FF:12-14D5: Difference between revisions

Latest revision as of 18:31, 4 June 2020

Name:	cortex, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10473
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	cortex
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		SAMD00005968

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10473		CAGE		DRX008947		DRR009821

Accession ID Mm9

Library id		BAM		CTSS
CNhs10473		DRZ001246		DRZ002629

Accession ID Mm10

Library id		BAM		CTSS
CNhs10473		DRZ012596		DRZ013979

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

CNhs10473

0	0
1	0.839
10	0
100	0
1000	0
1001	0
1002	-0.0592
1003	0.265
1004	0
1005	0.13
1006	0.739
1007	-0.0572
1008	0
1009	-0.0774
101	-0.05
1010	0
1011	0.985
1012	0.34
1013	0.147
1014	-0.0155
1015	-0.133
1016	-0.166
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	-0.016
1023	0
1024	0
1025	-0.0312
1026	0
1027	0.375
1028	0
1029	-0.0369
103	-0.0861
1030	0
1031	-0.502
1032	0.0951
1033	0.0696
1034	0
1035	0.0106
1036	-0.255
1037	0
1038	0.0186
1039	0.092
104	0
1040	-0.165
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: CNhs10473

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00288
MA0003.1	MA0003.1	0.298
MA0004.1	MA0004.1	0.596
MA0006.1	MA0006.1	0.137
MA0007.1	MA0007.1	0.382
MA0009.1	MA0009.1	0.792
MA0014.1	MA0014.1	0.711
MA0017.1	MA0017.1	7.90756e-7
MA0018.2	MA0018.2	0.00495
MA0019.1	MA0019.1	0.312
MA0024.1	MA0024.1	0.0641
MA0025.1	MA0025.1	0.00195
MA0027.1	MA0027.1	0.0669
MA0028.1	MA0028.1	0.0928
MA0029.1	MA0029.1	0.964
MA0030.1	MA0030.1	0.902
MA0031.1	MA0031.1	0.183
MA0035.2	MA0035.2	0.0157
MA0038.1	MA0038.1	0.397
MA0039.2	MA0039.2	0.0312
MA0040.1	MA0040.1	0.128
MA0041.1	MA0041.1	0.274
MA0042.1	MA0042.1	0.35
MA0043.1	MA0043.1	0.0695
MA0046.1	MA0046.1	3.20088e-10
MA0047.2	MA0047.2	4.70009e-4
MA0048.1	MA0048.1	0.0549
MA0050.1	MA0050.1	1.95729e-4
MA0051.1	MA0051.1	0.0278
MA0052.1	MA0052.1	0.459
MA0055.1	MA0055.1	0.0112
MA0057.1	MA0057.1	0.522
MA0058.1	MA0058.1	0.456
MA0059.1	MA0059.1	0.147
MA0060.1	MA0060.1	0.651
MA0061.1	MA0061.1	0.035
MA0062.2	MA0062.2	0.0033
MA0065.2	MA0065.2	1.03847e-6
MA0066.1	MA0066.1	0.032
MA0067.1	MA0067.1	0.518
MA0068.1	MA0068.1	0.615
MA0069.1	MA0069.1	0.0531
MA0070.1	MA0070.1	0.498
MA0071.1	MA0071.1	0.0195
MA0072.1	MA0072.1	0.138
MA0073.1	MA0073.1	0.856
MA0074.1	MA0074.1	0.132
MA0076.1	MA0076.1	0.223
MA0077.1	MA0077.1	0.675
MA0078.1	MA0078.1	0.704
MA0079.2	MA0079.2	0.376
MA0080.2	MA0080.2	1.84505e-9
MA0081.1	MA0081.1	0.321
MA0083.1	MA0083.1	0.0231
MA0084.1	MA0084.1	0.832
MA0087.1	MA0087.1	0.485
MA0088.1	MA0088.1	0.346
MA0090.1	MA0090.1	0.157
MA0091.1	MA0091.1	0.165
MA0092.1	MA0092.1	0.271
MA0093.1	MA0093.1	0.638
MA0099.2	MA0099.2	0.0116
MA0100.1	MA0100.1	0.317
MA0101.1	MA0101.1	0.0218
MA0102.2	MA0102.2	0.51
MA0103.1	MA0103.1	0.205
MA0104.2	MA0104.2	0.886
MA0105.1	MA0105.1	0.0117
MA0106.1	MA0106.1	0.0518
MA0107.1	MA0107.1	0.0423
MA0108.2	MA0108.2	7.43124e-4
MA0111.1	MA0111.1	0.917
MA0112.2	MA0112.2	5.77001e-4
MA0113.1	MA0113.1	0.355
MA0114.1	MA0114.1	4.51823e-6
MA0115.1	MA0115.1	2.2026e-5
MA0116.1	MA0116.1	0.0683
MA0117.1	MA0117.1	0.908
MA0119.1	MA0119.1	0.11
MA0122.1	MA0122.1	0.907
MA0124.1	MA0124.1	0.522
MA0125.1	MA0125.1	0.0383
MA0131.1	MA0131.1	0.778
MA0135.1	MA0135.1	0.496
MA0136.1	MA0136.1	8.37649e-11
MA0137.2	MA0137.2	0.283
MA0138.2	MA0138.2	9.61154e-4
MA0139.1	MA0139.1	0.643
MA0140.1	MA0140.1	2.20598e-4
MA0141.1	MA0141.1	4.62552e-4
MA0142.1	MA0142.1	0.473
MA0143.1	MA0143.1	0.623
MA0144.1	MA0144.1	0.148
MA0145.1	MA0145.1	0.138
MA0146.1	MA0146.1	0.0178
MA0147.1	MA0147.1	0.765
MA0148.1	MA0148.1	2.81477e-4
MA0149.1	MA0149.1	0.0903
MA0150.1	MA0150.1	0.209
MA0152.1	MA0152.1	0.302
MA0153.1	MA0153.1	8.39011e-11
MA0154.1	MA0154.1	0.0472
MA0155.1	MA0155.1	0.338
MA0156.1	MA0156.1	2.94094e-7
MA0157.1	MA0157.1	0.11
MA0159.1	MA0159.1	0.00121
MA0160.1	MA0160.1	0.00331
MA0162.1	MA0162.1	0.145
MA0163.1	MA0163.1	6.3365e-4
MA0164.1	MA0164.1	0.957
MA0258.1	MA0258.1	0.0168
MA0259.1	MA0259.1	0.921

