FF:11808-124D8: Difference between revisions

Latest revision as of 18:21, 4 June 2020

Name:	neurospheres - parasympathetic neuron derived, biol_rep2
Species:	Mouse (Mus musculus)
Library ID:	CNhs13085
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	para2
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		SAMD00005530

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13085		CAGE		DRX008866		DRR009738

Accession ID Mm9

Library id		BAM		CTSS
CNhs13085		DRZ001163		DRZ002548

Accession ID Mm10

Library id		BAM		CTSS
CNhs13085		DRZ012513		DRZ013898

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

CNhs13085

0	0
1	0.00311
10	0
100	0
1000	-0.0279
1001	0.00433
1002	-0.101
1003	-0.0687
1004	0
1005	-0.0666
1006	-0.074
1007	0.0353
1008	0
1009	-0.0399
101	0.0119
1010	0
1011	-0.012
1012	0
1013	-0.118
1014	0
1015	0.205
1016	0.456
1017	0
1018	0
1019	0
102	0
1020	0.277
1021	0.16
1022	-0.177
1023	0
1024	0
1025	-0.0611
1026	0
1027	0.444
1028	0
1029	-0.0228
103	-0.0787
1030	0
1031	0.385
1032	0.117
1033	0.0874
1034	0
1035	0
1036	-0.0061
1037	0
1038	0.0344
1039	-0.29
104	0
1040	0.159
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: CNhs13085

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00206
MA0003.1	MA0003.1	0.00358
MA0004.1	MA0004.1	0.854
MA0006.1	MA0006.1	0.275
MA0007.1	MA0007.1	0.816
MA0009.1	MA0009.1	0.0397
MA0014.1	MA0014.1	0.805
MA0017.1	MA0017.1	3.58791e-5
MA0018.2	MA0018.2	9.13955e-4
MA0019.1	MA0019.1	0.878
MA0024.1	MA0024.1	0.0254
MA0025.1	MA0025.1	0.504
MA0027.1	MA0027.1	0.664
MA0028.1	MA0028.1	0.24
MA0029.1	MA0029.1	0.286
MA0030.1	MA0030.1	0.915
MA0031.1	MA0031.1	0.185
MA0035.2	MA0035.2	2.70397e-4
MA0038.1	MA0038.1	0.375
MA0039.2	MA0039.2	0.268
MA0040.1	MA0040.1	0.662
MA0041.1	MA0041.1	0.0545
MA0042.1	MA0042.1	0.798
MA0043.1	MA0043.1	0.0398
MA0046.1	MA0046.1	1.11785e-17
MA0047.2	MA0047.2	0.00352
MA0048.1	MA0048.1	0.742
MA0050.1	MA0050.1	0.00303
MA0051.1	MA0051.1	0.00394
MA0052.1	MA0052.1	0.00294
MA0055.1	MA0055.1	0.842
MA0057.1	MA0057.1	0.154
MA0058.1	MA0058.1	0.527
MA0059.1	MA0059.1	0.357
MA0060.1	MA0060.1	0.0011
MA0061.1	MA0061.1	0.0448
MA0062.2	MA0062.2	0.46
MA0065.2	MA0065.2	4.18308e-5
MA0066.1	MA0066.1	0.596
MA0067.1	MA0067.1	0.272
MA0068.1	MA0068.1	0.533
MA0069.1	MA0069.1	0.401
MA0070.1	MA0070.1	0.0195
MA0071.1	MA0071.1	0.156
MA0072.1	MA0072.1	0.459
MA0073.1	MA0073.1	0.988
MA0074.1	MA0074.1	0.642
MA0076.1	MA0076.1	0.124
MA0077.1	MA0077.1	0.0307
MA0078.1	MA0078.1	0.157
MA0079.2	MA0079.2	0.295
MA0080.2	MA0080.2	4.9489e-8
MA0081.1	MA0081.1	0.737
MA0083.1	MA0083.1	0.0994
MA0084.1	MA0084.1	0.92
MA0087.1	MA0087.1	0.53
MA0088.1	MA0088.1	0.661
MA0090.1	MA0090.1	0.994
MA0091.1	MA0091.1	0.841
MA0092.1	MA0092.1	0.72
MA0093.1	MA0093.1	0.745
MA0099.2	MA0099.2	0.347
MA0100.1	MA0100.1	0.472
MA0101.1	MA0101.1	0.26
MA0102.2	MA0102.2	0.874
MA0103.1	MA0103.1	2.26963e-4
MA0104.2	MA0104.2	0.963
MA0105.1	MA0105.1	4.96889e-5
MA0106.1	MA0106.1	0.13
MA0107.1	MA0107.1	0.0952
MA0108.2	MA0108.2	0.0129
MA0111.1	MA0111.1	0.8
MA0112.2	MA0112.2	9.57361e-5
MA0113.1	MA0113.1	0.286
MA0114.1	MA0114.1	7.00781e-5
MA0115.1	MA0115.1	0.143
MA0116.1	MA0116.1	9.73195e-4
MA0117.1	MA0117.1	0.739
MA0119.1	MA0119.1	0.0971
MA0122.1	MA0122.1	0.9
MA0124.1	MA0124.1	0.664
MA0125.1	MA0125.1	0.181
MA0131.1	MA0131.1	0.337
MA0135.1	MA0135.1	0.556
MA0136.1	MA0136.1	4.24004e-5
MA0137.2	MA0137.2	0.465
MA0138.2	MA0138.2	0.0115
MA0139.1	MA0139.1	0.021
MA0140.1	MA0140.1	3.79431e-4
MA0141.1	MA0141.1	0.00653
MA0142.1	MA0142.1	0.0966
MA0143.1	MA0143.1	0.123
MA0144.1	MA0144.1	0.697
MA0145.1	MA0145.1	0.11
MA0146.1	MA0146.1	0.669
MA0147.1	MA0147.1	0.786
MA0148.1	MA0148.1	0.00448
MA0149.1	MA0149.1	0.417
MA0150.1	MA0150.1	0.187
MA0152.1	MA0152.1	0.915
MA0153.1	MA0153.1	2.60193e-11
MA0154.1	MA0154.1	0.00487
MA0155.1	MA0155.1	0.668
MA0156.1	MA0156.1	0.00559
MA0157.1	MA0157.1	0.0253
MA0159.1	MA0159.1	0.363
MA0160.1	MA0160.1	0.0689
MA0162.1	MA0162.1	0.185
MA0163.1	MA0163.1	0.0131
MA0164.1	MA0164.1	0.5
MA0258.1	MA0258.1	0.023
MA0259.1	MA0259.1	0.723

