FF:11807-124D7: Difference between revisions

Latest revision as of 18:21, 4 June 2020

Name:	neurospheres - parasympathetic neuron derived, biol_rep1
Species:	Mouse (Mus musculus)
Library ID:	CNhs13084
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	para1
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		SAMD00005929

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13084		CAGE		DRX008865		DRR009737

Accession ID Mm9

Library id		BAM		CTSS
CNhs13084		DRZ001162		DRZ002547

Accession ID Mm10

Library id		BAM		CTSS
CNhs13084		DRZ012512		DRZ013897

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

CNhs13084

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0356
1002	-0.0986
1003	-0.102
1004	0
1005	-0.0389
1006	-0.09
1007	-0.0036
1008	0
1009	-0.0572
101	0.0203
1010	0
1011	-0.0145
1012	0
1013	-0.066
1014	0
1015	0.133
1016	0.447
1017	0
1018	0
1019	0
102	0
1020	0.386
1021	0.0931
1022	-0.284
1023	0
1024	0
1025	-0.0611
1026	0
1027	0.341
1028	0.0931
1029	-0.0217
103	-0.0754
1030	0
1031	0.377
1032	-0.052
1033	0.17
1034	0
1035	0
1036	0.0254
1037	0
1038	0
1039	-0.293
104	0
1040	0.148
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: CNhs13084

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00104
MA0003.1	MA0003.1	0.00807
MA0004.1	MA0004.1	0.619
MA0006.1	MA0006.1	0.387
MA0007.1	MA0007.1	0.852
MA0009.1	MA0009.1	0.0336
MA0014.1	MA0014.1	0.669
MA0017.1	MA0017.1	3.63867e-5
MA0018.2	MA0018.2	0.00971
MA0019.1	MA0019.1	0.974
MA0024.1	MA0024.1	0.00149
MA0025.1	MA0025.1	0.747
MA0027.1	MA0027.1	0.732
MA0028.1	MA0028.1	0.114
MA0029.1	MA0029.1	0.279
MA0030.1	MA0030.1	0.794
MA0031.1	MA0031.1	0.312
MA0035.2	MA0035.2	0.00228
MA0038.1	MA0038.1	0.307
MA0039.2	MA0039.2	0.296
MA0040.1	MA0040.1	0.978
MA0041.1	MA0041.1	0.0809
MA0042.1	MA0042.1	0.658
MA0043.1	MA0043.1	0.163
MA0046.1	MA0046.1	3.34815e-18
MA0047.2	MA0047.2	0.00213
MA0048.1	MA0048.1	0.809
MA0050.1	MA0050.1	0.0183
MA0051.1	MA0051.1	0.0273
MA0052.1	MA0052.1	0.00363
MA0055.1	MA0055.1	0.663
MA0057.1	MA0057.1	0.19
MA0058.1	MA0058.1	0.281
MA0059.1	MA0059.1	0.554
MA0060.1	MA0060.1	1.72033e-6
MA0061.1	MA0061.1	0.0368
MA0062.2	MA0062.2	0.14
MA0065.2	MA0065.2	2.3043e-5
MA0066.1	MA0066.1	0.216
MA0067.1	MA0067.1	0.489
MA0068.1	MA0068.1	0.41
MA0069.1	MA0069.1	0.508
MA0070.1	MA0070.1	0.115
MA0071.1	MA0071.1	0.263
MA0072.1	MA0072.1	0.286
MA0073.1	MA0073.1	0.986
MA0074.1	MA0074.1	0.973
MA0076.1	MA0076.1	0.0555
MA0077.1	MA0077.1	0.00516
MA0078.1	MA0078.1	0.074
MA0079.2	MA0079.2	0.276
MA0080.2	MA0080.2	5.49205e-7
MA0081.1	MA0081.1	0.975
MA0083.1	MA0083.1	0.0915
MA0084.1	MA0084.1	0.8
MA0087.1	MA0087.1	0.517
MA0088.1	MA0088.1	0.725
MA0090.1	MA0090.1	0.568
MA0091.1	MA0091.1	0.691
MA0092.1	MA0092.1	0.627
MA0093.1	MA0093.1	0.506
MA0099.2	MA0099.2	0.459
MA0100.1	MA0100.1	0.28
MA0101.1	MA0101.1	0.329
MA0102.2	MA0102.2	0.297
MA0103.1	MA0103.1	2.28132e-4
MA0104.2	MA0104.2	0.859
MA0105.1	MA0105.1	1.94939e-5
MA0106.1	MA0106.1	0.0925
MA0107.1	MA0107.1	0.0978
MA0108.2	MA0108.2	7.21559e-4
MA0111.1	MA0111.1	0.973
MA0112.2	MA0112.2	4.46611e-5
MA0113.1	MA0113.1	0.551
MA0114.1	MA0114.1	7.84356e-5
MA0115.1	MA0115.1	0.113
MA0116.1	MA0116.1	2.45625e-4
MA0117.1	MA0117.1	0.654
MA0119.1	MA0119.1	0.0595
MA0122.1	MA0122.1	0.731
MA0124.1	MA0124.1	0.585
MA0125.1	MA0125.1	0.21
MA0131.1	MA0131.1	0.341
MA0135.1	MA0135.1	0.778
MA0136.1	MA0136.1	0.00196
MA0137.2	MA0137.2	0.381
MA0138.2	MA0138.2	0.00616
MA0139.1	MA0139.1	0.0249
MA0140.1	MA0140.1	0.00132
MA0141.1	MA0141.1	0.0218
MA0142.1	MA0142.1	0.147
MA0143.1	MA0143.1	0.06
MA0144.1	MA0144.1	0.857
MA0145.1	MA0145.1	0.0893
MA0146.1	MA0146.1	0.893
MA0147.1	MA0147.1	0.843
MA0148.1	MA0148.1	0.0128
MA0149.1	MA0149.1	0.295
MA0150.1	MA0150.1	0.218
MA0152.1	MA0152.1	0.89
MA0153.1	MA0153.1	7.31059e-13
MA0154.1	MA0154.1	0.00169
MA0155.1	MA0155.1	0.577
MA0156.1	MA0156.1	0.0305
MA0157.1	MA0157.1	0.122
MA0159.1	MA0159.1	0.397
MA0160.1	MA0160.1	0.121
MA0162.1	MA0162.1	0.318
MA0163.1	MA0163.1	0.00589
MA0164.1	MA0164.1	0.886
MA0258.1	MA0258.1	0.0268
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: CNhs13084

