9@Tcf4!1.27!26.33!Tcf4;;chr5:120120667..120120685,+!p3@Tbx3!1.26!33.12!Tbx3;;chr14:17407878..17407926,-!p1@Rarb!1.24!36.52!Rarb;;chr17:44951553..44951586,-!p2@Runx2!1.21!16.70!Runx2;;chr16:91270091..91270143,+!p2@Olig1!1.19!14.44!Olig1;;chr11:85646263..85646278,+!p2@Tbx2!1.18!35.95!Tbx2;;chr12:39510206..39510249,+!p3@Etv1!1.16!13.59!Etv1;;chr2:71367142..71367167,+!p2@Dlx1!1.16!13.59!Dlx1;;chr17:44872561..44872615,-!p1@Runx2!1.14!28.87!Runx2;;chr11:85646303..85646329,+!p1@Tbx2!1.13!82.66!Tbx2;;chr12:28027561..28027591,-!p1@Sox11!1.13!82.09!Sox11;;chr12:12948633..12948651,-!p1@Mycn!1.12!117.48!Mycn;;chr2:71384458..71384526,-!p2@Dlx2!1.12!12.17!Dlx2;;chr7:38558544..38558566,-!p4@Zfp536!1.09!13.02!Zfp536;;chrX:58146612..58146615,-!p1@Sox3!1.09!11.32!Sox3;;chr7:38554763..38554780,-!p1@Zfp536!1.08!20.10!Zfp536;;chr13:44936126..44936164,+!p6@Jarid2!1.08!12.74!Jarid2;;chr1:179374784..179374800,+!p2@Zfp238!1.07!12.74!Zfp238;;chr3:34548946..34548972,+!p2@Sox2!1.07!11.89!Sox2;;chr17:25707623..25707639,-!p1@Sox8!1.06!45.01!Sox8;;chr13:40829137..40829205,-!p1@Tfap2a!1.05!11.61!Tfap2a;;chr6:6832076..6832092,-!p1@Dlx5!1.04!11.61!Dlx5;;chr5:120121169..120121171,+!p4@Tbx3!1.02!16.98!Tbx3;;chr12:86814833..86814846,+!p1@Fos!1.01!218.25!Fos;;chr6:53523358..53523388,+!p1@Creb5!1.01!112.10!Creb5;;chr5:67490346..67490357,-!p4@Phox2b!0.99!8.78!Phox2b;;chr4:150503457..150503498,-!p3@Camta1!0.98!9.62!Camta1;;chr3:107398056..107398082,+!p1@Alx3!0.98!8.49!Alx3;;chr11:85646469..85646488,+!p5@Tbx2!0.97!12.74!Tbx2;;chr4:84320893..84320910,-!p1@Bnc2!0.96!18.40!Bnc2;;chr7:38557752..38557793,-!p3@Zfp536!0.96!9.62!Zfp536;;chr11:85646341..85646352,+!p3@Tbx2!0.95!15.85!Tbx2;;chr18:69752864..69752875,+!p25@Tcf4!0.95!7.93!Tcf4;;chr14:17407970..17408015,-!p2@Rarb!0.94!21.23!Rarb;;chr2:44968775..44968795,-!p4@Zeb2!0.93!36.80!Zeb2;;chr19:7342725..7342784,+!p1@Rcor2!0.93!32.27!Rcor2;;chr9:106356278..106356292,+!p3@Pcbp4!0.93!13.30!Pcbp4;;chr14:17407549..17407575,-!p3@Rarb!0.93!11.61!Rarb;;chr1:38684260..38684312,-!p2@Aff3!0.92!53.78!Aff3;;chr7:122968213..122968266,-!p4@Sox6!0.92!8.78!Sox6;;chr13:40826150..40826167,-!p3@Tfap2a!0.91!7.93!Tfap2a;;chr5:67490447..67490458,-!p7@Phox2b!0.91!7.08!Phox2b;;chr2:71384401..71384424,-!p3@Dlx2!0.91!7.08!Dlx2;;chr4:122911086..122911112,+!p1@Heyl!0.90!84.92!Heyl;;chr2:44965856..44965896,-!p5@Zeb2!0.90!28.31!Zeb2;;chr18:69752638..69752665,+!p19@Tcf4!0.90!7.64!Tcf4;;chr16:91225808..91225824,+!p1@Olig2!0.89!6.79!Olig2;;chr9:71743854..71743909,-!p1@Tcf12!0.88!55.48!Tcf12;;chr16:43363190..43363242,+!p2@Zbtb20!0.88!20.95!Zbtb20;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.88!18.40!Zfhx3;;chr11:33103563..33103583,-!p1@Tlx3!0.88!6.