FF:24-13C9: Difference between revisions

Latest revision as of 19:09, 4 June 2020

Name:	spinal cord, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10505
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	spinal cord
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		SAMD00005286

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10505		CAGE		DRX009083		DRR009957

Accession ID Mm9

Library id		BAM		CTSS
CNhs10505		DRZ001382		DRZ002765

Accession ID Mm10

Library id		BAM		CTSS
CNhs10505		DRZ012732		DRZ014115

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

CNhs10505

0	0
1	0.726
10	0
100	0
1000	0.117
1001	0.179
1002	-0.00984
1003	0.171
1004	0
1005	0.035
1006	0.587
1007	-0.0769
1008	0
1009	-0.0676
101	-0.0779
1010	0
1011	0.403
1012	0.19
1013	0.292
1014	-0.0851
1015	-0.116
1016	-0.138
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	0.268
1023	0
1024	0.195
1025	0
1026	0.0644
1027	0.578
1028	0
1029	0.0932
103	-0.0736
1030	0
1031	-0.306
1032	0.438
1033	-0.0665
1034	0
1035	0.137
1036	-0.258
1037	0
1038	-0.0134
1039	0.113
104	0
1040	-0.142
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: CNhs10505

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00197
MA0003.1	MA0003.1	0.369
MA0004.1	MA0004.1	0.408
MA0006.1	MA0006.1	0.283
MA0007.1	MA0007.1	0.234
MA0009.1	MA0009.1	0.708
MA0014.1	MA0014.1	0.911
MA0017.1	MA0017.1	2.46035e-6
MA0018.2	MA0018.2	0.0136
MA0019.1	MA0019.1	0.811
MA0024.1	MA0024.1	0.0672
MA0025.1	MA0025.1	0.00143
MA0027.1	MA0027.1	0.137
MA0028.1	MA0028.1	0.0721
MA0029.1	MA0029.1	0.984
MA0030.1	MA0030.1	0.598
MA0031.1	MA0031.1	0.472
MA0035.2	MA0035.2	0.0193
MA0038.1	MA0038.1	0.242
MA0039.2	MA0039.2	0.078
MA0040.1	MA0040.1	0.56
MA0041.1	MA0041.1	0.0875
MA0042.1	MA0042.1	0.29
MA0043.1	MA0043.1	0.0664
MA0046.1	MA0046.1	5.04426e-11
MA0047.2	MA0047.2	1.60614e-4
MA0048.1	MA0048.1	0.0273
MA0050.1	MA0050.1	6.03212e-4
MA0051.1	MA0051.1	0.0044
MA0052.1	MA0052.1	0.608
MA0055.1	MA0055.1	0.0066
MA0057.1	MA0057.1	0.27
MA0058.1	MA0058.1	0.501
MA0059.1	MA0059.1	0.104
MA0060.1	MA0060.1	0.348
MA0061.1	MA0061.1	0.024
MA0062.2	MA0062.2	0.00145
MA0065.2	MA0065.2	3.1389e-6
MA0066.1	MA0066.1	0.0189
MA0067.1	MA0067.1	0.271
MA0068.1	MA0068.1	0.457
MA0069.1	MA0069.1	0.136
MA0070.1	MA0070.1	0.207
MA0071.1	MA0071.1	0.0906
MA0072.1	MA0072.1	0.602
MA0073.1	MA0073.1	0.821
MA0074.1	MA0074.1	0.0612
MA0076.1	MA0076.1	0.176
MA0077.1	MA0077.1	0.17
MA0078.1	MA0078.1	0.681
MA0079.2	MA0079.2	0.198
MA0080.2	MA0080.2	3.51035e-9
MA0081.1	MA0081.1	0.268
MA0083.1	MA0083.1	0.0685
MA0084.1	MA0084.1	0.591
MA0087.1	MA0087.1	0.0672
MA0088.1	MA0088.1	0.359
MA0090.1	MA0090.1	0.0774
MA0091.1	MA0091.1	0.192
MA0092.1	MA0092.1	0.168
MA0093.1	MA0093.1	0.509
MA0099.2	MA0099.2	0.0233
MA0100.1	MA0100.1	0.124
MA0101.1	MA0101.1	0.0113
MA0102.2	MA0102.2	0.544
MA0103.1	MA0103.1	0.102
MA0104.2	MA0104.2	0.579
MA0105.1	MA0105.1	0.00119
MA0106.1	MA0106.1	0.0535
MA0107.1	MA0107.1	0.0345
MA0108.2	MA0108.2	0.0129
MA0111.1	MA0111.1	0.875
MA0112.2	MA0112.2	0.00175
MA0113.1	MA0113.1	0.377
MA0114.1	MA0114.1	3.86651e-6
MA0115.1	MA0115.1	5.44215e-5
MA0116.1	MA0116.1	0.0422
MA0117.1	MA0117.1	0.897
MA0119.1	MA0119.1	0.132
MA0122.1	MA0122.1	0.873
MA0124.1	MA0124.1	0.358
MA0125.1	MA0125.1	0.028
MA0131.1	MA0131.1	0.736
MA0135.1	MA0135.1	0.247
MA0136.1	MA0136.1	1.7104e-11
MA0137.2	MA0137.2	0.534
MA0138.2	MA0138.2	8.39219e-5
MA0139.1	MA0139.1	0.553
MA0140.1	MA0140.1	4.80814e-5
MA0141.1	MA0141.1	0.00981
MA0142.1	MA0142.1	0.375
MA0143.1	MA0143.1	0.912
MA0144.1	MA0144.1	0.153
MA0145.1	MA0145.1	0.276
MA0146.1	MA0146.1	0.0411
MA0147.1	MA0147.1	0.394
MA0148.1	MA0148.1	7.90758e-4
MA0149.1	MA0149.1	0.162
MA0150.1	MA0150.1	0.372
MA0152.1	MA0152.1	0.264
MA0153.1	MA0153.1	7.49996e-12
MA0154.1	MA0154.1	0.035
MA0155.1	MA0155.1	0.574
MA0156.1	MA0156.1	5.03258e-7
MA0157.1	MA0157.1	0.293
MA0159.1	MA0159.1	0.00486
MA0160.1	MA0160.1	0.0259
MA0162.1	MA0162.1	0.285
MA0163.1	MA0163.1	3.1194e-4
MA0164.1	MA0164.1	0.862
MA0258.1	MA0258.1	0.0272
MA0259.1	MA0259.1	0.602