Novel motif	Logo	P-value
1	1	0.145
10	10	0.136
100	100	0.821
101	101	0.768
102	102	0.914
103	103	0.0815
104	104	0.884
105	105	0.0573
106	106	0.0117
107	107	0.0325
108	108	0.918
109	109	0.104
11	11	0.116
110	110	0.3
111	111	0.0101
112	112	0.0399
113	113	0.453
114	114	0.035
115	115	0.456
116	116	0.711
117	117	0.664
118	118	0.623
119	119	0.0621
12	12	0.479
120	120	0.696
121	121	0.252
122	122	0.44
123	123	0.678
124	124	0.578
125	125	0.644
126	126	0.253
127	127	0.462
128	128	0.00834
129	129	0.0928
13	13	0.155
130	130	0.679
131	131	0.547
132	132	0.145
133	133	0.464
134	134	0.819
135	135	0.47
136	136	0.653
137	137	0.361
138	138	0.254
139	139	0.0688
14	14	0.39
140	140	0.00292
141	141	0.0818
142	142	0.937
143	143	0.668
144	144	0.805
145	145	0.357
146	146	0.424
147	147	0.854
148	148	0.585
149	149	0.272
15	15	0.126
150	150	0.518
151	151	0.374
152	152	0.0973
153	153	0.583
154	154	0.616
155	155	0.863
156	156	0.368
157	157	0.512
158	158	0.736
159	159	0.366
160	160	0.181
161	161	0.602
162	162	0.909
163	163	0.823
164	164	0.139
165	165	0.258
166	166	0.478
167	167	0.549
168	168	0.704
169	169	0.0238
17	17	0.0686
18	18	0.728
19	19	0.0814
2	2	0.326
20	20	0.997
21	21	0.36
22	22	0.563
23	23	0.345
24	24	0.415
25	25	0.347
26	26	0.0502
27	27	0.26
28	28	0.437
29	29	0.931
3	3	0.101
30	30	0.519
31	31	0.69
32	32	0.0779
33	33	0.471
34	34	0.357
35	35	0.602
36	36	0.689
37	37	0.126
38	38	0.366
39	39	0.437
4	4	0.877
40	40	0.428
41	41	0.987
42	42	0.282
43	43	0.197
44	44	0.309
45	45	0.33
46	46	0.197
47	47	0.169
48	48	0.206
49	49	0.135
5	5	0.209
50	50	0.81
51	51	0.51
52	52	0.211
53	53	0.323
54	54	0.461
55	55	0.983
56	56	0.557
57	57	0.484
58	58	0.0617
59	59	0.0381
6	6	0.855
60	60	0.0898
61	61	0.645
62	62	0.0211
63	63	0.15
64	64	0.395
65	65	0.23
66	66	0.431
67	67	0.792
68	68	0.505
69	69	0.734
7	7	0.126
70	70	0.0172
71	71	0.193
72	72	0.421
73	73	0.288
74	74	0.172
75	75	0.338
76	76	0.963
77	77	0.229
78	78	0.132
79	79	0.327
8	8	0.146
80	80	0.717
81	81	0.474
82	82	0.0198
83	83	0.125
84	84	0.735
85	85	0.0673
86	86	0.372
87	87	0.35
88	88	0.512
89	89	0.0307
9	9	0.357
90	90	0.742
91	91	0.288
92	92	0.0436
93	93	0.53
94	94	0.264
95	95	0.294
96	96	0.252
97	97	0.622
98	98	0.168
99	99	0.186

