FF:17-12C2: Difference between revisions

Latest revision as of 19:08, 4 June 2020

Name:	medulla oblongata, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10477
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	medulla oblongata
dev stage	adult
sex	male
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

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

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005853

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10477		CAGE		DRX009046		DRR009920

Accession ID Mm9

Library id		BAM		CTSS
CNhs10477		DRZ001345		DRZ002728

Accession ID Mm10

Library id		BAM		CTSS
CNhs10477		DRZ012695		DRZ014078

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

CNhs10477

0	0
1	0.728
10	0
100	0
1000	0.0138
1001	0.0534
1002	0
1003	0.0884
1004	0
1005	0.0863
1006	0.61
1007	-0.0594
1008	0
1009	-0.0691
101	-0.0826
1010	0
1011	0.423
1012	0.0647
1013	0.295
1014	-0.0299
1015	-0.135
1016	-0.153
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.0505
1023	0
1024	0.203
1025	0.0598
1026	0
1027	0.443
1028	0
1029	-0.00378
103	-0.0813
1030	0
1031	-0.304
1032	0.457
1033	-0.0105
1034	0
1035	0
1036	-0.279
1037	0
1038	-0.112
1039	0.181
104	0
1040	-0.151
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: CNhs10477

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00138
MA0003.1	MA0003.1	0.4
MA0004.1	MA0004.1	0.412
MA0006.1	MA0006.1	0.26
MA0007.1	MA0007.1	0.287
MA0009.1	MA0009.1	0.796
MA0014.1	MA0014.1	0.941
MA0017.1	MA0017.1	2.88822e-6
MA0018.2	MA0018.2	0.00566
MA0019.1	MA0019.1	0.65
MA0024.1	MA0024.1	0.0398
MA0025.1	MA0025.1	6.74289e-4
MA0027.1	MA0027.1	0.199
MA0028.1	MA0028.1	0.122
MA0029.1	MA0029.1	0.684
MA0030.1	MA0030.1	0.637
MA0031.1	MA0031.1	0.496
MA0035.2	MA0035.2	0.0216
MA0038.1	MA0038.1	0.247
MA0039.2	MA0039.2	0.0887
MA0040.1	MA0040.1	0.671
MA0041.1	MA0041.1	0.0358
MA0042.1	MA0042.1	0.183
MA0043.1	MA0043.1	0.0332
MA0046.1	MA0046.1	1.98885e-10
MA0047.2	MA0047.2	0.00105
MA0048.1	MA0048.1	0.0189
MA0050.1	MA0050.1	5.37196e-4
MA0051.1	MA0051.1	0.0036
MA0052.1	MA0052.1	0.419