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: CNhs10505

Novel motif	Logo	P-value
1	1	0.304
10	10	0.0421
100	100	0.271
101	101	0.913
102	102	0.9
103	103	0.111
104	104	0.983
105	105	0.632
106	106	0.0434
107	107	0.127
108	108	0.606
109	109	0.0142
11	11	0.119
110	110	0.0403
111	111	0.196
112	112	0.00771
113	113	0.462
114	114	0.492
115	115	0.683
116	116	0.266
117	117	0.00292
118	118	0.199
119	119	0.186
12	12	0.749
120	120	0.889
121	121	0.76
122	122	0.954
123	123	7.07387e-5
124	124	0.0229
125	125	0.0785
126	126	0.0232
127	127	0.386
128	128	0.0253
129	129	0.467
13	13	3.27406e-7
130	130	0.202
131	131	0.426
132	132	0.77
133	133	0.543
134	134	0.143
135	135	0.0674
136	136	0.138
137	137	0.781
138	138	0.988
139	139	0.432
14	14	0.585
140	140	0.113
141	141	0.879
142	142	0.424
143	143	0.244
144	144	0.798
145	145	8.32693e-5
146	146	0.502
147	147	0.498
148	148	0.998
149	149	0.749
15	15	0.166
150	150	0.0793
151	151	0.916
152	152	0.175
153	153	0.864
154	154	0.776
155	155	0.48
156	156	0.0343
157	157	0.344
158	158	0.33
159	159	0.739
160	160	0.188
161	161	0.213
162	162	0.742
163	163	0.624
164	164	0.0206
165	165	0.515
166	166	0.678
167	167	0.989
168	168	0.743
169	169	0.00583
17	17	0.106
18	18	0.913
19	19	0.226
2	2	0.604
20	20	0.0134
21	21	0.183
22	22	0.238
23	23	0.815
24	24	0.0672
25	25	0.813
26	26	5.29694e-11
27	27	0.316
28	28	0.831
29	29	0.0225
3	3	0.12
30	30	0.832
31	31	0.716
32	32	0.63
33	33	0.145
34	34	0.904
35	35	1
36	36	0.122
37	37	0.0684
38	38	0.476
39	39	0.503
4	4	0.263
40	40	0.138
41	41	0.46
42	42	0.235
43	43	0.15
44	44	0.506
45	45	0.804
46	46	0.0254
47	47	0.641
48	48	0.41
49	49	0.136
5	5	0.237
50	50	0.28
51	51	0.721
52	52	0.434
53	53	0.3
54	54	0.874
55	55	0.989
56	56	0.565
57	57	0.48
58	58	0.337
59	59	0.156
6	6	0.867
60	60	0.0508
61	61	0.0831
62	62	0.229
63	63	0.195
64	64	0.632
65	65	0.387
66	66	0.803
67	67	0.967
68	68	0.355
69	69	0.577
7	7	0.0239
70	70	0.0746
71	71	0.00224
72	72	0.667
73	73	0.0682
74	74	0.811
75	75	0.0437
76	76	0.204
77	77	0.571
78	78	0.00334
79	79	0.1
8	8	0.0599
80	80	0.664
81	81	0.494
82	82	0.403
83	83	0.528
84	84	0.837
85	85	0.225
86	86	0.145
87	87	0.502
88	88	0.63
89	89	0.489
9	9	0.584
90	90	0.0621
91	91	0.0457
92	92	0.309
93	93	0.167
94	94	0.454
95	95	0.0803
96	96	0.513
97	97	0.895
98	98	0.687
99	99	0.54

