FF:1396-42A3: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	medulla oblongata, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11200
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	medulla oblongata
dev stage	30 days neonate
sex	mixture
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		SAMD00005654

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11200		CAGE		DRX009047		DRR009921

Accession ID Mm9

Library id		BAM		CTSS
CNhs11200		DRZ001346		DRZ002729

Accession ID Mm10

Library id		BAM		CTSS
CNhs11200		DRZ012696		DRZ014079

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

CNhs11200

0	0
1	0.718
10	0
100	0
1000	0.0343
1001	0.1
1002	-0.0161
1003	0.0268
1004	0.0241
1005	0.00926
1006	0.6
1007	-0.0214
1008	0
1009	-0.152
101	-0.0749
1010	0
1011	0.287
1012	0.131
1013	0.328
1014	-0.037
1015	-0.184
1016	-0.0983
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.0857
1023	0
1024	0.17
1025	0
1026	0
1027	0.464
1028	0
1029	0.0527
103	-0.0799
1030	0
1031	-0.317
1032	0.46
1033	-0.0142
1034	0
1035	0.0481
1036	-0.233
1037	0
1038	-0.0942
1039	0.116
104	0
1040	-0.168
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: CNhs11200

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	2.7993e-4
MA0003.1	MA0003.1	0.291
MA0004.1	MA0004.1	0.437
MA0006.1	MA0006.1	0.259
MA0007.1	MA0007.1	0.379
MA0009.1	MA0009.1	0.879
MA0014.1	MA0014.1	0.854
MA0017.1	MA0017.1	2.63946e-6
MA0018.2	MA0018.2	0.00504
MA0019.1	MA0019.1	0.447
MA0024.1	MA0024.1	0.0638
MA0025.1	MA0025.1	0.00179
MA0027.1	MA0027.1	0.224
MA0028.1	MA0028.1	0.125
MA0029.1	MA0029.1	0.911
MA0030.1	MA0030.1	0.604
MA0031.1	MA0031.1	0.417
MA0035.2	MA0035.2	0.0179
MA0038.1	MA0038.1	0.206
MA0039.2	MA0039.2	0.0762
MA0040.1	MA0040.1	0.485
MA0041.1	MA0041.1	0.0489
MA0042.1	MA0042.1	0.151
MA0043.1	MA0043.1	0.0282
MA0046.1	MA0046.1	2.47318e-12
MA0047.2	MA0047.2	1.63525e-4
MA0048.1	MA0048.1	0.0365
MA0050.1	MA0050.1	3.79163e-5
MA0051.1	MA0051.1	5.45499e-4
MA0052.1	MA0052.1	0.357
MA0055.1	MA0055.1	0.0162
MA0057.1	MA0057.1	0.234
MA0058.1	MA0058.1	0.536
MA0059.1	MA0059.1	0.131
MA0060.1	MA0060.1	0.281
MA0061.1	MA0061.1	0.0172
MA0062.2	MA0062.2	0.00506
MA0065.2	MA0065.2	1.58615e-6
MA0066.1	MA0066.1	0.022
MA0067.1	MA0067.1	0.246
MA0068.1	MA0068.1	0.938
MA0069.1	MA0069.1	0.0581
MA0070.1	MA0070.1	0.341
MA0071.1	MA0071.1	0.181
MA0072.1	MA0072.1	0.918
MA0073.1	MA0073.1	0.826
MA0074.1	MA0074.1	0.109
MA0076.1	MA0076.1	0.308
MA0077.1	MA0077.1	0.159
MA0078.1	MA0078.1	0.747
MA0079.2	MA0079.2	0.262
MA0080.2	MA0080.2	1.25764e-9
MA0081.1	MA0081.1	0.208
MA0083.1	MA0083.1	0.014
MA0084.1	MA0084.1	0.657
MA0087.1	MA0087.1	0.0642
MA0088.1	MA0088.1	0.358
MA0090.1	MA0090.1	0.0844
MA0091.1	MA0091.1	0.157
MA0092.1	MA0092.1	0.227
MA0093.1	MA0093.1	0.525
MA0099.2	MA0099.2	0.0105
MA0100.1	MA0100.1	0.19
MA0101.1	MA0101.1	0.0123
MA0102.2	MA0102.2	0.461
MA0103.1	MA0103.1	0.104
MA0104.2	MA0104.2	0.632
MA0105.1	MA0105.1	0.0012
MA0106.1	MA0106.1	0.0618
MA0107.1	MA0107.1	0.024
MA0108.2	MA0108.2	9.57768e-4
MA0111.1	MA0111.1	0.815
MA0112.2	MA0112.2	8.70092e-4
MA0113.1	MA0113.1	0.497
MA0114.1	MA0114.1	6.48243e-6
MA0115.1	MA0115.1	5.76756e-5
MA0116.1	MA0116.1	0.0382
MA0117.1	MA0117.1	0.982
MA0119.1	MA0119.1	0.127
MA0122.1	MA0122.1	0.98
MA0124.1	MA0124.1	0.476
MA0125.1	MA0125.1	0.00717
MA0131.1	MA0131.1	0.802
MA0135.1	MA0135.1	0.368
MA0136.1	MA0136.1	3.77549e-11
MA0137.2	MA0137.2	0.305
MA0138.2	MA0138.2	1.48988e-4
MA0139.1	MA0139.1	0.521
MA0140.1	MA0140.1	1.58628e-5
MA0141.1	MA0141.1	0.0204
MA0142.1	MA0142.1	0.434
MA0143.1	MA0143.1	0.74
MA0144.1	MA0144.1	0.0795
MA0145.1	MA0145.1	0.217
MA0146.1	MA0146.1	0.0528
MA0147.1	MA0147.1	0.435
MA0148.1	MA0148.1	5.51366e-4
MA0149.1	MA0149.1	0.237
MA0150.1	MA0150.1	0.255
MA0152.1	MA0152.1	0.259
MA0153.1	MA0153.1	1.92247e-12
MA0154.1	MA0154.1	0.0235
MA0155.1	MA0155.1	0.454
MA0156.1	MA0156.1	5.23882e-7
MA0157.1	MA0157.1	0.287
MA0159.1	MA0159.1	0.00324
MA0160.1	MA0160.1	0.0279
MA0162.1	MA0162.1	0.265
MA0163.1	MA0163.1	5.39927e-4
MA0164.1	MA0164.1	0.895
MA0258.1	MA0258.1	0.015
MA0259.1	MA0259.1	0.679