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: CNhs13084

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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000073,UBERON:0002410,UBERON:0004121,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0000010,UBERON:0000011,UBERON:0001016,UBERON:0000924,UBERON:0005743,UBERON:0006601
+|DRA_sample_Accession=CAGE@SAMD00005929
-|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:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0000107,CL:0000133
+|accession_numbers=CAGE;DRX008865;DRR009737;DRZ001162;DRZ002547;DRZ012512;DRZ013897
+|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
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0011143
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:59799772..59799789,+!p1@Hand2!2.13!368.01!Hand2;;chr10:86956396..86956411,-!p1@Ascl1!2.05!166.80!Ascl1;;chr15:78994907..78994926,-!p1@Sox10!2.00!244.23!Sox10;;chr4:99322820..99322845,+!p1@Foxd3!1.85!88.42!Foxd3;;chr5:67490284..67490302,-!p1@Phox2b!1.82!65.24!Phox2b;;chr16:91270004..91270023,+!p1@Olig1!1.64!48.75!Olig1;;chr2:71384802..71384815,-!p1@Dlx2!1.62!49.94!Dlx2;;chr5:67490474..67490494,-!p2@Phox2b!1.62!40.62!Phox2b;;chr2:71367871..71367898,+!p1@Dlx1!1.53!33.22!Dlx1;;chr14:17407878..17407926,-!p1@Rarb!1.49!65.00!Rarb;;chr5:138199361..138199441,+!p2@Tsc22d4!1.47!53.29!Tsc22d4;;chr3:34548909..34548927,+!p1@Sox2!1.43!43.49!Sox2;;chr11:85646263..85646278,+!p2@Tbx2!1.35!53.29!Tbx2;;chr5:120120667..120120685,+!p3@Tbx3!1.31!36.80!Tbx3;;chr5:67490391..67490404,-!p3@Phox2b!1.30!18.88!Phox2b;;chr7:108966820..108966835,+!p1@Phox2a!1.30!18.88!Phox2a;;chr11:85646303..85646329,+!p1@Tbx2!1.29!118.29!Tbx2;;chr2:146047829..146047847,+!p1@Insm1!1.29!33.22!Insm1;;chr7:38557887..38557910,-!p5@Zfp536!1.27!17.44!Zfp536;;chr2:71384458..71384526,-!p2@Dlx2!1.26!17.21!Dlx2;;chr2:71367142..71367167,+!p2@Dlx1!1.21!15.29!Dlx1;;chr14:34791937..34791977,-!p1@Zfp488!1.21!15.06!Zfp488;;chr12:12948633..12948651,-!p1@Mycn!1.20!139.56!Mycn;;chr5:67490346..67490357,-!p4@Phox2b!1.19!14.58!Phox2b;;chr18:69752912..69752928,+!p9@Tcf4!1.17!20.79!Tcf4;;chrX:58146612..58146615,-!p1@Sox3!1.16!13.38!Sox3;;chr2:71384401..71384424,-!p3@Dlx2!1.12!12.19!Dlx2;;chr14:17407970..17408015,-!p2@Rarb!1.09!30.35!Rarb;;chr9:71743854..71743909,-!p1@Tcf12!1.08!87.70!Tcf12;;chr11:85646341..85646352,+!p3@Tbx2!1.08!21.75!Tbx2;;chr5:120121169..120121171,+!p4@Tbx3!1.08!19.83!Tbx3;;chr11:85646469..85646488,+!p5@Tbx2!1.06!15.77!Tbx2;;chr3:34548946..34548972,+!p2@Sox2!1.04!10.99!Sox2;;chr1:193007123..193007139,-!p1@Atf3!1.01!52.57!Atf3;;chr12:39510206..39510249,+!p3@Etv1!0.99!8.84!Etv1;;chr14:17407857..17407875,-!p4@Rarb!0.99!8.84!Rarb;;chr12:28027561..28027591,-!p1@Sox11!0.98!57.59!Sox11;;chr5:67490447..67490458,-!p7@Phox2b!0.98!8.60!Phox2b;;chr7:38557752..38557793,-!p3@Zfp536!0.97!9.80!Zfp536;;chr1:179374784..179374800,+!p2@Zfp238!0.95!9.32!Zfp238;;chr14:17407549..