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: CNhs10505

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011305 mouse spinal cord- 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)
0002240 (spinal cord)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001137 (dorsum)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011305 (mouse spinal cord- 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:0006241 (future spinal cord)
UBERON:0003057 (chordal neural plate)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0002240,UBERON:0002100,UBERON:0000483,UBERON:0000479,UBERON:0002346,UBERON:0000073,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0003103,UBERON:0005291,UBERON:0005174,UBERON:0000489,UBERON:0005177,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0000924,UBERON:0005743,UBERON:0001137,UBERON:0003075,UBERON:0001049,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003076,UBERON:0007284,UBERON:0003057,UBERON:0007135
+|DRA_sample_Accession=CAGE@SAMD00005286
+|accession_numbers=CAGE;DRX009083;DRR009957;DRZ001382;DRZ002765;DRZ012732;DRZ014115
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0002240,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0000489,UBERON:0005174,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001137
 |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:0011305
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr16:91270004..91270023,+!p1@Olig1!2.51!368.07!Olig1;;chr11:96143666..96143725,+!p1@Hoxb8!2.29!223.25!Hoxb8;;chr5:138199361..138199441,+!p2@Tsc22d4!2.14!251.81!Tsc22d4;;chr16:91225808..91225824,+!p1@Olig2!1.83!66.01!Olig2;;chr11:96143962..96144035,+!p2@Hoxb8!1.74!53.59!Hoxb8;;chrX:34442872..34442899,-!p1@Nkrf!1.63!53.40!Nkrf;;chr15:78994907..78994926,-!p1@Sox10!1.58!92.71!Sox10;;chr15:76353005..76353021,-!p2@Scrt1!1.55!34.67!Scrt1;;chr1:6477388..6477419,+!p3@St18!1.53!33.19!St18;;chr17:25707623..25707639,-!p1@Sox8!1.52!132.02!Sox8;;chr7:146768691..146768707,-!p1@Nkx6-2!1.52!32.26!Nkx6-2;;chr15:76352434..76352488,-!p4@Scrt1!1.49!30.04!Scrt1;;chr2:127347067..127347093,-!p1@Kcnip3!1.47!47.10!Kcnip3;;chr17:48015839..48015915,-!p3@Foxp4!1.44!30.97!Foxp4;;chr10:84218895..84218909,+!p1@Rfx4!1.41!24.48!Rfx4;;chr3:95032091..95032183,-!p1@Mllt11!1.40!200.82!Mllt11;;chr2:127347042..127347058,-!p3@Kcnip3!1.40!23.92!Kcnip3;;chr12:30219426..30219506,+!p2@Myt1l!1.38!22.81!Myt1l;;chr6:52176164..52176195,-!p1@Hoxa9!1.37!27.81!Hoxa9;;chr16:91270091..91270143,+!p2@Olig1!1.36!22.07!Olig1;;chr18:36441119..36441158,+!p2@Pura!1.35!51.36!Pura;;chr11:96160360..96160397,+!p3@Hoxb6!1.35!21.51!Hoxb6;;chr19:19185671..19185693,-!p1@Rorb!1.34!48.95!Rorb;;chr11:96685444..96685473,-!p5@Nfe2l1!1.31!19.28!Nfe2l1;;chr15:102828658..102828678,+!p1@Hoxc6!1.31!19.28!Hoxc6;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.30!23.92!Pou3f3;;chr15:76352677..76352737,-!p3@Scrt1!1.30!18.73!Scrt1;;chr7:116154364..116154444,+!p1@Tub!1.29!31.34!Tub;;chr2:74542