FF:11811-124E2: Difference between revisions

Latest revision as of 18:21, 4 June 2020

Name:	neurospheres - enteric neuron derived, biol_rep2
Species:	Mouse (Mus musculus)
Library ID:	CNhs13088
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	EN2
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		SAMD00005784

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13088		CAGE		DRX008863		DRR009735

Accession ID Mm9

Library id		BAM		CTSS
CNhs13088		DRZ001160		DRZ002545

Accession ID Mm10

Library id		BAM		CTSS
CNhs13088		DRZ012510		DRZ013895

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

CNhs13088

0	0
1	0.0216
10	0
100	0
1000	0
1001	-0.0749
1002	-0.116
1003	-0.0693
1004	0
1005	-0.0824
1006	0
1007	-0.144
1008	0
1009	-0.0468
101	0.0454
1010	0
1011	-0.132
1012	0
1013	-0.0382
1014	-0.0229
1015	0.101
1016	0.289
1017	0
1018	0
1019	0
102	0
1020	0.251
1021	0.202
1022	-0.124
1023	0
1024	-0.164
1025	0
1026	0
1027	0.476
1028	0
1029	-0.115
103	-0.0532
1030	0
1031	0.322
1032	0.112
1033	0.143
1034	0
1035	0
1036	0.129
1037	0
1038	-0.0109
1039	-0.13
104	0
1040	0.26
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: CNhs13088

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	6.33801e-4
MA0003.1	MA0003.1	0.0133
MA0004.1	MA0004.1	0.731
MA0006.1	MA0006.1	0.421
MA0007.1	MA0007.1	0.497
MA0009.1	MA0009.1	0.0337
MA0014.1	MA0014.1	0.699
MA0017.1	MA0017.1	6.96045e-6
MA0018.2	MA0018.2	0.00458
MA0019.1	MA0019.1	0.218
MA0024.1	MA0024.1	0.00185
MA0025.1	MA0025.1	0.508
MA0027.1	MA0027.1	0.207
MA0028.1	MA0028.1	0.315
MA0029.1	MA0029.1	0.0627
MA0030.1	MA0030.1	0.13
MA0031.1	MA0031.1	0.0163
MA0035.2	MA0035.2	9.2183e-4
MA0038.1	MA0038.1	0.00527
MA0039.2	MA0039.2	0.138
MA0040.1	MA0040.1	0.971
MA0041.1	MA0041.1	0.407
MA0042.1	MA0042.1	0.857
MA0043.1	MA0043.1	0.253
MA0046.1	MA0046.1	5.23907e-16
MA0047.2	MA0047.2	1.39905e-4
MA0048.1	MA0048.1	0.801
MA0050.1	MA0050.1	0.00193
MA0051.1	MA0051.1	0.0093
MA0052.1	MA0052.1	0.00581
MA0055.1	MA0055.1	0.878
MA0057.1	MA0057.1	0.0532
MA0058.1	MA0058.1	0.385
MA0059.1	MA0059.1	0.719
MA0060.1	MA0060.1	9.26713e-8
MA0061.1	MA0061.1	0.0525
MA0062.2	MA0062.2	0.82
MA0065.2	MA0065.2	1.68393e-6
MA0066.1	MA0066.1	0.189
MA0067.1	MA0067.1	0.573
MA0068.1	MA0068.1	0.073
MA0069.1	MA0069.1	0.367
MA0070.1	MA0070.1	0.316
MA0071.1	MA0071.1	0.541
MA0072.1	MA0072.1	0.605
MA0073.1	MA0073.1	0.866
MA0074.1	MA0074.1	0.76
MA0076.1	MA0076.1	0.244
MA0077.1	MA0077.1	0.026
MA0078.1	MA0078.1	0.155
MA0079.2	MA0079.2	0.802
MA0080.2	MA0080.2	1.36667e-8
MA0081.1	MA0081.1	0.539
MA0083.1	MA0083.1	0.95
MA0084.1	MA0084.1	0.91
MA0087.1	MA0087.1	0.824
MA0088.1	MA0088.1	0.736
MA0090.1	MA0090.1	0.77
MA0091.1	MA0091.1	0.63
MA0092.1	MA0092.1	0.953
MA0093.1	MA0093.1	0.678
MA0099.2	MA0099.2	0.141
MA0100.1	MA0100.1	0.537
MA0101.1	MA0101.1	0.254
MA0102.2	MA0102.2	0.776
MA0103.1	MA0103.1	7.03716e-4
MA0104.2	MA0104.2	0.7
MA0105.1	MA0105.1	9.87127e-4
MA0106.1	MA0106.1	0.148
MA0107.1	MA0107.1	0.105
MA0108.2	MA0108.2	0.14
MA0111.1	MA0111.1	0.751
MA0112.2	MA0112.2	1.59787e-5
MA0113.1	MA0113.1	0.084
MA0114.1	MA0114.1	3.12686e-5
MA0115.1	MA0115.1	0.013
MA0116.1	MA0116.1	6.74547e-4
MA0117.1	MA0117.1	0.817
MA0119.1	MA0119.1	0.0617
MA0122.1	MA0122.1	0.988
MA0124.1	MA0124.1	0.913
MA0125.1	MA0125.1	0.376
MA0131.1	MA0131.1	0.461
MA0135.1	MA0135.1	0.234
MA0136.1	MA0136.1	2.61218e-5
MA0137.2	MA0137.2	0.564
MA0138.2	MA0138.2	0.178
MA0139.1	MA0139.1	0.106
MA0140.1	MA0140.1	6.79003e-5
MA0141.1	MA0141.1	0.0129
MA0142.1	MA0142.1	0.019
MA0143.1	MA0143.1	0.0565
MA0144.1	MA0144.1	0.352
MA0145.1	MA0145.1	0.0444
MA0146.1	MA0146.1	0.44
MA0147.1	MA0147.1	0.945
MA0148.1	MA0148.1	0.00255
MA0149.1	MA0149.1	0.509
MA0150.1	MA0150.1	0.141
MA0152.1	MA0152.1	0.521
MA0153.1	MA0153.1	1.04044e-13
MA0154.1	MA0154.1	0.00358
MA0155.1	MA0155.1	0.354
MA0156.1	MA0156.1	0.00466
MA0157.1	MA0157.1	0.05
MA0159.1	MA0159.1	0.263
MA0160.1	MA0160.1	0.104
MA0162.1	MA0162.1	0.38
MA0163.1	MA0163.1	0.00939
MA0164.1	MA0164.1	0.932
MA0258.1	MA0258.1	0.00976
MA0259.1	MA0259.1	0.796