17407575,-!p3@Rarb!0.94!11.95!Rarb;;chr17:25707623..25707639,-!p1@Sox8!0.92!32.26!Sox8;;chr7:38554763..38554780,-!p1@Zfp536!0.92!13.62!Zfp536;;chr13:40826150..40826167,-!p3@Tfap2a!0.92!8.12!Tfap2a;;chr9:106356211..106356242,+!p1@Pcbp4!0.91!143.86!Pcbp4;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.89!8.60!Pou3f3;;chr12:86814833..86814846,+!p1@Fos!0.88!160.11!Fos;;chr12:39507680..39507715,+!p2@Etv1!0.86!12.90!Etv1;;chr13:40829137..40829205,-!p1@Tfap2a!0.86!7.17!Tfap2a;;chr6:83020355..83020371,-!p1@Tlx2!0.86!6.21!Tlx2;;chr5:67490333..67490342,-!p5@Phox2b!0.86!6.21!Phox2b;;chr18:69752864..69752875,+!p25@Tcf4!0.86!6.21!Tcf4;;chr4:84320893..84320910,-!p1@Bnc2!0.85!14.10!Bnc2;;chr13:44936126..44936164,+!p6@Jarid2!0.84!6.93!Jarid2;;chr5:67490412..67490421,-!p6@Phox2b!0.84!5.97!Phox2b;;chr14:52935788..52935817,-!p2@Sall2!0.83!13.14!Sall2;;chr3:107398056..107398082,+!p1@Alx3!0.83!5.74!Alx3;;chr6:53523358..53523388,+!p1@Creb5!0.82!72.65!Creb5;;chr2:44968775..44968795,-!p4@Zeb2!0.82!28.44!Zeb2;;chr11:85646427..85646451,+!p4@Tbx2!0.82!10.04!Tbx2;;chr9:106356278..106356292,+!p3@Pcbp4!0.82!10.04!Pcbp4;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.80!15.06!Zfhx3;;chr7:38558544..38558566,-!p4@Zfp536!0.79!5.97!Zfp536;;chr9:106356243..106356264,+!p2@Pcbp4!0.78!23.42!Pcbp4;;chr19:7342725..7342784,+!p1@Rcor2!0.78!22.46!Rcor2;;chr10:119913278..119913298,-!p2@Hmga2!0.78!11.95!Hmga2;;chr2:71384425..71384456,-!p4@Dlx2!0.78!5.02!Dlx2;;chr9:96653072..96653154,-!p1@Zbtb38!0.77!14.10!Zbtb38;;chr3:90097275..90097302,+!p2@Gatad2b!0.77!12.19!Gatad2b;;chr18:3281034..3281104,-!p1@Crem!0.76!37.52!Crem;;chr1:38684260..38684312,-!p2@Aff3!0.76!36.56!Aff3;;chr14:65568469..65568511,-!p2@Hmbox1!0.76!16.97!Hmbox1;;chr13:78339476..78339515,-!p1@Nr2f1!0.76!7.65!Nr2f1;;chr1:193041811..193041838,-!p2@Atf3!0.76!4.78!Atf3;;chr3:32264565..32264613,-!p1@Zmat3!0.75!56.64!Zmat3;;chr3:51144477..51144506,-!p6@Elf2!0.75!7.41!Elf2;;chr13:15555670..15555771,+!p2@Gli3!0.74!12.43!Gli3;;chr16:43503594..43503634,+!p15@Zbtb20!0.74!5.50!Zbtb20;;chr4:99322855..99322867,+!p2@Foxd3!0.74!4.54!Foxd3;;chr2:44968737..44968758,-!p2@Zeb2!0.73!27.72!Zeb2;;chr14:52634234..52634281,-!p3@Zfp219!0.73!13.14!Zfp219;;chr7:38558574..38558611,-!p2@Zfp536!0.72!5.50!Zfp536;;chr7:52471143..52471186,+!p1@Tead2!0.71!49.94!Tead2;;chr3:51144740..51144743,-!p7@Elf2!0.71!7.17!Elf2;;chr3:32264530..32264544,-!p2@Zmat3!0.71!6.93!Zmat3;;chr18:69752638..69752665,+!p19@Tcf4!0.71!4.54!Tcf4;;chr1:57029281..57029326,-!p1@Satb2!0.70!6.69!Satb2;;chr7:122968213..122968266,-!p4@Sox6!0.69!4.78!Sox6;;chr12:39506873..39506913,+!p1@Etv1!0.68!44.69!Etv1;;chr14:34791987..34791998,-!p2@Zfp488!0.68!3.82!Zfp488;;chr4:99323046..99323073,+!p3@Foxd3!0.68!3.82!Foxd3;;chr5:120120834..120120845,+!p8@Tbx3!0.66!3.58!Tbx3;;chr7:38554684..38554696,-!p10@Zfp536!0.66!3.58!Zfp536;;chr10:119913546..119913583,-!p3@Hmga2!0.65!7.89!Hmga2;;chr3:95032091..95032183,-!p1@Mllt11!0.64!33.69!Mllt11;;chr3:5218629..5218684,+!p1@Zfhx4!0.64!12.43!Zfhx4;;chr9:106356265..106356276,+!p4@Pcbp4!0.64!5.97!Pcbp4;;chr17:44951553..44951586,-!p2@Runx2!0.64!3.82!Runx2;;chr12:39510290..39510309,+!p5@Etv1!0.64!3.35!Etv1;;chr6:144157968..144157989,-!p7@Sox5!0.64!3.35!Sox5;;chr16:43363190..43363242,+!p2@Zbtb20!0.62!11.23!Zbtb20;;chr15:97738692..97738747,-!p1@Vdr!0.61!19.83!Vdr;;chr16:91270091..91270143,+!p2@Olig1!0.61!3.11!Olig1;;chr7:130644017..130644092,-!p1@Zkscan2!0.60!6.45!Zkscan2;;chr12:39507404..39507441,+!p4@Etv1!0.60!4.54!Etv1;;chr7:123174606..123174636,-!p5@Sox6!0.60!4.06!Sox6;;chr10:76424613..76424689,-!p1@Pcbp3!0.59!74.80!Pcbp3;;chr7:25292331..25292421,+!p1@Zfp428!0.59!24.61!Zfp428;;chr10:67375368..67375433,-!p1@Zfp365!0.59!5.74!Zfp365;;chr14:17407671..17407684,-!p7@Rarb!0.59!2.87!Rarb;;chr4:22415443..22415506,-!p1@Pou3f2!0.59!2.87!Pou3f2;;chr16:15887371..15887385,+!p1@Cebpd!0.58!117.33!Cebpd;;chr1:92895299..92895373,+!p2@Lrrfip1!0.58!71.93!Lrrfip1;;chr16:43503493..43503570,+!p9@Zbtb20!0.58!5.26!Zbtb20;;chr2:163028808..163028869,+!p1@Tox2!0.57!11.47!Tox2;;chr8:125778192..125778217,+!p2@Zfp276!0.57!9.08!Zfp276;;chr7:30954700..30954715,-!p2@LOC677248,p2@Zfp146!0.57!7.41!Zfp146;;chr13:78339428..78339466,-!p2@Nr2f1!0.57!4.06!Nr2f1;;chr5:120121020..120121049,+!p1@Tbx3!0.55!19.12!Tbx3;;chr13:22036953..22037009,+!p1@Zfp184!0.55!8.12!Zfp184;;chr10:13686815..13686846,+!p3@Hivep2!0.55!6.69!Hivep2;;chr18:83079981..83080037,+!p6@Zfp516!0.55!5.02!Zfp516;;chr2:44968721..44968734,-!p6@Zeb2!0.54!11.23!Zeb2;;chr4:54957910..54957954,+!p2@Zfp462!0.54!8.84!Zfp462;;chr10:67000609..67000625,+!p1@Egr2!0.54!6.69!Egr2;;chr4:122911086..122911112,+!p1@Heyl!0.53!36.08!Heyl;;chr13:15555496..15555544,+!p1@Gli3!0.53!10.04!Gli3;;chr17:44872561..44872615,-!p1@Runx2!0.53!6.45!Runx2;;chr18:76401789..76401814,+!p4@Smad2!0.53!6.21!Smad2;;chr11:3189683..3189744,+!p2@Patz1!0.53!5.74!Patz1;;chr9:72380594..72380635,+!p3@Rfx7!0.53!4.78!Rfx7;;chr14:65568567..65568588,-!p3@Hmbox1!0.53!4.06!Hmbox1;;chr7:123177120..123177138,-!p10@Sox6!0.53!3.11!Sox6;;chr13:40825465..40825469,-!p2@Tfap2a!0.53!2.39!Tfap2a;;chr13:44936077..44936096,+!p9@Jarid2!0.53!2.39!Jarid2;;chr12:30213247..30213333,+!p1@Myt1l!0.53!2.39!Myt1l;;chr16:91225808..91225824,+!p1@Olig2!0.53!2.39!Olig2;;chr2:71367646..71367658,+!p11@Dlx1!0.53!2.39!Dlx1;;chr2:71367855..71367864,+!p6@Dlx1!0.53!2.39!Dlx1;;chr5:134790507..134790546,-!p1@Gtf2i!0.52!73.36!Gtf2i;;chr19:55816546..55816556,+!p3@Tcf7l2!0.52!10.99!Tcf7l2;;chr16:43363152..43363186,+!p3@Zbtb20!0.52!6.21!Zbtb20;;chr13:78338076..78338104,-!p4@Nr2f1!0.52!3.11!Nr2f1;;chr6:6832076..6832092,-!p1@Dlx5!0.52!2.87!Dlx5;;chr9:63605740..63605771,-!p1@Smad3!0.51!42.54!Smad3;;chr16:22439654..22439676,-!p2@Etv5!0.51!16.97!Etv5;;chr2:44965856..44965896,-!p5@Zeb2!0.51!10.75!Zeb2;;chr15:102034446..102034506,+!p2@Zfp740!0.51!9.80!Zfp740;;chr9:122775033..122775044,-!p2@Zfp445!0.51!4.54!Zfp445