FF:11636-122C7: Difference between revisions

Latest revision as of 18:12, 4 June 2020

Name:	Mouse Granule cells, donor3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12108
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	brain
dev stage	NA
sex	NA
age	NA
cell type	neuron, granule cell
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNAMG1
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004673

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12108		CAGE		DRX008822		DRR009694

Accession ID Mm9

Library id		BAM		CTSS
CNhs12108		DRZ001119		DRZ002504

Accession ID Mm10

Library id		BAM		CTSS
CNhs12108		DRZ012469		DRZ013854

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

CNhs12108

0	0
1	0.356
10	0
100	0.441
1000	0
1001	-0.0749
1002	0.00879
1003	-0.102
1004	0
1005	-0.0389
1006	0.243
1007	-0.09
1008	0
1009	-0.19
101	-0.233
1010	0
1011	0.355
1012	0
1013	0.0793
1014	0
1015	0.367
1016	0.315
1017	0
1018	0
1019	0
102	0
1020	0.826
1021	0
1022	-0.0704
1023	0
1024	-0.205
1025	-0.0611
1026	0
1027	0.213
1028	0
1029	-0.176
103	-0.0754
1030	0
1031	-0.333
1032	-0.0798
1033	0.032
1034	0
1035	0
1036	-0.183
1037	0
1038	0.0249
1039	-0.138
104	0
1040	-0.121
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: CNhs12108

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00637
MA0003.1	MA0003.1	0.204
MA0004.1	MA0004.1	0.678
MA0006.1	MA0006.1	0.0807
MA0007.1	MA0007.1	0.106
MA0009.1	MA0009.1	0.769
MA0014.1	MA0014.1	0.472
MA0017.1	MA0017.1	3.68511e-5
MA0018.2	MA0018.2	0.013
MA0019.1	MA0019.1	0.345
MA0024.1	MA0024.1	0.987
MA0025.1	MA0025.1	0.833
MA0027.1	MA0027.1	0.833
MA0028.1	MA0028.1	0.227
MA0029.1	MA0029.1	0.857
MA0030.1	MA0030.1	0.476
MA0031.1	MA0031.1	0.0963
MA0035.2	MA0035.2	0.228
MA0038.1	MA0038.1	0.511
MA0039.2	MA0039.2	0.0184
MA0040.1	MA0040.1	0.777
MA0041.1	MA0041.1	0.216
MA0042.1	MA0042.1	0.454
MA0043.1	MA0043.1	0.117
MA0046.1	MA0046.1	1.39928e-6
MA0047.2	MA0047.2	0.00242
MA0048.1	MA0048.1	0.22
MA0050.1	MA0050.1	1.53129e-11
MA0051.1	MA0051.1	1.01478e-5
MA0052.1	MA0052.1	0.0981
MA0055.1	MA0055.1	0.322
MA0057.1	MA0057.1	0.117
MA0058.1	MA0058.1	0.65
MA0059.1	MA0059.1	0.463
MA0060.1	MA0060.1	0.00366
MA0061.1	MA0061.1	0.0478
MA0062.2	MA0062.2	0.0175
MA0065.2	MA0065.2	9.21863e-5
MA0066.1	MA0066.1	0.22
MA0067.1	MA0067.1	0.935
MA0068.1	MA0068.1	0.991
MA0069.1	MA0069.1	0.113
MA0070.1	MA0070.1	0.182
MA0071.1	MA0071.1	0.309
MA0072.1	MA0072.1	0.297
MA0073.1	MA0073.1	0.821
MA0074.1	MA0074.1	0.37
MA0076.1	MA0076.1	0.704
MA0077.1	MA0077.1	0.00163
MA0078.1	MA0078.1	0.0256
MA0079.2	MA0079.2	0.689
MA0080.2	MA0080.2	6.44829e-10
MA0081.1	MA0081.1	0.302
MA0083.1	MA0083.1	0.0199
MA0084.1	MA0084.1	0.549
MA0087.1	MA0087.1	0.592
MA0088.1	MA0088.1	0.113
MA0090.1	MA0090.1	0.0226
MA0091.1	MA0091.1	0.286
MA0092.1	MA0092.1	0.197
MA0093.1	MA0093.1	0.683
MA0099.2	MA0099.2	2.34104e-4
MA0100.1	MA0100.1	0.668
MA0101.1	MA0101.1	0.0272
MA0102.2	MA0102.2	0.411
MA0103.1	MA0103.1	0.255
MA0104.2	MA0104.2	0.583
MA0105.1	MA0105.1	0.0386
MA0106.1	MA0106.1	0.0529
MA0107.1	MA0107.1	0.0262
MA0108.2	MA0108.2	0.647
MA0111.1	MA0111.1	0.861
MA0112.2	MA0112.2	1.52346e-4
MA0113.1	MA0113.1	0.214
MA0114.1	MA0114.1	1.18299e-4
MA0115.1	MA0115.1	0.0289
MA0116.1	MA0116.1	0.0922
MA0117.1	MA0117.1	0.7
MA0119.1	MA0119.1	0.0951
MA0122.1	MA0122.1	0.754
MA0124.1	MA0124.1	0.892
MA0125.1	MA0125.1	0.159
MA0131.1	MA0131.1	0.943
MA0135.1	MA0135.1	0.143
MA0136.1	MA0136.1	1.63631e-9
MA0137.2	MA0137.2	0.00255
MA0138.2	MA0138.2	0.124
MA0139.1	MA0139.1	0.402
MA0140.1	MA0140.1	0.00655
MA0141.1	MA0141.1	0.0153
MA0142.1	MA0142.1	0.00324
MA0143.1	MA0143.1	0.00259
MA0144.1	MA0144.1	0.0086
MA0145.1	MA0145.1	0.0702
MA0146.1	MA0146.1	0.047
MA0147.1	MA0147.1	0.654
MA0148.1	MA0148.1	5.61224e-6
MA0149.1	MA0149.1	0.109
MA0150.1	MA0150.1	0.027
MA0152.1	MA0152.1	0.0665
MA0153.1	MA0153.1	7.41492e-6
MA0154.1	MA0154.1	0.0163
MA0155.1	MA0155.1	0.784
MA0156.1	MA0156.1	2.16272e-7
MA0157.1	MA0157.1	0.0504
MA0159.1	MA0159.1	0.00641
MA0160.1	MA0160.1	0.0769
MA0162.1	MA0162.1	0.328
MA0163.1	MA0163.1	0.00721
MA0164.1	MA0164.1	0.832
MA0258.1	MA0258.1	0.01
MA0259.1	MA0259.1	0.515

