FF:11805-124D5: Difference between revisions

Latest revision as of 18:21, 4 June 2020

Name:	neurospheres - sympathetic neuron derived, biol_rep2
Species:	Mouse (Mus musculus)
Library ID:	CNhs13082
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	sym2
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		SAMD00005733

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13082		CAGE		DRX008869		DRR009741

Accession ID Mm9

Library id		BAM		CTSS
CNhs13082		DRZ001166		DRZ002551

Accession ID Mm10

Library id		BAM		CTSS
CNhs13082		DRZ012516		DRZ013901

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

CNhs13082

0	0
1	0.111
10	0
100	0.05
1000	0
1001	-0.0356
1002	-0.0941
1003	-0.0467
1004	0
1005	0
1006	0
1007	-0.0275
1008	0
1009	0.0833
101	-0.00347
1010	0
1011	0
1012	0
1013	0.0653
1014	-0.0851
1015	0.145
1016	0.397
1017	0
1018	0
1019	0
102	0
1020	0.391
1021	0.111
1022	-0.124
1023	0
1024	-0.14
1025	-0.0611
1026	0
1027	0.44
1028	0
1029	-0.0363
103	0
1030	0
1031	0.514
1032	0.0262
1033	0.0743
1034	0
1035	0
1036	-0.0419
1037	0
1038	0.0367
1039	-0.162
104	0
1040	0.319
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: CNhs13082

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	3.22114e-6
MA0003.1	MA0003.1	0.0103
MA0004.1	MA0004.1	0.971
MA0006.1	MA0006.1	0.446
MA0007.1	MA0007.1	0.361
MA0009.1	MA0009.1	0.0625
MA0014.1	MA0014.1	0.894
MA0017.1	MA0017.1	3.38682e-6
MA0018.2	MA0018.2	0.0341
MA0019.1	MA0019.1	0.359
MA0024.1	MA0024.1	0.0423
MA0025.1	MA0025.1	0.265
MA0027.1	MA0027.1	0.711
MA0028.1	MA0028.1	0.915
MA0029.1	MA0029.1	0.48
MA0030.1	MA0030.1	0.342
MA0031.1	MA0031.1	0.0107
MA0035.2	MA0035.2	2.83557e-4
MA0038.1	MA0038.1	0.263
MA0039.2	MA0039.2	0.101
MA0040.1	MA0040.1	0.51
MA0041.1	MA0041.1	0.487
MA0042.1	MA0042.1	0.42
MA0043.1	MA0043.1	0.326
MA0046.1	MA0046.1	2.8135e-14
MA0047.2	MA0047.2	6.4813e-5
MA0048.1	MA0048.1	0.725
MA0050.1	MA0050.1	0.00896
MA0051.1	MA0051.1	0.00442
MA0052.1	MA0052.1	3.13642e-6
MA0055.1	MA0055.1	0.473
MA0057.1	MA0057.1	0.123
MA0058.1	MA0058.1	0.594
MA0059.1	MA0059.1	0.425
MA0060.1	MA0060.1	0.00459
MA0061.1	MA0061.1	0.0514
MA0062.2	MA0062.2	0.262
MA0065.2	MA0065.2	1.93051e-6
MA0066.1	MA0066.1	0.239
MA0067.1	MA0067.1	0.61
MA0068.1	MA0068.1	0.23
MA0069.1	MA0069.1	0.527
MA0070.1	MA0070.1	0.0173
MA0071.1	MA0071.1	0.281
MA0072.1	MA0072.1	0.269
MA0073.1	MA0073.1	0.887
MA0074.1	MA0074.1	0.642
MA0076.1	MA0076.1	0.843
MA0077.1	MA0077.1	0.0768
MA0078.1	MA0078.1	0.359
MA0079.2	MA0079.2	0.49
MA0080.2	MA0080.2	3.66839e-9
MA0081.1	MA0081.1	0.392
MA0083.1	MA0083.1	0.829
MA0084.1	MA0084.1	0.457
MA0087.1	MA0087.1	0.771
MA0088.1	MA0088.1	0.844
MA0090.1	MA0090.1	0.673
MA0091.1	MA0091.1	0.712
MA0092.1	MA0092.1	0.978
MA0093.1	MA0093.1	0.889
MA0099.2	MA0099.2	0.226
MA0100.1	MA0100.1	0.84
MA0101.1	MA0101.1	0.135
MA0102.2	MA0102.2	0.568
MA0103.1	MA0103.1	7.5403e-4
MA0104.2	MA0104.2	0.758
MA0105.1	MA0105.1	5.24016e-4
MA0106.1	MA0106.1	0.0478
MA0107.1	MA0107.1	0.059
MA0108.2	MA0108.2	0.00835
MA0111.1	MA0111.1	0.871
MA0112.2	MA0112.2	4.14692e-5
MA0113.1	MA0113.1	0.102
MA0114.1	MA0114.1	1.39601e-5
MA0115.1	MA0115.1	0.00505
MA0116.1	MA0116.1	0.0024
MA0117.1	MA0117.1	0.658
MA0119.1	MA0119.1	0.0895
MA0122.1	MA0122.1	0.756
MA0124.1	MA0124.1	0.233
MA0125.1	MA0125.1	0.186
MA0131.1	MA0131.1	0.533
MA0135.1	MA0135.1	0.144
MA0136.1	MA0136.1	1.13197e-7
MA0137.2	MA0137.2	0.718
MA0138.2	MA0138.2	0.179
MA0139.1	MA0139.1	0.0934
MA0140.1	MA0140.1	5.77652e-5
MA0141.1	MA0141.1	0.00195
MA0142.1	MA0142.1	0.0596
MA0143.1	MA0143.1	0.284
MA0144.1	MA0144.1	0.354
MA0145.1	MA0145.1	0.0591
MA0146.1	MA0146.1	0.413
MA0147.1	MA0147.1	0.522
MA0148.1	MA0148.1	5.31719e-4
MA0149.1	MA0149.1	0.683
MA0150.1	MA0150.1	0.0656
MA0152.1	MA0152.1	0.439
MA0153.1	MA0153.1	1.09888e-14
MA0154.1	MA0154.1	0.00326
MA0155.1	MA0155.1	0.477
MA0156.1	MA0156.1	4.22661e-5
MA0157.1	MA0157.1	0.0116
MA0159.1	MA0159.1	0.133
MA0160.1	MA0160.1	0.0229
MA0162.1	MA0162.1	0.316
MA0163.1	MA0163.1	0.00414
MA0164.1	MA0164.1	0.702
MA0258.1	MA0258.1	0.00796
MA0259.1	MA0259.1	0.889