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: CNhs11200

Novel motif	Logo	P-value
1	1	0.276
10	10	0.0529
100	100	0.357
101	101	0.752
102	102	0.914
103	103	0.0717
104	104	0.948
105	105	0.581
106	106	0.0306
107	107	0.126
108	108	0.591
109	109	0.0181
11	11	0.121
110	110	0.0394
111	111	0.2
112	112	0.00867
113	113	0.526
114	114	0.459
115	115	0.782
116	116	0.25
117	117	0.00379
118	118	0.255
119	119	0.215
12	12	0.786
120	120	0.646
121	121	0.606
122	122	0.812
123	123	4.86989e-4
124	124	0.0428
125	125	0.215
126	126	0.0274
127	127	0.209
128	128	0.0282
129	129	0.298
13	13	6.21618e-7
130	130	0.182
131	131	0.507
132	132	0.67
133	133	0.537
134	134	0.204
135	135	0.14
136	136	0.27
137	137	0.627
138	138	0.853
139	139	0.261
14	14	0.741
140	140	0.0969
141	141	0.74
142	142	0.527
143	143	0.326
144	144	0.937
145	145	1.6809e-4
146	146	0.406
147	147	0.364
148	148	0.88
149	149	0.988
15	15	0.164
150	150	0.0792
151	151	0.984
152	152	0.156
153	153	0.852
154	154	0.789
155	155	0.475
156	156	0.00763
157	157	0.283
158	158	0.326
159	159	0.617
160	160	0.183
161	161	0.243
162	162	0.864
163	163	0.471
164	164	0.028
165	165	0.517
166	166	0.454
167	167	0.774
168	168	0.496
169	169	0.00356
17	17	0.0884
18	18	0.935
19	19	0.164
2	2	0.78
20	20	0.0271
21	21	0.178
22	22	0.207
23	23	0.7
24	24	0.098
25	25	0.718
26	26	3.73002e-10
27	27	0.45
28	28	0.846
29	29	0.0272
3	3	0.0935
30	30	0.906
31	31	0.758
32	32	0.533
33	33	0.179
34	34	0.818
35	35	0.884
36	36	0.163
37	37	0.066
38	38	0.49
39	39	0.415
4	4	0.237
40	40	0.153
41	41	0.442
42	42	0.217
43	43	0.126
44	44	0.494
45	45	0.716
46	46	0.0249
47	47	0.495
48	48	0.338
49	49	0.167
5	5	0.19
50	50	0.294
51	51	0.724
52	52	0.384
53	53	0.354
54	54	0.924
55	55	0.949
56	56	0.539
57	57	0.473
58	58	0.284
59	59	0.098
6	6	0.88
60	60	0.0383
61	61	0.0785
62	62	0.157
63	63	0.168
64	64	0.622
65	65	0.358
66	66	0.818
67	67	0.845
68	68	0.514
69	69	0.606
7	7	0.018
70	70	0.0922
71	71	0.00258
72	72	0.586
73	73	0.0826
74	74	0.906
75	75	0.0589
76	76	0.256
77	77	0.498
78	78	0.00266
79	79	0.167
8	8	0.0519
80	80	0.861
81	81	0.576
82	82	0.305
83	83	0.3
84	84	0.586
85	85	0.239
86	86	0.134
87	87	0.652
88	88	0.596
89	89	0.511
9	9	0.495
90	90	0.208
91	91	0.0585
92	92	0.279
93	93	0.14
94	94	0.779
95	95	0.12
96	96	0.479
97	97	0.893
98	98	0.452
99	99	0.465

