FF:627-43G1: Difference between revisions

Latest revision as of 19:18, 4 June 2020

Name:	hippocampus, neonate N00
Species:	Mouse (Mus musculus)
Library ID:	CNhs11228
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	hippocampus
dev stage	0 day 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		SAMD00005607

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11228		CAGE		DRX008987		DRR009861

Accession ID Mm9

Library id		BAM		CTSS
CNhs11228		DRZ001286		DRZ002669

Accession ID Mm10

Library id		BAM		CTSS
CNhs11228		DRZ012636		DRZ014019

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

CNhs11228

0	0
1	0.423
10	0
100	0.369
1000	-0.0142
1001	0.0441
1002	0.139
1003	0.729
1004	0.0425
1005	0
1006	0.267
1007	0.121
1008	0
1009	-0.19
101	0.0323
1010	0
1011	0.335
1012	0.285
1013	-0.031
1014	-0.0133
1015	0.274
1016	0.262
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.04
1022	-0.0704
1023	0
1024	-0.0583
1025	0.0425
1026	0
1027	0.568
1028	0
1029	0.131
103	-0.0754
1030	0
1031	-0.275
1032	-0.0953
1033	0.0425
1034	0
1035	0
1036	-0.106
1037	0
1038	0.0666
1039	-0.127
104	0
1040	-0.134
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: CNhs11228

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00107
MA0003.1	MA0003.1	0.157
MA0004.1	MA0004.1	0.665
MA0006.1	MA0006.1	0.125
MA0007.1	MA0007.1	0.325
MA0009.1	MA0009.1	0.582
MA0014.1	MA0014.1	0.454
MA0017.1	MA0017.1	1.89779e-6
MA0018.2	MA0018.2	0.0647
MA0019.1	MA0019.1	0.159
MA0024.1	MA0024.1	0.631
MA0025.1	MA0025.1	0.515
MA0027.1	MA0027.1	0.0816
MA0028.1	MA0028.1	0.526
MA0029.1	MA0029.1	0.259
MA0030.1	MA0030.1	0.986
MA0031.1	MA0031.1	0.1
MA0035.2	MA0035.2	0.0065
MA0038.1	MA0038.1	0.0921
MA0039.2	MA0039.2	0.0837
MA0040.1	MA0040.1	0.55
MA0041.1	MA0041.1	0.255
MA0042.1	MA0042.1	0.59
MA0043.1	MA0043.1	0.091
MA0046.1	MA0046.1	2.86319e-14
MA0047.2	MA0047.2	2.88853e-5
MA0048.1	MA0048.1	0.4
MA0050.1	MA0050.1	1.88117e-4
MA0051.1	MA0051.1	0.0189
MA0052.1	MA0052.1	1.37714e-4
MA0055.1	MA0055.1	0.392
MA0057.1	MA0057.1	0.134
MA0058.1	MA0058.1	0.543
MA0059.1	MA0059.1	0.354
MA0060.1	MA0060.1	0.0071
MA0061.1	MA0061.1	0.0659
MA0062.2	MA0062.2	0.132
MA0065.2	MA0065.2	1.32893e-6
MA0066.1	MA0066.1	0.0732
MA0067.1	MA0067.1	0.79
MA0068.1	MA0068.1	0.767
MA0069.1	MA0069.1	0.0353
MA0070.1	MA0070.1	0.44
MA0071.1	MA0071.1	0.0475
MA0072.1	MA0072.1	0.0382
MA0073.1	MA0073.1	0.689
MA0074.1	MA0074.1	0.164
MA0076.1	MA0076.1	0.951
MA0077.1	MA0077.1	0.078
MA0078.1	MA0078.1	0.601
MA0079.2	MA0079.2	0.576
MA0080.2	MA0080.2	3.5459e-10
MA0081.1	MA0081.1	0.494
MA0083.1	MA0083.1	6.77577e-4
MA0084.1	MA0084.1	0.323
MA0087.1	MA0087.1	0.73
MA0088.1	MA0088.1	0.341
MA0090.1	MA0090.1	0.0318
MA0091.1	MA0091.1	0.255
MA0092.1	MA0092.1	0.23
MA0093.1	MA0093.1	0.688
MA0099.2	MA0099.2	3.4404e-5
MA0100.1	MA0100.1	0.989
MA0101.1	MA0101.1	0.0993
MA0102.2	MA0102.2	0.893
MA0103.1	MA0103.1	0.0371
MA0104.2	MA0104.2	0.767
MA0105.1	MA0105.1	0.0178
MA0106.1	MA0106.1	0.158
MA0107.1	MA0107.1	0.0916
MA0108.2	MA0108.2	7.16136e-4
MA0111.1	MA0111.1	0.857
MA0112.2	MA0112.2	5.68311e-5
MA0113.1	MA0113.1	0.286
MA0114.1	MA0114.1	3.13334e-5
MA0115.1	MA0115.1	4.64768e-4
MA0116.1	MA0116.1	0.0392
MA0117.1	MA0117.1	0.894
MA0119.1	MA0119.1	0.169
MA0122.1	MA0122.1	0.972
MA0124.1	MA0124.1	0.729
MA0125.1	MA0125.1	0.13
MA0131.1	MA0131.1	0.767
MA0135.1	MA0135.1	0.435
MA0136.1	MA0136.1	5.06838e-9
MA0137.2	MA0137.2	0.139
MA0138.2	MA0138.2	0.557
MA0139.1	MA0139.1	0.221
MA0140.1	MA0140.1	5.09718e-4
MA0141.1	MA0141.1	1.98965e-4
MA0142.1	MA0142.1	0.221
MA0143.1	MA0143.1	0.114
MA0144.1	MA0144.1	0.0624
MA0145.1	MA0145.1	0.0542
MA0146.1	MA0146.1	0.041
MA0147.1	MA0147.1	0.876
MA0148.1	MA0148.1	1.20069e-6
MA0149.1	MA0149.1	0.0515
MA0150.1	MA0150.1	0.0273
MA0152.1	MA0152.1	0.261
MA0153.1	MA0153.1	9.34583e-13
MA0154.1	MA0154.1	0.017
MA0155.1	MA0155.1	0.412
MA0156.1	MA0156.1	4.80416e-5
MA0157.1	MA0157.1	0.0346
MA0159.1	MA0159.1	3.36566e-4
MA0160.1	MA0160.1	0.00578
MA0162.1	MA0162.1	0.267
MA0163.1	MA0163.1	2.29065e-4
MA0164.1	MA0164.1	0.926
MA0258.1	MA0258.1	0.00188
MA0259.1	MA0259.1	0.557