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: CNhs13082

Novel motif	Logo	P-value
1	1	0.153
10	10	0.0757
100	100	0.954
101	101	0.869
102	102	0.941
103	103	0.202
104	104	0.657
105	105	0.0739
106	106	0.0382
107	107	0.0614
108	108	0.997
109	109	0.0375
11	11	0.132
110	110	0.13
111	111	0.0171
112	112	0.0246
113	113	0.503
114	114	0.0822
115	115	0.629
116	116	0.487
117	117	0.359
118	118	0.697
119	119	0.0371
12	12	0.663
120	120	0.607
121	121	0.119
122	122	0.354
123	123	0.469
124	124	0.398
125	125	0.733
126	126	0.205
127	127	0.219
128	128	0.0242
129	129	0.372
13	13	0.0134
130	130	0.975
131	131	0.72
132	132	0.315
133	133	0.517
134	134	0.953
135	135	0.726
136	136	0.69
137	137	0.319
138	138	0.938
139	139	0.165
14	14	0.444
140	140	0.152
141	141	0.275
142	142	0.663
143	143	0.93
144	144	0.912
145	145	0.333
146	146	0.374
147	147	0.653
148	148	0.424
149	149	0.118
15	15	0.0736
150	150	0.461
151	151	0.338
152	152	0.113
153	153	0.85
154	154	0.944
155	155	0.636
156	156	1.2857e-11
157	157	0.253
158	158	0.32
159	159	0.23
160	160	0.106
161	161	0.321
162	162	0.9
163	163	0.683
164	164	0.0939
165	165	0.173
166	166	0.857
167	167	0.395
168	168	0.706
169	169	0.00729
17	17	0.0854
18	18	0.864
19	19	0.194
2	2	0.554
20	20	0.775
21	21	0.363
22	22	0.288
23	23	0.289
24	24	0.0691
25	25	0.342
26	26	0.0213
27	27	0.228
28	28	0.417
29	29	0.389
3	3	0.123
30	30	0.641
31	31	0.797
32	32	0.199
33	33	0.268
34	34	0.406
35	35	0.885
36	36	0.643
37	37	0.0721
38	38	0.225
39	39	0.572
4	4	0.524
40	40	0.414
41	41	0.165
42	42	0.288
43	43	0.25
44	44	0.226
45	45	0.351
46	46	0.251
47	47	0.19
48	48	0.113
49	49	0.158
5	5	0.23
50	50	0.711
51	51	0.558
52	52	0.337
53	53	0.382
54	54	0.692
55	55	0.661
56	56	0.644
57	57	0.784
58	58	0.104
59	59	0.0313
6	6	0.58
60	60	0.0743
61	61	0.324
62	62	0.0373
63	63	0.115
64	64	0.399
65	65	0.108
66	66	0.676
67	67	0.598
68	68	0.67
69	69	0.976
7	7	0.0404
70	70	0.00599
71	71	0.111
72	72	0.203
73	73	0.224
74	74	0.97
75	75	0.15
76	76	0.83
77	77	0.185
78	78	0.0661
79	79	0.167
8	8	0.098
80	80	0.328
81	81	0.67
82	82	0.0158
83	83	0.0773
84	84	0.295
85	85	0.149
86	86	0.326
87	87	0.985
88	88	0.568
89	89	0.069
9	9	0.453
90	90	0.465
91	91	0.333
92	92	0.223
93	93	0.317
94	94	0.389
95	95	0.131
96	96	0.544
97	97	0.77
98	98	0.0988
99	99	0.299