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: CNhs13088

Novel motif	Logo	P-value
1	1	0.142
10	10	0.109
100	100	0.728
101	101	0.972
102	102	0.794
103	103	0.136
104	104	0.851
105	105	0.0655
106	106	0.0167
107	107	0.114
108	108	0.824
109	109	0.0573
11	11	0.131
110	110	0.206
111	111	0.0298
112	112	0.0297
113	113	0.424
114	114	0.0534
115	115	0.642
116	116	0.685
117	117	0.35
118	118	0.353
119	119	0.0223
12	12	0.676
120	120	0.643
121	121	0.323
122	122	0.315
123	123	0.53
124	124	0.549
125	125	0.941
126	126	0.247
127	127	0.124
128	128	0.0501
129	129	0.13
13	13	0.0371
130	130	0.542
131	131	0.292
132	132	0.289
133	133	0.549
134	134	0.895
135	135	0.824
136	136	0.999
137	137	0.295
138	138	0.747
139	139	0.122
14	14	0.37
140	140	3.30797e-4
141	141	0.502
142	142	0.712
143	143	0.573
144	144	0.81
145	145	0.533
146	146	0.692
147	147	0.888
148	148	0.455
149	149	0.169
15	15	0.141
150	150	0.495
151	151	0.325
152	152	0.0857
153	153	0.64
154	154	0.886
155	155	0.974
156	156	3.82151e-9
157	157	0.599
158	158	0.251
159	159	0.0451
160	160	0.127
161	161	0.275
162	162	0.981
163	163	0.806
164	164	0.212
165	165	0.363
166	166	0.759
167	167	0.472
168	168	0.688
169	169	0.00654
17	17	0.0457
18	18	0.718
19	19	0.138
2	2	0.457
20	20	0.796
21	21	0.483
22	22	0.236
23	23	0.161
24	24	0.181
25	25	0.432
26	26	0.0303
27	27	0.37
28	28	0.318
29	29	0.694
3	3	0.0996
30	30	0.459
31	31	0.626
32	32	0.0499
33	33	0.578
34	34	0.337
35	35	0.791
36	36	0.933
37	37	0.0545
38	38	0.255
39	39	0.253
4	4	0.682
40	40	0.53
41	41	0.79
42	42	0.313
43	43	0.176
44	44	0.248
45	45	0.3
46	46	0.218
47	47	0.208
48	48	0.121
49	49	0.137
5	5	0.249
50	50	0.526
51	51	0.437
52	52	0.364
53	53	0.324
54	54	0.428
55	55	0.781
56	56	0.584
57	57	0.697
58	58	0.0819
59	59	0.0234
6	6	0.864
60	60	0.0942
61	61	0.205
62	62	0.0408
63	63	0.076
64	64	0.463
65	65	0.112
66	66	0.487
67	67	0.577
68	68	0.304
69	69	0.497
7	7	0.0993
70	70	0.00192
71	71	0.181
72	72	0.358
73	73	0.203
74	74	0.989
75	75	0.175
76	76	0.84
77	77	0.172
78	78	0.0645
79	79	0.147
8	8	0.157
80	80	0.504
81	81	0.607
82	82	0.0165
83	83	0.369
84	84	0.343
85	85	0.0783
86	86	0.256
87	87	0.267
88	88	0.607
89	89	0.0317
9	9	0.373
90	90	0.604
91	91	0.231
92	92	0.194
93	93	0.611
94	94	0.573
95	95	0.19
96	96	0.645
97	97	0.634
98	98	0.133
99	99	0.29