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: CNhs11200

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011465 mouse medulla oblongata- neonate N30 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011465 (mouse medulla oblongata- neonate N30 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)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005654
+|accession_numbers=CAGE;DRX009047;DRR009921;DRZ001346;DRZ002729;DRZ012696;DRZ014079
 |ancestors_in_anatomy_facet=UBERON:0000468,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=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.44!308.62!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!2.18!277.44!Tsc22d4;;chr16:91225808..91225824,+!p1@Olig2!1.88!75.60!Olig2;;chr11:96143666..96143725,+!p1@Hoxb8!1.61!45.83!Hoxb8;;chr15:78994907..78994926,-!p1@Sox10!1.57!89.67!Sox10;;chr7:146768691..146768707,-!p1@Nkx6-2!1.57!35.98!Nkx6-2;;chrX:34442872..34442899,-!p1@Nkrf!1.56!45.13!Nkrf;;chr15:76353005..76353021,-!p2@Scrt1!1.54!33.52!Scrt1;;chr16:91270091..91270143,+!p2@Olig1!1.54!33.29!Olig1;;chr17:25707623..25707639,-!p1@Sox8!1.45!112.76!Sox8;;chr12:30219426..30219506,+!p2@Myt1l!1.44!26.72!Myt1l;;chr8:24780125..24780143,+!p1@Zmat4!1.41!35.16!Zmat4;;chr17:48015839..48015915,-!p3@Foxp4!1.41!28.72!Foxp4;;chr7:116154364..116154444,+!p1@Tub!1.40!40.67!Tub;;chr15:76352434..76352488,-!p4@Scrt1!1.40!23.91!Scrt1;;chr2:127347067..127347093,-!p1@Kcnip3!1.38!38.33!Kcnip3;;chr1:6477388..6477419,+!p3@St18!1.38!22.86!St18;;chr3:95032091..95032183,-!p1@Mllt11!1.37!184.26!Mllt11;;chr18:36441119..36441158,+!p2@Pura!1.36!52.39!Pura;;chr9:91260594..91260612,-!p1@Zic1!1.33!20.51!Zic1;;chr2:127347042..127347058,-!p3@Kcnip3!1.33!20.16!Kcnip3;;chr10:67375146..67375208,-!p2@Zfp365!1.32!30.01!Zfp365;;chr19:19185671..19185693,-!p1@Rorb!1.31!45.36!Rorb;;chr2:65683890..65683907,+!p1@Csrnp3!1.31!36.45!Csrnp3;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.29!23.56!Pou3f3;;chr15:76352677..76352737,-!p3@Scrt1!1.28!18.05!Scrt1;;chr4:150482563..150482655,-!p2@Camta1!1.27!62.59!Camta1;;chr7:148008023..148008092,-!p1@Zfp941!1.27!41.96!Zfp941;;chr9:91260616..91260653,-!p2@Zic1!1.26!17.00!Zic1;;chr11:96685444..96685473,-!p5@Nfe2l1!1.23!15.94!Nfe2l1;;chr2:168427068..168427115,-!p3@Nfatc2!1.22!15.59!Nfatc2;;chr4:58956447..58956510,+!p1@Zkscan16!1.21!33.05!Zkscan16;;chr7:38554763..38554780,-!p1@Zfp536!1.21!27.54!Zfp536;;chr14:34791937..34791977,-!p1@Zfp488!1.18!14.07!Zfp488;;chr10:84218895..84218909,+!p1@Rfx4!1.16!13.60!Rfx4;;chr19:10315179..10315241,-!p1@Gm98!1.13!129.40!Gm98;;chrX:34442842..34442866,-!p3@Nkrf!1.13!12.54!Nkrf;;chr12:54349410..54349461,+!p1@Npas3!1.11!14.30!Npas3;;chr10:67375368..67375433,-!p1@Zfp365!1.10!20.39!Zfp365;;chr6:52154414..52154462,-!p1@Hoxa5!1.10!15.94!Hoxa5;;chr10:84218800