918..74542971,+!p1@Hoxd8!1.29!27.81!Hoxd8;;chr6:52167459..52167492,-!p1@Hoxa7!1.28!21.69!Hoxa7;;chr12:54349410..54349461,+!p1@Npas3!1.27!21.32!Npas3;;chr11:96143728..96143745,+!p4@Hoxb8!1.27!17.80!Hoxb8;;chr11:96143843..96143868,+!p3@Hoxb8!1.27!17.43!Hoxb8;;chr19:10315179..10315241,-!p1@Gm98!1.26!174.11!Gm98;;chr8:107793688..107793736,+!p1@Hsf4!1.26!22.25!Hsf4;;chr11:96145450..96145517,+!p2@Hoxb7!1.25!24.85!Hoxb7;;chr2:168427068..168427115,-!p3@Nfatc2!1.24!16.50!Nfatc2;;chr2:65683890..65683907,+!p1@Csrnp3!1.23!30.60!Csrnp3;;chr15:102820964..102821006,+!p1@Hoxc8!1.23!16.13!Hoxc8;;chr4:150482563..150482655,-!p2@Camta1!1.22!54.70!Camta1;;chr8:24780125..24780143,+!p1@Zmat4!1.22!22.62!Zmat4;;chr6:52190467..52190500,-!p1@Hoxa10!1.20!14.83!Hoxa10;;chr4:58956447..58956510,+!p1@Zkscan16!1.19!31.34!Zkscan16;;chr10:67375146..67375208,-!p2@Zfp365!1.19!21.88!Zfp365;;chr2:163030219..163030258,+!p5@Tox2!1.19!14.46!Tox2;;chr8:87297878..87297935,-!p3@Nfix!1.15!29.30!Nfix;;chr9:91260594..91260612,-!p1@Zic1!1.15!13.17!Zic1;;chrX:34442842..34442866,-!p3@Nkrf!1.14!12.79!Nkrf;;chr6:145814003..145814056,-!p1@Bhlhe41!1.13!35.79!Bhlhe41;;chr9:91260616..91260653,-!p2@Zic1!1.13!12.61!Zic1;;chr7:148008023..148008092,-!p1@Zfp941!1.12!29.67!Zfp941;;chr3:34548946..34548972,+!p2@Sox2!1.12!13.54!Sox2;;chr3:95032515..95032553,-!p5@Mllt11!1.10!13.91!Mllt11;;chrX:137083127..137083138,-!p9@Tsc22d3!1.10!11.68!Tsc22d3;;chr6:52161666..52161711,-!p1@Hoxa6!1.09!11.31!Hoxa6;;chr2:74550015..74550057,+!p2@Hoxd3!1.09!11.31!Hoxd3;;chr15:102821007..102821021,+!p2@Hoxc8!1.08!11.13!Hoxc8;;chr6:52167434..52167450,-!p3@Hoxa7!1.08!10.94!Hoxa7;;chr10:80893711..80893784,-!p3@Nfic!1.04!53.03!Nfic;;chr2:25562263..25562314,+!p2@Bmyc!1.04!39.31!Bmyc;;chr15:103170533..103170556,-!p1@Zfp385a!1.03!36.90!Zfp385a;;chr7:38554763..38554780,-!p1@Zfp536!1.03!17.99!Zfp536;;chr3:34548909..34548927,+!p1@Sox2!1.03!16.69!Sox2;;chr3:95032197..95032208,-!p3@Mllt11!1.02!11.87!Mllt11;;chr11:96147952..96147967,+!p1@Hoxb7!1.02!11.87!Hoxb7;;chr2:163051181..163051205,+!p2@Tox2!1.02!9.46!Tox2;;chr16:91225654..91225671,+!p2@Olig2!1.02!9.46!Olig2;;chr3:95032213..95032226,-!p6@Mllt11!1.01!11.13!Mllt11;;chr7:122968213..122968266,-!p4@Sox6!1.01!10.94!Sox6;;chr10:84218800..84218829,+!p2@Rfx4!1.01!9.27!Rfx4;;chr7:91558392..91558434,-!p1@Arnt2!1.00!25.40!Arnt2;;chr6:145813905..145813932,-!p2@Bhlhe41!1.00!17.43!Bhlhe41;;chr14:34791937..34791977,-!p1@Zfp488!1.00!9.09!Zfp488;;chr11:96685487..96685512,-!p7@Nfe2l1!1.00!9.09!Nfe2l1;;chr11:96160426..96160443,+!p2@Hoxb6!1.00!9.09!Hoxb6;;chr2:163030186..163030204,+!p4@Tox2!1.00!8.90!Tox2;;chr15:102820946..102820961,+!p3@Hoxc8!0.99!8.71!Hoxc8;;chr11:98636531..98636559,-!p1@Nr1d1!0.97!49.32!Nr1d1;;chr10:67375368..67375433,-!p1@Zfp365!0.97!15.02!Zfp365;;chr2:74517742..74517758,+!p2@Hoxd11!0.97!8.34!Hoxd11;;chr5:122499831..122499891,-!p1@Cux2!0.96!12.61!Cux2;;chr2:115890294..115890334,-!p9@Meis2!0.96!11.13!Meis2;;chr2:147012101..147012118,-!p3@Nkx2-