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: CNhs13085

Novel motif	Logo	P-value
1	1	0.158
10	10	0.151
100	100	0.715
101	101	0.785
102	102	0.746
103	103	0.0886
104	104	0.986
105	105	0.104
106	106	0.0183
107	107	0.0904
108	108	0.79
109	109	0.0748
11	11	0.0918
110	110	0.302
111	111	0.019
112	112	0.0488
113	113	0.377
114	114	0.0423
115	115	0.378
116	116	0.545
117	117	0.528
118	118	0.57
119	119	0.0508
12	12	0.512
120	120	0.44
121	121	0.0841
122	122	0.603
123	123	0.829
124	124	0.732
125	125	0.704
126	126	0.309
127	127	0.427
128	128	0.0247
129	129	0.0796
13	13	0.1
130	130	0.609
131	131	0.425
132	132	0.374
133	133	0.281
134	134	0.736
135	135	0.316
136	136	0.752
137	137	0.372
138	138	0.376
139	139	0.163
14	14	0.402
140	140	0.0315
141	141	0.168
142	142	0.52
143	143	0.903
144	144	0.54
145	145	0.391
146	146	0.544
147	147	0.884
148	148	0.707
149	149	0.152
15	15	0.0991
150	150	0.617
151	151	0.334
152	152	0.0941
153	153	0.69
154	154	0.682
155	155	0.787
156	156	1.43764e-4
157	157	0.275
158	158	0.811
159	159	0.329
160	160	0.112
161	161	0.78
162	162	0.925
163	163	0.311
164	164	0.137
165	165	0.134
166	166	0.759
167	167	0.567
168	168	0.96
169	169	0.00958
17	17	0.0597
18	18	0.644
19	19	0.111
2	2	0.429
20	20	0.988
21	21	0.365
22	22	0.447
23	23	0.313
24	24	0.435
25	25	0.323
26	26	0.0563
27	27	0.234
28	28	0.591
29	29	0.676
3	3	0.119
30	30	0.59
31	31	0.757
32	32	0.105
33	33	0.371
34	34	0.365
35	35	0.534
36	36	0.614
37	37	0.146
38	38	0.27
39	39	0.353
4	4	0.738
40	40	0.415
41	41	0.739
42	42	0.296
43	43	0.249
44	44	0.349
45	45	0.391
46	46	0.219
47	47	0.164
48	48	0.2
49	49	0.182
5	5	0.233
50	50	0.831
51	51	0.49
52	52	0.224
53	53	0.342
54	54	0.555
55	55	0.568
56	56	0.618
57	57	0.417
58	58	0.0723
59	59	0.0282
6	6	0.998
60	60	0.0858
61	61	0.435
62	62	0.032
63	63	0.211
64	64	0.477
65	65	0.178
66	66	0.52
67	67	0.718
68	68	0.629
69	69	0.808
7	7	0.102
70	70	0.0304
71	71	0.147
72	72	0.462
73	73	0.212
74	74	0.222
75	75	0.236
76	76	0.839
77	77	0.258
78	78	0.0883
79	79	0.277
8	8	0.103
80	80	0.387
81	81	0.614
82	82	0.0306
83	83	0.161
84	84	0.506
85	85	0.0794
86	86	0.341
87	87	0.587
88	88	0.498
89	89	0.0603
9	9	0.375
90	90	0.73
91	91	0.227
92	92	0.0696
93	93	0.494
94	94	0.194
95	95	0.249
96	96	0.277
97	97	0.802
98	98	0.0835
99	99	0.109