MA0055.1	MA0055.1	0.00491
MA0057.1	MA0057.1	0.312
MA0058.1	MA0058.1	0.498
MA0059.1	MA0059.1	0.126
MA0060.1	MA0060.1	0.629
MA0061.1	MA0061.1	0.017
MA0062.2	MA0062.2	0.0042
MA0065.2	MA0065.2	1.86399e-6
MA0066.1	MA0066.1	0.0225
MA0067.1	MA0067.1	0.371
MA0068.1	MA0068.1	0.998
MA0069.1	MA0069.1	0.0438
MA0070.1	MA0070.1	0.178
MA0071.1	MA0071.1	0.19
MA0072.1	MA0072.1	0.733
MA0073.1	MA0073.1	0.85
MA0074.1	MA0074.1	0.0998
MA0076.1	MA0076.1	0.277
MA0077.1	MA0077.1	0.24
MA0078.1	MA0078.1	0.621
MA0079.2	MA0079.2	0.216
MA0080.2	MA0080.2	2.69538e-9
MA0081.1	MA0081.1	0.269
MA0083.1	MA0083.1	0.0224
MA0084.1	MA0084.1	0.451
MA0087.1	MA0087.1	0.081
MA0088.1	MA0088.1	0.421
MA0090.1	MA0090.1	0.0908
MA0091.1	MA0091.1	0.15
MA0092.1	MA0092.1	0.142
MA0093.1	MA0093.1	0.487
MA0099.2	MA0099.2	0.012
MA0100.1	MA0100.1	0.136
MA0101.1	MA0101.1	0.0103
MA0102.2	MA0102.2	0.532
MA0103.1	MA0103.1	0.123
MA0104.2	MA0104.2	0.656
MA0105.1	MA0105.1	0.00157
MA0106.1	MA0106.1	0.0417
MA0107.1	MA0107.1	0.0197
MA0108.2	MA0108.2	1.26154e-4
MA0111.1	MA0111.1	0.769
MA0112.2	MA0112.2	0.00123
MA0113.1	MA0113.1	0.395
MA0114.1	MA0114.1	4.04951e-6
MA0115.1	MA0115.1	2.31787e-5
MA0116.1	MA0116.1	0.0599
MA0117.1	MA0117.1	0.922
MA0119.1	MA0119.1	0.181
MA0122.1	MA0122.1	0.958
MA0124.1	MA0124.1	0.437
MA0125.1	MA0125.1	0.0176
MA0131.1	MA0131.1	0.728
MA0135.1	MA0135.1	0.123
MA0136.1	MA0136.1	4.20794e-10
MA0137.2	MA0137.2	0.546
MA0138.2	MA0138.2	2.71959e-5
MA0139.1	MA0139.1	0.703
MA0140.1	MA0140.1	1.43397e-5
MA0141.1	MA0141.1	0.025
MA0142.1	MA0142.1	0.222
MA0143.1	MA0143.1	0.695
MA0144.1	MA0144.1	0.144
MA0145.1	MA0145.1	0.25
MA0146.1	MA0146.1	0.0495
MA0147.1	MA0147.1	0.467
MA0148.1	MA0148.1	0.00137
MA0149.1	MA0149.1	0.169
MA0150.1	MA0150.1	0.405
MA0152.1	MA0152.1	0.24
MA0153.1	MA0153.1	7.75729e-11
MA0154.1	MA0154.1	0.0352
MA0155.1	MA0155.1	0.423
MA0156.1	MA0156.1	1.01848e-6
MA0157.1	MA0157.1	0.299
MA0159.1	MA0159.1	0.0051
MA0160.1	MA0160.1	0.0342
MA0162.1	MA0162.1	0.288
MA0163.1	MA0163.1	6.03178e-4
MA0164.1	MA0164.1	0.94
MA0258.1	MA0258.1	0.0166
MA0259.1	MA0259.1	0.698