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: CNhs12108

Novel motif	Logo	P-value
1	1	0.147
10	10	0.0984
100	100	0.656
101	101	0.91
102	102	0.997
103	103	0.0516
104	104	0.953
105	105	0.277
106	106	0.0104
107	107	0.0598
108	108	0.425
109	109	0.00571
11	11	0.106
110	110	0.061
111	111	0.0548
112	112	0.00285
113	113	0.924
114	114	0.368
115	115	0.583
116	116	0.638
117	117	0.017
118	118	0.6
119	119	0.134
12	12	0.634
120	120	0.749
121	121	0.322
122	122	0.541
123	123	0.0899
124	124	0.554
125	125	0.361
126	126	0.322
127	127	0.0888
128	128	0.0518
129	129	0.186
13	13	4.49477e-6
130	130	0.233
131	131	0.435
132	132	0.763
133	133	0.602
134	134	0.464
135	135	0.738
136	136	0.321
137	137	0.197
138	138	0.565
139	139	0.141
14	14	0.671
140	140	0.0135
141	141	0.239
142	142	0.00826
143	143	0.962
144	144	0.911
145	145	0.0114
146	146	0.461
147	147	0.769
148	148	0.801
149	149	0.344
15	15	0.127
150	150	0.138
151	151	0.49
152	152	0.0507
153	153	0.555
154	154	0.581
155	155	0.645
156	156	0.0127
157	157	0.0555
158	158	0.124
159	159	0.0361
160	160	0.29
161	161	0.328
162	162	0.681
163	163	0.437
164	164	0.00561
165	165	0.0622
166	166	0.507
167	167	0.912
168	168	0.77
169	169	0.00368
17	17	0.0114
18	18	0.511
19	19	0.0692
2	2	0.859
20	20	0.341
21	21	0.595
22	22	0.116
23	23	0.314
24	24	0.0342
25	25	0.663
26	26	9.6553e-5
27	27	0.918
28	28	0.318
29	29	0.0846
3	3	0.0602
30	30	0.849
31	31	0.896
32	32	0.56
33	33	0.143
34	34	0.675
35	35	0.479
36	36	0.35
37	37	0.0102
38	38	0.345
39	39	0.2
4	4	0.618
40	40	0.357
41	41	0.967
42	42	0.196
43	43	0.142
44	44	0.874
45	45	0.622
46	46	0.102
47	47	0.295
48	48	0.154
49	49	0.171
5	5	0.163
50	50	0.228
51	51	0.55
52	52	0.117
53	53	0.655
54	54	0.778
55	55	0.73
56	56	0.382
57	57	0.835
58	58	0.203
59	59	0.0964
6	6	0.705
60	60	0.00878
61	61	0.168
62	62	0.116
63	63	0.109
64	64	0.787
65	65	0.331
66	66	0.691
67	67	0.908
68	68	0.108
69	69	0.757
7	7	0.0195
70	70	0.035
71	71	0.00972
72	72	0.376
73	73	0.0219
74	74	0.618
75	75	0.0749
76	76	0.683
77	77	0.242
78	78	0.0144
79	79	0.548
8	8	0.138
80	80	0.975
81	81	0.577
82	82	0.155
83	83	0.358
84	84	0.738
85	85	0.0928
86	86	0.225
87	87	0.309
88	88	0.193
89	89	0.321
9	9	0.409
90	90	0.077
91	91	0.538
92	92	0.295
93	93	0.0153
94	94	0.833
95	95	0.0446
96	96	0.318
97	97	0.96
98	98	0.987
99	99	0.348