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: CNhs13085

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:0000010,UBERON:0000011,UBERON:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
+|DRA_sample_Accession=CAGE@SAMD00005530
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000031,CL:0000034,CL:0000047,CL:0000048,CL:0000055,CL:0000107,CL:0000133,CL:0000144,CL:0000211,CL:0000220,CL:0000221,CL:0000255,CL:0000393,CL:0000404,CL:0000540,CL:0000548,CL:0000723,CL:0002319,CL:0002321,CL:0002371
+|accession_numbers=CAGE;DRX008866;DRR009738;DRZ001163;DRZ002548;DRZ012513;DRZ013898
+|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!2.21!438.69!Hand2;;chr16:91270004..91270023,+!p1@Olig1!2.16!163.98!Olig1;;chr10:86956396..86956411,-!p1@Ascl1!2.14!207.20!Ascl1;;chr15:78994907..78994926,-!p1@Sox10!2.05!274.27!Sox10;;chr4:99322820..99322845,+!p1@Foxd3!1.97!115.63!Foxd3;;chr5:67490284..67490302,-!p1@Phox2b!1.83!65.95!Phox2b;;chr7:108966820..108966835,+!p1@Phox2a!1.70!49.02!Phox2a;;chr5:67490474..67490494,-!p2@Phox2b!1.58!36.76!Phox2b;;chr5:138199361..138199441,+!p2@Tsc22d4!1.52!59.04!Tsc22d4;;chr3:34548909..34548927,+!p1@Sox2!1.51!52.80!Sox2;;chr2:71384802..71384815,-!p1@Dlx2!1.51!38.77!Dlx2;;chr1:193007123..193007139,-!p1@Atf3!1.47!153.73!Atf3;;chr2:71367871..71367898,+!p1@Dlx1!1.40!23.84!Dlx1;;chr2:146047829..146047847,+!p1@Insm1!1.35!37.88!Insm1;;chr1:193041811..193041838,-!p2@Atf3!1.35!21.17!Atf3;;chr7:38557887..38557910,-!p5@Zfp536!1.34!20.94!Zfp536;;chr14:17407878..17407926,-!p1@Rarb!1.33!45.45!Rarb;;chr11:85646263..85646278,+!p2@Tbx2!1.25!42.11!Tbx2;;chr18:69752912..69752928,+!p9@Tcf4!1.25!25.40!Tcf4;;chr5:120120667..120120685,+!p3@Tbx3!1.23!30.52!Tbx3;;chr14:34791937..34791977,-!p1@Zfp488!1.23!15.82!Zfp488;;chr5:67490391..67490404,-!p3@Phox2b!1.21!15.37!Phox2b;;chr11:85646303..85646329,+!p1@Tbx2!1.18!93.13!Tbx2;;chr2:71384458..71384526,-!p2@Dlx2!1.17!13.81!Dlx2;;chr2:71367142..71367167,+!p2@Dlx1!1.17!13.81!Dlx1;;chr14:17407970..17408015,-!p2@Rarb!1.16!35.65!Rarb;;chr6:83020355..83020371,-!p1@Tlx2!1.16!13.37!Tlx2;;chr16:91270091..91270143,+!p2@Olig1!1.14!12.92!Olig1;;chr3:34548946..34548972,+!p2@Sox2!1.13!14.04!Sox2;;chr5:67490346..67490357,-!p4@Phox2b!1.13!12.48!Phox2b;;chr13:40829137..40829205,-!p1@Tfap2a!1.12!13.59!Tfap2a;;chr12:39510206..39510249,+!p3@Etv1!1.11!11.81!Etv1;;chrX:58146612..58146615,-!p1@Sox3!1.10!11.59!Sox3;;chr12:12948633..12948651,-!p1@Mycn!1.09!109.39!Mycn;;chr17:44872561..44872615,-!p1@Runx2!1.07!24.51!Runx2;;chr12:28027561..28027591,-!p1@Sox11!1.06!69.07!Sox11;;chr7:38557752..38557793,-!p3@Zfp536!1.06!12.25!Zfp536;;chr17:44951553..44951586,-!p2@Runx2!1.06!11.59!Runx2;;chr1:179374784..179374800,+!p2@Zfp238!1.04!11.81!Zfp238;;chr7:38558544..38558566,-!p4@Zfp536!1.04!11.36!Zfp536;;chr9:71743854..71743909,-!p1@Tcf12!1.02!76.64!Tcf12;;chr5:120121169..120121171,+!p4@Tbx3!1.02!17.38!Tbx