FF:1392-42F2: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	cortex, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11107
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	cortex
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		SAMD00004720

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11107		CAGE		DRX008948		DRR009822

Accession ID Mm9

Library id		BAM		CTSS
CNhs11107		DRZ001247		DRZ002630

Accession ID Mm10

Library id		BAM		CTSS
CNhs11107		DRZ012597		DRZ013980

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

CNhs11107

0	0
1	0.828
10	0
100	0
1000	0
1001	0.0729
1002	-0.0956
1003	0.16
1004	0
1005	0.114
1006	0.696
1007	0.0595
1008	0
1009	-0.179
101	-0.0521
1010	0
1011	0.879
1012	0.512
1013	0.152
1014	0
1015	-0.0015
1016	-0.2
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0229
1022	-0.0251
1023	0
1024	0
1025	0
1026	0
1027	0.306
1028	0
1029	0.0704
103	-0.0788
1030	0
1031	-0.441
1032	0.129
1033	-0.0647
1034	0
1035	0
1036	-0.249
1037	0
1038	0.00542
1039	0.0996
104	0
1040	-0.318
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: CNhs11107

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00325
MA0003.1	MA0003.1	0.28
MA0004.1	MA0004.1	0.572
MA0006.1	MA0006.1	0.135
MA0007.1	MA0007.1	0.359
MA0009.1	MA0009.1	0.95
MA0014.1	MA0014.1	0.691
MA0017.1	MA0017.1	7.55596e-7
MA0018.2	MA0018.2	0.00908
MA0019.1	MA0019.1	0.25
MA0024.1	MA0024.1	0.0506
MA0025.1	MA0025.1	0.015
MA0027.1	MA0027.1	0.0563
MA0028.1	MA0028.1	0.0897
MA0029.1	MA0029.1	0.922
MA0030.1	MA0030.1	0.773
MA0031.1	MA0031.1	0.185
MA0035.2	MA0035.2	0.0127
MA0038.1	MA0038.1	0.552
MA0039.2	MA0039.2	0.0209
MA0040.1	MA0040.1	0.0876
MA0041.1	MA0041.1	0.765
MA0042.1	MA0042.1	0.414
MA0043.1	MA0043.1	0.149
MA0046.1	MA0046.1	4.35054e-11
MA0047.2	MA0047.2	3.0384e-4
MA0048.1	MA0048.1	0.0571
MA0050.1	MA0050.1	1.61357e-4
MA0051.1	MA0051.1	0.0127
MA0052.1	MA0052.1	0.672
MA0055.1	MA0055.1	0.0162
MA0057.1	MA0057.1	0.507
MA0058.1	MA0058.1	0.448
MA0059.1	MA0059.1	0.169
MA0060.1	MA0060.1	0.488
MA0061.1	MA0061.1	0.0371
MA0062.2	MA0062.2	0.00267
MA0065.2	MA0065.2	1.31542e-6
MA0066.1	MA0066.1	0.0203
MA0067.1	MA0067.1	0.511
MA0068.1	MA0068.1	0.333
MA0069.1	MA0069.1	0.0534
MA0070.1	MA0070.1	0.511
MA0071.1	MA0071.1	0.0283
MA0072.1	MA0072.1	0.331
MA0073.1	MA0073.1	0.726
MA0074.1	MA0074.1	0.104
MA0076.1	MA0076.1	0.219
MA0077.1	MA0077.1	0.716
MA0078.1	MA0078.1	0.66
MA0079.2	MA0079.2	0.453
MA0080.2	MA0080.2	5.42935e-10
MA0081.1	MA0081.1	0.223
MA0083.1	MA0083.1	0.00763
MA0084.1	MA0084.1	0.741
MA0087.1	MA0087.1	0.665
MA0088.1	MA0088.1	0.315
MA0090.1	MA0090.1	0.197
MA0091.1	MA0091.1	0.182
MA0092.1	MA0092.1	0.305
MA0093.1	MA0093.1	0.6
MA0099.2	MA0099.2	0.00745
MA0100.1	MA0100.1	0.337
MA0101.1	MA0101.1	0.0223
MA0102.2	MA0102.2	0.386
MA0103.1	MA0103.1	0.217
MA0104.2	MA0104.2	0.901
MA0105.1	MA0105.1	0.0117
MA0106.1	MA0106.1	0.0693
MA0107.1	MA0107.1	0.0421
MA0108.2	MA0108.2	3.64563e-4
MA0111.1	MA0111.1	0.887
MA0112.2	MA0112.2	7.78892e-4
MA0113.1	MA0113.1	0.297
MA0114.1	MA0114.1	6.94097e-6
MA0115.1	MA0115.1	3.38497e-5
MA0116.1	MA0116.1	0.0685
MA0117.1	MA0117.1	0.891
MA0119.1	MA0119.1	0.112
MA0122.1	MA0122.1	0.897
MA0124.1	MA0124.1	0.544
MA0125.1	MA0125.1	0.0304
MA0131.1	MA0131.1	0.828
MA0135.1	MA0135.1	0.794
MA0136.1	MA0136.1	3.76654e-11
MA0137.2	MA0137.2	0.122
MA0138.2	MA0138.2	0.00167
MA0139.1	MA0139.1	0.475
MA0140.1	MA0140.1	4.02241e-4
MA0141.1	MA0141.1	4.74423e-4
MA0142.1	MA0142.1	0.438
MA0143.1	MA0143.1	0.683
MA0144.1	MA0144.1	0.0992
MA0145.1	MA0145.1	0.12
MA0146.1	MA0146.1	0.02
MA0147.1	MA0147.1	0.774
MA0148.1	MA0148.1	2.14096e-4
MA0149.1	MA0149.1	0.154
MA0150.1	MA0150.1	0.184
MA0152.1	MA0152.1	0.16
MA0153.1	MA0153.1	1.1127e-11
MA0154.1	MA0154.1	0.0481
MA0155.1	MA0155.1	0.347
MA0156.1	MA0156.1	8.91241e-8
MA0157.1	MA0157.1	0.07
MA0159.1	MA0159.1	0.00151
MA0160.1	MA0160.1	0.00324
MA0162.1	MA0162.1	0.151
MA0163.1	MA0163.1	0.00108
MA0164.1	MA0164.1	0.876
MA0258.1	MA0258.1	0.0192
MA0259.1	MA0259.1	0.969