51!Tlx3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.87!8.21!Pou3f3;;chr9:106356211..106356242,+!p1@Pcbp4!0.86!129.93!Pcbp4;;chr10:119913546..119913583,-!p3@Hmga2!0.86!13.59!Hmga2;;chr1:57029281..57029326,-!p1@Satb2!0.86!9.91!Satb2;;chr14:17407857..17407875,-!p4@Rarb!0.86!6.23!Rarb;;chr2:127347067..127347093,-!p1@Kcnip3!0.85!10.47!Kcnip3;;chr10:30562571..30562597,-!p1@Hey2!0.84!14.72!Hey2;;chr2:71384425..71384456,-!p4@Dlx2!0.84!5.94!Dlx2;;chr7:130644017..130644092,-!p1@Zkscan2!0.83!11.61!Zkscan2;;chr3:95032091..95032183,-!p1@Mllt11!0.82!51.52!Mllt11;;chr15:97738692..97738747,-!p1@Vdr!0.81!31.99!Vdr;;chr12:39507680..39507715,+!p2@Etv1!0.81!11.32!Etv1;;chr2:44968737..44968758,-!p2@Zeb2!0.80!32.84!Zeb2;;chr2:44968721..44968734,-!p6@Zeb2!0.80!21.51!Zeb2;;chr7:38558574..38558611,-!p2@Zfp536!0.80!6.79!Zfp536;;chr16:43503594..43503634,+!p15@Zbtb20!0.80!6.51!Zbtb20;;chr4:99322855..99322867,+!p2@Foxd3!0.80!5.38!Foxd3;;chr7:123174606..123174636,-!p5@Sox6!0.79!6.79!Sox6;;chr7:38554684..38554696,-!p10@Zfp536!0.79!5.10!Zfp536;;chr5:120121020..120121049,+!p1@Tbx3!0.78!33.40!Tbx3;;chr12:39507404..39507441,+!p4@Etv1!0.77!7.08!Etv1;;chr7:123177120..123177138,-!p10@Sox6!0.76!5.94!Sox6;;chr5:67490412..67490421,-!p6@Phox2b!0.76!4.81!Phox2b;;chr17:44873599..44873623,-!p7@Runx2!0.76!4.81!Runx2;;chr9:96653072..96653154,-!p1@Zbtb38!0.74!13.02!Zbtb38;;chr11:85646427..85646451,+!p4@Tbx2!0.74!8.21!Tbx2;;chr10:66998213..66998240,+!p4@Egr2!0.74!4.53!Egr2;;chr12:39510090..39510114,+!p6@Etv1!0.74!4.53!Etv1;;chr18:3281034..3281104,-!p1@Crem!0.73!34.82!Crem;;chr9:106356243..106356264,+!p2@Pcbp4!0.73!20.95!Pcbp4;;chr3:90097275..90097302,+!p2@Gatad2b!0.73!11.04!Gatad2b;;chr12:39510290..39510309,+!p5@Etv1!0.72!4.25!Etv1;;chr14:17407671..17407684,-!p7@Rarb!0.72!4.25!Rarb;;chr10:66998241..66998263,+!p2@Egr2!0.72!4.25!Egr2;;chr3:32264565..32264613,-!p1@Zmat3!0.71!51.24!Zmat3;;chr13:44826634..44826645,+!p7@Jarid2!0.71!8.49!Jarid2;;chr7:123177377..123177409,-!p7@Sox6!0.71!5.38!Sox6;;chr4:94718861..94718872,-!p2@Jun!0.70!33.69!Jun;;chr14:34791987..34791998,-!p2@Zfp488!0.70!3.96!Zfp488;;chr18:83079981..83080037,+!p6@Zfp516!0.69!7.36!Zfp516;;chr8:125778192..125778217,+!p2@Zfp276!0.68!11.89!Zfp276;;chr10:67000609..67000625,+!p1@Egr2!0.68!9.62!Egr2;;chr16:43363152..43363186,+!p3@Zbtb20!0.68!9.62!Zbtb20;;chr16:43503493..43503570,+!p9@Zbtb20!0.68!6.79!Zbtb20;;chr13:78339476..78339515,-!p1@Nr2f1!0.68!6.23!Nr2f1;;chr3:5218629..5218684,+!p1@Zfhx4!0.67!13.59!Zfhx4;;chr14:52935788..52935817,-!p2@Sall2!0.67!8.78!Sall2;;chr18:69752608..69752625,+!p17@Tcf4!0.66!4.25!Tcf4;;chr4:94718879..94718898,-!p1@Jun!0.65!296.38!Jun;;chr16:15887371..15887385,+!p1@Cebpd!0.65!138.99!Cebpd;;chr7:52471143..52471186,+!p1@Tead2!0.65!43.31!Tead2;;chr12:39506873..39506913,+!p1@Etv1!0.65!41.33!Etv1;;chr11:87881569..87881633,+!p2@Vezf1!0.65!31.42!Vezf1;;chr13:15555670..15555771,+!p2@Gli3!0.65!9.91!Gli3;;chr7:20408047..20408125,-!p1@Bcl3!0.64!45.29!Bcl3;;chr13:40829337..40829360,-!p5@Tfap2a!0.64!3.40!Tfap2a;;chr12:30213247..30213333,+!p1@Myt1l!0.64!3.40!Myt1l;;chr17:44951431..44951445,-!p3@Runx2!0.64!3.40!Runx2;;chr5:67490333..67490342,-!p5@Phox2b!0.64!3.40!Phox2b;;chr4:99323046..99323073,+!p3@Foxd3!0.64!3.40!Foxd3;;chr4:22415443..22415506,-!p1@Pou3f2!0.64!3.40!Pou3f2;;chr4:54960870..54960926,+!p1@Zfp462!0.63!13.59!Zfp462;;chr11:3189683..3189744,+!p2@Patz1!0.63!7.36!Patz1;;chr6:6831950..6831985,-!p2@Dlx5!0.63!3.68!Dlx5;;chr10:76424613..76424689,-!p1@Pcbp3!0.62!79.54!Pcbp3;;chr16:92697560..92697592,-!p2@Runx1!0.62!23.21!Runx1;;chr3:32264530..32264544,-!p2@Zmat3!0.62!5.38!Zmat3;;chr6:53523332..53523343,+!p2@Creb5!0.62!4.81!Creb5;;chr5:134790507..134790546,-!p1@Gtf2i!0.61!90.58!Gtf2i;;chr14:65568469..65568511,-!p2@Hmbox1!0.61!11.61!Hmbox1;;chr14:52634234..52634281,-!p3@Zfp219!0.61!9.62!Zfp219;;chr2:181501988..181502026,+!p3@Myt1!0.61!3.11!Myt1;;chr2:181501710..181501742,+!p2@Myt1!0.61!3.11!Myt1;;chr10:129717274..129717298,-!p1@Neurod4!0.61!3.11!Neurod4;;chr6:53523346..53523353,+!p3@Creb5!0.60!4.53!Creb5;;chr19:10315179..10315241,-!p1@Gm98!0.59!36.80!Gm98;;chr7:25292331..25292421,+!p1@Zfp428!0.59!24.91!Zfp428;;chr15:102034446..102034506,+!p2@Zfp740!0.59!11.89!Zfp740;;chr18:55149986..55150009,-!p7@Zfp608!0.59!6.23!Zfp608;;chr14:65568567..65568588,-!p3@Hmbox1!0.59!4.81!Hmbox1;;chr2:163028808..163028869,+!p1@Tox2!0.58!11.89!Tox2;;chr17:44873393..44873418,-!p4@Runx2!0.58!5.38!Runx2;;chr10:119913792..119913820,-!p5@Hmga2!0.58!5.38!Hmga2;;chr5:120121091..120121100,+!p7@Tbx3!0.58!3.40!Tbx3;;chr5:120120834..120120845,+!p8@Tbx3!0.58!2.83!Tbx3;;chr6:6831928..6831949,-!p3@Dlx5!0.58!2.83!Dlx5;;chr13:40826119..40826131,-!p7@Tfap2a!0.58!2.83!Tfap2a;;chr13:44936077..44936096,+!p9@Jarid2!0.58!2.83!Jarid2;;chr13:40826236..40826248,-!p8@Tfap2a!0.58!2.83!Tfap2a;;chr10:13685585..13685645,+!p2@Hivep2!0.57!11.32!Hivep2;;chr3:51144477..51144506,-!p6@Elf2!0.57!4.53!Elf2;;chr13:78339428..78339466,-!p2@Nr2f1!0.57!3.96!Nr2f1;;chr16:43503720..43503739,+!p18@Zbtb20!0.57!3.11!Zbtb20;;chr10:13685899..13685916,+!p1@Hivep2!0.56!34.54!Hivep2;;chr10:114821393..114821431,-!p5@Thap2!0.56!8.49!Thap2;;chr2:127347094..127347111,-!p2@Kcnip3!0.56!4.81!Kcnip3;;chr13:40825465..40825469,-!p2@Tfap2a!0.55!2.55!Tfap2a;;chr16:91225654..91225671,+!p2@Olig2!0.55!2.55!Olig2;;chr3:34548845..34548856,+!p4@Sox2!0.55!2.55!Sox2;;chr2:81893535..81893548,+!p1@Zfp804a!0.55!2.55!