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: CNhs13088

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011142 mouse neurospheres - enteric neuron derived sample

part_of relathionship
UBERON:0002005 enteric 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)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0002005 (enteric 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)
0011142 (mouse neurospheres - enteric 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:0000061,UBERON:0000073,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001016,UBERON:0001017,UBERON:0001062,UBERON:0002005,UBERON:0002050,UBERON:0002410,UBERON:0002532,UBERON:0004121,UBERON:0005423,UBERON:0005743
+|DRA_sample_Accession=CAGE@SAMD00005784
-|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;DRX008863;DRR009735;DRZ001160;DRZ002545;DRZ012510;DRZ013895
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0002005,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:0011142
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:59799772..59799789,+!p1@Hand2!2.37!632.90!Hand2;;chr5:67490284..67490302,-!p1@Phox2b!2.05!111.67!Phox2b;;chr11:96164821..96164865,+!p1@Hoxb5!2.00!98.39!Hoxb5;;chr10:86956396..86956411,-!p1@Ascl1!1.91!122.21!Ascl1;;chr6:52154386..52154407,-!p2@Hoxa5!1.83!83.94!Hoxa5;;chr6:52154414..52154462,-!p1@Hoxa5!1.82!88.24!Hoxa5;;chr2:74583776..74583815,+!p3@Hoxd3!1.75!54.66!Hoxd3;;chr15:78994907..78994926,-!p1@Sox10!1.74!133.92!Sox10;;chr4:99322820..99322845,+!p1@Foxd3!1.63!51.93!Foxd3;;chr11:96160426..96160443,+!p2@Hoxb6!1.63!41.39!Hoxb6;;chr12:39510206..39510249,+!p3@Etv1!1.62!40.22!Etv1;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.56!44.12!Pou3f3;;chr14:17407549..17407575,-!p3@Rarb!1.55!51.54!Rarb;;chr5:120120667..120120685,+!p3@Tbx3!1.54!63.25!Tbx3;;chr2:146047829..146047847,+!p1@Insm1!1.53!57.78!Insm1;;chr7:108966820..108966835,+!p1@Phox2a!1.47!28.50!Phox2a;;chr2:71384802..71384815,-!p1@Dlx2!1.45!33.19!Dlx2;;chr5:120121169..120121171,+!p4@Tbx3!1.43!45.29!Tbx3;;chr6:52158644..52158677,-!p2@Hoxa6!1.43!26.16!Hoxa6;;chr14:17407878..17407926,-!p1@Rarb!1.42!55.44!Rarb;;chr15:102865088..102865107,+!p1@Hoxc4!1.41!32.80!Hoxc4;;chr5:67490474..67490494,-!p2@Phox2b!1.32!19.91!Phox2b;;chr15:102865131..102865151,+!p2@Hoxc4!1.30!21.47!Hoxc4;;chr5:67490391..67490404,-!p3@Phox2b!1.25!16.79!Phox2b;;chr11:96160360..96160397,+!p3@Hoxb6!1.24!16.40!Hoxb6;;chr11:96164905..96164919,+!p2@Hoxb5!1.21!15.23!Hoxb5;;chrX:58146612..58146615,-!p1@Sox3!1.21!15.23!Sox3;;chr9:71743854..71743909,-!p1@Tcf12!1.20!115.18!Tcf12;;chr2:71384458..71384526,-!p2@Dlx2!1.19!14.45!Dlx2;;chr11:96160451..96160462,+!p5@Hoxb6!1.18!14.06!Hoxb6;;chr7:38557887..38557910,-!p5@Zfp536!1.18!14.06!Zfp536;;chr11:85646303..85646329,+!p1@Tbx2!1.14!83.94!Tbx2;;chr3:34548909..34548927,+!p1@Sox2!1.14!21.86!Sox2;;chr12:39510090..39510114,+!p6@Etv1!1.14!12.88!Etv1;;chr6:52134126..52134150,-!p3@Hoxa3!1.13!12.49!Hoxa3;;chr6:52114821..52114828,-!p1@Hoxa2!1.12!18.35!Hoxa2;;chr18:69752912..69752928,+!p9@Tcf4!1.12!18.35!Tcf4;;chr11:96143666..96143725,+!p1@Hoxb8!1.10!13.27!Hoxb8;;chr12:30213247..30213333,+!p1@Myt1l!1.10!11.71!Myt1l;;chr2:71367871..71367898,+!p1@Dlx1!1.09!11.32!Dlx1;;chr11:96145450..96145517,+!p2@Hoxb7!1.07!16.40!Hoxb7;;chr11:85646469..85646488,+!p5@Tbx2!1.07!16.01!Tbx2;;chr11:85646263..85646278,+!p2@Tbx2!1.06!27.33!Tbx2;;chr12:39510290..39510309,+!p5@Etv1!1.05!10.15!Etv1;;chr3:5218629..5218684,+!p1@Zfhx4!1.04!32.80!Zfhx4;;chr3:95032091..95032183,-!p1@Mllt11!1.03!83.55!Mllt11;;chr15:102865048..102865073,+!p3@Hoxc4!1.03!12.49!Hoxc4;;chr3:34548946..34548972,+!p2@Sox2!1.03!10.93!Sox2;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!1.02!12.49!Hoxb2;;chr11:96160403..96160416,+!p4@Hoxb6!1.02!9.37!Hoxb6;;chr14:17407857..17407875,-!p4@Rarb!1.02!9.37!Rarb;;chr12:12948633..12948651,-!p1@Mycn!1.01!90.19!Mycn;;chr10:119913278..119913298,-!p2@Hmga2!1.00!20.30!Hmga2;;chr11:85646341..85646352,+!p3@Tbx2!1.00!17.96!Tbx2;;chr14:34791937..34791977,-!p1@Zfp488!1.00!8.98!Zfp488;;chr5:67490346..67490357,-!p4@Phox2b!1.00!8.98!Phox2b;;chr11:96213183..96213188,+!p@chr11:96213183..96213188,+!0.98!8.59!Hoxb2;;chr12:28027561..28027591,-!p1@Sox11!0.96!54.66!Sox11;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.96!14.06!Hoxb2;;chr12:39507680..39507715,+!p2@Etv1!0.94!15.62!Etv1;;chr5:138199361..138199441,+!p2@Tsc22d4!0.92!14.06!Tsc22d4;;chr11:96180045..96180059,+!p1@Hoxb4!0.92!10.54!Hoxb4;;chr2:74565306..74565327,+!p2@Hoxd4!0.90!7.03!Hoxd4;;chr2:71384401..71384424,-!p3@Dlx2!0.90!7.03!Dlx2;;chr4:22415443..22415506,-!p1@Pou3f2!0.90!7.03!Pou3f2;;chr5:67490412..67490421,-!p6@Phox2b!0.90!7.03!Phox2b;;chr11:85646427..85646451,+!p4@Tbx2!0.88!11.71!Tbx2;;chr1:179374784..179374800,+!p2@Zfp238!0.88!7.81!Zfp238;;chr13:40829137..40829205,-!p1@Tfap2a!0.88!7.42!Tfap2a;;chr11:96143843..96143868,+!p3@Hoxb8!0.88!6.64!Hoxb8;;chr5:67490333..67490342,-!p5@Phox2b!0.88!6.64!Phox2b;;chr13:44936126..44936164,+!p6@Jarid2!0.87!7.42!Jarid2;;chr18:84255841..84255883,-!p1@Tshz1!0.86!46.07!Tshz1;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.86!17.57!Zfhx3;;chr13:40826150..40826167,-!p3@Tfap2a!0.86!7.03!Tfap2a;;chr1:6720216..6720232,+!p1@St18!0.86!6.25!St18;;chr5:120121020..120121049,+!p1@Tbx3!0.85!39.04!Tbx3;;chr2:163028808..163028869,+!p1@Tox2!0.85!23.04!Tox2;;chr6:52141694..52141715,-!p1@Hoxa4!0.83!7.42!Hoxa4;;chr7:38554763..38554780,-!p1@Zfp536!0.82!10.54!Zfp536;;chr11:96180069..96180089,+!p3@Hoxb4!0.81!5.47!Hoxb4;;chr11:96164887..96164894,+!p4@Hoxb5!0.81!5.47!Hoxb5;;chr2:74583741..74583750,+!p10@Hoxd3!0.81!5.47!Hoxd3;;chr9:106356211..106356242,+!p1@Pcbp4!0.80!111.67!Pcbp4;;chr19:7342725..7342784,+!p1@Rcor2!0.80!23.43!Rcor2;;chr12:39507404..39507441,+!p4@Etv1!0.79!7.42!Etv1;;chr17:25707623..25707639,-!p1@Sox8!0.75!21.47!Sox8;;chr7:38558544..38558566,-!p4@Zfp536!0.75!5.47!Zfp536;;chr18:69752638..69752665,+!p19@Tcf4!0.75!5.08!Tcf4;;chr5:120120834..120120845,+!p8@Tbx3!0.75!4.69!Tbx3;;chr6:52158693..52158704,-!p3@Hoxa6!0.75!4.69!Hoxa6;;chr13:40825465.