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: CNhs11228

Novel motif	Logo	P-value
1	1	0.161
10	10	0.12
100	100	0.727
101	101	0.975
102	102	0.852
103	103	0.103
104	104	0.957
105	105	0.188
106	106	0.0118
107	107	0.0551
108	108	0.853
109	109	0.00533
11	11	0.0465
110	110	0.0643
111	111	0.0236
112	112	0.0053
113	113	0.776
114	114	0.127
115	115	0.591
116	116	0.352
117	117	0.0404
118	118	0.438
119	119	0.11
12	12	0.914
120	120	0.665
121	121	0.368
122	122	0.899
123	123	0.355
124	124	0.356
125	125	0.338
126	126	0.0615
127	127	0.0828
128	128	0.0217
129	129	0.0638
13	13	8.14349e-5
130	130	0.754
131	131	0.679
132	132	0.937
133	133	0.816
134	134	0.379
135	135	0.875
136	136	0.104
137	137	0.645
138	138	0.847
139	139	0.181
14	14	0.603
140	140	0.0699
141	141	0.151
142	142	0.154
143	143	0.283
144	144	0.721
145	145	0.0214
146	146	0.414
147	147	0.918
148	148	0.508
149	149	0.0618
15	15	0.147
150	150	0.14
151	151	0.413
152	152	0.0596
153	153	0.681
154	154	0.957
155	155	0.572
156	156	0.0112
157	157	0.454
158	158	0.201
159	159	0.96
160	160	0.196
161	161	0.0773
162	162	0.996
163	163	0.232
164	164	0.0435
165	165	0.0105
166	166	0.782
167	167	0.621
168	168	0.275
169	169	0.00595
17	17	0.0268
18	18	0.696
19	19	0.0749
2	2	0.667
20	20	0.463
21	21	0.49
22	22	0.108
23	23	0.323
24	24	0.035
25	25	0.566
26	26	3.53023e-4
27	27	0.738
28	28	0.447
29	29	0.0901
3	3	0.0505
30	30	0.807
31	31	0.706
32	32	0.289
33	33	0.222
34	34	0.621
35	35	0.915
36	36	0.484
37	37	0.0166
38	38	0.374
39	39	0.219
4	4	0.296
40	40	0.21
41	41	0.364
42	42	0.215
43	43	0.121
44	44	0.239
45	45	0.549
46	46	0.136
47	47	0.136
48	48	0.118
49	49	0.148
5	5	0.118
50	50	0.304
51	51	0.625
52	52	0.137
53	53	0.918
54	54	0.583
55	55	0.578
56	56	0.316
57	57	0.683
58	58	0.253
59	59	0.0329
6	6	0.974
60	60	0.0214
61	61	0.18
62	62	0.139
63	63	0.126
64	64	0.6
65	65	0.215
66	66	0.923
67	67	0.478
68	68	0.894
69	69	0.348
7	7	0.0321
70	70	0.0125
71	71	0.0174
72	72	0.433
73	73	0.0264
74	74	0.521
75	75	0.0936
76	76	0.942
77	77	0.197
78	78	0.00791
79	79	0.468
8	8	0.106
80	80	0.945
81	81	0.487
82	82	0.104
83	83	0.0778
84	84	0.854
85	85	0.0399
86	86	0.185
87	87	0.0626
88	88	0.209
89	89	0.292
9	9	0.383
90	90	0.161
91	91	0.177
92	92	0.141
93	93	0.0381
94	94	0.521
95	95	0.0478
96	96	0.203
97	97	0.976
98	98	0.522
99	99	0.244

