FF:12157-128G6: Difference between revisions

Latest revision as of 18:32, 4 June 2020

Name:	Sox2+ Supporting cells - organ of corti, pool1
Species:	Mouse (Mus musculus)
Library ID:	CNhs12532
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	organ of corti
dev stage	NA
sex	mixed
age	NA
cell type	SELECT CELL TYPE
cell line	NA
company	NA
collaboration	Albert Edge (Department of Otolaryngology, Harvard Medical School)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	total RNA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005538

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12532		CAGE		DRX008778		DRR009650

Accession ID Mm9

Library id		BAM		CTSS
CNhs12532		DRZ001075		DRZ002460

Accession ID Mm10

Library id		BAM		CTSS
CNhs12532		DRZ012425		DRZ013810

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

CNhs12532

0	0
1	0.0637
10	0
100	0
1000	0
1001	-0.0749
1002	0.464
1003	-0.132
1004	0
1005	-0.0389
1006	0.0334
1007	0.205
1008	0
1009	0.0414
101	-0.0684
1010	0
1011	0.0866
1012	0
1013	0.0777
1014	-0.0874
1015	0.223
1016	0.296
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.0125
1023	0
1024	0
1025	0
1026	0
1027	0.517
1028	0
1029	-0.12
103	-0.0721
1030	0
1031	0
1032	0.325
1033	0.0572
1034	0
1035	0.0572
1036	0.0124
1037	0.0572
1038	0.0456
1039	-0.0717
104	0
1040	-0.121
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: CNhs12532