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: CNhs10477

Novel motif	Logo	P-value
1	1	0.259
10	10	0.0434
100	100	0.254
101	101	0.859
102	102	0.996
103	103	0.0897
104	104	0.999
105	105	0.644
106	106	0.0355
107	107	0.146
108	108	0.54
109	109	0.0262
11	11	0.138
110	110	0.0339
111	111	0.232
112	112	0.0129
113	113	0.451
114	114	0.516
115	115	0.915
116	116	0.274
117	117	0.00243
118	118	0.197
119	119	0.255
12	12	0.762
120	120	0.891
121	121	0.683
122	122	0.746
123	123	2.19989e-4
124	124	0.0206
125	125	0.123
126	126	0.0246
127	127	0.186
128	128	0.0529
129	129	0.356
13	13	1.87954e-7
130	130	0.179
131	131	0.571
132	132	0.723
133	133	0.678
134	134	0.214
135	135	0.0713
136	136	0.294
137	137	0.713
138	138	0.695
139	139	0.251
14	14	0.634
140	140	0.101
141	141	0.95
142	142	0.572
143	143	0.314
144	144	0.982
145	145	8.44091e-5
146	146	0.498
147	147	0.363
148	148	0.935
149	149	0.848
15	15	0.198
150	150	0.0691
151	151	0.94
152	152	0.166
153	153	0.845
154	154	0.719
155	155	0.416
156	156	0.00972
157	157	0.27
158	158	0.297
159	159	0.67
160	160	0.237
161	161	0.327
162	162	0.773
163	163	0.612
164	164	0.0329
165	165	0.544
166	166	0.446
167	167	0.922
168	168	0.782
169	169	0.00432
17	17	0.0895
18	18	0.927
19	19	0.185
2	2	0.589
20	20	0.0127
21	21	0.189
22	22	0.225
23	23	0.831
24	24	0.115
25	25	0.786
26	26	5.54404e-10
27	27	0.283
28	28	0.853
29	29	0.0272
3	3	0.098
30	30	0.799
31	31	0.715
32	32	0.65
33	33	0.201
34	34	0.908
35	35	0.952
36	36	0.168
37	37	0.0703
38	38	0.527
39	39	0.403
4	4	0.22
40	40	0.154
41	41	0.535
42	42	0.238
43	43	0.132
44	44	0.504
45	45	0.777
46	46	0.034
47	47	0.634
48	48	0.418
49	49	0.137
5	5	0.193
50	50	0.298
51	51	0.757
52	52	0.4
53	53	0.27
54	54	0.966
55	55	0.807
56	56	0.64
57	57	0.475
58	58	0.342
59	59	0.169
6	6	0.981
60	60	0.0461
61	61	0.0735
62	62	0.229
63	63	0.197
64	64	0.741
65	65	0.427
66	66	0.802
67	67	0.857
68	68	0.31
69	69	0.655
7	7	0.0184
70	70	0.1
71	71	0.00221
72	72	0.633
73	73	0.0748
74	74	0.805
75	75	0.0558
76	76	0.198
77	77	0.563
78	78	0.0022
79	79	0.213
8	8	0.0476
80	80	0.976
81	81	0.542
82	82	0.372
83	83	0.401
84	84	0.874
85	85	0.299
86	86	0.149
87	87	0.746
88	88	0.61
89	89	0.712
9	9	0.538
90	90	0.103
91	91	0.0778
92	92	0.387
93	93	0.129
94	94	0.585
95	95	0.107
96	96	0.515
97	97	0.92
98	98	0.702
99	99	0.61