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: CNhs11228

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011391 mouse hippocampus- neonate N00 sample

part_of relathionship
UBERON:0002421 hippocampal formation

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)
0001954 (Ammon's horn)
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)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011391 (mouse hippocampus- neonate N00 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0000483,UBERON:0001954,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:0002619,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002780,UBERON:0003022,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0002421,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0005743,UBERON:0000349,UBERON:0002600,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@SAMD00005607
+|accession_numbers=CAGE;DRX008987;DRR009861;DRZ001286;DRZ002669;DRZ012636;DRZ014019
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0001954,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:0002619,UBERON:0001062,UBERON:0000480,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0003022,UBERON:0010317,UBERON:0001017,UBERON:0002421,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0000203,UBERON:0000349,UBERON:0002600
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000304,FF:0011391
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr6:55631042..55631102,-!p1@Neurod6!2.65!447.22!Neurod6;;chr1:179374784..179374800,+!p2@Zfp238!2.34!255.62!Zfp238;;chr2:79296783..79296801,-!p1@Neurod1!2.30!196.86!Neurod1;;chr11:98190918..98190951,-!p1@Neurod2!2.24!172.47!Neurod2;;chr8:87297280..87297326,-!p2@Nfix!2.13!303.57!Nfix;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.84!86.23!Pou3f3;;chr3:95032091..95032183,-!p1@Mllt11!1.82!520.18!Mllt11;;chr12:30213247..30213333,+!p1@Myt1l!1.81!64.11!Myt1l;;chr19:59533221..59533271,+!p1@Emx2!1.76!69.67!Emx2;;chr2:38206744..38206766,+!p1@Lhx2!1.76!68.23!Lhx2;;chr5:98609885..98609900,+!p1@Prdm8!1.76!56.80!Prdm8;;chr2:38206580..38206600,+!p2@Lhx2!1.75!67.40!Lhx2;;chr7:116154364..116154444,+!p1@Tub!1.74!89.84!Tub;;chr2:61642631..61642684,+!p1@Tbr1!1.67!45.79!Tbr1;;chr8:87297330..87297365,-!p5@Nfix!1.66!44.66!Nfix;;chr3:17954233..17954249,+!p1@Bhlhe22!1.66!44.56!Bhlhe22;;chr12:28027561..28027591,-!p1@Sox11!1.65!272.59!Sox11;;chr3:101814061..101814094,+!p1@Nhlh2!1.65!43.63!Nhlh2;;chr17:48015839..48015915,-!p3@Foxp4!1.63!49.09!Foxp4;;chr3:17954392..17954407,+!p2@Bhlhe22!1.63!41.99!Bhlhe22;;chr4:48058129..48058179,+!p2@Nr4a3!1.62!76.15!Nr4a3;;chr16:91270004..91270023,+!p1@Olig1!1.60!44.35!Olig1;;chr9:118387300..118387317,+!p1@Eomes!1.58!37.05!Eomes;;chr1:140739