3;;chr13:44936126..44936164,+!p6@Jarid2!1.02!10.92!Jarid2;;chr17:25707623..25707639,-!p1@Sox8!1.01!39.88!Sox8;;chr7:38554763..38554780,-!p1@Zfp536!1.00!16.49!Zfp536;;chr12:86814833..86814846,+!p1@Fos!0.99!208.99!Fos;;chr2:44968775..44968795,-!p4@Zeb2!0.99!42.55!Zeb2;;chr9:106356278..106356292,+!p3@Pcbp4!0.99!15.15!Pcbp4;;chr13:40826150..40826167,-!p3@Tfap2a!0.99!9.80!Tfap2a;;chr11:85646341..85646352,+!p3@Tbx2!0.97!16.71!Tbx2;;chr2:71384401..71384424,-!p3@Dlx2!0.97!8.24!Dlx2;;chr5:67490447..67490458,-!p7@Phox2b!0.96!8.02!Phox2b;;chr9:96653072..96653154,-!p1@Zbtb38!0.94!21.39!Zbtb38;;chr9:106356211..106356242,+!p1@Pcbp4!0.93!153.06!Pcbp4;;chr4:150503457..150503498,-!p3@Camta1!0.92!8.24!Camta1;;chr16:91225808..91225824,+!p1@Olig2!0.92!7.35!Olig2;;chr7:38554684..38554696,-!p10@Zfp536!0.91!7.13!Zfp536;;chr5:67490412..67490421,-!p6@Phox2b!0.90!6.91!Phox2b;;chr19:7342725..7342784,+!p1@Rcor2!0.89!28.74!Rcor2;;chr11:85646469..85646488,+!p5@Tbx2!0.89!10.47!Tbx2;;chr18:69752864..69752875,+!p25@Tcf4!0.89!6.68!Tcf4;;chr6:53523358..53523388,+!p1@Creb5!0.88!83.33!Creb5;;chr12:39507680..39507715,+!p2@Etv1!0.88!13.37!Etv1;;chr7:122968213..122968266,-!p4@Sox6!0.88!7.80!Sox6;;chr10:119913546..119913583,-!p3@Hmga2!0.87!13.81!Hmga2;;chr16:43363190..43363242,+!p2@Zbtb20!0.86!20.05!Zbtb20;;chr2:71384425..71384456,-!p4@Dlx2!0.86!6.24!Dlx2;;chr9:106356243..106356264,+!p2@Pcbp4!0.85!27.85!Pcbp4;;chr14:17407857..17407875,-!p4@Rarb!0.85!6.02!Rarb;;chr2:44965856..44965896,-!p5@Zeb2!0.84!24.29!Zeb2;;chr18:3281034..3281104,-!p1@Crem!0.83!43.45!Crem;;chr4:122911086..122911112,+!p1@Heyl!0.82!69.96!Heyl;;chr5:67490333..67490342,-!p5@Phox2b!0.82!5.57!Phox2b;;chr4:84320893..84320910,-!p1@Bnc2!0.81!12.70!Bnc2;;chr1:57029281..57029326,-!p1@Satb2!0.81!8.69!Satb2;;chr18:69752638..69752665,+!p19@Tcf4!0.81!6.02!Tcf4;;chr2:44968737..44968758,-!p2@Zeb2!0.80!32.97!Zeb2;;chr4:99323046..99323073,+!p3@Foxd3!0.80!5.35!Foxd3;;chr4:99322855..99322867,+!p2@Foxd3!0.80!5.35!Foxd3;;chr14:17407671..17407684,-!p7@Rarb!0.80!5.35!Rarb;;chr14:17407549..17407575,-!p3@Rarb!0.79!8.24!Rarb;;chr3:95032091..95032183,-!p1@Mllt11!0.78!47.23!Mllt11;;chr2:127347067..127347093,-!p1@Kcnip3!0.78!8.91!Kcnip3;;chr1:38684260..38684312,-!p2@Aff3!0.77!38.10!Aff3;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.77!13.81!Zfhx3;;chr13:78339476..78339515,-!p1@Nr2f1!0.77!7.80!Nr2f1;;chr3:127336052..127336058,+!p1@Neurog2!0.77!4.90!Neurog2;;chr11:33103563..33103583,-!p1@Tlx3!0.77!4.90!Tlx3;;chr15:97738692..97738747,-!p1@Vdr!0.76!28.74!Vdr;;chr14:65568469..65568511,-!p2@Hmbox1!0.76!16.71!Hmbox1;;chr7:38558574..38558611,-!p2@Zfp536!0.76!6.02!Zfp536;;chr14:52634234..52634281,-!p3@Zfp219!0.75!13.81!Zfp219;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!0.75!6.02!Pou3f3;;chr19:5447886..5447905,+!p1@Fosl1!0.75!4.68!Fosl1;;chr17:44951431..44951445,-!p3@Runx2!0.75!4.68!Runx2;;chr2:44968721..44968734