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: CNhs10477

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011284 mouse medulla oblongata- adult 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0007023 (adult organism)
0000955 (brain)
0001896 (medulla oblongata)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0002298 (brainstem)
0002028 (hindbrain)
0005290 (myelencephalon)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011284 (mouse medulla oblongata- adult 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
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+|DRA_sample_Accession=CAGE@SAMD00005853
+|accession_numbers=CAGE;DRX009046;DRR009920;DRZ001345;DRZ002728;DRZ012695;DRZ014078
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000955,UBERON:0001896,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0004733,UBERON:0004732,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0002298,UBERON:0002028,UBERON:0005290
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000998,FF:0000004,FF:0011284
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.40!280.64!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.07!213.21!Tsc22d4;;chr11:96143666..96143725,+!p1@Hoxb8!1.82!74.50!Hoxb8;;chr16:91225808..91225824,+!p1@Olig2!1.81!62.94!Olig2;;chrX:34442872..34442899,-!p1@Nkrf!1.62!52.18!Nkrf;;chr15:76353005..76353021,-!p2@Scrt1!1.59!38.05!Scrt1;;chr15:76352434..76352488,-!p4@Scrt1!1.55!34.68!Scrt1;;chr2:127347067..127347093,-!p1@Kcnip3!1.52!52.66!Kcnip3;;chr17:48015839..48015915,-!p3@Foxp4!1.48!34.20!Foxp4;;chr15:78994907..78994926,-!p1@Sox10!1.44!66.63!Sox10;;chr7:116154364..116154444,+!p1@Tub!1.44!45.44!Tub;;chr8:24780125..24780143,+!p1@Zmat4!1.42!36.28!Zmat4;;chr15:76352677..76352737,-!p3@Scrt1!1.42!25.53!Scrt1;;chr7:146768691..146768707,-!p1@Nkx6-2!1.42!25.21!Nkx6-2;;chr2:127347042..127347058,-!p3@Kcnip3!1.41!24.89!Kcnip3;;chr1:6477388..6477419,+!p3@St18!1.41!24.56!St18;;chr18:36441119..36441158,+!p2@Pura!1.37!53.62!Pura;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.36!27.78!Pou3f3;;chr12:30219426..30219506,+!p2@Myt1l!1.36!21.83!Myt1l;;chr19:19185671..19185693,-!p1@Rorb!1.34!49.45!Rorb;;chr10:67375146..67375208,-!p2@Zfp365!1.34!31.47!Zfp365;;chr3:95032091..95032183,-!p1@Mllt11!1.33!167.13!Mllt11;;chr11:96685444..96685473,-!p5@Nfe2l1!1.33!20.55!Nfe2l1;;chr9:91260594..91260612,-!p1@Zic1!1.33!20.55!Zic1;;chr17:25707623..25707639,-!p1@Sox8!1.32!83.49!Sox8;;chr9:91260616..91260653,-!p2@Zic1!1.30!19.11!Zic1;;chr16:91270091..91270143,+!p2@Olig1!1.29!18.46!Olig1;;chr2:168427068..168427115,-!p3@Nfatc2!1.29!18.30!Nfatc2;;chr12:54349410..54349461,+!p1@Npas3!1.26!20.71!Npas3;;chr4:150482563..150482655,-!p2@Camta1!1.25!59.72!Camta1;;chr2:65683890..65683907,+!p1@Csrnp3!1.25!32.11!Csrnp3;;chr11:96143962..96144035,+!p2@Hoxb8!1.22!15.57!Hoxb8;;chr6:52154414..52154462,-!p1@Hoxa5!1.21!21.03!Hoxa5;;chr7:148008023..148008