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: CNhs11107

Novel motif	Logo	P-value
1	1	0.23
10	10	0.0575
100	100	0.408
101	101	0.849
102	102	0.883
103	103	0.0627
104	104	0.769
105	105	0.618
106	106	0.0497
107	107	0.159
108	108	0.725
109	109	0.00437
11	11	0.075
110	110	0.0443
111	111	0.113
112	112	0.0093
113	113	0.392
114	114	0.449
115	115	0.959
116	116	0.252
117	117	0.00402
118	118	0.493
119	119	0.29
12	12	0.942
120	120	0.983
121	121	0.427
122	122	0.798
123	123	0.00352
124	124	0.0426
125	125	0.309
126	126	0.0269
127	127	0.422
128	128	0.0477
129	129	0.298
13	13	2.07711e-7
130	130	0.0848
131	131	0.507
132	132	0.703
133	133	0.596
134	134	0.0983
135	135	0.421
136	136	0.038
137	137	0.711
138	138	0.858
139	139	0.246
14	14	0.94
140	140	0.071
141	141	0.525
142	142	0.814
143	143	0.416
144	144	0.674
145	145	2.64552e-4
146	146	0.316
147	147	0.247
148	148	0.368
149	149	0.468
15	15	0.226
150	150	0.0507
151	151	0.849
152	152	0.106
153	153	0.825
154	154	0.983
155	155	0.307
156	156	0.00225
157	157	0.353
158	158	0.207
159	159	0.605
160	160	0.162
161	161	0.0435
162	162	0.581
163	163	0.741
164	164	0.0689
165	165	0.0971
166	166	0.964
167	167	0.585
168	168	0.586
169	169	0.00365
17	17	0.0527
18	18	0.862
19	19	0.0691
2	2	0.874
20	20	0.0521
21	21	0.199
22	22	0.134
23	23	0.741
24	24	0.0322
25	25	0.777
26	26	5.7437e-7
27	27	0.604
28	28	0.687
29	29	0.0212
3	3	0.0455
30	30	0.933
31	31	0.986
32	32	0.503
33	33	0.194
34	34	0.594
35	35	0.805
36	36	0.297
37	37	0.0239
38	38	0.533
39	39	0.309
4	4	0.193
40	40	0.151
41	41	0.417
42	42	0.163
43	43	0.127
44	44	0.443
45	45	0.662
46	46	0.133
47	47	0.323
48	48	0.253
49	49	0.245
5	5	0.181
50	50	0.24
51	51	0.777
52	52	0.247
53	53	0.493
54	54	0.967
55	55	0.903
56	56	0.418
57	57	0.726
58	58	0.374
59	59	0.101
6	6	0.978
60	60	0.0388
61	61	0.0345
62	62	0.255
63	63	0.133
64	64	0.619
65	65	0.408
66	66	0.553
67	67	0.487
68	68	0.553
69	69	0.23
7	7	0.0207
70	70	0.121
71	71	0.00588
72	72	0.607
73	73	0.0332
74	74	0.928
75	75	0.049
76	76	0.568
77	77	0.34
78	78	0.00232
79	79	0.546
8	8	0.0627
80	80	0.568
81	81	0.858
82	82	0.229
83	83	0.066
84	84	0.792
85	85	0.176
86	86	0.196
87	87	0.0529
88	88	0.462
89	89	0.789
9	9	0.442
90	90	0.276
91	91	0.0984
92	92	0.24
93	93	0.114
94	94	0.895
95	95	0.0236
96	96	0.47
97	97	0.97
98	98	0.409
99	99	0.411