,-!p6@Zeb2!0.74!18.72!Zeb2;;chr10:119913278..119913298,-!p2@Hmga2!0.74!10.69!Hmga2;;chr13:40826236..40826248,-!p8@Tfap2a!0.74!4.46!Tfap2a;;chr9:106356265..106356276,+!p4@Pcbp4!0.73!7.58!Pcbp4;;chr12:39507404..39507441,+!p4@Etv1!0.73!6.46!Etv1;;chr16:43503594..43503634,+!p15@Zbtb20!0.73!5.35!Zbtb20;;chr10:67000609..67000625,+!p1@Egr2!0.72!10.69!Egr2;;chr16:43363152..43363186,+!p3@Zbtb20!0.72!10.47!Zbtb20;;chr14:52935788..52935817,-!p2@Sall2!0.72!10.03!Sall2;;chr3:51144477..51144506,-!p6@Elf2!0.72!6.91!Elf2;;chr7:123177120..123177138,-!p10@Sox6!0.72!5.35!Sox6;;chr13:40829337..40829360,-!p5@Tfap2a!0.72!4.23!Tfap2a;;chr12:39510290..39510309,+!p5@Etv1!0.72!4.23!Etv1;;chr8:125778192..125778217,+!p2@Zfp276!0.71!12.70!Zfp276;;chr10:30562571..30562597,-!p1@Hey2!0.71!10.47!Hey2;;chr10:119913792..119913820,-!p5@Hmga2!0.70!7.35!Hmga2;;chr12:30213247..30213333,+!p1@Myt1l!0.70!4.01!Myt1l;;chr12:39510090..39510114,+!p6@Etv1!0.70!4.01!Etv1;;chr5:120121020..120121049,+!p1@Tbx3!0.69!26.96!Tbx3;;chr10:13686815..13686846,+!p3@Hivep2!0.69!9.58!Hivep2;;chr14:65568567..65568588,-!p3@Hmbox1!0.69!6.24!Hmbox1;;chr3:32264530..32264544,-!p2@Zmat3!0.68!6.24!Zmat3;;chr10:119914001..119914078,-!p4@Hmga2!0.68!5.35!Hmga2;;chr7:52471143..52471186,+!p1@Tead2!0.67!45.23!Tead2;;chr3:5218629..5218684,+!p1@Zfhx4!0.67!13.59!Zfhx4;;chr3:90097275..90097302,+!p2@Gatad2b!0.67!9.36!Gatad2b;;chr4:94718879..94718898,-!p1@Jun!0.66!301.67!Jun;;chr10:76424613..76424689,-!p1@Pcbp3!0.66!87.78!Pcbp3;;chr10:114821393..114821431,-!p5@Thap2!0.66!10.92!Thap2;;chr16:43503493..43503570,+!p9@Zbtb20!0.66!6.46!Zbtb20;;chr3:32264565..32264613,-!p1@Zmat3!0.65!45.01!Zmat3;;chr12:39506873..39506913,+!p1@Etv1!0.65!41.89!Etv1;;chr4:94718861..94718872,-!p2@Jun!0.65!30.08!Jun;;chr18:55149986..55150009,-!p7@Zfp608!0.65!7.35!Zfp608;;chr7:130644017..130644092,-!p1@Zkscan2!0.65!7.35!Zkscan2;;chr5:120120834..120120845,+!p8@Tbx3!0.64!3.34!Tbx3;;chr3:107398056..107398082,+!p1@Alx3!0.64!3.34!Alx3;;chr1:179374820..179374831,+!p3@Zfp238!0.64!3.34!Zfp238;;chr13:22036953..22037009,+!p1@Zfp184!0.63!9.80!Zfp184;;chr11:85646427..85646451,+!p4@Tbx2!0.63!6.24!Tbx2;;chr2:127347094..127347111,-!p2@Kcnip3!0.63!5.79!Kcnip3;;chr2:44965761..44965785,-!p13@Zeb2!0.62!5.12!Zeb2;;chr18:69752608..69752625,+!p17@Tcf4!0.62!3.79!Tcf4;;chr19:55816546..55816556,+!p3@Tcf7l2!0.61!13.81!Tcf7l2;;chr13:78339428..78339466,-!p2@Nr2f1!0.61!4.46!Nr2f1;;chr14:34791987..34791998,-!p2@Zfp488!0.61!3.12!Zfp488;;chr10:66998241..66998263,+!p2@Egr2!0.61!3.12!Egr2;;chr10:119913954..119913972,-!p8@Hmga2!0.61!3.12!Hmga2;;chr18:55150011..55150059,-!p3@Zfp608!0.60!11.36!Zfp608;;chr9:72380594..72380635,+!p3@Rfx7!0.60!5.79!Rfx7;;chr16:43503720..43503739,+!p18@Zbtb20!0.60!3.34!Zbtb20;;chr17:44873599..44873623,-!p7@Runx2!0.59!2.90!Runx2;;chr18:3281015..3281028,-!p18@Crem!0.59!2.90!Crem;;chr13:40826119..40826131,-!p7@Tfap2a!0.59!2.90!Tfap2a;;chr13