014..140739032,-!p1@Lhx9!1.57!45.28!Lhx9;;chr2:65683890..65683907,+!p1@Csrnp3!1.55!63.90!Csrnp3;;chr16:91225808..91225824,+!p1@Olig2!1.55!34.16!Olig2;;chrX:90531838..90531861,+!p1@Arx!1.54!41.47!Arx;;chr14:13178147..13178185,-!p1@Fezf2!1.48!29.53!Fezf2;;chr1:179374820..179374831,+!p3@Zfp238!1.47!28.40!Zfp238;;chr2:146047829..146047847,+!p1@Insm1!1.46!49.60!Insm1;;chr4:48058016..48058032,+!p3@Nr4a3!1.46!46.00!Nr4a3;;chr18:69680960..69681007,+!p10@Tcf4!1.46!36.43!Tcf4;;chr3:34548909..34548927,+!p1@Sox2!1.45!44.87!Sox2;;chr4:154335024..154335039,+!p1@Hes5!1.45!32.93!Hes5;;chr15:76352832..76352900,-!p1@Scrt1!1.43!26.14!Scrt1;;chr8:12395603..12395621,+!p1@Sox1!1.43!26.03!Sox1;;chr2:71384802..71384815,-!p1@Dlx2!1.41!30.46!Dlx2;;chr8:87297878..87297935,-!p3@Nfix!1.39!50.63!Nfix;;chr7:30088977..30089002,+!p2@Dpf1!1.39!32.00!Dpf1;;chr2:71367142..71367167,+!p2@Dlx1!1.39!23.67!Dlx1;;chr16:43503493..43503570,+!p9@Zbtb20!1.38!38.49!Zbtb20;;chr4:82145196..82145229,-!p7@Nfib!1.38!23.26!Nfib;;chr1:179374862..179374873,+!p6@Zfp238!1.38!23.05!Zfp238;;chr7:30092993..30093076,+!p1@Dpf1!1.37!37.87!Dpf1;;chr11:116196664..116196679,-!p1@Foxj1!1.37!34.27!Foxj1;;chr9:91260594..91260612,-!p1@Zic1!1.36!21.92!Zic1;;chr3:127336052..127336058,+!p1@Neurog2!1.35!21.20!Neurog2;;chr2:56967334..56967366,-!p1@Nr4a2!1.34!42.50!Nr4a2;;chr9:91260616..91260653,-!p2@Zic1!1.34!20.68!Zic1;;chr13:29045321..29045337,-!p2@Sox4!1.32!26.55!Sox4;;chr14:122874619..122874634,+!p1@Zic2!1.32!20.07!Zic2;;chr4:150482563..150482655,-!p2@Camta1!1.30!65.96!Camta1;;chr10:86956396..86956411,-!p1@Ascl1!1.30!29.12!Ascl1;;chr4:48058047..48058062,+!p1@Nr4a3!1.30!28.61!Nr4a3;;chr14:13178361..13178386,-!p2@Fezf2!1.30!18.83!Fezf2;;chr12:54349410..54349461,+!p1@Npas3!1.22!18.73!Npas3;;chrX:58146612..58146615,-!p1@Sox3!1.22!15.64!Sox3;;chr4:82145232..82145259,-!p9@Nfib!1.20!14.92!Nfib;;chr11:23978111..23978134,+!p3@Bcl11a!1.18!29.43!Bcl11a;;chr1:179374764..179374776,+!p5@Zfp238!1.18!14.30!Zfp238;;chr2:151907338..151907360,+!p2@Scrt2!1.18!14.00!Scrt2;;chr4:122673278..122673336,+!p1@Mycl1!1.17!43.43!Mycl1;;chr4:124334894..124334899,+!p1@Pou3f1!1.17!18.01!Pou3f1;;chr12:72149359..72149406,+!p4@Arid4a!1.17!18.01!Arid4a;;chr8:87298020..87298041,-!p9@Nfix!1.17!13.69!Nfix;;chr12:109242266..109242295,-!p1@Bcl11b!1.16!111.34!Bcl11b;;chr7:91558472..91558512,-!p2@Arnt2!1.15!18.63!Arnt2;;chr1:173987720..173987729,-!p1@Nhlh1!1.13!12.45!Nhlh1;;chr4:119960301..119960359,-!p1@Foxo6!1.12!39.31!Foxo6;;chr6:85137520..85137563,+!p1@Emx1!1.09!11.32!Emx1;;chr12:50483639..50483654,+!p1@Foxg1!1.09!11.22!Foxg1;;chr2:71367871..71367898,+!p1@Dlx1!1.08!11.01!Dlx1;;chr11:21901608..21901634,-!p1@Otx1!1.08!11.01!Otx1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