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: CNhs12108

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000108 mouse granule cell 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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000120 (granule cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000108 (mouse granule cell 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
CL:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000073,UBERON:0004121,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0001017,UBERON:0001016,UBERON:0000924,UBERON:0005743,UBERON:0006601
+|DRA_sample_Accession=CAGE@SAMD00004673
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000540,CL:0000055,CL:0000047,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002371,CL:0002319,CL:0000221,CL:0000117,CL:0000393,CL:0000220,CL:0000004,CL:0000031,CL:0000211,CL:0000404,CL:0000255,CL:0000120,CL:0000133,CL:0000337
+|accession_numbers=CAGE;DRX008822;DRR009694;DRZ001119;DRZ002504;DRZ012469;DRZ013854
+|ancestors_in_anatomy_facet=
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0000120
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000108
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr1:140739014..140739032,-!p1@Lhx9!2.03!133.74!Lhx9;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.93!103.95!Pou3f3;;chr19:55969923..55969944,+!p6@Tcf7l2!1.91!81.13!Tcf7l2;;chr9:91260594..91260612,-!p1@Zic1!1.91!79.86!Zic1;;chrX:108009761..108009788,+!p1@Pou3f4!1.88!74.16!Pou3f4;;chr14:104867201..104867258,-!p1@Pou4f1!1.86!98.24!Pou4f1;;chr5:28492230..28492257,+!p1@En2!1.83!67.19!En2;;chr16:91270004..91270023,+!p1@Olig1!1.79!69.72!Olig1;;chr12:28027561..28027591,-!p1@Sox11!1.78!367.62!Sox11;;chr4:154335024..154335039,+!p1@Hes5!1.78!70.36!Hes5;;chr7:56892217..56892221,-!p1@Dbx1!1.76!57.04!Dbx1;;chr14:49287186..49287225,-!p1@Otx2!1.76!56.41!Otx2;;chr9:99776566..99776612,-!p1@Sox14!1.75!55.78!Sox14;;chr2:38206580..38206600,+!p2@Lhx2!1.74!65.92!Lhx2;;chr19:55969946..55969973,+!p8@Tcf7l2!1.72!51.34!Tcf7l2;;chr3:95032091..95032183,-!p1@Mllt11!1.71!403.12!Mllt11;;chr7:30088977..30089002,+!p2@Dpf1!1.71!67.82!Dpf1;;chr11:84339016..84339044,-!p1@Lhx1!1.70!49.44!Lhx1;;chr9:91260616..91260653,-!p2@Zic1!1.70!48.81!Zic1;;chr13:72766250..72766273,+!p1@Irx2!1.67!69.72!Irx2;;chr7:116154364..116154444,+!p1@Tub!1.65!72.89!Tub;;chr12:54349410..54349461,+!p1@Npas3!1.64!50.71!Npas3;;chr1:19199236..19199258,+!p1@Tfap2b!1.64!42.47!Tfap2b;;chr17:48015839..48015915,-!p3@Foxp4!1.59!44.37!Foxp4;;chr19:55968967..55968991,+!p7@Tcf7l2!1.59!38.03!Tcf7l2;;chr1:19199151..19199170,+!p3@Tfap2b!1.58!37.40!Tfap2b;;chr7:25292331..25292421,+!p1@Zfp428!1.57!244.03!Zfp428;;chr3:101814061..101814094,+!p1@Nhlh2!1.57!36.13