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00452
MA0003.1	MA0003.1	0.519
MA0004.1	MA0004.1	0.589
MA0006.1	MA0006.1	0.968
MA0007.1	MA0007.1	0.454
MA0009.1	MA0009.1	0.279
MA0014.1	MA0014.1	0.0981
MA0017.1	MA0017.1	2.11564e-9
MA0018.2	MA0018.2	3.08379e-4
MA0019.1	MA0019.1	0.499
MA0024.1	MA0024.1	0.88
MA0025.1	MA0025.1	0.868
MA0027.1	MA0027.1	0.846
MA0028.1	MA0028.1	0.472
MA0029.1	MA0029.1	0.335
MA0030.1	MA0030.1	0.678
MA0031.1	MA0031.1	0.429
MA0035.2	MA0035.2	0.0626
MA0038.1	MA0038.1	0.245
MA0039.2	MA0039.2	0.192
MA0040.1	MA0040.1	0.241
MA0041.1	MA0041.1	0.142
MA0042.1	MA0042.1	0.909
MA0043.1	MA0043.1	0.00496
MA0046.1	MA0046.1	5.32088e-11
MA0047.2	MA0047.2	0.00932
MA0048.1	MA0048.1	0.509
MA0050.1	MA0050.1	0.016
MA0051.1	MA0051.1	0.0497
MA0052.1	MA0052.1	0.138
MA0055.1	MA0055.1	0.955
MA0057.1	MA0057.1	0.475
MA0058.1	MA0058.1	0.845
MA0059.1	MA0059.1	0.152
MA0060.1	MA0060.1	6.62129e-10
MA0061.1	MA0061.1	0.0128
MA0062.2	MA0062.2	0.868
MA0065.2	MA0065.2	2.22353e-4
MA0066.1	MA0066.1	0.0269
MA0067.1	MA0067.1	0.148
MA0068.1	MA0068.1	0.0987
MA0069.1	MA0069.1	0.303
MA0070.1	MA0070.1	0.508
MA0071.1	MA0071.1	0.0929
MA0072.1	MA0072.1	0.584
MA0073.1	MA0073.1	0.88
MA0074.1	MA0074.1	0.08
MA0076.1	MA0076.1	0.289
MA0077.1	MA0077.1	0.0131
MA0078.1	MA0078.1	0.803
MA0079.2	MA0079.2	0.0789
MA0080.2	MA0080.2	3.95037e-10
MA0081.1	MA0081.1	0.252
MA0083.1	MA0083.1	0.0592
MA0084.1	MA0084.1	0.0888
MA0087.1	MA0087.1	0.0555
MA0088.1	MA0088.1	0.259
MA0090.1	MA0090.1	0.216
MA0091.1	MA0091.1	0.31
MA0092.1	MA0092.1	0.413
MA0093.1	MA0093.1	0.709
MA0099.2	MA0099.2	0.0164
MA0100.1	MA0100.1	0.835
MA0101.1	MA0101.1	0.105
MA0102.2	MA0102.2	0.696
MA0103.1	MA0103.1	0.975
MA0104.2	MA0104.2	0.292
MA0105.1	MA0105.1	1.30973e-6
MA0106.1	MA0106.1	0.0487
MA0107.1	MA0107.1	0.0395
MA0108.2	MA0108.2	0.855
MA0111.1	MA0111.1	0.905
MA0112.2	MA0112.2	1.69995e-5
MA0113.1	MA0113.1	0.795
MA0114.1	MA0114.1	8.47883e-6
MA0115.1	MA0115.1	7.88156e-5
MA0116.1	MA0116.1	5.11268e-5
MA0117.1	MA0117.1	0.97
MA0119.1	MA0119.1	0.14
MA0122.1	MA0122.1	0.93
MA0124.1	MA0124.1	0.412
MA0125.1	MA0125.1	0.0233
MA0131.1	MA0131.1	0.711
MA0135.1	MA0135.1	0.155
MA0136.1	MA0136.1	1.90304e-7
MA0137.2	MA0137.2	0.612
MA0138.2	MA0138.2	0.204
MA0139.1	MA0139.1	0.186
MA0140.1	MA0140.1	0.00195
MA0141.1	MA0141.1	0.00473
MA0142.1	MA0142.1	0.782
MA0143.1	MA0143.1	0.0607
MA0144.1	MA0144.1	0.214
MA0145.1	MA0145.1	0.123
MA0146.1	MA0146.1	0.897
MA0147.1	MA0147.1	0.185
MA0148.1	MA0148.1	0.00202
MA0149.1	MA0149.1	0.783
MA0150.1	MA0150.1	0.0272
MA0152.1	MA0152.1	0.81
MA0153.1	MA0153.1	6.33411e-8
MA0154.1	MA0154.1	0.00328
MA0155.1	MA0155.1	0.843
MA0156.1	MA0156.1	1.57498e-4
MA0157.1	MA0157.1	0.326
MA0159.1	MA0159.1	6.00836e-4
MA0160.1	MA0160.1	0.0112
MA0162.1	MA0162.1	0.204
MA0163.1	MA0163.1	2.04606e-4
MA0164.1	MA0164.1	0.47
MA0258.1	MA0258.1	0.00148
MA0259.1	MA0259.1	0.569