;;chr4:150503457..150503498,-!p3@Camta1!0.51!2.63!Camta1;;chr10:30562571..30562597,-!p1@Hey2!0.50!6.21!Hey2;;chr10:66998241..66998263,+!p2@Egr2!0.50!2.15!Egr2;;chr7:38559002..38559009,-!p15@Zfp536!0.50!2.15!Zfp536;;chr12:39510090..39510114,+!p6@Etv1!0.50!2.15!Etv1;;chr13:40829337..40829360,-!p5@Tfap2a!0.50!2.15!Tfap2a;;chr2:71367605..71367621,+!p9@Dlx1!0.50!2.15!Dlx1;;chr1:179374820..179374831,+!p3@Zfp238!0.50!2.15!Zfp238;;chr4:94718879..94718898,-!p1@Jun!0.49!205.75!Jun;;chr4:54960870..54960926,+!p1@Zfp462!0.49!9.56!Zfp462;;chr15:75447162..75447217,+!p2@Zfp41!0.49!7.65!Zfp41;;chr10:119914001..119914078,-!p4@Hmga2!0.49!3.11!Hmga2;;chr16:22439681..22439698,-!p1@Etv5!0.48!47.55!Etv5;;chr5:138187341..138187406,+!p3@Tsc22d4!0.48!29.15!Tsc22d4;;chr10:114821393..114821431,-!p5@Thap2!0.48!6.93!Thap2;;chr13:44826634..44826645,+!p7@Jarid2!0.48!4.54!Jarid2;;chr10:119913792..119913820,-!p5@Hmga2!0.48!4.06!Hmga2;;chr10:79896129..79896163,-!p6@Tcf3!0.48!3.58!Tcf3;;chr16:4594740..4594759,+!p1@Glis2!0.47!30.11!Glis2;;chr7:123177377..123177409,-!p7@Sox6!0.47!2.63!Sox6;;chr18:69752608..69752625,+!p17@Tcf4!0.47!2.39!Tcf4;;chr13:29045559..29045574,-!p1@Sox4!0.46!217.46!Sox4;;chr18:69753015..69753104,+!p1@Tcf4!0.46!34.65!Tcf4;;chr17:27693788..27693803,+!p3@Hmga1,p4@Hmga1-rs1!0.46!11.23!Hmga1;;chr7:25292076..25292114,+!p4@Zfp428!0.46!6.45!Zfp428;;chr18:55149986..55150009,-!p7@Zfp608!0.46!4.30!Zfp608;;chr10:62327990..62328025,-!p2@Tet1!0.46!3.35!Tet1;;chr6:47998938..47998955,-!p2@Zfp777!0.46!2.87!Zfp777;;chr10:66998213..66998240,+!p4@Egr2!0.46!1.91!Egr2;;chr13:40826119..40826131,-!p7@Tfap2a!0.46!1.91!Tfap2a;;chr14:70477113..70477173,+!p1@Egr3!0.46!1.91!Egr3;;chr3:34548845..34548856,+!p4@Sox2!0.46!1.91!Sox2;;chr12:77471524..77471607,+!p1@Zbtb1!0.45!32.26!Zbtb1;;chr10:13685899..13685916,+!p1@Hivep2!0.45!26.29!Hivep2;;chr15:61816932..61816952,+!p2@Myc!0.45!20.55!Myc;;chr13:30077847..30077906,-!p1@E2f3!0.45!19.36!E2f3;;chr7:134376558..134376587,+!p2@Zfp553!0.45!3.58!Zfp553;;chr2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+|ffid_belonging_in_development=CL:0000133,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:11807-124D7
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011143
+|is_a=EFO:0002091;;FF:0011143
+|is_obsolete=
+|library_id=CNhs13084
+|library_id_phase_based=2:CNhs13084
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11807
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11807
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep1.CNhs13084.11807-124D7.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_rep1.CNhs13084.11807-124D7.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_rep1.CNhs13084.11807-124D7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep1.CNhs13084.11807-124D7.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_rep1.CNhs13084.11807-124D7.mm9.nobarcode.rdna.fa.gz
 |name=neurospheres - parasympathetic neuron derived, biol_rep1