092,-!p1@Zfp941!1.19!34.52!Zfp941;;chr4:58956447..58956510,+!p1@Zkscan16!1.19!31.47!Zkscan16;;chr3:95032515..95032553,-!p5@Mllt11!1.18!17.18!Mllt11;;chr8:107793688..107793736,+!p1@Hsf4!1.17!18.14!Hsf4;;chr2:163051181..163051205,+!p2@Tox2!1.17!13.65!Tox2;;chr1:189821714..189821761,+!p1@Esrrg!1.14!23.92!Esrrg;;chr3:95032213..95032226,-!p6@Mllt11!1.14!15.41!Mllt11;;chrX:34442842..34442866,-!p3@Nkrf!1.12!12.20!Nkrf;;chr10:84218800..84218829,+!p2@Rfx4!1.12!12.20!Rfx4;;chr2:115890294..115890334,-!p9@Meis2!1.11!16.22!Meis2;;chr19:10315179..10315241,-!p1@Gm98!1.09!118.33!Gm98;;chr8:87297878..87297935,-!p3@Nfix!1.09!25.21!Nfix;;chr15:102865048..102865073,+!p3@Hoxc4!1.08!13.97!Hoxc4;;chr2:163030219..163030258,+!p5@Tox2!1.07!10.76!Tox2;;chr15:103170533..103170556,-!p1@Zfp385a!1.06!39.66!Zfp385a;;chrX:137083127..137083138,-!p9@Tsc22d3!1.06!10.44!Tsc22d3;;chr6:52161666..52161711,-!p1@Hoxa6!1.05!10.28!Hoxa6;;chr11:96160360..96160397,+!p3@Hoxb6!1.05!10.11!Hoxb6;;chr13:72766250..72766273,+!p1@Irx2!1.04!15.41!Irx2;;chr4:150513630..150513686,-!p4@Camta1!1.04!11.56!Camta1;;chr6:145814003..145814056,-!p1@Bhlhe41!1.03!28.42!Bhlhe41;;chr10:67375368..67375433,-!p1@Zfp365!1.03!17.34!Zfp365;;chr3:34548946..34548972,+!p2@Sox2!1.02!10.44!Sox2;;chr11:96164821..96164865,+!p1@Hoxb5!1.02!9.47!Hoxb5;;chr7:91558392..91558434,-!p1@Arnt2!1.01!26.17!Arnt2;;chr16:91225654..91225671,+!p2@Olig2!1.01!9.31!Olig2;;chr5:122499831..122499891,-!p1@Cux2!1.00!13.97!Cux2;;chr15:102865088..102865107,+!p1@Hoxc4!1.00!12.04!Hoxc4;;chr3:95032197..95032208,-!p3@Mllt11!0.99!11.08!Mllt11;;chr2:162769220..162769252,+!p1@L3mbtl1!0.99!8.83!L3mbtl1;;chr11:96685487..96685512,-!p7@Nfe2l1!0.99!8.67!Nfe2l1;;chr14:122874619..122874634,+!p1@Zic2!0.99!8.67!Zic2;;chr14:104867201..104867258,-!p1@Pou4f1!0.98!12.04!Pou4f1;;chr11:98190918..98190951,-!p1@Neurod2!0.98!8.51!Neurod2;;chr6:145813905..145813932,-!p2@Bhlhe41!0.97!16.06!Bhlhe41;;chr7:38554763..38554780,-!p1@Zfp536!0.97!15.41!Zfp536;;chr2:65768174..65768247,+!p2@Csrnp3!0.95!7.87!Csrnp3;;chr11:90252223..90252240,-!p1@Hlf!0.94!67.11!Hlf;;chrX:108009761..108009788,+!p1@Pou3f4!0.94!7.71!Pou3f4;;chr11:98636531..98636559,-!p1@Nr1d1!0.93!44.47!Nr1d1;;chr10:84218895..84218909,+!p1@Rfx4!0.93!7.55!Rfx4;;chr3:34548909..34548927,+!p1@Sox2!0.92!12.68!Sox2;;chr3:95032558..95032641,-!p2@Mllt11!0.91!41.90!Mllt11;;chr2:25562263..25562314,+!p2@Bmyc!0.91!28.90!Bmyc;;chr12:72149325..72149343,+!p2@Arid4a!0.91!10.28!Arid4a;;chr2:151907546..151907561,+!p1@Scrt2!0.91!7.06!Scrt2;;chr6:134780163..134780197,+!p2@Crebl2!0.90!16.70!Crebl2;;chr2:163030186..163030204,+!p4@Tox2!0.89!6.74!Tox2;;chr9:106362954..106362977,+!p6@Pcbp4!0.88!6.58!Pcbp4;;chr13:44936126..44936164,+!p6@Jarid2!0.87!7.55!Jarid2;;chr2:127347094..127347111,-!p2@Kcnip3!0.86!10.60!Kcnip3;;chr6:52154386..52154407,-!p2@Hoxa5!0.86!8.03!Hoxa5;;chr3:101814061..101814094,+!p1@Nhlh2!0.86!6.26!Nhlh2;;chr12:30213247..30213333