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: CNhs12532

Novel motif	Logo	P-value
1	1	0.0367
10	10	0.0255
100	100	0.894
101	101	0.642
102	102	0.593
103	103	0.106
104	104	0.646
105	105	0.641
106	106	0.158
107	107	0.219
108	108	0.653
109	109	0.163
11	11	0.154
110	110	0.0227
111	111	6.99748e-4
112	112	0.0122
113	113	0.984
114	114	0.00894
115	115	0.89
116	116	0.571
117	117	0.0453
118	118	0.617
119	119	0.0613
12	12	0.995
120	120	0.497
121	121	0.589
122	122	0.934
123	123	0.895
124	124	0.817
125	125	0.143
126	126	0.588
127	127	0.333
128	128	0.105
129	129	0.0973
13	13	0.0771
130	130	0.267
131	131	0.858
132	132	0.536
133	133	0.845
134	134	0.29
135	135	0.249
136	136	0.331
137	137	0.195
138	138	0.657
139	139	0.0567
14	14	0.991
140	140	0.2
141	141	0.733
142	142	0.238
143	143	0.355
144	144	0.693
145	145	0.113
146	146	0.364
147	147	0.566
148	148	0.254
149	149	0.515
15	15	0.113
150	150	0.423
151	151	0.388
152	152	0.977
153	153	0.161
154	154	0.452
155	155	0.579
156	156	0.0133
157	157	0.507
158	158	0.421
159	159	0.0137
160	160	0.195
161	161	0.66
162	162	0.64
163	163	0.313
164	164	0.00284
165	165	0.944
166	166	0.795
167	167	0.163
168	168	0.957
169	169	0.00501
17	17	0.16
18	18	0.176
19	19	0.0922
2	2	0.811
20	20	0.548
21	21	0.207
22	22	0.418
23	23	0.115
24	24	0.951
25	25	0.453
26	26	0.0134
27	27	0.876
28	28	0.624
29	29	0.0573
3	3	0.0537
30	30	0.94
31	31	0.584
32	32	0.0435
33	33	0.586
34	34	0.931
35	35	0.161
36	36	0.104
37	37	0.149
38	38	0.269
39	39	0.825
4	4	0.28
40	40	0.811
41	41	0.678
42	42	0.0696
43	43	0.0928
44	44	0.618
45	45	0.927
46	46	0.0207
47	47	0.272
48	48	0.26
49	49	0.0939
5	5	0.198
50	50	0.664
51	51	0.518
52	52	0.901
53	53	0.854
54	54	0.697
55	55	0.847
56	56	0.257
57	57	0.502
58	58	0.287
59	59	0.0423
6	6	0.891
60	60	0.4
61	61	0.317
62	62	0.118
63	63	0.107
64	64	0.301
65	65	0.144
66	66	0.268
67	67	0.648
68	68	0.00706
69	69	0.661
7	7	0.177
70	70	0.0177
71	71	0.0148
72	72	0.578
73	73	0.541
74	74	0.227
75	75	0.0597
76	76	0.428
77	77	0.344
78	78	0.00275
79	79	0.833
8	8	0.101
80	80	0.842
81	81	0.505
82	82	0.0987
83	83	0.476
84	84	0.615
85	85	0.0506
86	86	0.622
87	87	0.0253
88	88	0.944
89	89	0.128
9	9	0.345
90	90	0.0573
91	91	0.219
92	92	0.185
93	93	0.231
94	94	0.32
95	95	0.385
96	96	0.226
97	97	0.795
98	98	0.373
99	99	0.339

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: CNhs12532

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000279 mouse Sox2-positive supporting cell- organ of corti sample