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: CNhs10473

Novel motif	Logo	P-value
1	1	0.215
10	10	0.0492
100	100	0.39
101	101	0.698
102	102	0.925
103	103	0.0467
104	104	0.94
105	105	0.881
106	106	0.059
107	107	0.195
108	108	0.599
109	109	0.00468
11	11	0.086
110	110	0.0612
111	111	0.118
112	112	0.00607
113	113	0.38
114	114	0.38
115	115	0.975
116	116	0.302
117	117	0.00367
118	118	0.373
119	119	0.249
12	12	0.993
120	120	0.921
121	121	0.517
122	122	0.772
123	123	0.0026
124	124	0.0629
125	125	0.223
126	126	0.0206
127	127	0.361
128	128	0.038
129	129	0.223
13	13	1.43024e-7
130	130	0.112
131	131	0.622
132	132	0.756
133	133	0.833
134	134	0.106
135	135	0.373
136	136	0.063
137	137	0.692
138	138	0.874
139	139	0.305
14	14	0.952
140	140	0.0479
141	141	0.667
142	142	0.837
143	143	0.391
144	144	0.731
145	145	3.06758e-4
146	146	0.279
147	147	0.256
148	148	0.399
149	149	0.553
15	15	0.195
150	150	0.0579
151	151	0.826
152	152	0.125
153	153	0.831
154	154	0.983
155	155	0.294
156	156	0.00336
157	157	0.289
158	158	0.131
159	159	0.902
160	160	0.17
161	161	0.093
162	162	0.67
163	163	0.699
164	164	0.0699
165	165	0.0916
166	166	0.884
167	167	0.674
168	168	0.549
169	169	0.00363
17	17	0.0497
18	18	0.756
19	19	0.0911
2	2	0.775
20	20	0.0483
21	21	0.244
22	22	0.142
23	23	0.731
24	24	0.0315
25	25	0.779
26	26	4.52714e-7
27	27	0.53
28	28	0.712
29	29	0.0234
3	3	0.0406
30	30	0.829
31	31	0.967
32	32	0.55
33	33	0.216
34	34	0.679
35	35	0.895
36	36	0.25
37	37	0.0203
38	38	0.551
39	39	0.252
4	4	0.172
40	40	0.12
41	41	0.524
42	42	0.15
43	43	0.141
44	44	0.398
45	45	0.717
46	46	0.133
47	47	0.463
48	48	0.323
49	49	0.213
5	5	0.186
50	50	0.243
51	51	0.777
52	52	0.25
53	53	0.434
54	54	0.92
55	55	0.903
56	56	0.468
57	57	0.657
58	58	0.364
59	59	0.114
6	6	0.952
60	60	0.0368
61	61	0.028
62	62	0.284
63	63	0.156
64	64	0.632
65	65	0.464
66	66	0.769
67	67	0.614
68	68	0.789
69	69	0.15
7	7	0.016
70	70	0.0963
71	71	0.00606
72	72	0.59
73	73	0.0339
74	74	0.893
75	75	0.0427
76	76	0.501
77	77	0.307
78	78	0.00306
79	79	0.633
8	8	0.0648
80	80	0.626
81	81	0.904
82	82	0.238
83	83	0.0947
84	84	0.73
85	85	0.163
86	86	0.195
87	87	0.16
88	88	0.467
89	89	0.798
9	9	0.506
90	90	0.215
91	91	0.0789
92	92	0.258
93	93	0.195
94	94	0.806
95	95	0.0262
96	96	0.45
97	97	0.972
98	98	0.496
99	99	0.429