..84218829,+!p2@Rfx4!1.09!11.25!Rfx4;;chr1:189821714..189821761,+!p1@Esrrg!1.08!20.75!Esrrg;;chr15:103170533..103170556,-!p1@Zfp385a!1.06!39.38!Zfp385a;;chr13:72766250..72766273,+!p1@Irx2!1.05!16.06!Irx2;;chrX:137083127..137083138,-!p9@Tsc22d3!1.05!10.31!Tsc22d3;;chr8:112603658..112603674,+!p2@Zfp612!1.03!18.05!Zfp612;;chr5:122499831..122499891,-!p1@Cux2!1.03!15.00!Cux2;;chr16:91225654..91225671,+!p2@Olig2!1.03!9.61!Olig2;;chr2:162769220..162769252,+!p1@L3mbtl1!1.02!9.49!L3mbtl1;;chr2:163051181..163051205,+!p2@Tox2!1.02!9.38!Tox2;;chr3:95032515..95032553,-!p5@Mllt11!1.01!11.14!Mllt11;;chr8:107793688..107793736,+!p1@Hsf4!1.00!11.96!Hsf4;;chr3:95032213..95032226,-!p6@Mllt11!1.00!10.78!Mllt11;;chr11:96143962..96144035,+!p2@Hoxb8!1.00!9.03!Hoxb8;;chr4:150513630..150513686,-!p4@Camta1!0.99!10.20!Camta1;;chr6:145814003..145814056,-!p1@Bhlhe41!0.98!25.32!Bhlhe41;;chr2:65768174..65768247,+!p2@Csrnp3!0.97!8.44!Csrnp3;;chr11:98190918..98190951,-!p1@Neurod2!0.97!8.32!Neurod2;;chr11:96160360..96160397,+!p3@Hoxb6!0.96!8.20!Hoxb6;;chr15:102865088..102865107,+!p1@Hoxc4!0.95!10.67!Hoxc4;;chr15:102865048..102865073,+!p3@Hoxc4!0.95!10.08!Hoxc4;;chr7:122968213..122968266,-!p4@Sox6!0.95!9.38!Sox6;;chr11:96164821..96164865,+!p1@Hoxb5!0.95!7.85!Hoxb5;;chr14:122874619..122874634,+!p1@Zic2!0.95!7.85!Zic2;;chr3:34548946..34548972,+!p2@Sox2!0.94!8.67!Sox2;;chr2:163030219..163030258,+!p5@Tox2!0.94!7.74!Tox2;;chr2:163030186..163030204,+!p4@Tox2!0.94!7.74!Tox2;;chr3:34548909..34548927,+!p1@Sox2!0.93!13.01!Sox2;;chr2:25562263..25562314,+!p2@Bmyc!0.92!29.54!Bmyc;;chr2:127347094..127347111,-!p2@Kcnip3!0.92!12.31!Kcnip3;;chr7:91558392..91558434,-!p1@Arnt2!0.91!20.51!Arnt2;;chr8:87297878..87297935,-!p3@Nfix!0.91!16.41!Nfix;;chr14:104867201..104867258,-!p1@Pou4f1!0.90!9.85!Pou4f1;;chr12:30213247..30213333,+!p1@Myt1l!0.90!6.92!Myt1l;;chr3:95032558..95032641,-!p2@Mllt11!0.89!39.15!Mllt11;;chr12:72149325..72149343,+!p2@Arid4a!0.89!9.61!Arid4a;;chr2:115890294..115890334,-!p9@Meis2!0.89!9.49!Meis2;;chr2:81893535..81893548,+!p1@Zfp804a!0.89!6.68!Zfp804a;;chr10:80893711..80893784,-!p3@Nfic!0.88!35.75!Nfic;;chr3:95032197..95032208,-!p3@Mllt11!0.88!8.44!Mllt11;;chr3:95032184..95032195,-!p4@Mllt11!0.88!8.32!Mllt11;;chr6:145813905..145813932,-!p2@Bhlhe41!0.87!12.66!Bhlhe41;;chr15:103170516..103170531,-!p2@Zfp385a!0.86!15.47!Zfp385a;;chr2:77654815..77654872,-!p2@Zfp385b!0.84!7.50!Zfp385b;;chr12:3806003..3806031,+!p11@Dnmt3a!0.84!5.86!Dnmt3a;;chr6:52161666..52161711,-!p1@Hoxa6!0.84!5.86!Hoxa6;;chr4:150482353..150482386,-!p6@Camta1!0.83!5.74!Camta1;;chr11:96685487..96685512,-!p7@Nfe2l1!0.83!5.74!Nfe2l1;;chrX:137077151..137077227,-!p2@Tsc22d3!0.82!42.31!Tsc22d3;;chr2:151907546..151907561,+!p1@Scrt2!0.82!5.63!Scrt2;;chr6:117813087..117813121,+!p1@Zfp239!0.81!22.04!Zfp239;;chrX:108009