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)
0000197 (receptor cell)
0000003 (native cell)
0000548 (animal cell)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000710 (neurecto-epithelial cell)
0002491 (auditory epithelial cell)
0000630 (supportive cell)
0000255 (eukaryotic cell)
0002077 (ecto-epithelial cell)
0000098 (sensory epithelial cell)
0005014 (auditory epithelial support cell)
0002315 (supporting cell of cochlea)
0002490 (organ of Corti supporting cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0000033 (head)
0000058 (duct)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0004766 (cranial bone)
0008193 (pneumatized bone)
0005913 (zone of bone organ)
0005744 (cranial conduit)
0001032 (sensory system)
0003457 (head bone)
0008001 (irregular bone)
0007914 (head or neck bone)
0010317 (germ layer / neural crest derived structure)
0002227 (spiral organ of cochlea)
0001846 (internal ear)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0004456 (entire sense organ system)
0004339 (calvarium)
0002105 (vestibulo-auditory system)
0001678 (temporal bone)
0003128 (cranium)
0001694 (petrous part of temporal bone)
0004681 (vestibular system)
0001839 (bony labyrinth)
0001690 (ear)
0001844 (cochlea)
0001849 (membranous labyrinth)
0002499 (cochlear labyrinth)
0001855 (cochlear duct of membranous labyrinth)
0011137 (axial skeletal system)
0010323 (cranial skeletal system)
0003129 (skull)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000279 (mouse Sox2-positive supporting cell- organ of corti 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:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008668
+|DRA_sample_Accession=CAGE@SAMD00005538
+|accession_numbers=CAGE;DRX008778;DRR009650;DRZ001075;DRZ002460;DRZ012425;DRZ013810
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0000033,UBERON:0000058,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0000075,UBERON:0004765,UBERON:0004766,UBERON:0008193,UBERON:0005913,UBERON:0005744,UBERON:0001032,UBERON:0003457,UBERON:0008001,UBERON:0007914,UBERON:0010317,UBERON:0002227,UBERON:0001846,UBERON:0000153,UBERON:0007811,UBERON:0002204,UBERON:0001434,UBERON:0004456,UBERON:0004339,UBERON:0002105,UBERON:0001678,UBERON:0003128,UBERON:0001694,UBERON:0004681,UBERON:0001839,UBERON:0001690,UBERON:0001844,UBERON:0001849,UBERON:0002499,UBERON:0001855,UBERON:0011137,UBERON:0010323,UBERON:0003129
 |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000197,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0000710,CL:0002491,CL:0000630,CL:0000255,CL:0002077,CL:0000098,CL:0005014,CL:0002315,CL:0002490