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: CNhs13082

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011144 mouse neurospheres - sympathetic neuron derived sample

part_of relathionship
UBERON:0000013 sympathetic 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)
0000013 (sympathetic nervous system)
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)
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)
0011144 (mouse neurospheres - sympathetic 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:0000013,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:0001016,UBERON:0000924,UBERON:0005743,UBERON:0006601
+|DRA_sample_Accession=CAGE@SAMD00005733
-|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;DRX008869;DRR009741;DRZ001166;DRZ002551;DRZ012516;DRZ013901
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000013,UBERON:0004121,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,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:0011144
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:59799772..59799789,+!p1@Hand2!2.32!564.05!Hand2;;chr5:67490284..67490302,-!p1@Phox2b!2.13!135.31!Phox2b;;chr10:86956396..86956411,-!p1@Ascl1!2.11!194.93!Ascl1;;chr2:74583776..74583815,+!p3@Hoxd3!1.91!80.08!Hoxd3;;chr11:96164821..96164865,+!p1@Hoxb5!1.83!66.63!Hoxb5;;chr15:78994907..78994926,-!p1@Sox10!1.80!152.27!Sox10;;chr12:39510206..39510249,+!p3@Etv1!1.80!62.54!Etv1;;chr7:108966820..108966835,+!p1@Phox2a!1.80!62.25!Phox2a;;chr4:99322820..99322845,+!p1@Foxd3!1.79!76.57!Foxd3;;chr5:67490474..67490494,-!p2@Phox2b!1.62!40.33!Phox2b;;chr2:146047829..146047847,+!p1@Insm1!1.61!69.26!Insm1;;chr2:71384802..71384815,-!p1@Dlx2!1.58!45.30!Dlx2;;chr2:71367871..71367898,+!p1@Dlx1!1.57!35.95!Dlx1;;chr12:39510090..39510114,+!p6@Etv1!1.45!26.89!Etv1;;chr5:120120667..120120685,+!p3@Tbx3!1.41!47.05!Tbx3;;chr15:102865131..102865151,+!p2@Hoxc4!1.41!28.06!Hoxc4;;chr6:52154414..52154462,-!p1@Hoxa5!1.40!32.73!Hoxa5;;chr6:52154386..52154407,-!p2@Hoxa5!1.40!30.39!Hoxa5;;chr5:67490391..67490404,-!p3@Phox2b!1.40!23.96!Phox2b;;chr14:17407549..17407575,-!p3@Rarb!1.37!33.90!Rarb;;chr14:17407878..17407926,-!p1@Rarb!1.34!46.76!Rarb;;chr5:120121169..120121171,+!p4@Tbx3!1.34!36.82!Tbx3;;chr15:102865088..102865107,+!p1@Hoxc4!1.33!27.18!Hoxc4;;chr12:39510290..39510309,+!p5@Etv1!1.33!20.17!Etv1;;chr7:38557887..38557910,-!p5@Zfp536!1.32!19.87!Zfp536;;chr5:138199361..138199441,+!p2@Tsc22d4!1.30!35.66!Tsc22d4;;chr2:74565306..74565327,+!p2@Hoxd4!1.24!16.37!Hoxd4;;chr3:34548909..34548927,+!p1@Sox2!1.21!25.43!Sox2;;chr2:71367142..71367167,+!p2@Dlx1!1.21!15.20!Dlx1;;chr11:85646303..85646329,+!p1@Tbx2!1.20!97.03!Tbx2;;chr13:44936126..44936164,+!p6@Jarid2!1.17!16.07!Jarid2;;chr2:71384458..71384526,-!p2@Dlx2!1.17!13.74!Dlx2;;chr10:119913278..119913298,-!p2@Hmga2!1.15!29.23!Hmga2;;chr11:85646263..85646278,+!p2@Tbx2!1.14!32.73!Tbx2;;chr5:67490346..67490357,-!p4@Phox2b!1.11!11.98!Phox2b;;chr3:34548946..34548972,+!p2@Sox2!1.08!12.27!Sox2;