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: CNhs11107

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011469 mouse cortex- 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)
0001851 (cortex)
0005889 (zygote cortex)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000470 (cell part)

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)
0011469 (mouse cortex- 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
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00004720
+|accession_numbers=CAGE;DRX008948;DRR009822;DRZ001247;DRZ002630;DRZ012597;DRZ013980
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001851,UBERON:0005889,UBERON:0000479,UBERON:0000064,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000470
 |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=chr10:67375368..67375433,-!p1@Zfp365!2.12!227.08!Zfp365;;chr16:91270004..91270023,+!p1@Olig1!1.91!90.78!Olig1;;chr6:55631042..55631102,-!p1@Neurod6!1.87!73.90!Neurod6;;chr5:138199361..138199441,+!p2@Tsc22d4!1.84!126.07!Tsc22d4;;chr12:30219426..30219506,+!p2@Myt1l!1.66!44.49!Myt1l;;chr10:67375342..67375365,-!p3@Zfp365!1.66!44.49!Zfp365;;chr2:61642631..61642684,+!p1@Tbr1!1.66!44.24!Tbr1;;chr19:19185671..19185693,-!p1@Rorb!1.64!98.19!Rorb;;chr11:98190918..98190951,-!p1@Neurod2!1.64!42.96!Neurod2;;chr2:127347067..127347093,-!p1@Kcnip3!1.63!68.79!Kcnip3;;chr7:116154364..116154444,+!p1@Tub!1.62!68.53!Tub;;chr17:48015839..48015915,-!p3@Foxp4!1.61!46.28!Foxp4;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.58!46.28!Pou3f3;;chr6:85463580..85463585,-!p1@Egr4!1.57!35.80!Egr4;;chr3:95032091..95032183,-!p1@Mllt11!1.54!272.59!Mllt11;;chr8:24780125..24780143,+!p1@Zmat4!1.54!47.82!Zmat4;;chr10:67375146..67375208,-!p2@Zfp365!1.53!49.10!Zfp365;;chr2:65683890..65683907,+!p1@Csrnp3!1.50!57.54!Csrnp3;;chr1:179374784..179374800,+!p2@Zfp238!1.49!35.29!Zfp238;;chr16:91225808..91225824,+!p1@Olig2!1.49!29.92!Olig2;;chr2:127347094..127347111,-!p2@Kcnip3!1.43!42.45!Kcnip3;;chr5:98609885..98609900,+!p1@Prdm8!1.43!25.83!Prdm8;;chr13:83663902..83663927,+!p1@Mef2c!1.39!544.16!Mef2c;;chr13:83663868..83663894,+!p2@Mef2c!1.39!327.57!Mef2c;;chr15:76352677..76352737,-!p3@Scrt1!1.37!22.50!Scrt1;;chr12:30220074..30220102,+!p3@Myt1l!1.37!22.25!Myt1l;;chr2:127347042..127347058,-!p3@Kcnip3!1.36!21.74!Kcnip3;;chr2:65768174..65768247,+!p2@Csrnp3!1.35!21.48!Csrnp3;;chr12:30213247..30213333,+!p1@Myt1l!1.35!21.48!Myt1l;;chr4:58956447..58956510,+!p1@Zkscan16!1.34!44.75!Zkscan16;;chr15:76353005..76353021,-!p2@Scrt1!1.34!20.97!Scrt1;;chr2:38206580..38206600,+!p2@Lhx2!1.32!24.29!Lhx2;;chr7:148008023..148008092,-!p1@Zfp941!1.31!46.54!Zfp941;;chr13:83663546..83663560,+!p4@Mef2c!1.29!23.78!Mef2c;;chrX:34442872..34442899,-!p1@Nkrf!1.29!23.78!Nkrf;;chr12:86939997..86940040,+!p4@Jdp2!1.28!18.16!Jdp2;;chr5:122452349..122452377,-!p4@Cux2!1.28!17.90!Cux2;;chr2:38206744..38206766,+!p1@Lhx2!1.26!20.71!Lhx2;;chr2:61642743..61642758,+!p2@Tbr1!1.26!17.39!Tbr1;;chr16:91270091..91270143,+!p2@Olig1!1.22!15.60!Olig1;;chr4:150