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr3:34548909..34548927,+!p1@Sox2!2.30!325.07!Sox2;;chr12:86814833..86814846,+!p1@Fos!2.24!3755.59!Fos;;chr7:19895384..19895399,-!p2@Fosb!2.16!198.45!Fosb;;chr7:19895354..19895369,-!p1@Fosb!2.16!193.38!Fosb;;chr5:138199361..138199441,+!p2@Tsc22d4!2.09!221.41!Tsc22d4;;chr15:78994907..78994926,-!p1@Sox10!1.99!236.48!Sox10;;chr10:67000609..67000625,+!p1@Egr2!1.97!206.34!Egr2;;chr12:74147689..74147711,-!p1@Six1!1.94!181.97!Six1;;chr15:101097270..101097290,+!p1@Nr4a1!1.81!609.01!Nr4a1;;chr3:34548946..34548972,+!p2@Sox2!1.73!58.31!Sox2;;chr4:99322820..99322845,+!p1@Foxd3!1.71!62.96!Foxd3;;chr13:117099847..117099907,-!p1@Isl1!1.69!86.48!Isl1;;chr2:9800207..9800234,-!p1@Gata3!1.65!129.72!Gata3;;chr2:9809357..9809371,-!p2@Gata3!1.62!40.42!Gata3;;chr4:154335024..154335039,+!p1@Hes5!1.60!46.20!Hes5;;chr18:35020854..35020869,+!p1@Egr1!1.59!1383.65!Egr1;;chr9:55388997..55389016,+!p1@Isl2!1.57!36.34!Isl2;;chr17:86087592..86087615,-!p1@Six2!1.51!31.41!Six2;;chr18:42554216..42554229,+!p1@Pou4f3!1.50!30.84!Pou4f3;;chr4:48058047..48058062,+!p1@Nr4a3!1.49!45.35!Nr4a3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.46!35.35!Pou3f3;;chr4:154010409..154010466,-!p2@Prdm16!1.34!48.45!Prdm16;;chr6:88143711..88143717,+!p2@Gata2!1.33!32.25!Gata2;;chr2:9809374..9809396,-!p4@Gata3!1.30!18.73!Gata3;;chr14:118636214..118636235,-!p1@Sox21!1.29!22.11!Sox21;;chr4:82351639..82351658,-!p14@Nfib!1.28!18.17!Nfib;;chr4:22415443..22415506,-!p1@Pou3f2!1.27!17.61!Pou3f2;;chr8:87502608..87502623,-!p1@Junb!1.26!272.95!Junb;;chr4:154010228..154010244,-!p4@Prdm16!1.23!21.83!Prdm16;;chr6:88148650..88148669,+!p1@Gata2!1.17!114.93!Gata2;;chr3:8666963..8666978,-!p1@Hey1!1.15!85.07!Hey1;;chr4:124334894..124334899,+!p1@Pou3f1!1.15!17.18!Pou3f1;;chr8:94325321..94325366,-!p1@Irx3!1.14!31.27!Irx3;;chr13:78339428..78339466,-!p2@Nr2f1!1.14!17.46!Nr2f1;;chr13:78339382..78339420,-!p3@Nr2f1!1.11!13.94!Nr2f1;;chr2:9809402..9809422,-!p5@Gata3!1.11!11.97!Gata3;;chr4:22415290..22415307,-!p2@Pou3f2!1.11!11.97!Pou3f2;;chr13:78339476..78339515,-!p1@Nr2f1!1.08!17.04!Nr2f1;;chr1:173987720..173987729,-!p1@Nhlh1!1.08!11.13!Nhlh1;;chr4:94718861..94718872,-!p2@Jun!1.07!80.42!Jun;;chr1:193007123..193007139,-!p1@Atf3!1.07!60.00!Atf3;;chr18:81183755..81183761,-!p1@Sall3!1.04!10.00!Sall3;;chr8:125778192..125778217,+!p2@Zfp276!1.03!27.89!Zfp276;;chr8:94325273..94325288,-!p5@Irx3!1.03!12.25!Irx3;;chr2:168427252..168427273,-!p2@Nfatc2!1.03!11.97!Nfatc2;;chr12:74147860..74147888,-!p2@Six1!1.03!9.72!Six1;;chr14:118636238..118636257,-!p2@Sox21!1.02!9.44!Sox21;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.01!11.97!Zbtb11;;chr13:78339134..78339185,-!p5@Nr2f1!1.01!11.55!Nr2f1;;chr14:52948124..52948148,-!p7@Sall2!1.01!9.30!Sall2;;chr6:64679112..64679126,+!p1@Atoh1!1.01!9.30!Atoh1;;chr6:85463580..85463585,-!p1@Egr4!1.01!9.15!Egr4;;chr11:85646303..85646329,+!p1@Tbx2!1.00!61.27!Tbx2;;chr19:19185671..19185693,-!p1@Rorb!1.00!22.11!Rorb;;chr3:90046995..90047031,-!p2@Creb3l4!1.00!11.27!Creb3l4;;chr10:30562571..30562597,-!p1@Hey2!0.99!21.27!Hey2;;chr19:59533221..59533271,+!p1@Emx2!0.99!10.99!Emx2;;chr8:94881872..94881887,+!p2@Irx5!0.99!9.58!Irx5;;chr2:9809579..9809627,-!p7@Gata3!0.98!8.59!Gata3;;chr4:82351566..82351607,-!p10@Nfib!0.98!8.59!Nfib;;chr9:106356211..106356242,+!p1@Pcbp4!0.97!165.91!Pcbp4;;chr4:154010918..154010931,-!p1@Prdm16!0.97!25.21!Prdm16;;chr11:85646263..85646278