.07!20.17!Tsc22d4;;chr11:98602203..98602266,+!p4@Thra!1.07!17.08!Thra;;chr3:34548946..34548972,+!p2@Sox2!1.07!12.04!Sox2;;chr18:69681020..69681032,+!p23@Tcf4!1.07!10.80!Tcf4;;chr14:49287186..49287225,-!p1@Otx2!1.07!10.80!Otx2;;chr12:30219426..30219506,+!p2@Myt1l!1.07!10.70!Myt1l;;chr2:71366660..71366702,+!p3@Dlx1!1.07!10.70!Dlx1;;chr1:6724908..6724955,+!p2@St18!1.07!10.70!St18;;chr11:98190955..98190968,-!p2@Neurod2!1.07!10.70!Neurod2;;chr4:13670499..13670526,+!p2@Runx1t1!1.06!23.15!Runx1t1;;chr13:78339428..78339466,-!p2@Nr2f1!1.06!14.51!Nr2f1;;chr17:37139472..37139514,+!p1@Zfp57!1.05!70.08!Zfp57;;chr13:29045252..29045271,-!p5@Sox4!1.04!12.45!Sox4;;chr13:78339382..78339420,-!p3@Nr2f1!1.03!11.42!Nr2f1;;chr12:50485973..50486015,+!p2@Foxg1!1.03!9.67!Foxg1;;chr11:23980664..23980706,+!p2@Bcl11a!1.02!41.99!Bcl11a;;chr2:127347067..127347093,-!p1@Kcnip3!1.02!16.16!Kcnip3;;chr8:87237732..87237745,-!p7@Nfix!1.02!15.23!Nfix;;chr11:23978229..23978268,+!p8@Bcl11a!1.02!10.80!Bcl11a;;chr6:55631251..55631265,-!p2@Neurod6!1.02!9.36!Neurod6;;chr19:59533429..59533470,+!p4@Emx2!1.01!9.26!Emx2;;chr16:43503594..43503634,+!p15@Zbtb20!1.00!10.91!Zbtb20;;chr5:24104540..24104584,-!p7@Smarcd3!0.99!8.75!Smarcd3;;chr17:25707623..25707639,-!p1@Sox8!0.98!37.35!Sox8;;chr18:69753108..69753139,+!p8@Tcf4!0.98!17.39!Tcf4;;chr13:29045274..29045293,-!p6@Sox4!0.98!10.39!Sox4;;chr5:24104751..24104773,-!p5@Smarcd3!0.98!8.54!Smarcd3;;chr1:6720216..6720232,+!p1@St18!0.98!8.54!St18;;chr19:59533163..59533185,+!p3@Emx2!0.98!8.54!Emx2;;chr4:13670571..13670625,+!p1@Runx1t1!0.97!23.57!Runx1t1;;chr2:152223783..152223812,-!p4@Sox12!0.97!19.45!Sox12;;chr4:54957886..54957907,+!p3@Zfp462!0.97!14.51!Zfp462;;chr18:69753168..69753186,+!p12@Tcf4!0.97!11.42!Tcf4;;chr6:6831950..6831985,-!p2@Dlx5!0.97!9.26!Dlx5;;chr6:6831928..6831949,-!p3@Dlx5!0.97!8.44!Dlx5;;chr2:127347042..127347058,-!p3@Kcnip3!0.97!8.44!Kcnip3;;chr11:23977742..23977794,+!p6@Bcl11a!0.96!10.19!Bcl11a;;chr2:71384458..71384526,-!p2@Dlx2!0.96!8.13!Dlx2;;chr4:13678482..13678505,+!p9@Runx1t1!0.96!8.13!Runx1t1;;chr2:38194778..38194798,+!p3@Lhx2!0.96!8.03!Lhx2;;chr16:43503417..43503436,+!p26@Zbtb20!0.96!8.03!Zbtb20;;chr7:30089006..30089022,+!p3@Dpf1!0.96!8.03!Dpf1;;chr3:95032197..95032208,-!p3@Mllt11!0.95!10.08!Mllt11;;chr11:23978270..23978290,+!p9@Bcl11a!0.95!7.82!Bcl11a;;chr9:18278055..18278126,-!p1@Zfp558!0.94!22.74!Zfp558;;chr18:69504195..69504213,+!p4@Tcf4!0.93!35.71!Tcf4;;chr4:109650609..109650653,+!p1@Dmrta2!0.93!7.51!Dmrta2;;chr7:17062114..17062141,-!p1@Npas1!0.93!7.51!Npas1;;chr7:25292331..25292421,+!p1@Zfp428!0.92!54.33!Zfp428;;chr2:35960919..35960954,-!p1@Lhx6!0.92!14.20!Lhx6;;chr18:69752912..69752928,+!p9@Tcf4!0.92!11.32!Tcf4;;chr1:42752654..42752