482563..150482655,-!p2@Camta1!1.21!54.21!Camta1;;chr2:61642558..61642595,+!p3@Tbr1!1.21!15.34!Tbr1;;chr5:122499831..122499891,-!p1@Cux2!1.19!21.99!Cux2;;chr1:57029281..57029326,-!p1@Satb2!1.18!21.74!Satb2;;chr2:115890294..115890334,-!p9@Meis2!1.18!19.18!Meis2;;chr15:76352434..76352488,-!p4@Scrt1!1.18!14.06!Scrt1;;chr11:90252223..90252240,-!p1@Hlf!1.17!114.56!Hlf;;chr12:72149325..72149343,+!p2@Arid4a!1.16!18.67!Arid4a;;chr17:25707623..25707639,-!p1@Sox8!1.15!55.49!Sox8;;chr11:90250944..90250982,-!p2@Hlf!1.14!21.48!Hlf;;chr18:36441119..36441158,+!p2@Pura!1.12!29.92!Pura;;chr2:56967334..56967366,-!p1@Nr4a2!1.12!24.80!Nr4a2;;chr3:95032197..95032208,-!p3@Mllt11!1.12!15.34!Mllt11;;chr13:83663500..83663519,+!p8@Mef2c!1.12!12.27!Mef2c;;chr6:117813087..117813121,+!p1@Zfp239!1.11!45.01!Zfp239;;chrX:90531838..90531861,+!p1@Arx!1.11!15.09!Arx;;chr19:4989964..4989972,-!p1@Npas4!1.10!11.51!Npas4;;chr2:77654815..77654872,-!p2@Zfp385b!1.09!14.06!Zfp385b;;chr8:87297878..87297935,-!p3@Nfix!1.07!23.78!Nfix;;chr7:30092993..30093076,+!p1@Dpf1!1.07!18.41!Dpf1;;chr18:69680960..69681007,+!p10@Tcf4!1.07!14.06!Tcf4;;chr4:22415443..22415506,-!p1@Pou3f2!1.07!10.74!Pou3f2;;chr12:54349410..54349461,+!p1@Npas3!1.06!12.53!Npas3;;chr19:59533221..59533271,+!p1@Emx2!1.05!12.79!Emx2;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!1.04!104.08!Camta2;;chr8:87297280..87297326,-!p2@Nfix!1.03!23.27!Nfix;;chr5:125342568..125342602,+!p2@Zfp664!1.03!16.11!Zfp664;;chr6:72850124..72850210,-!p7@Kcmf1!1.03!12.79!Kcmf1;;chr2:162769220..162769252,+!p1@L3mbtl1!1.03!9.72!L3mbtl1;;chr7:71083876..71083932,-!p2@Klf13!1.02!76.20!Klf13;;chr19:23216132..23216157,+!p3@Klf9!1.02!15.09!Klf9;;chr19:19185697..19185711,-!p2@Rorb!1.02!12.27!Rorb;;chr13:78339134..78339185,-!p5@Nr2f1!1.01!11.51!Nr2f1;;chr15:78994907..78994926,-!p1@Sox10!1.00!23.27!Sox10;;chr3:34548909..34548927,+!p1@Sox2!1.00!15.60!Sox2;;chr1:179372411..179372509,+!p1@Zfp238!0.99!113.79!Zfp238;;chr14:13178147..13178185,-!p1@Fezf2!0.99!8.69!Fezf2;;chr3:95032213..95032226,-!p6@Mllt11!0.98!10.23!Mllt11;;chr10:13685585..13685645,+!p2@Hivep2!0.97!29.66!Hivep2;;chr2:25562263..25562314,+!p2@Bmyc!0.96!32.22!Bmyc;;chr14:13178361..13178386,-!p2@Fezf2!0.96!8.18!Fezf2;;chr2:71367142..71367167,+!p2@Dlx1!0.96!8.18!Dlx1;;chr4:154335024..154335039,+!p1@Hes5!0.95!9.72!Hes5;;chr10:84218800..84218829,+!p2@Rfx4!0.95!7.93!Rfx4;;chr4:150513630..150513686,-!p4@Camta1!0.94!8.95!Camta1;;chr13:83643031..83643049,+!p11@Mef2c!0.94!7.67!Mef2c;;chr3:95032184..95032195,-!p4@Mllt11!0.93!9.46!Mllt11;;chr11:96685444..96685473,-!p5@Nfe2l1!0.93!7.42!Nfe2l1;;chr7:146768691..146768707,-!p1@Nkx6-2!0.93!7.42!Nkx6-2;;chr10:80893711..80893784,-!p3@Nfic!0.91!38.87!Nfic;;chr11:23980664..23980706,+!p2@Bcl11a!0.91!31.96!Bcl11a;;chr15:100430414..100430470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b2;;chr6:146744563..146744594,+!p1@Arntl2!0.50!4.60!Arntl2;;chr8:87324171..87324182,-!p6@Nfix!0.50!4.35!Nfix;;chr9:48644284..48644305,-!p4@Zbtb16!0.50!3.07!Zbtb16;;chr9:56266431..56266488,