 |namespace=
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13084,LSID1000,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.223885579629871,0,0,0,0,0,0.055728249476372,0,0,0,0,0.00872112889504958,0,0,0,0,0,0,0.0428532670859904,0,0,0,0,0,0,0,0,0,0,0,0,0.440647496388232,-0.46536242303244,0,0,0,0,0,-0.124494677047689,0.0406964861964167,-0.024403826273188,-0.749464748509261,-0.17680826871876,0.234746617968565,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0.0930603692915911,0,0,0,-0.0428469550828748,0,0.0149740036304489,0,0.169656096896275,0,-0.0259937656086298,-0.217590288047795,0.306063098590099,-0.0850131124406532,0,0,0.0254298029956996,0,0,0,0.0160506845002252,0.0159425708917197,0.397161663406513,-0.0788315948399074,0,0,0,0,0,0,0.143026204583491,-0.017347032174321,0.107944637530428,0,0,0,0.291341138162471,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=12
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=ANATOMICAL SYSTEM
 |top_motifs=SOX2:1.81469066945;SREBF1,2:1.76455258172;EN1,2:1.64093856807;SOX5:1.58527222208;RXR{A,B,G}:1.5832913054;TP53:1.52047930616;SOX17:1.32631572042;ZNF384:1.26903042607;ONECUT1,2:1.21623072452;ZNF143:1.19980021044;NRF1:1.08505221009;GFI1:1.01124836329;NKX2-1,4:0.982811169531;NANOG:0.979048554892;TFDP1:0.978265252453;HMX1:0.972338418089;PAX8:0.901814675686;AHR_ARNT_ARNT2:0.877898479125;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.818530465466;JUN:0.814657048886;PRRX1,2:0.802701208599;POU3F1..4:0.779572785436;NKX3-1:0.776152872332;FOXD3:0.762401597326;LHX3,4:0.722111448124;ELK1,4_GABP{A,B1}:0.720497584433;ZFP161:0.708016217011;NFY{A,B,C}:0.691613121001;DBP:0.670777065998;MTE{core}:0.660772308631;ZBTB16:0.657627384967;E2F1..5:0.653170781667;EP300:0.636796737885;GZF1:0.605766398428;SOX{8,9,10}:0.597193833617;RFX2..5_RFXANK_RFXAP:0.576544812108;TFAP2{A,C}:0.567822381461;FOSL2:0.560119863236;TFAP2B:0.546734108535;PDX1:0.544116244564;IKZF1:0.534856942492;MZF1:0.533425082632;LEF1_TCF7_TCF7L1,2:0.526588026858;ATF4:0.484965209791;TEF:0.473520005147;EVI1:0.470863277542;CDC5L:0.45851630513;PAX5:0.450685446912;AIRE:0.434084839979;FOS_FOS{B,L1}_JUN{B,D}:0.43179615282;TFCP2:0.428011388845;MED-1{core}:0.419574305947;NHLH1,2:0.393290475915;HES1:0.391977354329;EGR1..3:0.376098975769;RORA:0.35701837261;FOX{I1,J2}:0.343847304709;HBP1_HMGB_SSRP1_UBTF:0.338054086388;BACH2:0.32712690852;PATZ1:0.313585236992;UFEwm:0.306917639405;ZNF148:0.305582399007;NFE2:0.302168867264;FOXQ1:0.302033911937;NR1H4:0.301461476121;STAT1,3:0.298533359874;PBX1:0.296718778781;GTF2I:0.292301693409;VSX1,2:0.261718334866;BREu{core}:0.249518365352;CREB1:0.242985706113;ATF2:0.240227270727;OCT4_SOX2{dimer}:0.238233451445;SP1:0.18794861537;TEAD1:0.184518671103;HAND1,2:0.181722407519;MAZ:0.17357875847;HSF1,2:0.155641709147;ADNP_IRX_SIX_ZHX:0.140838062439;MYB:0.129924427253;ATF5_CREB3:0.10917390469;RFX1:0.104604344561;HIC1:0.0942447867704;TFAP4:0.094071636263;POU2F1..3:0.0809483826081;FOX{D1,D2}:0.0758054619913;ZBTB6:0.0557013985322;REST:0.0553509152891;POU5F1:0.0510960898841;GATA4:0.0485443314308;ZNF423:0.0450111334169;STAT5{A,B}:0.032534217869;XCPE1{core}:0.0291020778182;ESRRA:0.0264807889183;AR:0.0237171255813;KLF4:0.0150880323526;RREB1:-0.00786027355568;FOXM1:-0.0125645937495;ESR1:-0.0323879416841;NFE2L1:-0.0338575715217;CUX2:-0.0340517287116;GTF2A1,2:-0.0506464043192;TLX2:-0.0706532729599;MYFfamily:-0.0735093428069;HOXA9_MEIS1:-0.0774676650122;TOPORS:-0.102886562289;NFATC1..3:-0.10644169381;EBF1:-0.13799227559;SPIB:-0.139400003103;SMAD1..7,9:-0.149841494954;MTF1:-0.168486329913;ZIC1..3:-0.17029748679;PITX1..3:-0.174898397857;PAX1,9:-0.175306752226;FOXO1,3,4:-0.201194362587;FOXP3:-0.214088339449;RBPJ:-0.21520713164;PRDM1:-0.221089187925;SPZ1:-0.233018552499;HIF1A:-0.246414336618;NFIX:-0.265479773139;IKZF2:-0.265659182731;ELF1,2,4:-0.275859652371;ALX4:-0.289127389793;HMGA1,2:-0.289560015481;CRX:-0.290188892869;GFI1B:-0.296360401549;ATF6:-0.301612419272;DMAP1_NCOR{1,2}_SMARC:-0.305828610754;RUNX1..3:-0.342790936073;NKX3-2:-0.348487917462;ZNF238:-0.355407589092;YY1:-0.359155580948;IRF1,2:-0.396652764476;LMO2:-0.398922208307;PAX6:-0.399518630549;POU1F1:-0.400071268732;PAX4:-0.400418796037;SPI1:-0.400983730617;NR3C1:-0.402790280275;TLX1..3_NFIC{dimer}:-0.407655295273;FOXP1:-0.408914554443;HNF4A_NR2F1,2:-0.4207079618;FOXL1:-0.441372693236;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.445465231525;NFIL3:-0.450102992498;ALX1:-0.456988234192;MYBL2:-0.465589482832;HOX{A4,D4}:-0.469675592701;MEF2{A,B,C,D}:-0.484185156151;T:-0.512447576655;IRF7:-0.528449159434;bHLH_family:-0.529860991195;NANOG{mouse}:-0.538241434091;NR6A1:-0.542890963463;NFKB1_REL_RELA:-0.559469262239;BPTF:-0.571018079515;GCM1,2:-0.588647283537;SRF:-0.598317138449;HNF1A:-0.621303860607;HLF:-0.630356597153;ETS1,2:-0.667068143883;TAL1_TCF{3,4,12}:-0.673522202063;NR5A1,2:-0.674466593058;STAT2,4,6:-0.681859628255;NKX6-1,2:-0.698200736277;RXRA_VDR{dimer}:-0.721450776133;NFE2L2:-0.723266303801;CEBPA,B_DDIT3:-0.747754488316;TGIF1:-0.748667871979;ARID5B:-0.750567516349;NKX2-3_NKX2-5:-0.75915108083;GLI1..3:-0.774508794683;FOX{F1,F2,J1}:-0.780899989688;POU6F1:-0.815567569464;CDX1,2,4:-0.844361648162;MYOD1:-0.859800143204;NKX2-2,8:-0.875826615558;FOXA2:-0.889254715233;TBP:-0.936383176047;GATA6:-0.937665842747;HOX{A5,B5}:-0.943793810589;FOXN1:-0.960229420427;PAX2:-1.06981003087;MAFB:-1.19941717666;SNAI1..3:-1.22085666317;ZEB1:-1.46280247724;PPARG:-1.54248301058;TBX4,5:-1.86141398445
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11807-124D7;search_select_hide=table117:11807-124D7
 }}

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FF:11807-124D7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:21, 4 June 2020

CNhs13084

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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