!Nhlh2;;chr7:144505957..144505972,-!p2@Ebf3!1.56!43.73!Ebf3;;chr10:86956396..86956411,-!p1@Ascl1!1.53!49.44!Ascl1;;chr2:28771056..28771092,-!p1@Barhl1!1.53!32.96!Barhl1;;chr5:106887474..106887489,-!p1@Barhl2!1.53!32.96!Barhl2;;chr7:144506077..144506128,-!p1@Ebf3!1.50!68.45!Ebf3;;chr13:72766279..72766296,+!p2@Irx2!1.49!44.37!Irx2;;chr1:19199079..19199092,+!p7@Tfap2b!1.49!29.79!Tfap2b;;chrX:58146612..58146615,-!p1@Sox3!1.44!26.62!Sox3;;chr1:19199095..19199114,+!p5@Tfap2b!1.42!25.35!Tfap2b;;chr19:55969887..55969904,+!p9@Tcf7l2!1.42!25.35!Tcf7l2;;chr5:120881900..120881914,+!p1@Lhx5!1.42!25.35!Lhx5;;chr7:30092993..30093076,+!p1@Dpf1!1.41!41.83!Dpf1;;chr13:56353536..56353542,-!p1@Neurog1!1.40!24.09!Neurog1;;chr14:118636238..118636257,-!p2@Sox21!1.40!24.09!Sox21;;chr2:146047829..146047847,+!p1@Insm1!1.39!41.83!Insm1;;chr3:34548909..34548927,+!p1@Sox2!1.39!39.30!Sox2;;chr14:118636214..118636235,-!p1@Sox21!1.39!27.89!Sox21;;chr4:53792566..53792578,+!p1@Tal2!1.39!23.45!Tal2;;chr1:19199119..19199134,+!p4@Tfap2b!1.39!23.45!Tfap2b;;chr7:144505980..144506010,-!p3@Ebf3!1.38!27.89!Ebf3;;chr15:76352832..76352900,-!p1@Scrt1!1.38!22.82!Scrt1;;chr7:91558472..91558512,-!p2@Arnt2!1.37!31.69!Arnt2;;chr3:95032197..95032208,-!p3@Mllt11!1.36!27.25!Mllt11;;chr2:38206744..38206766,+!p1@Lhx2!1.36!26.62!Lhx2;;chr1:122499088..122499099,+!p2@En1!1.34!20.92!En1;;chr1:140739042..140739054,-!p2@Lhx9!1.34!20.92!Lhx9;;chr7:25292160..25292213,+!p3@Zfp428!1.33!49.44!Zfp428;;chr2:151907546..151907561,+!p1@Scrt2!1.33!20.28!Scrt2;;chr11:98190918..98190951,-!p1@Neurod2!1.33!20.28!Neurod2;;chr2:79296783..79296801,-!p1@Neurod1!1.33!20.28!Neurod1;;chr13:72101161..72101177,-!p2@Irx1!1.31!26.62!Irx1;;chr3:66785857..66785873,-!p1@Shox2!1.31!19.65!Shox2;;chr3:127336052..127336058,+!p1@Neurog2!1.31!19.65!Neurog2;;chr5:140019865..140019886,+!p1@Uncx!1.30!19.01!Uncx;;chr14:122874619..122874634,+!p1@Zic2!1.30!19.01!Zic2;;chr15:76352677..76352737,-!p3@Scrt1!1.29!18.38!Scrt1;;chr1:19199193..19199207,+!p11@Tfap2b!1.29!18.38!Tfap2b;;chr12:30213247..30213333,+!p1@Myt1l!1.27!17.75!Myt1l;;chr4:124334894..124334899,+!p1@Pou3f1!1.25!21.55!Pou3f1;;chr5:106887496..106887515,-!p2@Barhl2!1.24!16.48!Barhl2;;chr9:99776617..99776631,-!p2@Sox14!1.24!16.48!Sox14;;chr5:148000254..148000260,+!p1@Gsx1!1.24!16.48!Gsx1;;chr4:22415443..22415506,-!p1@Pou3f2!1.23!15.85!Pou3f2;;chr15:76352740..76352781,-!p5@Scrt1!1.23!15.85!Scrt1;;chr2:70313168..70313184,+!p1@Sp5!1.22!23.45!Sp5;;chr13:72101178..72101203,-!p1@Irx1!1.21!23.45!Irx1;;chr15:76353005..76353021,-!p2@Scrt1!1.21!15.21!Scrt1;;chr4:44717334..44717367,-!p5@Pax5!1.21!15.21!Pax5;;chr4:115612528..115612533,-!p1@Dmbx1!1.21!15.21!Dmbx1;;chrX:55283799..55283813,+!p1@Zic3!1.21!15.21!Zic3;;chr13:48356475..48356