+!p2@Hmg20a!0.49!28.90!Hmg20a;;chr14:76814601..76814630,+!p5@Tsc22d1!0.49!16.62!Tsc22d1;;chr17:27693525..27693538,+!p5@Hmga1!0.49!8.95!Hmga1;;chr13:31717548..31717596,+!p1@Foxf2!0.49!4.86!Foxf2;;chr10:22451100..22451111,-!p5@Tbpl1!0.49!4.35!Tbpl1;;chr4:135840623..135840632,+!p5@Zfp46!0.49!3.07!Zfp46;;chr4:129118044..129118067,-!p1@Zbtb8b!0.49!2.81!Zbtb8b;;chr2:48805082..48805137,+!p1@Mbd5!0.48!56.77!Mbd5;;chr7:148513409..148513455,-!p2@Deaf1!0.48!12.27!Deaf1;;chr11:62545367..62545412,-!p1@Zfp287!0.48!10.48!Zfp287;;chr4:108131994..108132056,+!p2@Zcchc11!0.48!8.44!Zcchc11;;chr7:135020324..135020368,-!p4@Zfp668!0.48!7.42!Zfp668;;chr15:98126545..98126588,-!p1@Zfp641!0.48!5.37!Zfp641;;chr4:102787521..102787588,+!p4@Mier1!0.48!4.35!Mier1;;chr4:119486912..119486954,+!p3@Hivep3!0.48!4.09!Hivep3;;chr3:8667033..8667046,-!p3@Hey1!0.48!3.07!Hey1;;chr1:38684414..38684427,-!p7@Aff3!0.48!2.56!Aff3;;chr12:109241852..109241873,-!p4@Bcl11b!0.48!2.56!Bcl11b;;chr2:77654793..77654805,-!p7@Zfp385b!0.48!2.05!Zfp385b;;chr4:82145232..82145259,-!p9@Nfib!0.48!2.05!Nfib;;chr8:12395629..12395644,+!p6@Sox1!0.48!2.05!Sox1;;chrX:70656436..70656464,+!p1@Zfp92!0.48!2.05!Zfp92;;chr15:82742573..82742620,-!p2@Tcf20!0.48!2.05!Tcf20;;chr2:181501710..181501742,+!p2@Myt1!0.48!2.05!Myt1;;chr2:181501745..181501778,+!p1@Myt1!0.48!2.05!Myt1;;chr1:179372514..179372525,+!p7@Zfp238!0.48!2.05!Zfp238;;chr6:6812962..6812979,+!p1@Dlx6!0.48!2.05!Dlx6;;chr6:144152701..144152714,-!p24@Sox5!0.48!2.05!Sox5;;chr12:3806003..3806031,+!p11@Dnmt3a!0.48!2.05!Dnmt3a;;chr11:62602904..62602945,-!p1@Zfp286!0.47!12.02!Zfp286;;chr16:33380881..33380909,+!p1@Zfp148!0.47!11.25!Zfp148;;chr2:44965856..44965896,-!p5@Zeb2!0.47!9.72!Zeb2;;chr3:30500978..30501018,+!p1@Mynn!0.47!6.65!Mynn;;chr19:26681226..26681299,+!p7@Smarca2!0.47!5.63!Smarca2;;chr6:134780163..134780197,+!p2@Crebl2!0.47!5.63!Crebl2;;chr10:127896265..127896276,+!p4@Smarcc2!0.47!4.09!Smarcc2;;chr6:146744595..146744613,+!p2@Arntl2!0.47!3.84!Arntl2;;chr15:81633139..81633152,+!p4@Tef!0.47!3.84!Tef;;chr16:43503493..43503570,+!p9@Zbtb20!0.47!3.84!Zbtb20;;chr12:4484016..4484074,-!p1@Ncoa1!0.46!42.19!Ncoa1;;chr9:121669118..121669179,+!p1@Zfp651!0.46!27.62!Zfp651;;chr1:38684260..38684312,-!p2@Aff3!0.46!17.90!Aff3;;chr4:149862477..149862553,+!p3@Rere!0.46!8.69!Rere;;chr2:25562315..25562344,+!p3@Bmyc!0.46!8.18!Bmyc;;chr6:92042363..92042413,+!p3@Nr2c2!0.46!5.63!Nr2c2;;chr10:67000609..67000625,+!p1@Egr2!0.46!5.37!Egr2;;chr9:87626083..87626108,-!p1@Tbx18!0.46!5.11!Tbx18;;chr17:46520518..46520571,+!p2@Zfp318!0.46!5.11!Zfp318;;chr18:3281750..3281776,-!p2@Crem!0.46!4.60!Crem;;chr9:106356278..106356292,+!p3@Pcbp4!0.46!3.84!Pcbp4;;chr17:46520492..46520515,+!p4@Zfp318!0.46!3.07!Zfp318;;chr3:87946458..87946467,+!p6@Mef2d!0.46!2.56!Mef2d;;chr7:38558544..38558566,-!p4@Zfp536!0.46!2.30!Zfp536;;chr11:23978229..23978268,+!p8@Bcl11a!0.46!2.30!Bcl11a;;chr5:67698180..67698216,+!p1@Slc30a9!0.45!65.72!Slc30a9;;chr2:25562346..25562433,+!p1@Bmyc!0.45!46.28!Bmyc;;chr16:23988711..23988727,-!p1@Bcl6!