2!0.96!8.16!Nkx2-2;;chr6:52167513..52167549,-!p2@Hoxa7!0.94!11.13!Hoxa7;;chr11:96132523..96132538,+!p3@Hoxb9!0.94!7.79!Hoxb9;;chrX:108009761..108009788,+!p1@Pou3f4!0.94!7.79!Pou3f4;;chr6:134780163..134780197,+!p2@Crebl2!0.92!17.43!Crebl2;;chr17:27693525..27693538,+!p5@Hmga1!0.91!24.85!Hmga1;;chr2:74549968..74549996,+!p1@Hoxd3!0.91!9.09!Hoxd3;;chr11:96160403..96160416,+!p4@Hoxb6!0.91!7.05!Hoxb6;;chr2:151907546..151907561,+!p1@Scrt2!0.91!7.05!Scrt2;;chr4:150513630..150513686,-!p4@Camta1!0.90!7.97!Camta1;;chr2:74529970..74529997,+!p1@Hoxd10!0.90!6.86!Hoxd10;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.89!74.36!Camta2;;chr9:106356278..106356292,+!p3@Pcbp4!0.89!12.05!Pcbp4;;chr11:96153767..96153822,+!p1@Hoxb6!0.88!10.38!Hoxb6;;chr3:95032184..95032195,-!p4@Mllt11!0.88!8.34!Mllt11;;chr8:112603658..112603674,+!p2@Zfp612!0.87!12.05!Zfp612;;chr6:52163319..52163342,-!p1@Hoxa3!0.87!9.64!Hoxa3;;chr4:22415443..22415506,-!p1@Pou3f2!0.86!6.30!Pou3f2;;chr3:95032558..95032641,-!p2@Mllt11!0.85!35.97!Mllt11;;chr15:103170516..103170531,-!p2@Zfp385a!0.85!15.02!Zfp385a;;chr12:30213247..30213333,+!p1@Myt1l!0.85!6.12!Myt1l;;chr4:150482353..150482386,-!p6@Camta1!0.85!6.12!Camta1;;chr2:65768174..65768247,+!p2@Csrnp3!0.85!6.12!Csrnp3;;chr11:96132637..96132652,+!p1@Hoxb9!0.85!6.12!Hoxb9;;chr5:77524250..77524300,-!p1@Hopx!0.84!128.50!Hopx;;chr3:54559496..54559511,+!p1@Smad9!0.84!13.72!Smad9;;chr14:52935860..52935874,-!p3@Sall2!0.83!8.53!Sall2;;chr12:57714257..57714278,-!p1@Nkx2-9!0.83!5.75!Nkx2-9;;chr2:163030164..163030178,+!p6@Tox2!0.83!5.75!Tox2;;chr11:116196664..116196679,-!p1@Foxj1!0.82!8.90!Foxj1;;chr6:145813964..145813994,-!p3@Bhlhe41!0.82!7.23!Bhlhe41;;chr2:181501745..181501778,+!p1@Myt1!0.82!5.56!Myt1;;chr2:127347094..127347111,-!p2@Kcnip3!0.81!9.27!Kcnip3;;chr11:90252223..90252240,-!p1@Hlf!0.80!47.65!Hlf;;chr14:104867201..104867258,-!p1@Pou4f1!0.80!7.60!Pou4f1;;chr6:52176144..52176161,-!p2@Hoxa9!0.80!5.38!Hoxa9;;chr19:26681865..26681900,+!p6@Smarca2!0.79!15.95!Smarca2;;chrX:95345005..95345053,+!p1@Ar!0.79!5.19!Ar;;chr14:122874619..122874634,+!p1@Zic2!0.79!5.19!Zic2;;chr2:162769220..162769252,+!p1@L3mbtl1!0.79!5.19!L3mbtl1;;chr6:117813087..117813121,+!p1@Zfp239!0.78!20.40!Zfp239;;chr8:79423672..79423727,+!p2@Nr3c2!0.78!6.49!Nr3c2;;chr18:36441100..36441113,+!p3@Pura!0.78!5.93!Pura;;chr15:102839976..102839989,+!p4@Hoxc6!0.78!5.01!Hoxc6;;chr7:91558472..91558512,-!p2@Arnt2!0.77!7.23!Arnt2;;chr13:44936126..44936164,+!p6@Jarid2!0.77!5.75!Jarid2;;chr15:102797288..102797302,+!p1@Hoxc10!0.77!4.82!Hoxc10;;chr13:44936077..44936096,+!p9@Jarid2!0.77!4.82!Jarid2;;chr2:151907338..151907360,+!p2@Scrt2!0.77!4.82!Scrt2;;chr2:81893535..81893548,+!p1@Zfp804a!0.77!4.82!Zfp804a;;chr19:26679615..26679646,+!p3@Smarca2!0.76!35.97!Smarca2;;chr7:17200307..17200370,-!p2@Grlf1!0.75!37.64!Grlf1;;chr14:19071466..19071550,-!p1@Nr1d2!0.75!35.05!Nr1d2;;chr16:25684232..25684285,+!p2@Trp63!0.75!4.64!Trp63;;chr11:96164821..96164865,+!p1@Hoxb5!0.75!