492,+!p1@Id4!1.19!309.94!Id4;;chr2:65683890..65683907,+!p1@Csrnp3!1.19!27.89!Csrnp3;;chr2:9809357..9809371,-!p2@Gata3!1.19!14.58!Gata3;;chr5:140019843..140019858,+!p2@Uncx!1.19!14.58!Uncx;;chr8:12395603..12395621,+!p1@Sox1!1.19!14.58!Sox1;;chr16:91225808..91225824,+!p1@Olig2!1.19!14.58!Olig2;;chr2:9800207..9800234,-!p1@Gata3!1.17!41.83!Gata3;;chr13:44936126..44936164,+!p6@Jarid2!1.17!15.85!Jarid2;;chr4:13670499..13670526,+!p2@Runx1t1!1.16!29.79!Runx1t1;;chr1:19199221..19199234,+!p6@Tfap2b!1.16!13.31!Tfap2b;;chr1:78193687..78193692,-!p1@Pax3!1.16!13.31!Pax3;;chr13:72101141..72101158,-!p3@Irx1!1.15!16.48!Irx1;;chr4:13670571..13670625,+!p1@Runx1t1!1.14!34.86!Runx1t1;;chr7:91558392..91558434,-!p1@Arnt2!1.14!34.86!Arnt2;;chr19:59533221..59533271,+!p1@Emx2!1.14!15.85!Emx2;;chr2:28771380..28771413,-!p2@Barhl1!1.14!12.68!Barhl1;;chr1:19202352..19202354,+!p2@Tfap2b!1.14!12.68!Tfap2b;;chr10:84218895..84218909,+!p1@Rfx4!1.14!12.68!Rfx4;;chr11:21901608..21901634,-!p1@Otx1!1.12!12.04!Otx1;;chr4:139388835..139388867,-!p1@Pax7!1.12!12.04!Pax7;;chr2:115891534..115891589,-!p1@Meis2!1.10!162.26!Meis2;;chr1:170361991..170362015,-!p6@Pbx1!1.09!25.35!Pbx1;;chr1:173987720..173987729,-!p1@Nhlh1!1.09!11.41!Nhlh1;;chr7:30089006..30089022,+!p3@Dpf1!1.09!11.41!Dpf1;;chr12:30219426..30219506,+!p2@Myt1l!1.09!11.41!Myt1l;;chr3:95032184..95032195,-!p4@Mllt11!1.07!13.31!Mllt11;;chr4:13669922..13669957,+!p13@Runx1t1!1.07!10.78!Runx1t1;;chr9:74709695..74709722,+!p1@Onecut1!1.07!10.78!Onecut1;;chrX:55284180..55284195,+!p2@Zic3!1.07!10.78!Zic3;;chr1:19199064..19199075,+!p10@Tfap2b!1.07!10.78!Tfap2b;;chr1:122498955..122498968,+!p1@En1!1.07!10.78!En1;;chr12:87762578..87762612,+!p1@Esrrb!1.07!10.78!Esrrb;;chr2:34227446..34227511,-!p1@Pbx3!1.05!23.45!Pbx3;;chr4:107353376..107353452,-!p3@Dmrtb1!1.05!10.14!Dmrtb1;;chr10:79957600..79957618,+!p1@Onecut3!1.05!10.14!Onecut3;;chr19:55816546..55816556,+!p3@Tcf7l2!1.04!38.03!Tcf7l2;;chr8:94325321..94325366,-!p1@Irx3!1.04!24.72!Irx3;;chr8:94881872..94881887,+!p2@Irx5!1.04!10.78!Irx5;;chr7:25292141..25292158,+!p2@Zfp428!1.03!34.23!Zfp428;;chr5:107003725..107003746,-!p5@Zfp644!1.02!12.68!Zfp644;;chr4:150503457..150503498,-!p3@Camta1!1.02!10.78!Camta1;;chr4:13678482..13678505,+!p9@Runx1t1!1.02!9.51!Runx1t1;;chr2:181501745..181501778,+!p1@Myt1!1.02!9.51!Myt1;;chr3:130813200..130813252,+!p1@Lef1!1.01!41.83!Lef1;;chr13:78339428..78339466,-!p2@Nr2f1!1.01!12.68!Nr2f1;;chr4:129118044..129118067,-!p1@Zbtb8b!1.00!11.41!Zbtb8b;;chr17:37139472..37139514,+!p1@Zfp57!0.99!60.85!Zfp57;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.99!24.09!Zfhx3;;chr1:189821714..189821761,+!p1@Esrrg!0.99!16.48!Esrrg;;chr2:181501710..181501742,+!p2@Myt1!0.99!8.87!Myt1;;chr5:98609885..98609900,+!p1@Prdm