,+!p2@Tbx2!0.97!21.97!Tbx2;;chr8:94881733..94881790,+!p1@Irx5!0.97!16.48!Irx5;;chr4:94718879..94718898,-!p1@Jun!0.96!605.35!Jun;;chr2:26062055..26062100,-!p1@Lhx3!0.96!8.03!Lhx3;;chr1:194979315..194979359,+!p1@Irf6!0.95!50.14!Irf6;;chr9:106356278..106356292,+!p3@Pcbp4!0.94!13.38!Pcbp4;;chr8:24780125..24780143,+!p1@Zmat4!0.94!11.41!Zmat4;;chr2:71384802..71384815,-!p1@Dlx2!0.94!9.72!Dlx2;;chr12:54349410..54349461,+!p1@Npas3!0.93!9.01!Npas3;;chr18:42554021..42554024,+!p2@Pou4f3!0.91!7.18!Pou4f3;;chr2:9809451..9809469,-!p6@Gata3!0.90!6.90!Gata3;;chr3:8666997..8667012,-!p2@Hey1!0.89!16.06!Hey1;;chr1:194979361..194979373,+!p2@Irf6!0.89!9.30!Irf6;;chr4:82351544..82351563,-!p15@Nfib!0.89!6.76!Nfib;;chr10:42303385..42303401,-!p1@Nr2e1!0.89!6.76!Nr2e1;;chr2:152561980..152561997,+!p1@Id1!0.88!199.86!Id1;;chr13:48356475..48356492,+!p1@Id4!0.87!145.91!Id4;;chr18:35020615..35020641,+!p2@Egr1!0.87!7.75!Egr1;;chr9:106356243..106356264,+!p2@Pcbp4!0.86!28.73!Pcbp4;;chr13:78338076..78338104,-!p4@Nr2f1!0.86!8.03!Nr2f1;;chr13:78339096..78339116,-!p12@Nr2f1!0.86!6.20!Nr2f1;;chr18:52775562..52775650,+!p1@Zfp474!0.86!6.20!Zfp474;;chr10:30375579..30375616,-!p3@Ncoa7!0.85!15.07!Ncoa7;;chr2:28771380..28771413,-!p2@Barhl1!0.85!6.06!Barhl1;;chr8:94325486..94325510,-!p4@Irx3!0.84!7.89!Irx3;;chr15:79178060..79178074,+!p2@Maff!0.82!7.61!Maff;;chrX:108009761..108009788,+!p1@Pou3f4!0.82!5.63!Pou3f4;;chr8:91568074..91568094,-!p1@Sall1!0.82!5.63!Sall1;;chr2:71367871..71367898,+!p1@Dlx1!0.82!5.63!Dlx1;;chr14:52948033..52948045,-!p12@Sall2!0.82!5.63!Sall2;;chr2:9800094..9800108,-!p3@Gata3!0.81!5.49!Gata3;;chr3:34548845..34548856,+!p4@Sox2!0.81!5.49!Sox2;;chr4:154010313..154010324,-!p9@Prdm16!0.80!5.35!Prdm16;;chr14:118635860..118635885,-!p3@Sox21!0.80!5.35!Sox21;;chr4:48058016..48058032,+!p3@Nr4a3!0.79!9.15!Nr4a3;;chr2:56967334..56967366,-!p1@Nr4a2!0.77!10.56!Nr4a2;;chr9:106356265..106356276,+!p4@Pcbp4!0.77!8.31!Pcbp4;;chr4:48058129..48058179,+!p2@Nr4a3!0.76!9.58!Nr4a3;;chr8:94325847..94325869,-!p3@Irx3!0.75!7.75!Irx3;;chr4:99322855..99322867,+!p2@Foxd3!0.75!4.65!Foxd3;;chr2:9811653..9811662,-!p8@Gata3!0.74!4.51!Gata3;;chr4:6917921..6917970,-!p2@Tox!0.73!13.24!Tox;;chrX:58146612..58146615,-!p1@Sox3!0.73!4.37!Sox3;;chr13:78339241..78339273,-!p9@Nr2f1!0.73!4.37!Nr2f1;;chr4:135699731..135699747,+!p1@Id3!0.72!542.39!Id3;;chr11:116196664..116196679,-!p1@Foxj1!0.72!6.90!Foxj1;;chr4:97248607..97248649,+!p15@Nfia!0.72!4.23!Nfia;;chr4:150482563..150482655,-!p2@Camta1!0.71!16.34!Camta1;;chr12:86815639..86815664,+!p2@Fos!0.71!4.08!Fos;;chr7:119822957..119822980,+!p2@Tead1!0.70!21.97!Tead1;;chr1:135320962..135320981,-!p2@Sox13!0.70!15.07!Sox13;;chr16:43503720..43503739,+!p18@Zbtb20!0.70!4.51!Zbtb20;;chr2:71367142..71367167,+!p2@Dlx1!0.69!3.94!Dlx1;;chr3:34549096..34549111,+!p3@Sox2!0.68!3.80!Sox2;;chr18:42554126..42554135,+!p3@Pou4f3!0.68!3.80!Pou4f3;;chr12:28027561..28027591,-!p1@Sox11!0.67!27.89!Sox11;;chr11:85646341..85646352,+!p3@Tbx2!0.67!7.89!Tbx2;;chr10:42303410..42303422,-!p3@Nr2e1!0.67!3.66!Nr2e