Zfp804a;;chrX:108810678..108810736,-!p1@Hdx!0.54!10.19!Hdx;;chr1:92895299..92895373,+!p2@Lrrfip1!0.53!63.41!Lrrfip1;;chr7:5003165..5003203,+!p2@Zfp580!0.53!16.42!Zfp580;;chr6:97757008..97757061,+!p1@Mitf!0.53!12.74!Mitf;;chr2:44965788..44965815,-!p11@Zeb2!0.53!5.10!Zeb2;;chr2:17976799..17976829,+!p5@Mllt10!0.53!3.11!Mllt10;;chr7:123174485..123174514,-!p6@Sox6!0.53!3.11!Sox6;;chr7:91558392..91558434,-!p1@Arnt2!0.52!7.64!Arnt2;;chr8:111227738..111227793,+!p@chr8:111227738..111227793,+!0.52!6.79!Zfhx3;;chr9:106356265..106356276,+!p4@Pcbp4!0.52!4.25!Pcbp4;;chr1:179372625..179372654,+!p4@Zfp238!0.52!3.96!Zfp238;;chr1:38684383..38684394,-!p4@Aff3!0.52!3.40!Aff3;;chr13:78338076..78338104,-!p4@Nr2f1!0.52!3.11!Nr2f1;;chr18:69753015..69753104,+!p1@Tcf4!0.51!39.06!Tcf4;;chr4:119406389..119406411,+!p1@Hivep3!0.51!13.87!Hivep3;;chr18:55150011..55150059,-!p3@Zfp608!0.51!9.06!Zfp608;;c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p516;;chr7:30638630..30638702,-!p1@Zfp940!0.24!4.53!Zfp940;;chr11:74644716..74644780,+!p2@Mnt!0.24!3.96!Mnt;;chr19:28086084..28086124,-!p6@Rfx3!0.24!3.68!Rfx3;;chr18:83080255..83080277,+!p4@Zfp516!0.24!3.11!Zfp516;;chr13:65380103..65380116,+!p3@Zfp369!0.24!3.11!Zfp369;;chr18:14130694..14130697,-!p2@Zfp521!0.24!2.83!Zfp521;;chr4:128483731..128483757,-!p4@Zfp362!0.24!2.83!Zfp362;;chr7:30691543..30691586,-!p2@Zfp27!0.24!2.83!Zfp27;;chr2:169458496..169458516,+!p6@Tshz2!0.24!2.55!Tshz2;;chr2:153475178..153475196,+!p1@Dnmt3b!0.24!2.55!Dnmt3b;;chr5:122500142..122500167,-!p2@Cux2!0.24!2.55!Cux2;;chr5:22940353..22940372,+!p3@Mll5!0.24!2.26!Mll5;;chr11:106993257..106993268,-!p4@Bptf!0.24!1.98!Bptf;;chr13:53076382..53076393,-!p2@Nfil3!0.24!1.70!Nfil3;;chr13:30077917..30077928,-!p4@E2f3!0.24!1.13!E2f3;;chr5:77695181..77695196,+!p6@Rest!0.24!1.13!Rest;;chr2:168427252..168427273,-!p2@Nfatc2!0.24!1.13!Nfatc2;;chr9:21420674..21420725,+!p1@Smarca4!0.23!122.29!Smarca4;;chr12:112277544..112277610,+!p1@Rcor1!0.23!56.90!Rcor1;;chr6:64992569..64992656,+!p1@Smarcad1!0.23!45.29!Smarcad1;;chr11:87881744..87881791,+!p1@Vezf1!0.23!42.74!Vezf1;;chr2:164860270..164860320,-!p1@Ncoa5!0.23!30.01!Ncoa5;;chr9:30837968..30838036,+!p1@Zbtb44!0.23!26.33!Zbtb44;;chr12:86940338..86940357,+!p1@Jdp2!0.23!14.72!Jdp2;;chr4:97444590..97444607,+!p6@Nfia!0.23!10.47!Nfia;;chr14:19071466..19071550,-!p1@Nr1d2!0.23!9.91!Nr1d2;;chr3:135354384..135354443,-!p1@Nfkb1!0.23!8.78!Nfkb1;;chr3:135354476..135354528,-!p2@Nfkb1!0.23!7.93!Nfkb1;;chr9:65675351..65675383,-!p1@Zfp609!0.23!7.08!Zfp609;;chr10:5958538..5958568,+!p1@Zbtb2!0.23!6.23!Zbtb2;;chr7:135020060..135020124,-!p2@Zfp668!0.23!5.94!Zfp668;;chr17:84587167..84587239,-!p2@Zfp36l2!0.23!4.53!Zfp36l2;;chr4:119960