8!0.99!8.87!Prdm8;;chr4:13670626..13670657,+!p5@Runx1t1!0.98!13.31!Runx1t1;;chr2:152223734..152223756,-!p6@Sox12!0.98!10.14!Sox12;;chr6:55631042..55631102,-!p1@Neurod6!0.97!8.24!Neurod6;;chr6:64679112..64679126,+!p1@Atoh1!0.97!8.24!Atoh1;;chr4:22415600..22415616,-!p3@Pou3f2!0.97!8.24!Pou3f2;;chr17:37140628..37140631,+!p2@Zfp57!0.96!16.48!Zfp57;;chr13:29045559..29045574,-!p1@Sox4!0.95!677.57!Sox4;;chr19:7342725..7342784,+!p1@Rcor2!0.95!33.59!Rcor2;;chr2:152223783..152223812,-!p4@Sox12!0.95!18.38!Sox12;;chr3:34548946..34548972,+!p2@Sox2!0.95!8.87!Sox2;;chr9:21420744..21420755,+!p3@Smarca4!0.94!22.82!Smarca4;;chr4:122673278..122673336,+!p1@Mycl1!0.93!24.72!Mycl1;;chr7:135019147..135019187,-!p3@Zfp668!0.93!17.11!Zfp668;;chr2:56967334..56967366,-!p1@Nr4a2!0.93!15.85!Nr4a2;;chr7:25292246..25292259,+!p6@Zfp428!0.93!9.51!Zfp428;;chr13:78338076..78338104,-!p4@Nr2f1!0.93!9.51!Nr2f1;;chr10:84218800..84218829,+!p2@Rfx4!0.93!7.61!Rfx4;;chr4:107353563..107353590,-!p6@Dmrtb1!0.93!7.61!Dmrtb1;;chr18:77094894..77094905,+!p2@Skor2!0.93!7.61!Skor2;;chr9:106356211..106356242,+!p1@Pcbp4!0.91!144.51!Pcbp4;;chr8:111227738..111227793,+!p@chr8:111227738..111227793,+!0.91!18.38!Zfhx3;;chr7:25292310..25292329,+!p5@Zfp428!0.91!10.14!Zfp428;;chr7:91558537..91558558,-!p4@Arnt2!0.91!8.87!Arnt2;;chr5:107003699..107003717,-!p11@Zfp644!0.91!8.24!Zfp644;;chr2:163028808..163028869,+!p1@Tox2!0.90!25.99!Tox2;;chr8:111227354..111227401,+!p@chr8:111227354..111227401,+!0.90!9.51!Zfhx3;;chrX:108009734..108009752,+!p2@Pou3f4!0.90!6.97!Pou3f4;;chr17:35031631..35031645,+!p5@Zbtb12!0.90!6.97!Zbtb12;;chr17:86020156..86020183,+!p1@Six3!0.90!6.97!Six3;;chr13:40825465..40825469,-!p2@Tfap2a!0.90!6.97!Tfap2a;;chr2:65768174..65768247,+!p2@Csrnp3!0.90!6.97!Csrnp3;;chr2:147012125..147012149,-!p1@Nkx2-2!0.90!6.97!Nkx2-2;;chr19:55969687..55969714,+!p16@Tcf7l2!0.90!6.97!Tcf7l2;;chr19:55968937..55968951,+!p21@Tcf7l2!0.90!6.97!Tcf7l2;;chr1:19199021..19199048,+!p8@Tfap2b!0.90!6.97!Tfap2b;;chr3:95032558..95032641,-!p2@Mllt11!0.89!39.93!Mllt11;;chr5:122499831..122499891,-!p1@Cux2!0.89!10.78!Cux2;;chr11:116196664..116196679,-!p1@Foxj1!0.89!10.78!Foxj1;;chr8:24780125..24780143,+!p1@Zmat4!0.89!10.14!Zmat4;;chr3:95032213..95032226,-!p6@Mllt11!0.89!8.24!Mllt11;;chr8:94881733..94881790,+!p1@Irx5!0.88!13.31!Irx5;;chr8:94325273..94325288,-!p5@Irx3!0.88!8.24!Irx3;;chr15:100325682..100325698,-!p1@Csrnp2!0.87!31.06!Csrnp2;;chr4:150482563..150482655,-!p2@Camta1!0.87!24.09!Camta1;;chr12:3891810..3891829,+!p2@Dnmt3a!0.87!10.14!Dnmt3a;;chr2:152223586..152223604,-!p5@Sox12!0.87!9.51!Sox12;;chr15:40486883..40486903,+!p4@Zfpm2!0.87!8.87!Zfpm2;;chr4:114730254..114730276,+!p2@Tal1!0.87!8.24!Tal1;;chr4:107353508..107353547,-!p4@Dmrtb1!0.87!6.34!Dmrtb1;;chr4:44