1;;chr4:89354729..89354776,+!p1@Dmrta1!0.67!3.66!Dmrta1;;chr15:76287876..76287894,+!p1@Scx!0.66!22.25!Scx;;chr13:78338288..78338309,-!p7@Nr2f1!0.66!4.08!Nr2f1;;chr10:42303452..42303470,-!p2@Nr2e1!0.66!3.52!Nr2e1;;chr11:44430812..44430838,+!p1@Ebf1!0.65!39.72!Ebf1;;chr1:64579555..64579570,+!p3@Creb1!0.65!18.87!Creb1;;chr3:8667033..8667046,-!p3@Hey1!0.65!5.07!Hey1;;chr4:6917606..6917681,-!p1@Tox!0.64!16.06!Tox;;chr15:37162796..37162828,+!p1@Grhl2!0.64!6.06!Grhl2;;chr4:82351527..82351541,-!p16@Nfib!0.64!3.38!Nfib;;chr14:52634412..52634500,-!p2@Zfp219!0.63!17.18!Zfp219;;chr2:26063801..26063813,-!p2@Lhx3!0.63!3.24!Lhx3;;chr1:169528823..169528860,+!p5@Rxrg!0.63!3.24!Rxrg;;chr4:6917971..6918000,-!p3@Tox!0.62!6.90!Tox;;chr4:154010940..154010962,-!p3@Prdm16!0.61!7.61!Prdm16;;chr8:94325814..94325839,-!p2@Irx3!0.61!7.18!Irx3;;chr1:169528520..169528542,+!p2@Rxrg!0.61!3.10!Rxrg;;chr13:40825465..40825469,-!p2@Tfap2a!0.61!3.10!Tfap2a;;chr13:72766250..72766273,+!p1@Irx2!0.60!5.07!Irx2;;chr13:72766279..72766296,+!p2@Irx2!0.60!4.79!Irx2;;chr4:154011072..154011095,-!p6@Prdm16!0.60!3.66!Prdm16;;chr15:76352677..76352737,-!p3@Scrt1!0.60!2.96!Scrt1;;chr4:122673187..122673201,+!p2@Mycl1!0.59!5.77!Mycl1;;chr10:119913792..119913820,-!p5@Hmga2!0.59!5.49!Hmga2;;chr11:85646469..85646488,+!p5@Tbx2!0.58!4.51!Tbx2;;chr7:38557752..38557793,-!p3@Zfp536!0.58!3.38!Zfp536;;chrX:108009798..108009815,+!p3@Pou3f4!0.58!2.82!Pou3f4;;chr4:97248652..97248671,+!p19@Nfia!0.58!2.82!Nfia;;chr13:78335687..78335701,-!p16@Nr2f1!0.58!2.82!Nr2f1;;chr1:191994550..191994623,-!p1@Prox1!0.57!22.96!Prox1;;chr6:145814003..145814056,-!p1@Bhlhe41!0.57!9.15!Bhlhe41;;chr10:67000811..67000822,+!p3@Egr2!0.57!2.68!Egr2;;chr12:74147842..74147856,-!p3@Six1!0.57!2.68!Six1;;chr14:118636183..118636192,-!p4@Sox21!0.57!2.68!Sox21;;chr12:25780945..25780961,-!p1@Id2!0.56!555.35!Id2;;chr4:122911086..122911112,+!p1@Heyl!0.56!38.17!Heyl;;chr7:17647736..17647772,-!p1@Hif3a!0.56!11.13!Hif3a;;chrX:98449898..98449913,+!p2@Foxo4!0.56!10.14!Foxo4;;chr7:91558392..91558434,-!p1@Arnt2!0.56!8.59!Arnt2;;chr9:63869729..63869749,-!p4@Smad6!0.56!5.92!Smad6;;chr1:135320989..135321043,-!p1@Sox13!0.55!34.93!Sox13;;chr11:44430788..44430804,+!p3@Ebf1!0.55!7.46!Ebf1;;chr15:102087880..102087927,-!p2@Rarg!0.55!6.76!Rarg;;chr14:52935860..52935874,-!p3@Sall2!0.55!4.08!Sall2;;chr7:91558631..91558652,-!p3@Arnt2!0.55!4.08!Arnt2;;chr8:94881686..94881700,+!p4@Irx5!0.55!2.54!Irx5;;chr2:31495237..31495243,+!p1@Prdm12!0.55!2.54!Prdm12;;chr16:43508231..43508271,+!p21@Zbtb20!0.55!2.54!Zbtb20;;chr14:52935876..52935928,-!p1@Sall2!0.54!25.21!Sall2;;chr2:44968737..44968758,-!p2@Zeb2!0.54!17.61!Zeb2;;chr14:52634234..52634281,-!p3@Zfp219!0.54!8.17!Zfp219;;chr11:3189683..3189744,+!p2@Patz1!0.54!5.92!Patz1;;chr8:34496298..34496366,+!p1@Purg!0.53!25.35!Purg;;chr7:130644017..130644092,-!p1@Zkscan2!0.53!5.35!Zkscan2;;chr10:30562617..30562637,-!p2@Hey2!0.53!3.24!Hey2;;chr6:88143570..88143590,+!p4@Gata2!0.53!2.39!Gata2;;chr1:169528491..169528505,+!p4@Rxrg!0.53!2.39!Rxrg;;chr12:74