;chr12:30213247..30213333,+!p1@Myt1l!1.08!11.11!Myt1l;;chr3:95032091..95032183,-!p1@Mllt11!1.07!92.65!Mllt11;;chr12:39507680..39507715,+!p2@Etv1!1.07!21.33!Etv1;;chr18:69752912..69752928,+!p9@Tcf4!1.06!15.78!Tcf4;;chr17:25707623..25707639,-!p1@Sox8!1.05!43.84!Sox8;;chr5:67490333..67490342,-!p5@Phox2b!1.05!10.23!Phox2b;;chr5:67490412..67490421,-!p6@Phox2b!1.05!10.23!Phox2b;;chr12:12948633..12948651,-!p1@Mycn!1.04!97.61!Mycn;;chr11:85646341..85646352,+!p3@Tbx2!1.04!19.87!Tbx2;;chr1:179374784..179374800,+!p2@Zfp238!1.04!11.69!Zfp238;;chr15:102865048..102865073,+!p3@Hoxc4!1.03!12.27!Hoxc4;;chr1:6724908..6724955,+!p2@St18!1.03!9.64!St18;;chr12:28027561..28027591,-!p1@Sox11!1.02!63.71!Sox11;;chr9:71743854..71743909,-!p1@Tcf12!1.01!74.23!Tcf12;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!1.01!24.84!Zfhx3;;chr13:40829137..40829205,-!p1@Tfap2a!1.01!10.52!Tfap2a;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!1.00!15.49!Hoxb2;;chr11:96180045..96180059,+!p1@Hoxb4!1.00!12.86!Hoxb4;;chr4:150503457..150503498,-!p3@Camta1!1.00!10.23!Camta1;;chr18:69752638..69752665,+!p19@Tcf4!1.00!9.94!Tcf4;;chr2:74583741..74583750,+!p10@Hoxd3!1.00!9.06!Hoxd3;;chr11:85646469..85646488,+!p5@Tbx2!0.99!13.15!Tbx2;;chr18:84255841..84255883,-!p1@Tshz1!0.96!59.33!Tshz1;;chr13:40826150..40826167,-!p3@Tfap2a!0.96!9.06!Tfap2a;;chr12:39510042..39510069,+!p8@Etv1!0.95!7.89!Etv1;;chrX:58146612..58146615,-!p1@Sox3!0.95!7.89!Sox3;;chr2:71384401..71384424,-!p3@Dlx2!0.95!7.89!Dlx2;;chr2:71384425..71384456,-!p4@Dlx2!0.93!7.60!Dlx2;;chr5:67490447..67490458,-!p7@Phox2b!0.93!7.60!Phox2b;;chr3:5218629..5218684,+!p1@Zfhx4!0.92!24.55!Zfhx4;;chr11:96164905..96164919,+!p2@Hoxb5!0.90!7.01!Hoxb5;;chr11:96160426..96160443,+!p2@Hoxb6!0.89!6.72!Hoxb6;;chr14:34791937..34791977,-!p1@Zfp488!0.89!6.72!Zfp488;;chr9:106356211..106356242,+!p1@Pcbp4!0.88!135.90!Pcbp4;;chr14:17407857..17407875,-!p4@Rarb!0.87!6.43!Rarb;;chr6:53523358..53523388,+!p1@Creb5!0.85!77.16!Creb5;;chr10:119913546..119913583,-!p3@Hmga2!0.84!12.86!Hmga2;;chr7:38554763..38554780,-!p1@Zfp536!0.83!10.81!Zfp536;;chr16:91270004..91270023,+!p1@Olig1!0.83!6.72!Olig1;;chr5:120121446..120121461,+!p2@Tbx3!0.82!19.58!Tbx3;;chr2:127347067..127347093,-!p1@Kcnip3!0.82!9.64!Kcnip3;;chr5:120121262..120121282,+!p6@Tbx3!0.82!6.43!Tbx3;;chr6:83020355..83020371,-!p1@Tlx2!0.82!5.55!Tlx2;;chr11:96180069..96180089,+!p3@Hoxb4!0.82!5.55!Hoxb4;;chr10:76424613..76424689,-!p1@Pcbp3!0.81!125.09!Pcbp3;;chr10:119914001..119914078,-!p4@Hmga2!0.81!7.60!Hmga2;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.80!7.31!Hoxb2;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.80!5.26!Hoxb2;;chr12:39510260..39510271,+!p10@Etv1!0.80!5.26!Etv1;;chr18:3281034..3281104,-!p1@Crem!0.79!39.45!Crem;;chr19:7342725..7342784,+!p1@Rcor2!0.79!23.09!Rcor2;;chr14:17407970..17408015,-!p2@Rarb!0.79!14.91!Rarb;;chr5:120121020..120121049,+!p1@Tbx3!0.78!33.61!Tbx3;;chr18:84255649..84255661,-!p4@Tshz1!0.78!14.32!Tshz1;;chr11:96143666..96143725,+!p1@Hoxb8!0.78!5.85!Hoxb8;;chr19:5447886..5447905,+!p1@Fosl1!0.78!4.97!Fosl1;;chr2:81893535..81893548,+!p1@Zfp804a!0.78!4.97!Zfp804a;;chr7:116154364..116154444,+!p1@Tub!0.77!8.77!Tub;;chr12:86814833..86814846,+!p1@Fos!0.76!123.33!Fos;;chr11:96153767..96153822,+!p1@Hoxb6!0.76!7.60!Hoxb6;;chr10:80870405..80870428,-!p4@Nfic!0.75!13.44!Nfic;;chr9:106356243..106356264,+!p2@Pcbp4!0.74!21.33!Pcbp4;;chr1:57029281..57029326,-!p1@Satb2!0.74!7.31!Satb2;;chr3:32264565..32264613,-!p1@Zmat3!0.73!53.78!Zmat3;;chr2:44968775..44968795,-!p4@Zeb2!0.73!22.80!Zeb2;;chr13:44936077..44936096,+!p9@Jarid2!0.73!4.38!Jarid2;;chr3:90097275..90097302,+!p2@Gatad2b!0.72!10.52!Gatad2b;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.72!5.55!Hoxb2;;chr10:119913310..119913366,-!p1@Hmga2!0.71!35.95!Hmga2;;chr10:67375368..67375433,-!p1@Zfp365!0.71!7.89!Zfp365;;chr7:38558574..38558611,-!p2@Zfp536!0.71!5.26!Zfp536;;chr2:74565247..74565258,+!p3@Hoxd4!0.71!4.09!Hoxd4;;chr1:179374820..179374831,+!p3@Zfp238!0.71!4.09!Zfp238;;chr2:181501745..181501778,+!p1@Myt1!0.71!4.09!Myt1;;chr9:106356278..106356292,+!p3@Pcbp4!0.70!7.31!Pcbp4;;chr11:96145450..96145517,+!p2@Hoxb7!0.70!6.43!Hoxb7;;chr12:39507404..39507441,+!p4@Etv1!0.70!5.85!Etv1;;chr7:38558544..38558566,-!p4@Zfp536!0.70!4.68!Zfp536;;chr1:38684260..38684312,-!p2@Aff3!0.69!31.27!Aff3;;chr3:32264530..32264544,-!p2@Zmat3!0.69!6.43!Zmat3;;chr18:69752608..69752625,+!p17@Tcf4!0.69!4.68!Tcf4;;chr9:96653072..96653154,-!p1@Zbtb38!0.68!11.11!Zbtb38;;chr7:130644017..130644092,-!p1@Zkscan2!0.68!7.89!Zkscan2;;chr11:96164868..96164875,+!p5@Hoxb5!0.68!3.80!Hoxb5;;chr1:193007123..193007139,-!p1@Atf3!0.67!23.67!Atf3;;chr5:120120981..120120992,+!p5@Tbx3!0.66!4.97!Tbx3;;chr11:3189683..3189744,+!p2@Patz1!0.65!7.89!Patz1;;chr11:96160360..96160397,+!p3@Hoxb6!0.65!3.51!Hoxb6;;chr10:119913266..119913277,-!p6@Hmga2!0.65!3.51!Hmga2;;chr18:69752864..69752875,+!p25@Tcf4!0.65!3.51!Tcf4;;chr14:17407671..17407684,-!p7@Rarb!0.65!3.51!Rarb;;chr4:99322855..99322867,+!p2@Foxd3!0.65!3.51!Foxd3;;chr4:22415443..22415506,-!p1@Pou3f2!0.65!3.51!Pou3f2;;chr2:44968721..44968734,-!p6@Zeb2!0.64!14.61!Zeb2;;chr4:54960870..54960926,+!p1@Zfp462!0.64!14.03!Zfp462;;chr9:72380594..72380635,+!p3@Rfx7!0.64!6.43!Rfx7;;chr13:78339476..78339515,-!p1@Nr2f1!0.64!5.55!Nr2f1;;chr19:7342786..7342803,+!p2@Rcor2!0.64!4.68!Rcor2;;chr18:83079981..83080037,+!p6@Zfp516!0.63!6.14!Zfp516;;chr2:74542918..74542971,+!p1@Hoxd8!0.63!5.26!Hoxd8;;chr4:122911086..122911112,+!p1@Heyl!0.62!43.84!Heyl;;chr2:163028808..163028869,+!p1@Tox2!0.62!13.15!Tox2;;chr14:52634234..52634281,-!p3@Zfp219!0.62!9.94!Zfp219;;chr15:102844431..102844445,+!p1@Hoxc5!0.62!3.21!Hoxc5;;chr11:96143962..96144035,+!p2@Hoxb8!0.62!3.21!Hoxb8;;chr5:120120834..120120845,+!p8@Tbx3!0.62!3.21!Tbx3;;chr7:38554684..38554696,-!p10@Zfp536!0.62!3.21!Zfp536;;chr7:25292331..25292421,+!p1@Zfp428!0.61!26.01!Zfp428;;chr10:67375223..67375240,-!p4@Zfp365!0.61!3.51!Zfp365;;chr2:44968737..44968758,-!p2@Zeb2!0.60!20.46!Zeb2;;chr14:52935