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: CNhs10473

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000103 mouse sample
FF:0011525 cortex- 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)
0000956 (cerebral cortex)
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)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011525 (cortex- 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0000955,UBERON:0000483,UBERON:0000956,UBERON:0000033,UBERON:0000479,UBERON:0002346,UBERON:0000064,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:0002020,UBERON:0002791,UBERON:0003528,UBERON:0000481,UBERON:0000467,UBERON:0002616,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002780,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0005743,UBERON:0003075,UBERON:0003056,UBERON:0001049,UBERON:0006238,UBERON:0006601,UBERON:0005068,UBERON:0006241,UBERON:0003080,UBERON:0006240,UBERON:0007284,UBERON:0007135
+|DRA_sample_Accession=CAGE@SAMD00005968
+|accession_numbers=CAGE;DRX008947;DRR009821;DRZ001246;DRZ002629;DRZ012596;DRZ013979
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000955,UBERON:0000956,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203
 |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:0011525
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr10:67375368..67375433,-!p1@Zfp365!2.06!198.16!Zfp365;;chr6:55631042..55631102,-!p1@Neurod6!2.01!101.69!Neurod6;;chr16:91270004..91270023,+!p1@Olig1!1.95!99.78!Olig1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.78!109.51!Tsc22d4;;chr2:127347067..127347093,-!p1@Kcnip3!1.74!89.52!Kcnip3;;chr6:85463580..85463585,-!p1@Egr4!1.72!51.45!Egr4;;chr11:98190918..98190951,-!p1@Neurod2!1.70!49.37!Neurod2;;chr12:30219426..30219506,+!p2@Myt1l!1.70!49.02!Myt1l;;chr7:116154364..116154444,+!p1@Tub!1.69!81.52!Tub;;chr19:19185671..19185693,-!p1@Rorb!1.67!107.42!Rorb;;chr2:61642631..61642684,+!p1@Tbr1!1.67!45.54!Tbr1;;chr10:67375342..67375365,-!p3@Zfp365!1.63!41.37!Zfp365;;chr17:48015839..48015915,-!p3@Foxp4!1.61!46.24!Foxp4;;chr10:67375146..67375208,-!p2@Zfp365!1.59!56.67!Zfp365;;chr3:95032091..95032183,-!p1@Mllt11!1.56!285.07!Mllt11;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.56!44.67!Pou3f3;;chr2:65683890..65683907,+!p1@Csrnp3!1.50!58.06!Csrnp3;;chr2:38206744..38206766,+!p1@Lhx2!1.50!37.02!Lhx2;;chr5:98609885..98609900,+!p1@Prdm8!1.49!30.07!Prdm8;;chr8:24780125..24780143,+!p1@Zmat4!1.48!41.89!Zmat4;;chrX:34442872..34442899,-!p1@Nkrf!1.47!36.33!Nkrf;;chr2:38206580..38206600,+!p2@Lhx2!1.46!34.07!Lhx2;;chr15:76353005..76353021,-!p2@Scrt1!1.45!27.46!Scrt1;;chr2:127347094..127347111,-!p2@Kcnip3!1.42!41.02!Kcnip3;;chr4:58956447..58956510,+!p1@Zkscan16!1.41!52.32!Zkscan16;;chr15:76352677..76352737,-!p3@Scrt1!1.40!24.16!Scrt1;;chr12:30213247..30213333,+!p1@Myt1l!1.39!23.29!Myt1l;;chr13:83663546..83663560,+!p4@Mef2c!1.38!29.55!Mef2c;;chr1:179374784..179374800,+!p2@Zfp238!1.37!26.60!Zfp238;;chr13:83663902..83663927,+!p1@Mef2c!1.35!500.09!Mef2c;;chr19:4989964..4989972,-!p1@Npas4!1.35!21.38!Npas4;;chr16:91225808..91225824,+!p1@Olig2!1.32!19.99!Olig2;;chr13:83663868..83663894,+!p2@Mef2c!1.31!271.51!Mef2c;;chrX:90531838..90531861,+!p1@Arx!1.30!23.99!Arx;;chr2:127347042..127347058,-!p3@Kcnip3!1.30!19.12!Kcnip3;;chr2:61642558..61642595,+!p3@Tbr1!1.29!18.43!Tbr1;;chr11:98636531..98636559,-!p1@Nr1d1!1.27!98.38!Nr1d1;;chr1:57029281..57029326,-!p1@Satb2!1.27!26.94!Satb2;;chr12:86939997..86940040,+!p4@Jdp2!1.25!16.69!Jdp2;;chr7:148008023..148008092,-!p1@Zfp941!1.23!38.42!Zfp941;;chr2:56967334..56967366,-!p1@Nr4a2!1.23!32.51!Nr4a2;;chr11:90250944..90250982,-!p2@Hlf!1.23!26.77!Hlf;;chr2:61642743..61642758,+!p2@Tbr1!1.23!15.82!Tbr1;;chr11:90252223..90252240,-!p1@Hlf!1.22!126.54!Hlf;;chr4:150482563..150482655,-!p2@Camta1!1.22!55.10!Camta1;;chr2:65768174..65768247,+!p2@Csrnp3!1.21!15.12!Csrnp3;;chr4:48058129..48058179,+!p2@Nr4a3!1.20!27.81!Nr4a3;;chr15:76352434..76352488,-!p4@Scrt1!1.20!14.95!Scrt1;;chr6:117813087..117813121,+!p1@Zfp239!1.18!52.84!Zfp239;;chr18:35020854..35020869,+!p1@Egr1!1.17!515.22!Egr1;;chr2:77654815..77654872,-!p2@Zfp385b!1.17!17.21!Zfp385b;;chr12:30220074..30220102,+!p3@Myt1l!1.17!13.91!Myt1l;;chr17:25707623..25707639,-!p1@Sox8!1.15!55.80!Sox8;;chr12:72149325..72149343,+!p2@Arid4a!1.15!18.60!Arid4a;;chr14:13178147..13178185,-!p1@Fezf2!1.15!13.21!Fezf2;;chr13:83663500..83663519,+!p8@Mef2c!1.15!13.04!Mef2c;;chr18:36441119..36441158,+!p2@Pura!1.14!31.11!Pura;;chr5:122499831..122499891,-!p1@Cux2!1.14!19.82!Cux2;;chr3:95032197..95032208,-!p3@Mllt11!1.13!15.64!Mllt11;;chr5:122452349..122452377,-!p4@Cux2!1.13!12.52!Cux2;;chr8:87297878..87297935,-!p3@Nfix!1.12!26.94!Nfix;;chr11:98190955..98190968,-!p2@Neurod2!1.11!11.99!Neurod2;;chr19:23216132..23216157,+!p3@Klf9!1.08!17.21!Klf9;;chr19:19185697..19185711,-!p2@Rorb!1.08!14.25!Rorb;;chr2:162769220..162769252,+!p1@L3mbtl1!1.08!11.12!L3mbtl1;;chr19:59533221..59533271,+!p1@Emx2!1.07!13.38!Emx2;;chr12:54349410..54349461,+!p1@Npas3!1.07!12.86!Npas3;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!1.05!106.21!Camta2;;chr3:34548909..34548927,+!p1@Sox2!1.05!17.56!Sox2;;chr12:72149359..72149406,+!p4@Arid4a!1.05!13.56!Arid4a;;chr4:150513630..150513686,-!p4@Camta1!1.05!11.82!Camta1;;chr10:13685585..13685645,+!p2@Hivep2!1.04!35.29!Hivep2;;chr7:30092993..30093