665,+!p@chr1:42752654..42752665,+!0.92!7.41!Pou3f3;;chr2:79296907..79296918,-!p2@Neurod1!0.92!7.31!Neurod1;;chr4:13678514..13678539,+!p14@Runx1t1!0.91!7.10!Runx1t1;;chr10:84218895..84218909,+!p1@Rfx4!0.91!7.10!Rfx4;;chr16:43619057..43619078,+!p8@Zbtb20!0.90!15.02!Zbtb20;;chr13:78339476..78339515,-!p1@Nr2f1!0.90!10.80!Nr2f1;;chr12:50483663..50483678,+!p3@Foxg1!0.90!7.00!Foxg1;;chr2:61642558..61642595,+!p3@Tbr1!0.90!6.89!Tbr1;;chr6:38204214..38204267,-!p4@D630045J12Rik!0.89!13.17!D630045J12Rik;;chr10:129717274..129717298,-!p1@Neurod4!0.89!6.79!Neurod4;;chr19:59533139..59533152,+!p2@Emx2!0.89!6.79!Emx2;;chr11:98603160..98603171,+!p3@Thra!0.88!32.41!Thra;;chr14:13178241..13178254,-!p4@Fezf2!0.88!6.59!Fezf2;;chr16:43619101..43619151,+!p6@Zbtb20!0.87!16.05!Zbtb20;;chr3:95032184..95032195,-!p4@Mllt11!0.87!8.13!Mllt11;;chr11:23978353..23978379,+!p10@Bcl11a!0.87!7.82!Bcl11a;;chr6:6832076..6832092,-!p1@Dlx5!0.87!7.61!Dlx5;;chr18:69752608..69752625,+!p17@Tcf4!0.87!7.51!Tcf4;;chr2:61642743..61642758,+!p2@Tbr1!0.87!6.48!Tbr1;;chrX:55284180..55284195,+!p2@Zic3!0.87!6.38!Zic3;;chr12:109242296..109242307,-!p3@Bcl11b!0.86!9.36!Bcl11b;;chr12:72149325..72149343,+!p2@Arid4a!0.86!8.85!Arid4a;;chr4:48057987..48057996,+!p7@Nr4a3!0.86!7.31!Nr4a3;;chr4:48058102..48058110,+!p5@Nr4a3!0.86!7.20!Nr4a3;;chr2:73109983..73109996,+!p1@Sp9!0.86!6.28!Sp9;;chr9:96632719..96632745,-!p7@Zbtb38!0.86!6.28!Zbtb38;;chr11:23978291..23978323,+!p7@Bcl11a!0.86!6.17!Bcl11a;;chr2:152223881..152223933,-!p3@Sox12!0.85!21.40!Sox12;;chr1:179372625..179372654,+!p4@Zfp238!0.85!9.78!Zfp238;;chr18:69753145..69753159,+!p14@Tcf4!0.85!8.54!Tcf4;;chrX:34442872..34442899,-!p1@Nkrf!0.85!8.03!Nkrf;;chr7:25372631..25372684,-!p1@Zfp575!0.84!18.83!Zfp575;;chr10:84218800..84218829,+!p2@Rfx4!0.84!5.87!Rfx4;;chr12:50484072..50484092,+!p4@Foxg1!0.84!5.87!Foxg1;;chr4:13669922..13669957,+!p13@Runx1t1!0.84!5.87!Runx1t1;;chr11:98603185..98603208,+!p1@Thra!0.83!371.18!Thra;;chr4:82151178..82151262,-!p1@Nfib!0.82!245.22!Nfib;;chr12:12948633..12948651,-!p1@Mycn!0.82!58.04!Mycn;;chr3:95032558..95032641,-!p2@Mllt11!0.82!33.75!Mllt11;;chr8:87237711..87237727,-!p11@Nfix!0.82!7.61!Nfix;;chr8:79423672..79423727,+!p2@Nr3c2!0.82!7.20!Nr3c2;;chr4:82151274..82151290,-!p3@Nfib!0.81!95.39!Nfib;;chr10:13685585..13685645,+!p2@Hivep2!0.81!20.17!Hivep2;;chr8:87237692..87237703,-!p12@Nfix!0.81!7.41!Nfix;;chr18:69752638..69752665,+!p19@Tcf4!0.81!5.97!Tcf4;;chr16:43510380..43510393,+!p39@Zbtb20!0.81!5.45!Zbtb20;;chr6:55631324..55631335,-!p3@Neurod6!0.81!5.45!Neurod6;;chr2:151907546..151907561,+!p1@Scrt2!0.81!5.45!Scrt2;;chr11:23978022..23978076,+!p1@Bcl11a!0.80!124.62!Bcl11a;;chr5:38215819..38215823,-!p1@Msx1!0.80!14.82!Msx1;;chr5:110539286..110539317,+!p2