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p142;;chr11:53164285..53164302,+!p3@Aff4!0.14!9.76!Aff4;;chr9:71959634..71959702,-!p2@Tcf12!0.14!8.98!Tcf12;;chr7:28516392..28516416,+!p2@Zfp60!0.14!8.59!Zfp60;;chr3:52072315..52072327,+!p2@Foxo1!0.14!7.03!Foxo1;;chr2:181100154..181100181,+!p3@Zgpat!0.14!5.47!Zgpat;;chr11:62602904..62602945,-!p1@Zfp286!0.14!5.08!Zfp286;;chr1:13362515..13362538,-!p2@Ncoa2!0.14!3.51!Ncoa2;;chrX:71330995..71331011,-!p2@Mecp2!0.14!3.12!Mecp2;;chr8:92872242..92872285,-!p1@Tox3!0.14!2.34!Tox3;;chr10:75495410..75495444,+!p2@Zfp280b!0.14!2.34!Zfp280b;;chr14:55711114..55711159,-!p2@Zfhx2!0.14!1.95!Zfhx2;;chr7:74517732..74517743,-!p4@Mef2a!0.14!1.56!Mef2a;;chr8:81552528..81552553,+!p6@Zfp827!0.14!1.17!Zfp827;;chr5:9161608..9161619,-!p3@Dmtf1!0.14!1.17!Dmtf1;;chr5:31262699..31262712,-!p2@Preb!0.14!1.17!Preb;;chr7:17200403..17200416,-!p5@Grlf1!0.14!1.17!Grlf1;;chr18:14131045..14131062,-!p3@Zfp521!0.14!1.17!Zfp521;;chr13:31898496..31898519,+!p3@Foxc1!0.14!1.17!Foxc1;;chr2:91864449..91864492,-!p3@Creb3l1!0.14!1.17!Creb3l1;;chr3:96002383..96002407,-!p4@Bola1!0.14!0.78!Bola1;;chr5:22939909..22939948,+!p6@Mll5!0.14!0.78!Mll5;;chr7:5003069..5003078,+!p5@Zfp580!0.14!0.78!Zfp580;;chr9:68501549..68501564,+!p6@Rora!0.14!0.78!Rora;;chr13:83663546..83663560,+!p4@Mef2c!0.14!0.78!Mef2c;;chr16:43619156..43619171,+!p16@Zbtb20!0.14!0.78!Zbtb20;;chr18:14131020..14131033,-!p4@Zfp521!0.14!0.78!Zfp521;;chr1:120950269..120950287,-!p6@Gli2!0.14!0.78!Gli2;;chr1:64168030..64168037,-!p9@Klf7!0.14!0.78!Klf7;;chr2:163030186..163030204,+!p4@Tox2!0.14!0.39!Tox2;;chr2:168032254..168032259,-!p6@Adnp!0.14!0.39!Adnp;;chr2:154395524..154395535,-!p5@E2f1!0.14!0.39!E2f1;;chr1:179372666..179372678,+!p11@Zfp238!0.14!0.39!Zfp238;;chr2:163030219..163030258,+!p5@Tox2!0.14!0.39!Tox2;;chr2:163051181..163051205,+!p2@Tox2!0.14!0.39!Tox2;;chr1:179374764..179374776,+!p5@Zfp238!0.14!0.39!Zfp238;;chr2:172375081..172375105,+!p1@Tfap2c!0.14!0.39!Tfap2c;;chr2:169458593..169458603,+!p13@Tshz2!0.14!0.39!Tshz2;;chr2:156665551..156665562,+!p6@Tgif2!0.14!0.39!Tgif2;;chr2:104966983..104966990,+!p11@Wt1!0.14!0.39!Wt1;;chr1:57029076..57029098,-!p8@Satb2!0.14!0.39!Satb2;;chr1:92950128..92950139,+!p4@Lrrfip1!0.14!0.39!Lrrfip1;;chr2:65768149..65768173,+!p4@Csrnp3!0.14!0.39!Csrnp3;;chr1:91827728..91827743,-!p2@Gbx2!0.14!0.39!Gbx2;;chr19:55970060..55970071,+!p25@Tcf7l2!0.14!0.39!Tcf7l2;;chr1:135557400..135557421,-!p4@Zbed6!0.14!0.39!Zbed6;;chr19:55969946..55969973,+!p8@Tcf7l2!0.14!0.39!Tcf7l2;;chr2:105522840..105522844,+!p22@Pax6!0.14!0.39!Pax6;;chr2:26063801..26063813,-!p2@Lhx3!0.14!0.39!Lhx3;;chr2:56967316..56967327,-!p3@Nr4a2!0.14!0.39!Nr4a2;;chr2:163030164..163030178,+!p6@Tox2!0.14!0.39!Tox2;;chr2:127347042..127347058,-!p3@Kcnip3!0.14!0.39!Kcnip3;;chr2:56967381..56967386,-!p8@Nr4a2!0.14!0.39!Nr4a2;;chr2:65683842..65683856,+!p3@Csrnp3!0.14!0.39!Csrnp3;;chr2:104966933..104966966