4.64!Hoxb5;;chr2:168427120..168427138,-!p4@Nfatc2!0.75!4.64!Nfatc2;;chrX:137077151..137077227,-!p2@Tsc22d3!0.74!34.49!Tsc22d3;;chr9:68501522..68501538,+!p4@Rora!0.74!8.90!Rora;;chr8:12395603..12395621,+!p1@Sox1!0.74!4.45!Sox1;;chr15:102839948..102839975,+!p3@Hoxc6!0.74!4.45!Hoxc6;;chr12:30220074..30220102,+!p3@Myt1l!0.74!4.45!Myt1l;;chrX:55283799..55283813,+!p1@Zic3!0.74!4.45!Zic3;;chr6:52184901..52184959,-!p2@Hoxa10!0.74!4.45!Hoxa10;;chr3:54559463..54559493,+!p3@Smad9!0.73!8.53!Smad9;;chr12:72149325..72149343,+!p2@Arid4a!0.73!6.30!Arid4a;;chr15:102839912..102839938,+!p5@Hoxc6!0.72!4.26!Hoxc6;;chr10:84218931..84218942,+!p4@Rfx4!0.72!4.26!Rfx4;;chr11:44431115..44431132,+!p9@Ebf1!0.72!4.26!Ebf1;;chr11:84339016..84339044,-!p1@Lhx1!0.72!4.26!Lhx1;;chr6:53523358..53523388,+!p1@Creb5!0.71!56.00!Creb5;;chr15:10400245..10400282,-!p2@Dnajc21!0.71!15.39!Dnajc21;;chr6:52154414..52154462,-!p1@Hoxa5!0.71!5.93!Hoxa5;;chr8:107793737..107793757,+!p2@Hsf4!0.71!4.82!Hsf4;;chr14:33412570..33412586,+!p1@Prrxl1!0.71!4.08!Prrxl1;;chr16:91269972..91269978,+!p3@Olig1!0.71!4.08!Olig1;;chr8:112603610..112603656,+!p1@Zfp612!0.70!20.77!Zfp612;;chr11:44431016..44431045,+!p5@Ebf1!0.70!5.93!Ebf1;;chr15:103164702..103164778,-!p3@Zfp385a!0.70!4.82!Zfp385a;;chr15:103170561..103170572,-!p4@Zfp385a!0.69!5.93!Zfp385a;;chr14:67853425..67853454,+!p1@Ebf2!0.69!5.75!Ebf2;;chr11:98636508..98636524,-!p3@Nr1d1!0.69!5.01!Nr1d1;;chr14:118636214..118636235,-!p1@Sox21!0.69!4.82!Sox21;;chr15:102828642..102828653,+!p2@Hoxc6!0.69!3.89!Hoxc6;;chr15:102820912..102820923,+!p5@Hoxc8!0.69!3.89!Hoxc8;;chr15:76352832..76352900,-!p1@Scrt1!0.69!3.89!Scrt1;;chr2:147012125..147012149,-!p1@Nkx2-2!0.69!3.89!Nkx2-2;;chr8:12395892..12395919,+!p4@Sox1!0.69!3.89!Sox1;;chr9:96653072..96653154,-!p1@Zbtb38!0.68!11.31!Zbtb38;;chr11:44430989..44431015,+!p4@Ebf1!0.68!7.23!Ebf1;;chr7:52960700..52960719,+!p2@Dbp!0.68!4.82!Dbp;;chr2:169458192..169458247,+!p1@Tshz2!0.67!37.83!Tshz2;;chrX:66613481..66613562,+!p1@Aff2!0.67!17.80!Aff2;;chr11:44430877..44430899,+!p6@Ebf1!0.67!4.82!Ebf1;;chr11:96145393..96145407,+!p3@Hoxb7!0.67!3.71!Hoxb7;;chr6:55631042..55631102,-!p1@Neurod6!0.67!3.71!Neurod6;;chr2:74543397..74543435,+!p2@Hoxd8!0.67!3.71!Hoxd8;;chr3:32264565..32264613,-!p1@Zmat3!0.66!45.99!Zmat3;;chr2:44968737..44968758,-!p2@Zeb2!0.66!23.36!Zeb2;;chr11:69579401..69579427,+!p2@Zbtb4!0.66!15.76!Zbtb4;;chr14:76903992..76904056,+!p6@Tsc22d1!0.66!7.97!Tsc22d1;;chr5:125342568..125342602,+!p2@Zfp664!0.66!6.30!Zfp664;;chr2:25562241..25562250,+!p4@Bmyc!0.66!4.08!Bm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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0006241,UBERON:0003057,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:24-13C9
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011305
+|is_a=EFO:0002091;;FF:0011305
+|is_obsolete=
+|library_id=CNhs10505
+|library_id_phase_based=2:CNhs10505
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;24