076,+!p1@Dpf1!1.04!17.21!Dpf1;;chr2:163051181..163051205,+!p2@Tox2!1.04!9.91!Tox2;;chr2:115890294..115890334,-!p9@Meis2!1.03!13.21!Meis2;;chr10:84218800..84218829,+!p2@Rfx4!1.02!9.39!Rfx4;;chr18:69680960..69681007,+!p10@Tcf4!1.01!12.17!Tcf4;;chr16:91270091..91270143,+!p2@Olig1!1.01!9.21!Olig1;;chrX:95345005..95345053,+!p1@Ar!1.00!9.04!Ar;;chr15:100430414..100430470,-!p1@Pou6f1!0.99!27.99!Pou6f1;;chr4:154335024..154335039,+!p1@Hes5!0.99!10.78!Hes5;;chr3:95032213..95032226,-!p6@Mllt11!0.99!10.60!Mllt11;;chr11:90250894..90250916,-!p5@Hlf!0.99!8.69!Hlf;;chr7:71083876..71083932,-!p2@Klf13!0.98!70.57!Klf13;;chr15:101097270..101097290,+!p1@Nr4a1!0.97!88.30!Nr4a1;;chrX:108009761..108009788,+!p1@Pou3f4!0.97!8.34!Pou3f4;;chr4:22415443..22415506,-!p1@Pou3f2!0.96!8.17!Pou3f2;;chrX:34442842..34442866,-!p3@Nkrf!0.96!8.17!Nkrf;;chr14:70476975..70476997,+!p2@Egr3!0.96!8.17!Egr3;;chr14:122874619..122874634,+!p1@Zic2!0.95!7.82!Zic2;;chr12:109242266..109242295,-!p1@Bcl11b!0.94!67.62!Bcl11b;;chr11:23980664..23980706,+!p2@Bcl11a!0.94!34.24!Bcl11a;;chr11:96685487..96685512,-!p7@Nfe2l1!0.94!7.65!Nfe2l1;;chr10:84218895..84218909,+!p1@Rfx4!0.94!7.65!Rfx4;;chr7:146768691..146768707,-!p1@Nkx6-2!0.94!7.65!Nkx6-2;;chr11:98636575..98636607,-!p2@Nr1d1!0.93!28.33!Nr1d1;;chr7:91558472..91558512,-!p2@Arnt2!0.93!10.95!Arnt2;;chr6:55631251..55631265,-!p2@Neurod6!0.93!7.47!Neurod6;;chr2:25562263..25562314,+!p2@Bmyc!0.92!29.72!Bmyc;;chr8:79423672..79423727,+!p2@Nr3c2!0.92!9.39!Nr3c2;;chr3:95032184..95032195,-!p4@Mllt11!0.92!9.21!Mllt11;;chr15:78994907..78994926,-!p1@Sox10!0.91!18.77!Sox10;;chr13:78339134..78339185,-!p5@Nr2f1!0.91!8.87!Nr2f1;;chr14:13178361..13178386,-!p2@Fezf2!0.91!7.13!Fezf2;;chr11:96685444..96685473,-!p5@Nfe2l1!0.91!7.13!Nfe2l1;;chr8:87297280..87297326,-!p2@Nfix!0.90!17.03!Nfix;;chr5:125342568..125342602,+!p2@Zfp664!0.90!11.82!Zfp664;;chr7:52960780..52960793,+!p5@Dbp!0.90!8.34!Dbp;;chr1:6477388..6477419,+!p3@St18!0.90!6.95!St18;;chr1:179374820..179374831,+!p3@Zfp238!0.90!6.95!Zfp238;;chr13:83643031..83643049,+!p11@Mef2c!0.90!6.95!Mef2c;;chr11:90252108..90252134,-!p6@Hlf!0.89!6.78!Hlf;;chr7:91521166..91521194,-!p11@Arnt2!0.89!6.78!Arnt2;;chr14:70477113..70477173,+!p1@Egr3!0.88!6.61!Egr3;;chr7:91558537..91558558,-!p4@Arnt2!0.87!7.82!Arnt2;;chr7:30094448..30094481,+!p4@Dpf1!0.87!7.82!Dpf1;;chr11:21901608..21901634,-!p1@Otx1!0.87!6.43!Otx1;;chr14:18493386..18493464,+!p1@Thrb!0.86!25.20!Thrb;;chr6:108610766..108610781,+!p2@Bhlhe40!0.86!11.47!Bhlhe40;;chr7:52960700..52960719,+!p2@Dbp!0.86!7.82!Dbp;;chr7:91520922..91520956,-!p5@Arnt2!0.86!6.26!Arnt2;;chr15:81633165..81633188,+!p2@Tef!0.85!53.02!Tef;;chr1:57028556