0.45!29.66!Bcl6;;chr19:28085628..28085671,-!p1@Rfx3!0.45!17.13!Rfx3;;chr16:22439654..22439676,-!p2@Etv5!0.45!14.58!Etv5;;chr14:76903992..76904056,+!p6@Tsc22d1!0.45!4.60!Tsc22d1;;chr11:98602203..98602266,+!p4@Thra!0.45!3.32!Thra;;chr19:23215554..23215567,+!p5@Klf9!0.45!2.81!Klf9;;chr7:38557752..38557793,-!p3@Zfp536!0.45!2.30!Zfp536;;chr6:6832076..6832092,-!p1@Dlx5!0.45!2.30!Dlx5;;chr19:53403997..53404008,+!p7@Mxi1!0.45!2.05!Mxi1;;chr16:91225654..91225671,+!p2@Olig2!0.45!1.79!Olig2;;chr2:73110004..73110016,+!p2@Sp9!0.45!1.79!Sp9;;chr3:34549144..34549155,+!p5@Sox2!0.45!1.79!Sox2;;chr2:77541362..77541382,-!p8@Zfp385b!0.45!1.79!Zfp385b;;chr7:52960663..52960677,+!p6@Dbp!0.45!1.79!Dbp;;chr14:13178323..13178347,-!p3@Fezf2!0.45!1.79!Fezf2;;chr13:44936106..44936121,+!p13@Jarid2!0.45!1.79!Jarid2;;chr15:76352740..76352781,-!p5@Scrt1!0.45!1.79!Scrt1;;chr12:50483663..50483678,+!p3@Foxg1!0.45!1.79!Foxg1;;chr2:151907338..151907360,+!p2@Scrt2!0.45!1.79!Scrt2;;chr1:179374862..179374873,+!p6@Zfp238!0.45!1.79!Zfp238;;chr2:181501988..181502026,+!p3@Myt1!0.45!1.79!Myt1;;chr19:59533429..59533470,+!p4@Emx2!0.45!1.79!Emx2;;chr15:76701830..76701883,-!p1@Zfp251!0.44!33.50!Zfp251;;chr7:25292331..25292421,+!p1@Zfp428!0.44!17.39!Zfp428;;chr6:38204109..38204155,-!p1@D630045J12Rik!0.44!12.79!D630045J12Rik;;chr5:110539286..110539317,+!p2@Zfp605!0.44!5.37!Zfp605;;chr18:69753108..69753139,+!p8@Tcf4!0.44!4.35!Tcf4;;chr5:125659510..125659517,-!p3@Ncor2!0.44!2.81!Ncor2;;chr7:17200198..17200209,-!p8@Grlf1!0.44!2.56!Grlf1;;chr5:107003725..107003746,-!p5@Zfp644!0.44!2.56!Zfp644;;chr12:39506841..39506848,+!p7@Etv1!0.44!2.30!Etv1;;chr18:35721854..35721914,+!p1@Matr3!0.43!184.37!Matr3;;chr5:107125549..107125605,-!p1@Zfp644!0.43!42.19!Zfp644;;chr17:23723181..23723236,-!p1@Zfp13!0.43!22.76!Zfp13;;chr2:160698681..160698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Zfp420!0.32!10.48!Zfp420;;chr15:100325682..100325698,-!p1@Csrnp2!0.32!8.18!Csrnp2;;chrX:66613481..66613562,+!p1@Aff2!0.32!7.42!Aff2;;chr2:128769721..128769770,-!p1@Zc3h8!0.32!6.65!Zc3h8;;chr7:7124057..7124084,+!p1@Zfp418!0.32!5.88!Zfp418;;chr3:87945895..87945946,+!p2@Mef2d!0.32!5.37!Mef2d;;chr16:43619101..43619151,+!p6@Zbtb20!0.32!3.84!Zbtb20;;chr12:119539732..119539762,-!p3@Sp4!0.32!3.58!Sp4;;chr6:47827547..47827568,+!p4@Zfp282!0.32!3.58!Zfp282;;chr18:79306029..79306059,-!p2@Setbp1!0.32!3.32!Setbp1;;chr2:35960919..35960954,-!p1@Lhx6!0.32!2.81!Lhx6;;chr6:115310872..115310899,+!p2@Pparg!0.32!2.56!Pparg;;chr2:44965761..44965785,-!p13@Zeb2!0.32!2.05!Zeb2;;chr17:87153519..87153533,+!p5@Epas1!0.32!2.05!Epas1;;chr17:32501360..32501371,-!p5@Wiz!0.32!2.05!Wiz;;chr11:16952347..16952366,-!p2@Plek!0.32!2.05!Plek;;chr1:38684383..38684394,-!p4@Aff3!0.32!1.79!Aff3;;chr4:149610794..149610876,+!p2@LOC100045967,p2@LOC100503183,p3@Eno1,p3@Gm5506!0.32!1.79!Eno1;;chr18:69753145..69753159,+!p14@Tcf4!0.32!1.79!Tcf4;;chr7:31741624..31741643,-!p7@LOC100504922,p7@Usf2!0.32!1.53!Usf2;;chr11:121121297..121121369,+!p1@Foxk2!0.31!107.91!Foxk2;;chr9:122775056..122