761..108009788,+!p1@Pou3f4!0.81!5.51!Pou3f4;;chr2:79296783..79296801,-!p1@Neurod1!0.81!5.39!Neurod1;;chr8:112603610..112603656,+!p1@Zfp612!0.80!26.26!Zfp612;;chr9:106356278..106356292,+!p3@Pcbp4!0.80!9.61!Pcbp4;;chr15:103170561..103170572,-!p4@Zfp385a!0.80!7.97!Zfp385a;;chr14:52935860..52935874,-!p3@Sall2!0.80!7.85!Sall2;;chr2:181501745..181501778,+!p1@Myt1!0.80!5.27!Myt1;;chr14:19071466..19071550,-!p1@Nr1d2!0.79!38.68!Nr1d2;;chr6:134780163..134780197,+!p2@Crebl2!0.79!12.89!Crebl2;;chr11:116196664..116196679,-!p1@Foxj1!0.79!8.32!Foxj1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.78!57.20!Camta2;;chr10:67375342..67375365,-!p3@Zfp365!0.78!5.04!Zfp365;;chr3:101814061..101814094,+!p1@Nhlh2!0.78!5.04!Nhlh2;;chr8:12395603..12395621,+!p1@Sox1!0.77!4.92!Sox1;;chr13:72766279..72766296,+!p2@Irx2!0.76!7.38!Irx2;;chr7:38558544..38558566,-!p4@Zfp536!0.76!5.63!Zfp536;;chr7:91558472..91558512,-!p2@Arnt2!0.75!6.92!Arnt2;;chr7:38558574..38558611,-!p2@Zfp536!0.75!5.98!Zfp536;;chr13:44936126..44936164,+!p6@Jarid2!0.75!5.51!Jarid2;;chr6:55631042..55631102,-!p1@Neurod6!0.75!4.57!Neurod6;;chr17:27693525..27693538,+!p5@Hmga1!0.74!16.64!Hmga1;;chr7:130644017..130644092,-!p1@Zkscan2!0.73!9.03!Zkscan2;;chr15:102865131..102865151,+!p2@Hoxc4!0.73!5.04!Hoxc4;;chr9:106362954..106362977,+!p6@Pcbp4!0.73!4.34!Pcbp4;;chr11:90252223..90252240,-!p1@Hlf!0.72!39.15!Hlf;;chr6:145813964..145813994,-!p3@Bhlhe41!0.72!5.63!Bhlhe41;;chr2:168427120..168427138,-!p4@Nfatc2!0.72!4.22!Nfatc2;;chr3:54559496..54559511,+!p1@Smad9!0.71!9.85!Smad9;;chr5:125342568..125342602,+!p2@Zfp664!0.71!7.27!Zfp664;;chr2:77541432..77541474,-!p5@Zfp385b!0.71!4.10!Zfp385b;;chr8:125897750..125897758,+!p2@Tcf25!0.69!29.65!Tcf25;;chr10:67375223..67375240,-!p4@Zfp365!0.69!4.45!Zfp365;;chr15:10400245..10400282,-!p2@Dnajc21!0.68!14.30!Dnajc21;;chr9:68501522..68501538,+!p4@Rora!0.68!7.62!Rora;;chr11:96143843..96143868,+!p3@Hoxb8!0.68!3.75!Hoxb8;;chr4:22415443..22415506,-!p1@Pou3f2!0.68!3.75!Pou3f2;;chr2:74565247..74565258,+!p3@Hoxd4!0.68!3.75!Hoxd4;;chr3:34549096..34549111,+!p3@Sox2!0.68!3.75!Sox2;;chr19:26681865..26681900,+!p6@Smarca2!0.67!11.96!Smarca2;;chr8:125778192..125778217,+!p2@Zfp276!0.67!11.49!Zfp276;;chr4:154335024..154335039,+!p1@Hes5!0.67!4.57!Hes5;;chrX:55283799..55283813,+!p1@Zic3!0.67!3.63!Zic3;;chr2:181501710..181501742,+!p2@Myt1!0.67!3.63!Myt1;;chr2:65768149..65768173,+!p4@Csrnp3!0.67!3.63!Csrnp3;;chr18:36441165..36441172,+!p6@Pura!0.67!3.63!Pura;;chr11:84339016..84339044,-!p1@Lhx1!0.67!3.63!Lhx1;;chr7:17200307..17200370,-!p2@Grlf1!0.66!30.24!Grlf1;;chr6:52154386..52154407,-!p2@Hoxa5!0.66!4.69!Hoxa5;;chr18:36441100..36441113,+!p3@Pura!0.66!4.22!Pura;;chr8:107793737..107793757,+!p2@Hsf4!0.66!4.22!Hsf4;;chr11:98636531..98636559,-!p1@Nr1d1!0.65!22.86!Nr1d1;;chr16:91269972..91269978,+!