,+!p1@Myt1l!0.86!6.26!Myt1l;;chr9:106356278..106356292,+!p3@Pcbp4!0.85!10.76!Pcbp4;;chr10:80893711..80893784,-!p3@Nfic!0.84!33.07!Nfic;;chr6:117813087..117813121,+!p1@Zfp239!0.83!23.44!Zfp239;;chr15:103170516..103170531,-!p2@Zfp385a!0.83!14.29!Zfp385a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444;;chrX:137077653..137077669,-!p3@Tsc22d3!0.17!5.30!Tsc22d3;;chr9:21420596..21420607,+!p4@Smarca4!0.17!4.82!Smarca4;;chr19:28085485..28085544,-!p5@Rfx3!0.17!4.50!Rfx3;;chr6:92041399..92041417,+!p2@Nr2c2!0.17!3.69!Nr2c2;;chr1:170362437..170362478,-!p5@Pbx1!0.17!3.37!Pbx1;;chr7:37483021..37483078,+!p1@Tshz3!0.17!3.37!Tshz3;;chr9:21420610..21420621,+!p5@Smarca4!0.17!3.37!Smarca4;;chr2:38781916..38781974,-!p1@Nr6a1!0.17!3.21!Nr6a1;;chr2:115891409..115891425,-!p2@Meis2!0.17!3.05!Meis2;;chr9:113840082..113840105,+!p3@Ubp1!0.17!3.05!Ubp1;;chr2:160698668..160698679,-!p4@Zhx3!0.17!1.61!Zhx3;;chr11:98636657..98636668,-!p6@Nr1d1!0.17!1.44!Nr1d1;;chr11:18918434..18918489,-!p3@Meis1!0.17!1.28!Meis1;;chr12:16817785..16817796,+!p2@E2f6!0.17!1.28!E2f6;;chr8:123608252..123608268,+!p1@Foxf1a!0.17!1.12!Foxf1a;;chr8:118231350..118231385,-!p7@Maf!0.17!1.12!Maf;;chr7:16760434..16760453,+!p2@LOC100046899,p2@Meis3!0.17!0.96!Meis3;;chr6:47998938..47998955,-!p2@Zfp777!0.17!0.96!Zfp777;;chr17:46692970..46692977,-!p5@Srf!0.17!0.96!Srf;;chr1:64168228..64168250,-!p7@Klf7!0.17!0.96!Klf7;;chr2:169459017..169459029,+!p9@Tshz2!0.17!0.80!Tshz2;;chr18:65740031..65740054,+!p5@Zfp532!0.17!0.80!Zfp532;;chr16:55973994..55974005,+!p8@Rpl24,p8@Zbtb11!0.17!0.80!Zbtb11;;chr15:81633224..81633235,+!p5@Tef!0.17!0.80!Tef;;chr8:123640090..123640101,+!p2@Foxc2!0.17!0.64!Foxc2;;chr11:44431191..44431205,+!p11@Ebf1!0.17!0.64!Ebf1;;chr4:117354821..117354830,-!p3@Dmap1!0.17!0.64!Dmap1;;chr2:74543202..74543213,+!p3@Hoxd8!0.17!0.48!Hoxd8;;chr4:97248607..97248649,+!p15@Nfia!0.17!0.48!Nfia;;chr4:22415600..22415616,-!p3@Pou3f2!0.17!0.48!Pou3f2;;chr2:9809357..9809371,-!p2@Gata3!0.17!0.48!Gata3;;chr2:9809451..9809469,-!p6@Gata3!0.17!0.48!Gata3;;chr2:74583741..74583750,+!p10@Hoxd3!0.17!0.48!Hoxd3;;chr3:66785201..66785226,-!p3@Shox2!0.17!0.48!Shox2;;chr3:17954233..17954249,+!p1@Bhlhe22!0.17!0.48!Bhlhe22;;chr4:150503544..150503561,-!p8@Camta1!0.17!0.48!Camta1;;chr3:135257370..135257389,-!p9@Nfkb1!0.17!0.48!Nfkb1;;chr3:34548845..34548856,+!p4@Sox2!0.17!0.48!Sox2;;chr4:61869681..61869704,-!p3@Zfp37!0.17!0.48!Zfp37;;chr4:107107224..107107259,+!p2@Glis1!0.17!0.48!Glis1;;chr2:74543397..74543435,+!p2@Hoxd8!0.17!0.48!Hoxd8;;chr9:96632593..96632620,-!p12@Zbtb38!0.17!0.48!Zbtb38;;chr9:98855692..98855710,+!p2@Foxl2!0.17!0.48!Foxl2;;chr9:55388997..55389016,+!p1@Isl2!0.17!0.48!Isl2;;chr8:26958093..26958148,-!p2@Ash2l!0.17!0.48!Ash2l;;chr9:69608731..69608742,-!p2@Foxb1!0.17!0.48!Foxb1;;chrX:137077530..137077533,-!p11@Tsc22d3!0.17!0.48!Tsc22d3;;chr8:94325779..94325791,-!p7@Irx3!0.17!0.48!Irx3;;chr8:12395500..12395