:40825465..40825469,-!p2@Tfap2a!0.59!2.90!Tfap2a;;chr7:38559002..38559009,-!p15@Zfp536!0.59!2.90!Zfp536;;chr16:15887371..15887385,+!p1@Cebpd!0.58!117.64!Cebpd;;chr13:15555670..15555771,+!p2@Gli3!0.58!8.24!Gli3;;chr11:3189683..3189744,+!p2@Patz1!0.58!6.46!Patz1;;chr7:123174606..123174636,-!p5@Sox6!0.58!3.79!Sox6;;chr2:163028808..163028869,+!p1@Tox2!0.57!11.59!Tox2;;chr5:120121446..120121461,+!p2@Tbx3!0.57!10.69!Tbx3;;chr18:55149735..55149776,-!p4@Zfp608!0.57!7.58!Zfp608;;chr5:120121262..120121282,+!p6@Tbx3!0.57!3.12!Tbx3;;chrX:108009761..108009788,+!p1@Pou3f4!0.57!2.67!Pou3f4;;chr13:29045559..29045574,-!p1@Sox4!0.56!272.71!Sox4;;chr19:7342786..7342803,+!p2@Rcor2!0.56!3.79!Rcor2;;chr2:169458519..169458555,+!p2@Tshz2!0.55!12.48!Tshz2;;chr4:54960870..54960926,+!p1@Zfp462!0.55!11.14!Zfp462;;chr15:102034510..102034549,+!p4@Zfp740!0.55!7.35!Zfp740;;chr7:123174485..123174514,-!p6@Sox6!0.55!3.34!Sox6;;chr6:6832076..6832092,-!p1@Dlx5!0.55!3.12!Dlx5;;chr4:119406389..119406411,+!p1@Hivep3!0.54!15.15!Hivep3;;chr7:135019147..135019187,-!p3@Zfp668!0.54!6.24!Zfp668;;chr7:134376558..134376587,+!p2@Zfp553!0.54!4.68!Zfp553;;chr7:138697803..138697813,+!p1@Hmx2!0.54!2.45!Hmx2;;chr6:6831928..6831949,-!p3@Dlx5!0.54!2.45!Dlx5;;chr2:181501745..181501778,+!p1@Myt1!0.54!2.45!Myt1;;chr10:13685585..13685645,+!p2@Hivep2!0.53!10.25!Hivep2;;chr9:21420744..21420755,+!p3@Smarca4!0.53!8.24!Smarca4;;chr7:20408047..20408125,-!p1@Bcl3!0.52!34.09!Bcl3;;chr10:62327990..62328025,-!p2@Tet1!0.52!4.01!Tet1;;chr18:24113207..24113218,+!p3@Zfp397!0.52!4.01!Zfp397;;chr6:53523346..53523353,+!p3@Creb5!0.52!3.56!Creb5;;chr1:92895299..92895373,+!p2@Lrrfip1!0.51!61.05!Lrrfip1;;chr19:5637528..5637548,+!p2@Rela!0.51!16.93!Rela;;chr4:99323019..99323031,+!p4@Foxd3!0.51!2.23!Foxd3;;chr7:25292331..25292421,+!p1@Zfp428!0.50!20.05!Zfp428;;chr2:130120884..130120972,+!p1@Ebf4!0.50!16.26!Ebf4;;chr13:44826634..44826645,+!p7@Jarid2!0.50!4.90!Jarid2;;chr2:44965788..44965815,-!p11@Zeb2!0.50!4.68!Zeb2;;c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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:11808-124D8
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011143
+|is_a=EFO:0002091;;FF:0011143
+|is_obsolete=
+|library_id=CNhs13085
+|library_id_phase_based=2:CNhs13085
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11808
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11808
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep2.CNhs13085.11808-124D8.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_rep2.CNhs13085.11808-124D8.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_rep2.CNhs13085.11808-124D8.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520parasympathetic%2520neuron%2520derived%252c%2520biol_rep2.CNhs13085.11808-124D8.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_rep2.CNhs13085.11808-124D8.mm9.nobarcode.rdna.fa.gz