788..52935817,-!p2@Sall2!0.60!7.31!Sall2;;chr16:15887371..15887385,+!p1@Cebpd!0.59!120.99!Cebpd;;chr15:103170516..103170531,-!p2@Zfp385a!0.59!7.89!Zfp385a;;chr18:79306577..79306592,-!p3@Setbp1!0.59!6.43!Setbp1;;chr11:85646427..85646451,+!p4@Tbx2!0.59!5.55!Tbx2;;chr2:74549968..74549996,+!p1@Hoxd3!0.59!3.80!Hoxd3;;chr5:120121091..120121100,+!p7@Tbx3!0.59!3.51!Tbx3;;chr7:138697803..138697813,+!p1@Hmx2!0.59!2.92!Hmx2;;chr13:44936106..44936121,+!p13@Jarid2!0.59!2.92!Jarid2;;chr13:40825785..40825798,-!p9@Tfap2a!0.59!2.92!Tfap2a;;chr13:40825465..40825469,-!p2@Tfap2a!0.59!2.92!Tfap2a;;chr2:71367605..71367621,+!p9@Dlx1!0.59!2.92!Dlx1;;chr4:99323046..99323073,+!p3@Foxd3!0.59!2.92!Foxd3;;chr12:39506873..39506913,+!p1@Etv1!0.58!35.66!Etv1;;chr15:102034510..102034549,+!p4@Zfp740!0.58!7.89!Zfp740;;chr3:51144477..51144506,-!p6@Elf2!0.58!4.68!Elf2;;chr6:52141694..52141715,-!p1@Hoxa4!0.58!3.80!Hoxa4;;chr19:55816546..55816556,+!p3@Tcf7l2!0.57!12.27!Tcf7l2;;chr16:43363190..43363242,+!p2@Zbtb20!0.57!9.94!Zbtb20;;chr10:30562571..30562597,-!p1@Hey2!0.57!7.31!Hey2;;chrX:34442872..34442899,-!p1@Nkrf!0.57!3.80!Nkrf;;chr2:17976799..17976829,+!p5@Mllt10!0.57!3.51!Mllt10;;chr10:114821393..114821431,-!p5@Thap2!0.56!8.48!Thap2;;chrX:7341077..7341091,+!p5@Tfe3!0.56!4.97!Tfe3;;chr16:43503493..43503570,+!p9@Zbtb20!0.56!4.97!Zbtb20;;chr6:47998938..47998955,-!p2@Zfp777!0.56!3.80!Zfp777;;chr7:122968213..122968266,-!p4@Sox6!0.56!3.21!Sox6;;chr7:38557752..38557793,-!p3@Zfp536!0.56!3.21!Zfp536;;chrX:108009761..108009788,+!p1@Pou3f4!0.56!2.63!Pou3f4;;chr7:38559019..38559026,-!p21@Zfp536!0.56!2.63!Zfp536;;chr2:181501988..181502026,+!p3@Myt1!0.56!2.63!Myt1;;chr15:76353005..76353021,-!p2@Scrt1!0.56!2.63!Scrt1;;chr1:92949999..92950097,+!p1@Lrrfip1!0.55!85.05!Lrrfip1;;chr11:87881569..87881633,+!p2@Vezf1!0.55!25.13!Vezf1;;chr7:25292141..25292158,+!p2@Zfp428!0.55!10.81!Zfp428;;chr16:43503720..43503739,+!p18@Zbtb20!0.55!2.92!Zbtb20;;chr13:29045559..29045574,-!p1@Sox4!0.54!260.40!Sox4;;chr12:84828663..84828679,-!p1@Dpf3!0.54!23.67!Dpf3;;chr14:98568761..98568814,-!p2@Dach1!0.54!21.04!Dach1;;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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:11805-124D5
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011144
+|is_a=EFO:0002091;;FF:0011144
+|is_obsolete=
+|library_id=CNhs13082
+|library_id_phase_based=2:CNhs13082
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11805
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11805
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520sympathetic%2520neuron%2520derived%252c%2520biol_rep2.CNhs13082.11805-124D5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520sympathetic%2520neuron%2520derived%252c%2520biol_rep2.CNhs13082.11805-124D5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520sympathetic%2520neuron%2520derived%252c%2520biol_rep2.CNhs13082.11805-124D5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520sympathetic%2520neuron%2520derived%252c%2520biol_rep2.CNhs13082.11805-124D5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520sympathetic%2520neuron%2520derived%252c%2520biol_rep2.CNhs13082.11805-124D5.mm9.nobarcode.rdna.fa.gz