..57028583,-!p5@Satb2!0.85!6.08!Satb2;;chr7:30088977..30089002,+!p2@Dpf1!0.84!8.34!Dpf1;;chr2:65768149..65768173,+!p4@Csrnp3!0.84!5.91!Csrnp3;;chr6:144152648..144152680,-!p5@Sox5!0.83!5.74!Sox5;;chr6:85137520..85137563,+!p1@Emx1!0.83!5.74!Emx1;;chr2:71367871..71367898,+!p1@Dlx1!0.83!5.74!Dlx1;;chr2:79296783..79296801,-!p1@Neurod1!0.83!5.74!Neurod1;;chr9:91260594..91260612,-!p1@Zic1!0.83!5.74!Zic1;;chr15:81641878..81641921,+!p1@Tef!0.82!155.05!Tef;;chr10:80893711..80893784,-!p3@Nfic!0.82!31.64!Nfic;;chr11:23978078..23978096,+!p4@Bcl11a!0.82!18.25!Bcl11a;;chr8:107793688..107793736,+!p1@Hsf4!0.82!7.47!Hsf4;;chr4:124334894..124334899,+!p1@Pou3f1!0.82!7.47!Pou3f1;;chr10:42303385..42303401,-!p1@Nr2e1!0.82!5.56!Nr2e1;;chr7:52960888..52960902,+!p7@Dbp!0.82!5.56!Dbp;;chr1:179372411..179372509,+!p1@Zfp238!0.81!74.40!Zfp238;;chr15:99532568..99532636,+!p2@Smarcd1!0.81!53.54!Smarcd1;;chr14:118636214..118636235,-!p1@Sox21!0.81!6.61!Sox21;;chr13:44936126..44936164,+!p6@Jarid2!0.81!6.43!Jarid2;;chr3:34548946..34548972,+!p2@Sox2!0.81!6.08!Sox2;;chr4:22415290..22415307,-!p2@Pou3f2!0.81!5.39!Pou3f2;;chr14:13178241..13178254,-!p4@Fezf2!0.81!5.39!Fezf2;;chr19:19185429..19185440,-!p3@Rorb!0.81!5.39!Rorb;;chr15:103170533..103170556,-!p1@Zfp385a!0.80!21.38!Zfp385a;;chr1:170362437..170362478,-!p5@Pbx1!0.80!17.56!Pbx1;;chr19:23216166..23216191,+!p6@Klf9!0.80!7.30!Klf9;;chr10:30522690..30522752,-!p2@Ncoa7!0.79!33.72!Ncoa7;;chr10:67000609..67000625,+!p1@Egr2!0.79!12.52!Egr2;;chr10:13686815..13686846,+!p3@Hivep2!0.79!12.34!Hivep2;;chr2:77654936..77654988,-!p4@Zfp385b!0.79!6.43!Zfp385b;;chr4:150482353..150482386,-!p6@Camta1!0.79!5.21!Camta1;;chr9:91260616..91260653,-!p2@Zic1!0.79!5.21!Zic1;;chr9:36954842..36954908,-!p1@Pknox2!0.78!64.31!Pknox2;;chr1:39250584..39250643,+!p1@Npas2!0.78!27.46!Npas2;;chr7:91558392..91558434,-!p1@Arnt2!0.78!14.78!Arnt2;;chr4:154010409..154010466,-!p2@Prdm16!0.78!12.52!Prdm16;;chr11:23978111..23978134,+!p3@Bcl11a!0.78!11.12!Bcl11a;;chr11:90250999..90251013,-!p8@Hlf!0.78!5.04!Hlf;;chr1:57028606..57028625,-!p4@Satb2!0.78!5.04!Satb2;;chr10:13685657..13685677,+!p7@Hivep2!0.77!6.61!Hivep2;;chr10:67375223..67375240,-!p4@Zfp365!0.77!5.56!Zfp365;;chr2:77541432..77541474,-!p5@Zfp385b!0.77!4.87!Zfp385b;;chr12:39510042..39510069,+!p8@Etv1!0.77!4.87!Etv1;;chr15:82742573..82742620,-!p2@Tcf20!0.77!4.87!Tcf20;;chr11:98603119..98603130,+!p2@Thra!0.76!44.67!Thra;;chr15:81633139..81633152,+!p4@Tef!0.76!8.34!Tef;;chr9:96631820..96631834,-!p11@Zbtb38!0.76!4.69!Zbtb38;;chr12:39510290..39510309,+!p5@Etv1!0.76!4.69!Etv1;;chr15:76352832..76352900,-!p1@Scrt1!0.76!4.69!Scrt1;;chr2:168427068..168427115,-!p3@Nfatc2!0.