 |name=neurospheres - parasympathetic neuron derived, biol_rep2
 |namespace=
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13085,LSID1000,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.370295673645231,0,0,0,0,0,0.202378953745147,0,0,0,0,0.00301571873911587,0,0,0,0,0,0,0.0848428903839269,0,0,0,0,0,0,0,0,0,0,0,0,0.438775903795505,-0.189802726892465,0,0,0,0,0,0.0401949680072997,0.0880151420071128,0.049277193456926,-0.34652353667317,-0.269868638010351,0.22229914573975,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.135189868614564,0.0873549591356574,0.368620065431566,0,0.119342885928703,-0.310650657339386,0.406998942600499,-0.0912368485550605,0,-0.0176404686176167,0.0822906369537606,0,0,0,0.0207955997913607,0.135844515142306,0.380267659230652,0.00852336429574996,0,0,0,0,0,0,0.143703679522247,0.0509286280261558,0.188748132192918,0,0,0,0.284256462170925,0
 |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=SOX2:1.94861870455;SOX5:1.8834408657;RXR{A,B,G}:1.57888067216;EN1,2:1.50862319895;ONECUT1,2:1.49632849425;TP53:1.48278086486;SREBF1,2:1.45062829577;GZF1:1.32868598177;ZNF143:1.3071023975;ZNF384:1.24037851087;SOX17:1.22683956453;NKX2-1,4:1.11883782546;CDC5L:1.08161434332;JUN:1.0692222552;AHR_ARNT_ARNT2:1.04071242041;NRF1:1.01046577309;POU3F1..4:0.996938159159;NANOG:0.991622838768;PRRX1,2:0.963366795001;ZFP161:0.927077716951;ATF4:0.882746691023;FOXD3:0.835119920543;HMX1:0.834063899066;FOSL2:0.81854076182;GFI1:0.796050840208;DBP:0.759860294529;TFDP1:0.71008719143;MTE{core}:0.709870890223;SOX{8,9,10}:0.675318861124;MZF1:0.660146707151;TFAP2{A,C}:0.644511664855;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.644326370309;ELK1,4_GABP{A,B1}:0.634003901535;RORA:0.627592624861;EVI1:0.605694017339;LHX3,4:0.604249601787;FOXQ1:0.587566523964;HBP1_HMGB_SSRP1_UBTF:0.581039701085;PBX1:0.570556541796;AIRE:0.561441535045;LEF1_TCF7_TCF7L1,2:0.546164604375;PDX1:0.544928788839;MED-1{core}:0.543660977772;ZBTB16:0.538728726973;TFAP2B:0.512488917252;PAX8:0.512438014516;EGR1..3:0.511653810736;NHLH1,2:0.508329104225;IKZF1:0.503685104695;NFE2:0.503081091434;RFX2..5_RFXANK_RFXAP:0.50262246647;NKX3-1:0.501030138585;GATA4:0.496778706941;PATZ1:0.472789746613;ADNP_IRX_SIX_ZHX:0.45276322013;FOS_FOS{B,L1}_JUN{B,D}:0.446750486969;PAX5:0.44021332062;MAZ:0.425692174866;EP300:0.411736837845;SP1:0.391602344703;GTF2I:0.385915359277;HAND1,2:0.383452265836;VSX1,2:0.341950944559;ATF2:0.315840232552;NFY{A,B,C}:0.305799251242;ZNF148:0.300394991719;BREu{core}:0.299829239866;GTF2A1,2:0.293280631528;RBPJ:0.284120969208;CREB1:0.281831647367;TFAP4:0.278706125839;UFEwm:0.27515434975;TFCP2:0.273836928328;ZBTB6:0.26948603672;TEF:0.268986282981;BACH2:0.246170836072;E2F1..5:0.2236842021;HIC1:0.218253360134;IKZF2:0.210288237206;NR1H4:0.204766606529;PAX4:0.188019030811;OCT4_SOX2{dimer}:0.18015137096;EBF1:0.169253544273;TEAD1:0.151923153482;STAT1,3:0.149381216081