p3@Olig1!0.65!3.52!Olig1;;chr3:54559463..54559493,+!p3@Smad9!0.64!6.80!Smad9;;chr10:62328047..62328076,-!p3@Tet1!0.64!5.39!Tet1;;chr12:87762578..87762612,+!p1@Esrrb!0.64!3.40!Esrrb;;chr9:20385868..20385902,+!p3@Zfp846!0.63!5.04!Zfp846;;chr4:124334894..124334899,+!p1@Pou3f1!0.63!4.45!Pou3f1;;chr2:74583776..74583815,+!p3@Hoxd3!0.63!3.28!Hoxd3;;chr5:67490284..67490302,-!p1@Phox2b!0.63!3.28!Phox2b;;chr5:122500142..122500167,-!p2@Cux2!0.62!7.50!Cux2;;chr8:79423672..79423727,+!p2@Nr3c2!0.62!4.22!Nr3c2;;chr7:17062114..17062141,-!p1@Npas1!0.62!3.16!Npas1;;chr3:32264565..32264613,-!p1@Zmat3!0.61!40.67!Zmat3;;chr10:30522690..30522752,-!p2@Ncoa7!0.61!21.92!Ncoa7;;chr11:90252108..90252134,-!p6@Hlf!0.61!3.05!Hlf;;chr11:90252071..90252093,-!p7@Hlf!0.61!3.05!Hlf;;chr11:96143728..96143745,+!p4@Hoxb8!0.61!3.05!Hoxb8;;chr13:44936077..44936096,+!p9@Jarid2!0.61!3.05!Jarid2;;chr15:76352832..76352900,-!p1@Scrt1!0.61!3.05!Scrt1;;chr8:91568074..91568094,-!p1@Sall1!0.61!3.05!Sall1;;chr12:100631220..100631300,-!p2@Foxn3!0.60!32.23!Foxn3;;chrX:66613481..66613562,+!p1@Aff2!0.60!15.12!Aff2;;chr7:30092993..30093076,+!p1@Dpf1!0.60!5.63!Dpf1;;chr18:36440723..36440805,+!p1@Pura!0.59!57.20!Pura;;chr9:106356243..106356264,+!p2@Pcbp4!0.59!14.77!Pcbp4;;chr4:149611311..149611317,+!p2@Eno1!0.59!9.96!Eno1;;chr13:64253718..64253763,-!p2@Zfp367!0.59!8.56!Zfp367;;chr5:3648045..3648074,-!p2@Gatad1!0.59!5.27!Gatad1;;chr19:23215554..23215567,+!p5@Klf9!0.59!4.22!Klf9;;chr7:38557887..38557910,-!p5@Zfp536!0.59!2.93!Zfp536;;chr12:30220074..30220102,+!p3@Myt1l!0.59!2.93!Myt1l;;chr2:163030164..163030178,+!p6@Tox2!0.59!2.93!Tox2;;chr17:48015645..48015689,-!p9@Foxp4!0.58!3.87!Foxp4;;chr15:95485240..95485257,-!p1@Dbx2!0.58!2.81!Dbx2;;chr1:6477452..6477459,+!p8@St18!0.58!2.81!St18;;chr2:151907338..151907360,+!p2@Scrt2!0.58!2.81!Scrt2;;chr11:96160426..96160443,+!p2@Hoxb6!0.58!2.81!Hoxb6;;chr12:57714257..57714278,-!p1@Nkx2-9!0.58!2.81!Nkx2-9;;chr4:151235807..151235870,-!p1@Camta1!0.57!54.03!Camta1;;chr11:98636575..98636607,-!p2@Nr1d1!0.57!11.96!Nr1d1;;chrX:108810678..108810736,-!p1@Hdx!0.57!11.14!Hdx;;chr16:43363968..43364001,+!p7@Zbtb20!0.57!5.51!Zbtb20;;chr13:72101178..72101203,-!p1@Irx1!0.57!4.57!Irx1;;chr6:72850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chr11:98789099..98789124,+!p3@Rara!0.19!3.63!Rara;;chr5:147760339..147760350,+!p3@Gtf3a!0.19!3.28!Gtf3a;;chr1:172797934..172797945,-!p4@Atf6!0.19!3.28!Atf6;;chr10:82226613..82226641,-!p4@Nfyb!0.19!3.05!Nfyb;;chr7:13063643..13063662,+!p2@Zfp606!0.19!2.81!Zfp606;;chr6:92042363..92042413,+!p3@Nr2c2!0.19!2.58!Nr2c2;;chr16:55973899..55973913,+!p7@Rpl24,p7@Zbtb11!0.19!2.46!Zbtb11;;chr17:27693818..27693830,+!p7@Hmga1-rs1,p8@Hmga1!0.19!2.34!Hmga1;;chr1:64167811..64167826,-!p5@Klf7!0.19!2.23!Klf7;;chr16:43619057..43619078,+!p8@Zbtb20!0.