,+!p3@Wt1!0.14!0.39!Wt1;;chr7:17200230..17200240,-!p15@Grlf1!0.14!0.39!Grlf1;;chr6:98978428..98978450,-!p15@Foxp1!0.14!0.39!Foxp1;;chr6:144157893..144157905,-!p14@Sox5!0.14!0.39!Sox5;;chr5:120120708..120120713,+!p12@Tbx3!0.14!0.39!Tbx3;;chr6:144157880..144157889,-!p25@Sox5!0.14!0.39!Sox5;;chr7:116093986..116093999,+!p4@Tub!0.14!0.39!Tub;;chr5:120120409..120120416,+!p17@Tbx3!0.14!0.39!Tbx3;;chr5:77695258..77695269,+!p12@Rest!0.14!0.39!Rest;;chr6:83661226..83661282,+!p1@Vax2!0.14!0.39!Vax2;;chr6:144158183..144158210,-!p11@Sox5!0.14!0.39!Sox5;;chr7:17200127..17200137,-!p11@Grlf1!0.14!0.39!Grlf1;;chr5:137041573..137041594,-!p9@Cux1!0.14!0.39!Cux1;;chr6:88143570..88143590,+!p4@Gata2!0.14!0.39!Gata2;;chr5:108155007..108155034,-!p1@Gfi1!0.14!0.39!Gfi1;;chr5:42155788..42155800,-!p1@Nkx3-2!0.14!0.39!Nkx3-2;;chr11:96144050..96144065,+!p5@Hoxb8!0.14!0.39!Hoxb8;;chr10:75384163..75384185,-!p3@Smarcb1!0.14!0.39!Smarcb1;;chr11:52095821..52095836,-!p3@Tcf7!0.14!0.39!Tcf7;;chr11:90252071..90252093,-!p7@Hlf!0.14!0.39!Hlf;;chr10:67599527..67599530,-!p9@Arid5b!0.14!0.39!Arid5b;;chr11:90250999..90251013,-!p8@Hlf!0.14!0.39!Hlf;;chr11:96132767..96132796,+!p2@Hoxb9!0.14!0.39!Hoxb9;;chr10:12844757..12844771,+!p2@Plagl1!0.14!0.39!Plagl1;;chr11:52096260..52096274,-!p12@Tcf7!0.14!0.39!Tcf7;;chr11:95170996..95171026,-!p3@Myst2!0.14!0.39!Myst2;;chr11:58717647..58717659,-!p3@Zfp39!0.14!0.39!Zfp39;;chr10:20881239..20881254,-!p5@Myb!0.14!0.39!Myb;;chr10:102491694..102491714,-!p3@Alx1!0.14!0.39!Alx1;;chr11:106128919..106128933,-!p8@Smarcd2!0.14!0.39!Smarcd2;;chr11:23670864..23670877,-!p5@Rel!0.14!0.39!Rel;;chr10:20872753..20872775,-!p11@Myb!0.14!0.39!Myb;;chr11:96184567..96184569,+!p8@Hoxb3!0.14!0.39!Hoxb3;;chr10:119913301..119913302,-!p11@Hmga2!0.14!0.39!Hmga2;;chr10:30522660..30522671,-!p10@Ncoa7!0.14!0.39!Ncoa7;;chr11:98601909..98601922,+!p11@Thra!0.14!0.39!Thra;;chr11:97524329..97524348,+!p6@Mllt6!0.14!0.39!Mllt6;;chr11:50641158..50641165,-!p3@Zfp354c!0.14!0.39!Zfp354c;;chrX:70656436..70656464,+!p1@Zfp92!0.14!0.39!Zfp92;;chr3:17954496..17954515,+!p3@Bhlhe22!0.14!0.39!Bhlhe22;;chr4:97444557..97444558,+!p23@Nfia!0.14!0.39!Nfia;;chr3:133207614..133207630,-!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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:11811-124E2
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0011142
+|is_a=EFO:0002091;;FF:0011142
+|is_obsolete=
+|library_id=CNhs13088
+|library_id_phase_based=2:CNhs13088
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11811
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11811
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep2.CNhs13088.11811-124E2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep2.CNhs13088.11811-124E2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep2.CNhs13088.11811-124E2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep2.CNhs13088.11811-124E2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/neurospheres%2520-%2520enteric%2520neuron%2520derived%252c%2520biol_rep2.CNhs13088.11811-124E2.mm9.nobarcode.rdna.fa.gz