301..119960359,-!p1@Foxo6!0.23!4.25!Foxo6;;chr16:4214034..4214070,-!p@chr16:4214034..4214070,-!0.23!3.96!Crebbp;;chr18:74375772..74375799,+!p2@Cxxc1!0.23!3.68!Cxxc1;;chr11:49016816..49016846,+!p2@Zfp62!0.23!3.68!Zfp62;;chr8:72520225..72520248,-!p9@Gatad2a!0.23!3.40!Gatad2a;;chr8:81923398..81923409,-!p4@Smad1!0.23!3.11!Smad1;;chr5:34530277..34530292,-!p3@Mxd4!0.23!3.11!Mxd4;;chr2:148506935..148506954,+!p2@Gzf1!0.23!2.26!Gzf1;;chr19:55816278..55816287,+!p10@Tcf7l2!0.23!2.26!Tcf7l2;;chr13:96095124..96095144,+!p3@Zbed3!0.23!2.26!Zbed3;;chr6:98978189..98978198,-!p10@Foxp1!0.23!1.13!Foxp1;;chr7:25292223..25292234,+!p7@Zfp428!0.23!1.13!Zfp428;;chr19:19185697..19185711,-!p2@Rorb!0.23!1.13!Rorb;;chr17:71200967..71200983,-!p8@Tgif1!0.23!1.13!Tgif1;;chr5:104182943..104182954,+!p12@Aff1!0.23!1.13!Aff1;;chr2:165213716..165213732,-!p2@Zfp334!0.23!1.13!Zfp334;;chr10:75384307..75384370,-!p1@Smarcb1!0.22!116.06!Smarcb1;;chr2:83484681..83484704,+!p1@Zc3h15!0.22!68.50!Zc3h15;;chr5:106305551..106305604,+!p1@Zfp326!0.22!56.05!Zfp326;;chr7:134170235..134170294,-!p1@Maz!0.22!41.33!Maz;;chr1:64167972..64168026,-!p1@Klf7!0.22!35.38!Klf7;;chr19:47125313..47125405,-!p1@Pcgf6!0.22!31.70!Pcgf6;;chr9:72380021..72380078,+!p1@Rfx7!0.22!27.46!Rfx7;;chr17:32967140..32967197,-!p1@Zfp799!0.22!20.10!Zfp799;;chr11:59319701..59319741,-!p1@Zkscan17!0.22!16.70!Zkscan17;;chr2:37278415..37278478,-!p1@Rc3h2!0.22!12.74!Rc3h2;;chr8:81552152..81552208,+!p1@Zfp827!0.22!10.19!Zfp827;;chr7:88005795..88005858,+!p1@Zscan2!0.22!9.91!Zscan2;;chr7:11080671..11080750,-!p1@Zik1!0.22!9.62!Zik1;;chr6:133985993..133986029,+!p2@Etv6!0.22!9.06!Etv6;;chr7:6238191..6238224,+!p1@Zfp667!0.22!8.21!Zfp667;;chr11:50729638..50729681,-!p1@Zfp2!0.22!7.08!Zfp2;;chr10:92773818..92773906,-!p2@Elk3!0.22!6.51!Elk3;;chr11:62602904..62602945,-!p1@Zfp286!0.22!6.23!Zfp286;;chr8:125778131..125778178,+!p1@Zfp276!0.22!6.23!Zfp276;;chr18:55147667..55147746,-!p2@Zfp608!0.22!6.23!Zfp608;;chr7:6336020..6336068,+!p1@Zfp28!0.22!5.94!Zfp28;;chr9:69137672..69137702,+!p2@Rora!0.22!5.66!Rora;;chr7:6282837..6282892,-!p1@Zfp583!0.22!5.38!Zfp583;;chr15:25914114..25914128,+!p2@Zfp622!0.22!5.38!Zfp622;;chr7:134170541..134170569,-!p9@Maz!0.22!5.10!Maz;;chr2:152223881..152223933,-!p3@Sox12!0.22!4.25!Sox12;;chrX:71330995..71331011,-!p2@Mecp2!0.22!3.96!Mecp2;;chr18:83080305..83080335,+!p2@Zfp516!0.22!3.96!Zfp516;;chr17:45570631..45570658,-!p4@Cdc5l!0.22!3.68!Cdc5l;;chr8:107694596..107694619,+!p4@Cbfb!0.22!3.68!Cbfb;;chr7:30875418..30875454,-!p2@Zfp566,p2@Zfp82!0.22!3.40!Zfp566;;chr18:7004715..7004731,-!p1@Mkx!0.22!2.83!Mkx;;chr17:45692676..45692695,+!p2@Nfkbie!0.22!2.26!Nfkbie;;chr2:56967334..56967366,-!p1@Nr4a2!0.22!2.26!Nr