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;24
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spinal%2520cord%252c%2520adult.CNhs10505.24-13C9.mm9.nobarcode.rdna.fa.gz
 |name=spinal cord, adult
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10505,LSID648,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0628772532419645,0,0,0,0,0,0.122297429379438,0,0.0369370963453219,0,0,-0.0843392403965415,0,0,0,0,0,0,0.000193242956690015,0,0,0,0,0,0.0738741926906438,0,0,0,0,0,0,0,-0.317449139257749,0,0,0,0,0.0577028437001263,-0.103890565280398,0.186647495386143,-0.220396277247982,0.517950727536165,1.02521344167943,0,0,0.136990127740213,0,0,0,0,0,0,0,0.0738741926906438,0,-0.0660055475634404,0,0,0,0,0.0941431726573383,0,0,0,0,0.00429094606012561,-0.0119576426928977,-0.0257404316230725,0.324736583494908,0.0152235245027303,0,0.0143987823472837,0.160916457167857,0.0696222597762435,0,0,0.127679885887386,0.0918400216146348,0.0937429915281948,-0.0788315948399074,0,0,0,0,0,0,-0.0266298923127834,-0.353427461836899,-0.164370842015971,0,0,0.577650268894186,0,0
 |rna_box=13
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=spinal cord
 |top_motifs=NHLH1,2:2.73036278966;MTF1:2.61804793171;ZBTB6:2.51099921766;REST:2.50237810346;MYFfamily:2.42632051058;ATF2:2.41840142993;PRRX1,2:2.1577571017;SREBF1,2:2.07898055923;GFI1B:2.03950118786;HBP1_HMGB_SSRP1_UBTF:2.02019988165;LMO2:2.01590677614;NFE2L2:2.00119289991;BREu{core}:1.98954119215;TFAP2B:1.96065631861;PAX5:1.92043527689;ZIC1..3:1.91497641561;PBX1:1.89657688151;ZFP161:1.88989858255;MAFB:1.86813131418;HAND1,2:1.85945034928;AHR_ARNT_ARNT2:1.85725582556;HIC1:1.84731466385;MED-1{core}:1.83946584697;POU6F1:1.77632494628;FOX{I1,J2}:1.7618930107;SMAD1..7,9:1.71500093944;CUX2:1.67897429992;TFAP2{A,C}:1.66215478713;TGIF1:1.65470117106;KLF4:1.63627288439;RBPJ:1.61893223618;RORA:1.5942829406;EGR1..3:1.58017819698;ZNF143:1.48329831144;JUN:1.44762725064;NRF1:1.25524759818;OCT4_SOX2{dimer}:1.21640635201;RFX1:1.18574493459;TFDP1:1.18267693712;PRDM1:1.17036847129;STAT1,3:1.12532352414;SOX2:1.11844589357;GTF2A1,2:1.104518513;NKX2-2,8:1.087247183;MTE{core}:1.05715876715;ATF5_CREB3:1.04439872108;GTF2I:1.0436733017;FOXM1:1.0253966293;PATZ1:1.01253580908;POU3F1..4:1.00574475985;HSF1,2:0.995239719445;NR3C1:0.994342889081;MZF1:0.975240847114;MYOD1:0.957146532143;HES1:0.951085546417;PAX2:0.941103546172;RREB1:0.90646184169;FOXD3:0.901794574345;NFIL3:0.890891663813;IKZF1:0.885571858202;DBP:0.880546599605;NFE2:0.880081826443;ZEB1:0.875044340982;TFAP4:0.845842226943;ADNP_IRX_SIX_ZHX:0.836181446573;SOX5:0.812303555155;EVI1:0.771214279883;NANOG:0.767265374442;RFX2..5_RFXANK_RFXAP:0.767001044105;SOX{8,9,10}:0.759042616839;GATA4:0.75117610828;FOXN1:0.737275264817;MAZ:0.732825123498;ZNF423:0.711694315423;PAX6:0.693738207106;ONECUT1,2:0.650138715422;CREB1:0.604336937391;SP1:0.58732240975;YY1:0.571465592052;PAX4:0.484485819567;NKX3-2:0.462666037874;UFEwm:0.455930862598;PPARG:0.447405408654;NFATC1..3:0