 |name=neurospheres - sympathetic neuron derived, biol_rep2
 |namespace=
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13082,LSID1000,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.317687963838818,0,0,0,0,0.0130018044037329,0.185239094796407,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.368049490314937,0,0,0,0,0,0,0,0,0,0,0,0,0.273410491217492,-0.0747226925113157,0,0,0,0,0,-0.0169432251171325,0.0918152144157885,0.0501063721991339,-0.390641928458338,-0.158520128470455,0.336264243659775,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0.111348509539896,0.391160897340021,0,0.135329517320834,-0.310650657339386,0.729632271656643,-0.0656811758161899,0,0.0333399087879451,0.0484922062433519,0,0,0,0.0560638956519211,0.0869832449651379,0.465583245304425,0.032516914699989,0,0,0,0,0,0,0.193094461506184,0.108662252323942,0.191992359874771,0,0,0,0.288770557392231,0
 |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=GZF1:2.2833743789;TP53:1.93067757662;ONECUT1,2:1.88192375228;NKX3-1:1.82801678471;EN1,2:1.75018606826;SREBF1,2:1.68219677578;FOXQ1:1.66184994208;SOX2:1.62262668666;NKX2-1,4:1.45133228324;ZNF384:1.26598415163;POU3F1..4:1.25759353368;PRRX1,2:1.22029727463;HBP1_HMGB_SSRP1_UBTF:1.18954273345;JUN:1.17899112519;AHR_ARNT_ARNT2:1.09506085651;RXR{A,B,G}:1.09371254655;PAX5:1.07010497976;NANOG:1.05578524346;PBX1:1.04834015655;DBP:1.04492644556;FOXM1:1.04129320137;TEF:1.00858486973;NFE2L1:1.00206103629;MZF1:0.997983630619;MTE{core}:0.989270895217;SOX17:0.986017298726;ZBTB16:0.983931737366;ZFP161:0.966348599838;ZNF143:0.874257557914;UFEwm:0.870939486452;SOX5:0.863513909542;PDX1:0.860909853776;TFDP1:0.857983268578;HMX1:0.857365834192;TFAP2B:0.837768183996;NHLH1,2:0.833907124461;FOXP3:0.776577659566;NRF1:0.757172374738;FOX{I1,J2}:0.750949522718;LHX3,4:0.745549579835;PITX1..3:0.727701306488;FOXP1:0.720432472205;MED-1{core}:0.705179202399;ZIC1..3:0.690205933221;VSX1,2:0.676774651963;TFAP2{A,C}:0.671493613911;EGR1..3:0.662932053977;PAX4:0.654225364315;GTF2I:0.631190283408;NKX3-2:0.62994384401;LEF1_TCF7_TCF7L1,2:0.582049263532;CRX:0.578363698207;HMGA1,2:0.570129575872;TLX2:0.561892834355;FOXD3:0.5544043652;HIC1:0.530177219324;RORA:0.529757215528;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.529200188274;EP300:0.515996778829;PATZ1:0.506640323616;ADNP_IRX_SIX_ZHX:0.505796228491;ATF2:0.504810313561;EVI1:0.502478940373;IKZF1:0.484118132753;PAX8:0.48312178687;REST:0.476646447982;OCT4_SOX2{dimer}:0.467184137425;SP1:0.46469637079;ZNF423:0.425678279722;NFY{A,B,C}:0.394811314587;GTF2A1,2:0.394571021302;HOXA9_MEIS1:0.38986346874;BPTF:0.388550739445;POU6F1:0.378161884304;HAND1,2:0.371632090131;MAZ:0.368598228992;POU1F1:0.363130716438;ALX1:0.358203819064;SMAD1..7,9:0.349261961275;GFI1:0.343786893215;NFE2:0.335223324079;MYFfamily:0.330537279479;GATA4:0.320173281505;TEAD1:0.320074876645;SOX{8,9,10}:0.318880426259;RREB1:0.318125397124;E2F1..5:0.317584889335;RBPJ:0.314951867167;TFAP4:0.277303499889;STAT1,3:0.273429855971;ATF4:0.258649721724;POU5F1:0.205339027812;XCPE1{core}:0.200943411324;AIRE:0.199516225893;ELK1,4_GABP{A,B1}:0.198757402211;ZBTB6:0.192063865481;BREu{core}:0.178808200062;TAL1_TCF{3,4,12}:0.148817750891;PAX6:0.139255072857;ZNF148:0.137770081349;RFX2..5_RFXANK_RFXAP:0.131183789507;POU2F1..3:0.128183916077;CDC5L:0.124904746007;CREB1:0.121316752534;RFX1:0.119455242686;FOSL2:0.0979355962775;TFCP2:0.0975995360046;HSF1,2:0.0938460886871;FOS_FOS{B,L1}_JUN{B,D}:0.0821462938762;GFI1B:0.0775168124756;FOX{D1,D2}:0.0302301853385;TOPORS:0.0237633217024;KLF4:0.0122993473001;EBF1:-0.0216332290777;IRF7:-0.0274033190699;MTF1:-0.0613195830509;LMO2:-0.0625804798569;FOXO1,3,4:-0.0815957211705;MYB:-0.0830876738283;ATF5_CREB3:-0.104708498696;FOXL1:-0.112093191505;NR1H4:-0.117285645511;ATF6:-0.123522515103;YY1:-0.125463737476;CEBPA,B_DDIT3:-0.133970952938;NFIL3:-0.164578231006;TLX1..3_NFIC{dimer}:-0.168785485702;NFATC1..3:-0.173510643192;IKZF2:-0.199034562217;SRF:-0.20874465814;BACH2:-0.228619190536;ESRRA:-0.233700854466;PRDM1:-0.247589087353;DMAP1_NCOR{1,2}_SMARC:-0.276151832267;NKX6-1,2:-0.279789877916;bHLH_family:-0.289438197109;ZNF238:-0.317476709001;FOXN1:-0.321387482058;ESR1:-0.32239850777;STAT2,4,6:-0.348493869603;HOX{A4,D4}:-0.372943886716;CUX2:-0.389610145659;MYBL2:-0.396679419245;SPIB:-0.401239307464;T:-0.420832884384;HIF1A:-0.422787947283;HNF4A_NR2F1,2:-0.469324953962;RUNX1..3:-0.471781171663;GCM1,2:-0.477060552668;GLI1..3:-0.506861045079;NR6A1:-0.513208761004;RXRA_VDR{dimer}:-0.549219472366;TGIF1:-0.553588511308;HES1:-0.553804360489;MAFB:-0.563332638181;HNF1A:-0.565238337559;SPI1:-0.571789398046;IRF1,2:-0.639853532814;NANOG{mouse}:-0.657441346788;ELF1,2,4:-0.681696845468;NKX2-3_NKX2-5:-0.687770309573;NFKB1_REL_RELA:-0.691947537506;MEF2{A,B,C,D}:-0.699849350365;NR5A1,2:-0.712466907934;FOX{F1,F2,J1}:-0.718344381459;ETS1,2:-0.724689748386;AR:-0.732018153142;CDX1,2,4:-0.743302335315;HLF:-0.75007268094;TBP:-0.782335479965;NR3C1:-0.792815973901;FOXA2:-0.799650078933;ALX4:-0.811338787162;PAX1,9:-0.825627596181;HOX{A5,B5}:-0.827542312441;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.830547485586;NFE2L2:-0.86632341965;MYOD1:-0.876338462269;NFIX:-0.888421409223;PAX2:-0.899425430986;SNAI1..3:-1.01792048137;NKX2-2,8:-1.03607081967;ARID5B:-1.06960620331;STAT5{A,B}:-1.07757083433;GATA6:-1.10052475874;SPZ1:-1.19477201772;ZEB1:-1.38901504591;PPARG:-1.54810092254;TBX4,5:-1.98056404213
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11805-124D5;search_select_hide=table117:11805-124D5
 }}

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FF:11805-124D5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:21, 4 June 2020

CNhs13082

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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