;MYFfamily:0.142383452096;RFX1:0.14147561017;REST:0.140798301165;POU5F1:0.139638514821;ATF5_CREB3:0.131622739364;HES1:0.129502591948;CRX:0.125825502929;XCPE1{core}:0.121106304946;RREB1:0.109377534098;FOXP3:0.109112056923;HIF1A:0.10907924138;FOX{I1,J2}:0.0852726042196;NFE2L1:0.0627595469044;HMGA1,2:0.0528303231532;FOX{D1,D2}:0.0400796832841;NKX3-2:0.0243442843057;HSF1,2:0.0217834952106;PRDM1:0.00511996786593;ZNF238:-0.00472675640108;POU2F1..3:-0.0054427461347;MYB:-0.00600275026113;GFI1B:-0.00778703005267;SMAD1..7,9:-0.0233469074432;FOXO1,3,4:-0.0242365334244;HOX{A4,D4}:-0.0392263013844;ZNF423:-0.0458855824166;STAT5{A,B}:-0.0588092912837;KLF4:-0.0590372588381;FOXP1:-0.063566703052;ZIC1..3:-0.0743816289596;ATF6:-0.0901527946441;ESR1:-0.113619358712;TLX2:-0.129910814625;CUX2:-0.13475062451;DMAP1_NCOR{1,2}_SMARC:-0.140795951761;SPZ1:-0.141526468097;TLX1..3_NFIC{dimer}:-0.152054183008;ALX1:-0.160460476939;ESRRA:-0.165767346062;PAX1,9:-0.179085523227;MTF1:-0.186871096106;SPIB:-0.1951463749;YY1:-0.213822217625;PITX1..3:-0.216956354792;NKX2-2,8:-0.24275793477;MYBL2:-0.244255224354;NFIL3:-0.244416450536;NFATC1..3:-0.262077103987;FOXM1:-0.26934779535;RUNX1..3:-0.283517958878;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.291368830144;GCM1,2:-0.296222519538;FOXL1:-0.30926221525;HOXA9_MEIS1:-0.32029774867;BPTF:-0.345979545643;CEBPA,B_DDIT3:-0.376304909926;AR:-0.380315622669;IRF1,2:-0.387626670847;IRF7:-0.391890418752;ELF1,2,4:-0.401909209897;TOPORS:-0.407600310183;T:-0.410364258354;STAT2,4,6:-0.420302671891;POU1F1:-0.423827692659;TAL1_TCF{3,4,12}:-0.425387595078;HNF4A_NR2F1,2:-0.457838408033;PAX6:-0.464594763695;NR6A1:-0.487070440782;MEF2{A,B,C,D}:-0.490580291066;SPI1:-0.512095010703;bHLH_family:-0.555718431032;NFKB1_REL_RELA:-0.564369489139;HNF1A:-0.597220028122;LMO2:-0.604746853462;SRF:-0.605843119449;FOX{F1,F2,J1}:-0.609667374161;NKX6-1,2:-0.612455210182;NFIX:-0.613833319348;NR3C1:-0.642521114549;POU6F1:-0.64629613732;ALX4:-0.647344611921;FOXA2:-0.661056180289;ARID5B:-0.665785325281;CDX1,2,4:-0.679580327285;GLI1..3:-0.690663337996;NANOG{mouse}:-0.697539187604;NFE2L2:-0.725387981963;ETS1,2:-0.739821022559;MYOD1:-0.744006980047;HLF:-0.783532878859;TGIF1:-0.784331061327;TBP:-0.808154783463;PAX2:-0.820938165252;NKX2-3_NKX2-5:-0.823342273315;RXRA_VDR{dimer}:-0.824034158075;MAFB:-0.890140407264;NR5A1,2:-0.938580196604;GATA6:-0.991910316281;FOXN1:-1.03413893935;HOX{A5,B5}:-1.1381775571;PPARG:-1.15518599222;SNAI1..3:-1.23771791527;ZEB1:-1.5568442938;TBX4,5:-2.11423826572
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11808-124D8;search_select_hide=table117:11808-124D8
 }}

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FF:11808-124D8: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:21, 4 June 2020

CNhs13085

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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