.447069500088;FOX{F1,F2,J1}:0.425298077605;SOX17:0.374363493489;BPTF:0.357813071654;TFCP2:0.355675333446;NR5A1,2:0.333033544299;HOXA9_MEIS1:0.309864186758;POU5F1:0.279710510817;FOXP3:0.277801056685;PAX8:0.273511978732;ESR1:0.249936634312;EBF1:0.218561316915;EP300:0.167063785429;TLX1..3_NFIC{dimer}:0.150784308739;LHX3,4:0.143479133675;GLI1..3:0.135508478745;ESRRA:0.113534303332;LEF1_TCF7_TCF7L1,2:0.0995565041943;GCM1,2:0.0976183182583;HMGA1,2:0.0764889489648;ATF6:0.0706405746286;FOXA2:0.0684429614141;BACH2:0.0190872330389;STAT2,4,6:0.0179338692904;NKX2-3_NKX2-5:0.00386510537409;AR:-0.0534858113104;TBX4,5:-0.0721057575523;TOPORS:-0.0729726358178;ATF4:-0.0773150280116;VSX1,2:-0.077487625583;TAL1_TCF{3,4,12}:-0.0866057027063;HIF1A:-0.10021794364;GZF1:-0.112060402624;MEF2{A,B,C,D}:-0.115205082697;MYBL2:-0.121358717836;NFY{A,B,C}:-0.168675197295;PDX1:-0.185149466787;NANOG{mouse}:-0.201504787604;XCPE1{core}:-0.217144190152;NKX6-1,2:-0.224965350491;T:-0.230199703286;NFE2L1:-0.238525504758;RXR{A,B,G}:-0.298233342649;ZNF384:-0.313302213144;CDX1,2,4:-0.334545984899;SPZ1:-0.33492820513;ARID5B:-0.344775798779;FOSL2:-0.346290991557;HMX1:-0.389357538266;TP53:-0.406909233188;CEBPA,B_DDIT3:-0.414308462569;HLF:-0.440914080818;FOXP1:-0.445066184653;IRF7:-0.459975514642;SNAI1..3:-0.471565617586;PAX1,9:-0.478417247289;ZNF148:-0.487321792684;CRX:-0.488298782771;FOX{D1,D2}:-0.502821778408;NKX2-1,4:-0.514927857717;SPI1:-0.518278542576;ZBTB16:-0.522405710918;TEF:-0.529438495684;HOX{A4,D4}:-0.558210686924;bHLH_family:-0.563562734235;AIRE:-0.616198413442;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.625554698359;ELK1,4_GABP{A,B1}:-0.660289725313;FOXQ1:-0.665701912466;POU1F1:-0.677389708734;ALX1:-0.697636068061;EN1,2:-0.701311507258;TEAD1:-0.724042471722;GATA6:-0.745070761004;ZNF238:-0.787690377647;FOXO1,3,4:-0.820226867045;IRF1,2:-0.825741511929;HNF4A_NR2F1,2:-0.83259504581;FOS_FOS{B,L1}_JUN{B,D}:-0.858030411882;MYB:-0.859132542556;RUNX1..3:-0.860960333059;HOX{A5,B5}:-0.871928488175;FOXL1:-0.93490149197;NR6A1:-0.947935713378;HNF1A:-0.959302294558;NFKB1_REL_RELA:-0.963288517492;ETS1,2:-0.964283301055;NR1H4:-0.982719547916;GFI1:-1.02982618189;POU2F1..3:-1.08921934289;CDC5L:-1.09085534216;NKX3-1:-1.11915957543;PITX1..3:-1.15140665821;NFIX:-1.1586031043;TBP:-1.19095106348;SRF:-1.26286573766;ELF1,2,4:-1.26948506282;IKZF2:-1.38010733285;SPIB:-1.39150625798;RXRA_VDR{dimer}:-1.39481297072;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.45353624749;DMAP1_NCOR{1,2}_SMARC:-1.51381211566;E2F1..5:-1.52040984524;ALX4:-2.11040087807;TLX2:-2.30596562616;STAT5{A,B}:-2.44389988655
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:24-13C9;search_select_hide=table117:24-13C9
 }}

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FF:24-13C9: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:09, 4 June 2020

CNhs10505

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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