@Zfp605!0.80!13.58!Zfp605;;chr6:38204274..38204327,-!p3@D630045J12Rik!0.80!11.22!D630045J12Rik;;chr4:13670626..13670657,+!p5@Runx1t1!0.80!8.44!Runx1t1;;chr14:13178323..13178347,-!p3@Fezf2!0.80!5.25!Fezf2;;chr7:148513409..148513455,-!p2@Deaf1!0.79!26.45!Deaf1;;chr19:28085485..28085544,-!p5@Rfx3!0.79!22.02!Rfx3;;chr11:23978078..23978096,+!p4@Bcl11a!0.79!16.98!Bcl11a;;chr7:25292160..25292213,+!p3@Zfp428!0.79!13.79!Zfp428;;chr7:130644017..130644092,-!p1@Zkscan2!0.79!10.50!Zkscan2;;chr2:181501745..181501778,+!p1@Myt1!0.78!5.04!Myt1;;chr4:48058196..48058205,+!p4@Nr4a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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011391
 |is_obsolete=
+|library_id=CNhs11228
+|library_id_phase_based=2:CNhs11228
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;627
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;627
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/hippocampus%252c%2520neonate%2520N00.CNhs11228.627-43G1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/hippocampus%252c%2520neonate%2520N00.CNhs11228.627-43G1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/hippocampus%252c%2520neonate%2520N00.CNhs11228.627-43G1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/hippocampus%252c%2520neonate%2520N00.CNhs11228.627-43G1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/hippocampus%252c%2520neonate%2520N00.CNhs11228.627-43G1.mm9.nobarcode.rdna.fa.gz
 |name=hippocampus, neonate N00
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11228,LSID748,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.139072923758276,0,0,0,0,0,0.096169841100307,0,0.021268976479071,0,0,-0.0418012874383994,0,0,0,0,0,0,0.115398568541624,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.441578098056209,0,0,0,0,0.0425379529581421,0.105498783380314,0.164041650951529,-0.129519056898555,0.285224255158421,0.893990413048877,0,0,0,0,0,0,0,0,0,0,0,0.0425379529581421,-0.0660055475634404,0,0,0,0,0,0,0,0,0,0.0230413082077658,0.0125806044478246,0.0181265077169351,0.514428527039046,0.151938045607929,0,0,0.146009345730993,0.0190073371593207,0,0,0.152397144547042,0.109084371702505,-0.0429286257929932,-0.0362936418817653,0,0,0,0,0.021268976479071,0,-0.0490518619379706,0.00887443597125603,0.00164912753994668,0,0,0.0812786020093627,0,0
 |rna_box=43
 |rna_catalog_number=
@@ Line 59: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:627-43G1;search_select_hide=table117:627-43G1
 }}

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FF:627-43G1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:18, 4 June 2020

CNhs11228

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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