717308..44717321,-!p6@Pax5!0.87!6.34!Pax5;;chr5:106886962..106886973,-!p3@Barhl2!0.87!6.34!Barhl2;;chr2:31495237..31495243,+!p1@Prdm12!0.87!6.34!Prdm12;;chr11:21901587..21901604,-!p2@Otx1!0.87!6.34!Otx1;;chr13:44936077..44936096,+!p9@Jarid2!0.87!6.34!Jarid2;;chr14:4928710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@Smarce1!0.28!1.90!Smarce1;;chr11:23978353..23978379,+!p10@Bcl11a!0.28!1.27!Bcl11a;;chr16:43503594..43503634,+!p15@Zbtb20!0.28!1.27!Zbtb20;;chr6:14851344..14851364,+!p6@Foxp2!0.28!1.27!Foxp2;;chr5:31262571..31262582,-!p4@Preb!0.28!1.27!Preb;;chr19:9016729..9016740,+!p6@Mta2!0.28!1.27!Mta2;;chr2:168032563..168032642,-!p2@Adnp!0.27!100.78!Adnp;;chr19:55816300..55816332,+!p1@Tcf7l2!0.27!79.23!Tcf7l2;;chr7:13595144..13595205,-!p1@Zbtb45!0.27!32.33!Zbtb45;;chr10:57206160..57206220,+!p1@Hsf2!0.27!17.75!Hsf2;;chr6:48395426..48395504,-!p2@Zfp467!0.27!15.21!Zfp467;;chr7:134170310..134170341,-!p5@Maz!0.27!14.58!Maz;;chr8:108375881..108375936,-!p1@Cenpt!0.27!13.94!Cenpt;;chr7:6107541..6107572,-!p1@Zfp787!0.27!12.04!Zfp787;;chr7:30739068..30739108,-!p1@Zfp74!0.27!12.04!Zfp74;;chr15:100382390..100382441,-!p1@Tfcp2!0.27!10.78!Tfcp2;;chr10:5958538..5958568,+!p1@Zbtb2!0.27!6.97!Zbtb2;;chr1:64167851..64167886,-!p3@Klf7!0.27!6.34!Klf7;;chr8:72498134..72498156,-!p7@Gatad2a!0.27!5.70!Gatad2a;;chr4:151401710..151401733,-!p2@Zbtb48!0.27!4.44!Zbtb48;;chr17:13897299..13897342,+!p3@Mllt4!0.27!3.17!Mllt4;;chr18:14130694..14130697,-!p2@Zfp521!0.27!3.17!Zfp521;;chr11:3190303..3190351,+!p3@Patz1!0.27!2.54!Patz1;;chr13:31717548..31717596,+!p1@Foxf2!0.27!2.54!Foxf2;;chr5:65194810..65194819,+!p9@Klf3!0.27!2.54!Klf3;;chr11:98789140..98789168,+!p5@Rara!0.27!1.90!Rara;;chr12:100802129..100802145,-!p4@Foxn3!0.27!1.90!Foxn3;;chr11:44431710..44431725,+!p7@Ebf1!0.27!1.90!Ebf1;;chr3:5218563..5218587,+!p5@Zfhx4!0.27!1.90!Zfhx4;;chr2:17976799..17976829,+!p5@Mllt10!0.27!1.27!Mllt10;;chr2:168427252..168427273,-!p2@Nfatc2!0.27!1.27!Nfatc2;;chr13:29045252..29045271,-!p5@Sox4!0.27!1.27!Sox4;;chr15:50721503..50721514,-!p15@Trps1!0.27!1.27!Trps1;;chrX:20527671..20527719,-!p1@Elk1!0.26!36.76!Elk1;;chr10:85379647..85379751,-!p1@Prdm4!0.26!17.75!Prdm4;;chr17:4994904..4994953,+!p3@Arid1b!0.26!12.04!Arid1b;;chr6:72849946..72849979,-!p2@Kcmf1!0.26!8.87!Kcmf1;;chr2:181100154..181100181,+!p3@Zgpat!0.26!7.61!Zgpat;;chr17:4994697..4994730,+!p4@Arid1b!0.26!6.97!Arid1b;;chr9:65675514..65675547,-!p2@Zfp609!0.26!6.97!Zfp609;;chr11:98603160..98603171,+!p3@Thra!0.26!6.97!Thra;;chr16:55966525..55966543,+!p5@Rpl24,p5@Zbtb11!0.26!5.07!Zbtb11;;chr16:17531086..17531109,-!p3@Thap7!0.26!4.44!Thap7;;chrX:71330995..71331011,-!p2@Mecp2!0.26!4.44!Mecp2;;chr3:90097217..90097233,+!p3@Gatad2b!0.26!3.17!Gatad2b;;chr16:43619101..43619151