775117,-!p1@Zfp445!0.31!62.65!Zfp445;;chr15:99532709..99532743,+!p1@Smarcd1!0.31!48.07!Smarcd1;;chr6:98978245..98978289,-!p1@Foxp1!0.31!26.59!Foxp1;;chr2:115891534..115891589,-!p1@Meis2!0.31!25.83!Meis2;;chr13:65380118..65380146,+!p2@Zfp369!0.31!11.76!Zfp369;;chr11:69579472..69579529,+!p1@Zbtb4!0.31!8.69!Zbtb4;;chr14:19071567..19071612,-!p2@Nr1d2!0.31!6.39!Nr1d2;;chr15:99532528..99532550,+!p3@Smarcd1!0.31!5.88!Smarcd1;;chr17:33766353..33766393,+!p2@Zfp414!0.31!4.35!Zfp414;;chr6:35083731..35083742,-!p2@Cnot4!0.31!4.09!Cnot4;;chr13:99954688..99954710,+!p2@Zfp366!0.31!2.81!Zfp366;;chr7:74517732..74517743,-!p4@Mef2a!0.31!2.81!Mef2a;;chr3:103772552..103772584,+!p2@Phtf1!0.31!2.05!Phtf1;;chr15:81575472..81575481,+!p4@Zc3h7b!0.31!1.53!Zc3h7b;;chr18:39649174..39649196,-!p5@Nr3c1!0.31!1.53!Nr3c1;;chr18:69752598..69752607,+!p26@Tcf4!0.31!1.28!Tcf4;;chr17:51972530..51972571,-!p7@Satb1!0.31!1.02!Satb1;;chr17:51965928..51965960,-!p10@Satb1!0.31!1.02!Satb1;;chr17:51972400..51972428,-!p11@Satb1!0.31!1.02!Satb1;;chr17:51971991..51972003,-!p4@Satb1!0.31!1.02!Satb1;;chr18:69681009..69681014,+!p35@Tcf4!0.31!1.02!Tcf4;;chr16:43364036..43364047,+!p28@Zbtb20!0.31!1.02!Zbtb20;;chr4:22415600..22415616,-!p3@Pou3f2!0.31!1.02!Pou3f2;;chr3:98186461..98186476,+!p2@Zfp697!0.31!1.02!Zfp697;;chr4:82145196..82145229,-!p7@Nfib!0.31!1.02!Nfib;;chr6:6813769..6813781,+!p8@Dlx6!0.31!1.02!Dlx6;;chr10:62562530..62562540,+!p1@Atoh7!0.31!1.02!Atoh7;;chr11:50641158..50641165,-!p3@Zfp354c!0.31!1.02!Zfp354c;;chr9:91263649..91263666,+!p3@Zic4!0.31!1.02!Zic4;;chr8:87297330..87297365,-!p5@Nfix!0.31!1.02!Nfix;;chrX:137083127..137083138,-!p9@Tsc22d3!0.31!1.02!Tsc22d3;;chr8:12395670..12395682,+!p3@Sox1!0.31!1.02!Sox1;;chr9:96632593..96632620,-!p12@Zbtb38!0.31!1.02!Zbtb38;;chr13:31717597..31717613,+!p2@Foxf2!0.31!1.02!Foxf2;;chr14:69808725..69808748,+!p1@Nkx3-1!0.31!1.02!Nkx3-1;;chr13:83643232..83643254,+!p5@Mef2c!0.31!1.02!Mef2c;;chr14:70477182..70477191,+!p5@Egr3!0.31!1.02!Egr3;;chr14:76815156..76815181,+!p16@Tsc22d1!0.31!1.02!Tsc22d1;;chr2:163030164..163030178,+!p6@Tox2!0.31!1.02!Tox2;;chr7:13404186..13404214,-!p1@Zfp329!0.30!35.03!Zfp329;;chr5:146041333..146041379,+!p@chr5:146041333..146041379,+!0.30!13.30!Zfp498;;chr18:69504157..69504184,+!p3@Tcf4!0.30!10.74!Tcf4;;chr11:50872733..50872809,+!p1@Zfp354a!0.30!7.67!Zfp354a;;chrX:109714331..109714347,+!p1@Zfp711!0.30!6.65!Zfp711;;chr7:148513599..148513636,-!p3@Deaf1!0.30!6.39!Deaf1;;chr6:48552000..48552042,+!p@chr6:48552000..48552042,+!0.30!4.60!Zfp775;;chr9:55785981..55786009,-!p2@Scaper!0.30!4.09!Scaper;;chr15:50721616..50721632,-!p4@Trps1!0.30!4.09!Trps1;;chr11:50745114..50745144,-!p1@Zfp354b!0.30!3.84!Zfp354b;;chr1:33871319..33871333,-!p3@Zfp451!0.30!3.58!Zfp451;;chr8:4613211..4613224,+!p3@Zfp958!0.30!3.07!Zfp958;;chr13:67229127..67229153,+!p2@Zfp759!0.30!2.81!Zfp759;;chr7:74517982..74518012,-!p2@Mef2a!0.30!2.56!Mef2a;;chr8:87237732..87237745,-!p7@Nfix!0.30!2.05!Nfix;;chr7:148513548..148513560,-!p7@Deaf1!0.30!2.05!Deaf1;;chr6:92041506..92041517,+!p5@