19!2.11!Zbtb20;;chr8:4613211..4613224,+!p3@Zfp958!0.19!2.11!Zfp958;;chr11:18918982..18918993,-!p5@Meis1!0.19!2.11!Meis1;;chr6:38204274..38204327,-!p3@D630045J12Rik!0.19!1.99!D630045J12Rik;;chr2:34227524..34227547,-!p2@Pbx3!0.19!1.88!Pbx3;;chr14:65568567..65568588,-!p3@Hmbox1!0.19!1.29!Hmbox1;;chr6:53523332..53523343,+!p2@Creb5!0.19!1.17!Creb5;;chr18:65741911..65741929,+!p3@Zfp532!0.19!1.05!Zfp532;;chr1:140739014..140739032,-!p1@Lhx9!0.19!0.94!Lhx9;;chr10:5636374..5636421,-!p1@Esr1!0.19!0.94!Esr1;;chr11:100800901..100800921,-!p4@Stat3!0.19!0.82!Stat3;;chr9:72122748..72122757,+!p4@Zfp280d!0.19!0.82!Zfp280d;;chr5:125659525..125659599,-!p1@Ncor2!0.18!84.28!Ncor2;;chr3:54611692..54611726,-!p1@Rfxap!0.18!30.83!Rfxap;;chr3:103772250..103772317,+!p1@Phtf1!0.18!26.49!Phtf1;;chrX:98728131..98728214,+!p1@Taf1!0.18!18.99!Taf1;;chr5:142939972..142940026,+!p1@C330006K01Rik!0.18!17.58!C330006K01Rik;;chr15:57908011..57908070,-!p2@Zhx1,p3@9130401M01Rik!0.18!11.96!Zhx1;;chr5:137043177..137043190,-!p2@Cux1!0.18!10.67!Cux1;;chr5:36826883..36826951,-!p1@Tada2b!0.18!9.61!Tada2b;;chr1:38684260..38684312,-!p2@Aff3!0.18!9.03!Aff3;;chr19:12870598..12870636,-!p1@U05342,p1@Zfp91!0.18!6.21!Zfp91;;chr4:126698529..126698536,+!p2@Sfpq!0.18!5.51!Sfpq;;chr11:50872733..50872809,+!p1@Zfp354a!0.18!5.51!Zfp354a;;chr13:42147211..42147244,+!p2@Hivep1!0.18!3.75!Hivep1;;chr6:92041399..92041417,+!p2@Nr2c2!0.18!3.75!Nr2c2;;chr5:65194853..65194866,+!p5@Klf3!0.18!3.16!Klf3;;chr19:53384965..53384984,+!p4@Mxi1!0.18!3.16!Mxi1;;chr18:65741935..65741964,+!p2@Zfp532!0.18!2.93!Zfp532;;chr8:83262929..83262957,-!p1@Smarca5!0.18!2.93!Smarca5;;chr15:81575602..81575618,+!p3@Zc3h7b!0.18!2.81!Zc3h7b;;chr11:59285966..59285990,-!p2@Zfp867!0.18!2.70!Zfp867;;chr11:18918820..18918831,-!p4@Meis1!0.18!1.76!Meis1;;chr10:67599375..67599386,-!p3@Arid5b!0.18!1.64!Arid5b;;chr3:54611738..54611749,-!p3@Rfxap!0.18!1.64!Rfxap;;chr7:13404215..13404220,-!p2@Zfp329!0.18!1.52!Zfp329;;chr6:47785785..47785796,+!p4@Zfp398!0.18!1.29!Zfp398;;chr7:6238175..6238186,+!p2@Zfp667!0.18!1.29!Zfp667;;chr10:80600725..80600737,+!p9@Zbtb7a!0.18!1.29!Zbtb7a;;chrX:45245621..45245632,-!p3@Smarca1!0.18!1.05!Smarca1;;chr10:13685657..13685677,+!p7@Hivep2!0.18!0.94!Hivep2;;chr18:14131020..14131033,-!p4@Zfp521!0.18!0.94!Zfp521;;chr9:48644284..48644305,-!p4@Zbtb16!0.18!0.94!Zbtb16;;chr11:101646155..101646170,-!p3@Etv4!0.18!0.82!Etv4;;chr2:115888250..115888298,-!p10@Meis2!0.18!0.82!Meis2;;chr15:57527217..57527240,+!p6@Zhx2!0.18!0.82!Zhx2;;chr13:21454766..21454791,+!p3@Zscan12!0.18!0.70!Zscan12;;chr13:40829137..40829205,-!p1@Tfap2a!0.18!0.70!Tfap2a;;chr9:111020710..111020721,+!p2@Lrrfip2!0.18!0.70!Lrrfip2;;chr11:23978229..23978268,+!p8@Bcl11a!0.18!0.70!Bcl11a;;chr5:9161692..9161762,-!p1@Dmtf1!0.17!57.32!Dmtf1;;chr11:112643496..112643562,+