511,+!p5@Sox1!0.17!0.48!Sox1;;chrX:108009602..108009615,+!p4@Pou3f4!0.17!0.48!Pou3f4;;chr9:21992581..21992593,+!p1@Zfp872!0.17!0.48!Zfp872;;chr8:87298020..87298041,-!p9@Nfix!0.17!0.48!Nfix;;chr8:87297330..87297365,-!p5@Nfix!0.17!0.48!Nfix;;chr9:91263649..91263666,+!p3@Zic4!0.17!0.48!Zic4;;chr16:43508231..43508271,+!p21@Zbtb20!0.17!0.48!Zbtb20;;chr18:52775562..52775650,+!p1@Zfp474!0.17!0.48!Zfp474;;chr19:44831390..44831414,+!p1@Pax2!0.17!0.48!Pax2;;chr16:43503417..43503436,+!p26@Zbtb20!0.17!0.48!Zbtb20;;chr16:43364258..43364270,+!p27@Zbtb20!0.17!0.48!Zbtb20;;chr17:48015995..48016037,-!p12@Foxp4!0.17!0.48!Foxp4;;chr1:78193687..78193692,-!p1@Pax3!0.17!0.48!Pax3;;chr2:163028876..163028885,+!p7@Tox2!0.17!0.48!Tox2;;chr1:19202352..19202354,+!p2@Tfap2b!0.17!0.48!Tfap2b;;chr1:169528581..169528607,+!p7@Rxrg!0.17!0.48!Rxrg;;chr2:181501822..181501834,+!p8@Myt1!0.17!0.48!Myt1;;chr2:33496386..33496410,-!p1@Lmx1b!0.17!0.48!Lmx1b;;chr2:151907368..151907379,+!p8@Scrt2!0.17!0.48!Scrt2;;chr1:169619239..169619257,+!p4@Lmx1a!0.17!0.48!Lmx1a;;chr2:56967381..56967386,-!p8@Nr4a2!0.17!0.48!Nr4a2;;chr2:154395524..154395535,-!p5@E2f1!0.17!0.48!E2f1;;chr1:169528491..169528505,+!p4@Rxrg!0.17!0.48!Rxrg;;chr6:88143570..88143590,+!p4@Gata2!0.17!0.48!Gata2;;chr6:85463580..85463585,-!p1@Egr4!0.17!0.48!Egr4;;
+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011284
 |is_obsolete=
+|library_id=CNhs10477
+|library_id_phase_based=2:CNhs10477
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;17
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;17
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm9.nobarcode.rdna.fa.gz
 |name=medulla oblongata, adult
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10477,LSID646,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.076339866300382,0,0,0,0,0,-0.05272224564925,0,0.030936709486621,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.0211472067224795,0,0,0,0,0,0.170746144160095,0,0,0,0,0,0,0,-0.493758715628899,0,0,0,0,0.0327134645401244,-0.0813546180496645,0.149433103813338,-0.182629039615701,0.403896696646389,0.856015681534086,0,0,0.170746144160095,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0218171216122575,0,0.0323320383475661,0,0,0,-0.0569217626770165,-0.0176632077016166,0.308273376107523,-0.00064230896796749,0,0,0.101871956563477,0,0,0,0.0544723134119831,0.0715158543496048,0.0447218001602192,-0.0788315948399074,0,0,0,0,0,0,-0.020444838171606,-0.1216930865379,0.0458563641780491,0,0,0.589939622461393,0,0
 |rna_box=12
 |rna_catalog_number=
@@ Line 58: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:17-12C2;search_select_hide=table117:17-12C2
 }}

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FF:17-12C2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:08, 4 June 2020

CNhs10477

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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