76!4.69!Nfatc2;;chr14:19071466..19071550,-!p1@Nr1d2!0.75!34.76!Nr1d2;;chr9:48644306..48644364,-!p1@Zbtb16!0.75!20.34!Zbtb16;;chr4:48058016..48058032,+!p3@Nr4a3!0.75!8.34!Nr4a3;;chr3:95032558..95032641,-!p2@Mllt11!0.74!27.46!Mllt11;;chr12:109242296..109242307,-!p3@Bcl11b!0.74!6.78!Bcl11b;;chr13:78339428..78339466,-!p2@Nr2f1!0.74!6.43!Nr2f1;;chr12:39510206..39510249,+!p3@Etv1!0.74!4.52!Etv1;;chr17:51965903..51965926,-!p5@Satb1!0.74!4.52!Satb1;;chr6:98994408..98994420,-!p23@Foxp1!0.74!4.52!Foxp1;;chr9:96632719..96632745,-!p7@Zbtb38!0.74!4.52!Zbtb38;;chr9:96631780..96631791,-!p13@Zbtb38!0.74!4.52!Zbtb38;;chr11:90252071..90252093,-!p7@Hlf!0.74!4.52!Hlf;;chr2:65683842..65683856,+!p3@Csrnp3!0.74!4.52!Csrnp3;;chr2:151907338..151907360,+!p2@Scr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+|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:0000103;;FF:0011525
 |is_obsolete=
+|library_id=CNhs10473
+|library_id_phase_based=2:CNhs10473
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cortex%252c%2520adult.CNhs10473.12-14D5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cortex%252c%2520adult.CNhs10473.12-14D5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cortex%252c%2520adult.CNhs10473.12-14D5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cortex%252c%2520adult.CNhs10473.12-14D5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cortex%252c%2520adult.CNhs10473.12-14D5.mm9.nobarcode.rdna.fa.gz
 |name=cortex, adult
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10473,LSID646,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0530072575970185,0,0,0,0,0,0.0437022283880422,0,0.00169470880465219,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0.0696031033168343,0,0,0,0,0,0,0,-0.248165921753944,0,0,0,0,0.0405584488431633,-0.0598982411292005,0.129576677486723,-0.0923757418100477,0.577607219396095,0.0403882325597363,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.086729722403848,0,0,0,0,0.0202314716739472,0.0635415217930987,-0.181073979852663,0.828287230990896,0.0663070079442705,0,0,0.141133569990131,0.115149114136527,0,0,0.129576677486723,0.109000048140986,0.0199129375136624,0.0507450826468154,0,0,0,0,0,0,-0.0660154575426048,-0.328021339823248,-0.178670882963052,0,0,0.850269430443658,0,0
 |rna_box=14
 |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=table111:12-14D5;search_select_hide=table117:12-14D5
 }}

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FF:12-14D5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:31, 4 June 2020

CNhs10473

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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