!p1@Sox9!0.17!49.70!Sox9;;chr9:122775056..122775117,-!p1@Zfp445!0.17!44.77!Zfp445;;chr9:20297167..20297209,-!p1@Zfp426!0.17!31.30!Zfp426;;chrX:20527671..20527719,-!p1@Elk1!0.17!29.89!Elk1;;chrX:98449492..98449510,+!p1@Foxo4!0.17!13.48!Foxo4;;chr7:11080671..11080750,-!p1@Zik1!0.17!8.56!Zik1;;chr2:48805015..48805042,+!p2@Mbd5!0.17!7.38!Mbd5;;chr2:130120884..130120972,+!p1@Ebf4!0.17!7.15!Ebf4;;chr16:22439654..22439676,-!p2@Etv5!0.17!7.15!Etv5;;chr18:24178808..24178865,-!p2@Zfp191!0.17!6.56!Zfp191;;chr13:67585161..67585205,-!p1@Zfp874b!0.17!6.21!Zfp874b;;chr2:119698528..119698571,+!p3@Mga!0.17!3.99!Mga;;chr19:9016975..9017004,+!p2@Mta2!0.17!3.28!Mta2;;chr1:172797920..172797931,-!p3@Atf6!0.17!3.28!Atf6;;
+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011465
 |is_obsolete=
+|library_id=CNhs11200
+|library_id_phase_based=2:CNhs11200
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1396
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1396
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520neonate%2520N30.CNhs11200.1396-42A3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520neonate%2520N30.CNhs11200.1396-42A3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520neonate%2520N30.CNhs11200.1396-42A3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520neonate%2520N30.CNhs11200.1396-42A3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520neonate%2520N30.CNhs11200.1396-42A3.mm9.nobarcode.rdna.fa.gz
 |name=medulla oblongata, neonate N30
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11200,LSID747,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0386002970469516,0,0,0,0,0,0.143636305467745,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.0610339025606856,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.327139264661615,0,0,0,0,0.0481354699899057,-0.0101927188676489,0.166976485593938,-0.106658713382387,0.445601980671584,0.846500102524017,0,0,0.0914641362800683,0,0,0,0,0,0,0,0,0.0481354699899057,-0.0178700775735347,0,0,0,0,0,0,0,0,0.0481354699899057,0.0364001795194968,0.0123218781949209,-0.0504643143771036,0.596904235625436,0.170089832423677,0,0,0.162812678487456,0.1163826621023,0.0914641362800683,0,0.107935799463628,0.0733169633541559,-0.174152463286075,-0.0306961248500017,0,0,0,0,0,0,0,0.0639452229794855,0.0550344850534889,0.019573061087374,0,0.643367675867246,0,0
 |rna_box=42
 |rna_catalog_number=
@@ Line 60: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 80: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:1396-42A3;search_select_hide=table117:1396-42A3
 }}

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FF:1396-42A3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11200

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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