147444..74147463,-!p4@Six1!0.53!2.39!Six1;;chr17:48061584..48061601,-!p2@Foxp4!0.52!19.15!Foxp4;;chr18:55150011..55150059,-!p3@Zfp608!0.52!9.15!Zfp608;;chr9:63869751..63869767,-!p1@Smad6!0.52!7.32!Smad6;;chr1:189821714..189821761,+!p1@Esrrg!0.52!4.93!Esrrg;;chr6:51382677..51382783,+!p1@Nfe2l3!0.51!6.90!Nfe2l3;;chr10:119913546..119913583,-!p3@Hmga2!0.51!5.49!Hmga2;;chr4:154010334..154010347,-!p8@Prdm16!0.51!2.82!Prdm16;;chr4:97248473..97248496,+!p16@Nfia!0.51!2.25!Nfia;;chr12:50485973..50486015,+!p2@Foxg1!0.51!2.25!Foxg1;;chr15:37163124..37163153,+!p3@Grhl2!0.51!2.25!Grhl2;;chr15:7635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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000279
 |is_obsolete=
-|library_ids=CNhs12532
+|library_id=CNhs12532
+|library_id_phase_based=2:CNhs12532
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12157
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12157
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Sox2%252b%2520Supporting%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12532.12157-128G6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Sox2%252b%2520Supporting%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12532.12157-128G6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Sox2%252b%2520Supporting%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12532.12157-128G6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Sox2%252b%2520Supporting%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12532.12157-128G6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Sox2%252b%2520Supporting%2520cells%2520-%2520organ%2520of%2520corti%252c%2520pool1.CNhs12532.12157-128G6.mm9.nobarcode.rdna.fa.gz
 |name=Sox2+ Supporting cells - organ of corti, pool1
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12532,LSID919,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.0686102458237835,0,0,0,0,-0.0843392403965415,0,0,0,0,0.0286130208973782,0,-0.0841114259086656,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.36435999640495,0,0,0,0,0.00868329692581116,0.0554188522498211,0.0531196473196478,-0.113892720831148,-0.554439545710481,0.159903182756994,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0428469550828748,0,-0.0336651674912462,0,0,0,-0.0887767820109479,-0.0126924202373402,-0.00502952951747593,0.0406016495197159,0,0,0.0492504190792844,0,0,0,0.0104917417496376,-0.0693651005291375,-0.59591488074057,0.0289503301340015,0,0,0,0,0,0,-0.204963756277873,-0.460258162216312,-0.154040543036775,0,0,0,0,0
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12157-128G6;search_select_hide=table117:12157-128G6
-|DRA_sample_Accession=CAGE@DRS008668
-|accession_numbers=DRX008778;DRR009650;DRZ001075;DRZ002460;CAGE
-|library_id=CNhs12532
 }}

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FF:12157-128G6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:32, 4 June 2020

CNhs12532

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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