 |name=neurospheres - enteric neuron derived, biol_rep2
 |namespace=
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13088,LSID1000,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0462196659394792,0,0,0,0,0,-0.122652496695101,0,0,0,0,0.0588126204052594,0,0,0,0,0,0,-0.0487414900807737,0,0,0,0,0,0,0,0,0,0,0,0,0.429510429509109,-0.415270931522231,0,0,0,0,0,0.0306147444990647,0.0783446389000022,-0.00452705414569388,-0.575673777815696,-0.12671677720855,0,0,0,0,0,0,0,0,0,0,0.143151860801801,0,-0.0660055475634404,0,0,0,0,0,0,0.109240904544104,0.143151860801801,0.33672307918798,0,-0.0458138725074257,-0.310650657339386,0.678016578544388,-0.0365927089968535,0,0,0.00898545881712187,0,0,0,0,0.00623779693074775,0.672891024065844,0.0643202659618935,0,0,0,0,0,0,0.236280818395901,0,0.0368453543064463,0,0,0,0.250634044192069,0
 |rna_box=124
 |rna_catalog_number=
@@ Line 54: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=124E2
+|rna_tube_id=1.24E+04
 |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=GZF1:2.96186301507;PBX1:2.18122455862;EN1,2:1.84253556624;PRRX1,2:1.72270311471;ONECUT1,2:1.6516894892;NKX3-1:1.49775055626;SOX2:1.47575800279;DBP:1.35092808807;SREBF1,2:1.2719815601;FOX{I1,J2}:1.26696678865;ZNF143:1.23553851899;AHR_ARNT_ARNT2:1.22828320576;HBP1_HMGB_SSRP1_UBTF:1.17154720444;JUN:1.14425020102;TFDP1:1.04295355593;SOX17:1.04059866624;TP53:1.01337334142;NANOG:0.996360004645;POU3F1..4:0.991151989322;HOXA9_MEIS1:0.980235116541;NFE2L1:0.9703597839;NFY{A,B,C}:0.969577247288;NRF1:0.965996864732;PITX1..3:0.946207121015;MTE{core}:0.936803284477;NKX2-1,4:0.932084033907;OCT4_SOX2{dimer}:0.912773035905;GFI1:0.892865635383;RORA:0.884236752745;ZNF384:0.857563122722;NHLH1,2:0.83692794439;PAX8:0.807675616945;TLX2:0.796437373561;E2F1..5:0.78578787381;HSF1,2:0.77581562785;PDX1:0.763439524332;ADNP_IRX_SIX_ZHX:0.759427701442;SOX{8,9,10}:0.735394209894;ZBTB16:0.725229262007;ZFP161:0.705215168103;MZF1:0.70199537097;ATF2:0.687447989485;FOXD3:0.673000095419;POU6F1:0.637164895919;POU2F1..3:0.599943852444;TFAP2{A,C}:0.576478625657;LHX3,4:0.571027592165;LEF1_TCF7_TCF7L1,2:0.570190898115;SOX5:0.558374405518;TAL1_TCF{3,4,12}:0.554774144014;YY1:0.519676399629;IKZF1:0.516322987221;HMX1:0.516133970484;TEF:0.511129426886;ELK1,4_GABP{A,B1}:0.509788261991;MED-1{core}:0.494574152882;TFAP2B:0.492409182136;RXR{A,B,G}:0.472830008443;UFEwm:0.470991489749;FOXQ1:0.466128070258;HMGA1,2:0.463116838293;AIRE:0.436965820556;STAT1,3:0.433891022295;RBPJ:0.433284487471;ATF4:0.42336243632;HIC1:0.417489498371;PAX5:0.408689034255;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.40551591016;EGR1..3:0.402701350329;EP300:0.379224198106;GTF2I:0.357569746675;PAX6:0.350489427744;PATZ1:0.330791646291;NKX3-2:0.326379821851;BREu{core}:0.314053341077;CREB1:0.294971055479;ALX1:0.273323121102;REST:0.270892651009;GFI1B:0.246352133319;VSX1,2:0.245042487443;CRX:0.230628