4a2;;chr12:85534720..85534751,-!p4@C130039O16Rik!0.22!1.98!C130039O16Rik;;chr17:32501360..32501371,-!p5@Wiz!0.22!1.42!Wiz;;chr11:16952347..16952366,-!p2@Plek!0.22!1.42!Plek;;chr13:83663546..83663560,+!p4@Mef2c!0.22!1.13!Mef2c;;chr12:72149359..72149406,+!p4@Arid4a!0.22!1.13!Arid4a;;chr5:107003725..107003746,-!p5@Zfp644!0.22!1.13!Zfp644;;chr17:35031524..35031539,+!p4@Zbtb12!0.22!1.13!Zbtb12;;chr18:69504229..69504240,+!p16@Tcf4!0.22!1.13!Tcf4;;chr15:79178013..79178028,+!p3@Maff!0.22!1.13!Maff;;chr1:69732354..69732402,-!p1@Ikzf2!0.22!0.85!Ikzf2;;chr4:126698555..126698583,+!p1@Sfpq!0.21!79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@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011143
 |is_obsolete=
+|library_id=CNhs13086
+|library_id_phase_based=2:CNhs13086
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11809
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11809
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep3.CNhs13086.11809-124D9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep3.CNhs13086.11809-124D9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep3.CNhs13086.11809-124D9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep3.CNhs13086.11809-124D9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep3.CNhs13086.11809-124D9.mm9.nobarcode.rdna.fa.gz
 |name=neurospheres - parasympathetic neuron derived, biol_rep3
 |namespace=
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13086,LSID1000,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0466291806786836,0,0,0,0,0,0.00839495672522005,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.412143512064212,-0.291431957688506,0,0,0,0,0,-0.155196444889018,0.132237144995996,0.142019474181921,-0.434265852363447,-0.269868638010351,0.108252561213616,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0531295031996292,0,0.108252561213616,0.00308767647535552,0.266990834635525,0,-0.00913724169470995,-0.20239809612577,0.224894900321396,-0.140687683267293,0,-0.0780086007519514,0.11304484932921,0,0,0,0.0270936559625196,0.266865793289611,0.245732802176189,0.0294209663737088,0,0,0,0,0,0,0.108288271287686,-0.198814341847097,-0.118259619727169,0,0,0,0.328849554038127,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=12
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |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=table111:11809-124D9;search_select_hide=table117:11809-124D9
 }}

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FF:11809-124D9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:21, 4 June 2020

CNhs13086

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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