Nr2c2!0.30!1.79!Nr2c2;;chr16:18587076..18587106,-!p1@Tbx1!0.30!1.79!Tbx1;;chr18:3281725..3281740,-!p3@Crem!0.30!1.53!Crem;;chrX:109714433..109714444,+!p2@Zfp711!0.30!1.53!Zfp711;;chr4:13670661..13670681,+!p12@Runx1t1!0.30!1.28!Runx1t1;;chr6:99471206..99471219,-!p12@Foxp1!0.30!1.28!Foxp1;;chr2:120389531..120389614,-!p1@Zfp106!0.29!130.93!Zfp106;;chr8:28087578..28087599,+!p2@Zfp703!0.29!16.37!Zfp703;;chr6:99470943..99471024,-!p3@Foxp1!0.29!16.37!Foxp1;;chr7:5003165..5003203,+!p2@Zfp580!0.29!9.21!Zfp580;;chr4:61869460..61869521,-!p1@Zfp37!0.29!8.69!Zfp37;;chr10:30523091..30523182,-!p4@Ncoa7!0.29!5.37!Ncoa7;;chr6:14851287..14851342,+!p1@Foxp2!0.29!5.11!Foxp2;;chr7:30875490..30875555,-!p1@Zfp566,p1@Zfp82!0.29!4.35!Zfp566;;chr12:78063146..78063159,-!p2@Max!0.29!3.84!Max;;chr13:67229155..67229187,+!p1@Zfp759!0.29!3.58!Zfp759;;chr1:18173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+|ffid_belonging_in_development=FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 40: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011469
 |is_obsolete=
+|library_id=CNhs11107
+|library_id_phase_based=2:CNhs11107
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1392
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1392
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cortex%252c%2520neonate%2520N30.CNhs11107.1392-42F2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/cortex%252c%2520neonate%2520N30.CNhs11107.1392-42F2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cortex%252c%2520neonate%2520N30.CNhs11107.1392-42F2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cortex%252c%2520neonate%2520N30.CNhs11107.1392-42F2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/cortex%252c%2520neonate%2520N30.CNhs11107.1392-42F2.mm9.nobarcode.rdna.fa.gz
 |name=cortex, neonate N30
 |namespace=FANTOM5
@@ Line 45: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11107,LSID733,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.105007143608148,0,0,0,0,0,0.257230528340089,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0553791725433985,0,0,0,0,0,0.305966219492192,0,0,0,0,0,0,0,-0.459531552055981,0,0,0,0,0.0338557610151762,-0.0299344245062049,0.179388300989621,0.0242500436034698,0.711147156869823,0.311383363712143,0,0,0,0,0,0,0,0,0,0,0.09889124026805,0,-0.0660055475634404,0,0,0,0,0.0376836003944056,0,0,0,0,0.0320681718505592,-0.0788061589841934,-0.211759417071336,0.882230490805136,0.105897162996102,0,0,0.184471132311466,0.120505792362096,0,0,0.178022338646539,0.0755028374499913,0.0885473306023236,-0.0788315948399074,0.0103969186453698,0,0,0,0,0,0,0.0199579491165949,0.191477034124847,0,0,0.518703292570475,0,0
 |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=table111:1392-42F2;search_select_hide=table117:1392-42F2
 }}

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FF:1392-42F2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11107

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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