382782;NFE2:0.214892307872;CDC5L:0.198246462627;HES1:0.183191986201;FOXP1:0.178391518569;TFAP4:0.177460416545;RFX1:0.175249241833;ZIC1..3:0.169969080456;ALX4:0.147502065775;XCPE1{core}:0.125877494856;SP1:0.119525505694;MYB:0.113137882082;bHLH_family:0.110789877182;RFX2..5_RFXANK_RFXAP:0.105214546133;HAND1,2:0.0966375696185;NR1H4:0.0933818694322;TEAD1:0.082449945919;FOSL2:0.0749250607413;TFCP2:0.0741718726369;MYFfamily:0.0550557752858;BPTF:0.0534166460538;POU5F1:0.0401480547679;IKZF2:0.0146305168081;FOXP3:0.0103776718861;KLF4:-0.0297348284832;RREB1:-0.032862975664;MAZ:-0.0350615931487;ZBTB6:-0.0362182570453;POU1F1:-0.0452418612608;FOXM1:-0.0512221367004;FOXL1:-0.0544545814971;FOS_FOS{B,L1}_JUN{B,D}:-0.0672662820609;ATF5_CREB3:-0.0851120437463;NANOG{mouse}:-0.105489246184;CDX1,2,4:-0.107763740493;ESRRA:-0.109350152839;IRF7:-0.153137533293;SMAD1..7,9:-0.153494646467;FOX{D1,D2}:-0.201952109801;HOX{A5,B5}:-0.203449310537;LMO2:-0.204805280968;AR:-0.206288386714;BACH2:-0.209219882687;STAT5{A,B}:-0.210811506984;ESR1:-0.216283302625;HOX{A4,D4}:-0.217288817472;GTF2A1,2:-0.219421569491;T:-0.231967185488;SRF:-0.244401778886;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.250174036108;GATA4:-0.252533321875;ZNF238:-0.2566471761;DMAP1_NCOR{1,2}_SMARC:-0.26287921442;MYBL2:-0.268784553345;MTF1:-0.269319513894;NFATC1..3:-0.276713369261;EBF1:-0.286169166098;EVI1:-0.289138545472;RUNX1..3:-0.303597629388;TOPORS:-0.315876194502;PAX4:-0.32449922695;TLX1..3_NFIC{dimer}:-0.341664518234;PRDM1:-0.346944146807;ELF1,2,4:-0.391947791769;SPIB:-0.410478779926;TGIF1:-0.414860695637;CEBPA,B_DDIT3:-0.443107085676;NFIL3:-0.461994573174;ZNF148:-0.464614295681;NFKB1_REL_RELA:-0.472432454242;HNF4A_NR2F1,2:-0.501962516501;FOXN1:-0.507272796334;CUX2:-0.511338812479;MEF2{A,B,C,D}:-0.53055120404;FOXO1,3,4:-0.531180874373;ARID5B:-0.531532688849;ZNF423:-0.573703364731;NKX2-3_NKX2-5:-0.587449523668;ETS1,2:-0.611826395316;RXRA_VDR{dimer}:-0.614490006646;HNF1A:-0.615117533824;TBP:-0.616328271449;NFE2L2:-0.622966729557;MAFB:-0.625258801972;NR6A1:-0.672400162657;HLF:-0.678312360384;SPI1:-0.705785527703;FOXA2:-0.72815118274;SPZ1:-0.748494085597;NFIX:-0.762750209703;PAX2:-0.764279210067;FOX{F1,F2,J1}:-0.787035379802;GLI1..3:-0.806473427212;GCM1,2:-0.820641193721;NKX6-1,2:-0.822654504825;PAX1,9:-0.82630817318;STAT2,4,6:-0.849735769104;HIF1A:-0.867295525273;IRF1,2:-0.895253690587;ATF6:-0.915714359492;NR3C1:-0.952923240146;NR5A1,2:-0.975654073897;GATA6:-1.00198691647;MYOD1:-1.00209623541;SNAI1..3:-1.04197176991;ZEB1:-1.10393031109;NKX2-2,8:-1.16952995564;TBX4,5:-1.25632161047;PPARG:-1.29877754045
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11811-124E2;search_select_hide=table117:11811-124E2
 }}

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FF:11811-124E2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:21, 4 June 2020

CNhs13088

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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