,+!p6@Zbtb20!0.26!3.17!Zbtb20;;chrX:45947787..45947812,-!p3@Zfp280c!0.26!2.54!Zfp280c;;chr5:22939752..22939768,+!p5@Mll5!0.26!2.54!Mll5;;chr10:5958477..5958503,+!p4@Zbtb2!0.26!1.90!Zbtb2;;chr4:133310137..133310152,-!p12@Arid1a!0.26!1.90!Arid1a;;chr4:99322820..99322845,+!p1@Foxd3!0.26!1.27!Foxd3;;chr4:142802570..142802581,-!p2@Prdm2!0.26!1.27!Prdm2;;chr6:52141694..52141715,-!p1@Hoxa4!0.26!1.27!Hoxa4;;chr6:92041372..92041383,+!p6@Nr2c2!0.26!1.27!Nr2c2;;chr6:98978189..98978198,-!p10@Foxp1!0.26!1.27!Foxp1;;chr15:81575472..81575481,+!p4@Zc3h7b!0.26!1.27!Zc3h7b;;chr16:95923586..95923598,+!p5@Ets2!0.26!1.27!Ets2;;chr17:25152634..25152648,-!p8@Cramp1l!0.26!1.27!Cramp1l;;chr7:77511622..77511657,-!p5@Nr2f2!0.26!1.27!Nr2f2;;chr11:98614826..98614845,+!p9@Thra!0.26!1.27!Thra;;chr8:125897678..125897746,+!p1@Tcf25!0.25!323.89!Tcf25;;chr7:133839456..133839523,+!p1@Bola2!0.25!80.50!Bola2;;chr11:112643496..112643562,+!p1@Sox9!0.25!59.58!Sox9;;chr7:4966247..4966286,-!p1@Fiz1!0.25!31.06!Fiz1;;chr8:81923316..81923334,-!p1@Smad1!0.25!24.72!Smad1;;chr7:13551180..13551243,+!p1@Zfp324!0.25!12.68!Zfp324;;chr6:88148650..88148669,+!p1@Gata2!0.25!12.68!Gata2;;chr7:135019614..135019666,-!p1@Zfp668!0.25!12.68!Zfp668;;chr9:69137716..69137744,+!p1@Rora!0.25!9.51!Rora;;chr16:17530781..17530882,-!p2@Thap7!0.25!8.87!Thap7;;chr16:3847206..3847307,+!p1@Zfp174!0.25!6.97!Zfp174;;chr17:69732690..69732734,+!p1@Zfp161!0.25!5.70!Zfp161;;chr7:88138585..88138600,+!p2@Zfp592!0.25!3.80!Zfp592;;chr4:126703093..126703158,+!p3@Sfpq!0.25!3.80!Sfpq;;chr7:16986617..16986632,+!p2@Zc3h4!0.25!3.80!Zc3h4;;chr15:102034510..102034549,+!p4@Zfp740!0.25!3.17!Zfp740;;
+|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000108
 |is_obsolete=
+|library_id=CNhs12108
+|library_id_phase_based=2:CNhs12108
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11636
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11636
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Granule%2520cells%252c%2520donor3.CNhs12108.11636-122C7.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Granule cells, donor3
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12108,LSID839,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0111919767001525,0,0,0,0,0,-0.56560648034262,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.574336056956007,-0.558422792324031,0,0,0,0,0,-0.209322725495826,0.274717397313647,-0.0668600171762983,0.10952420234914,0.695794320357973,0.681511539650463,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,-0.0240929458105596,0,0,0,-0.0958388010569529,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,0.115833574805628,0.213207239280454,0,0,0.0973991026720268,0.206166971266778,-0.0474854609494575,-0.0788315948399074,0,0,0,0,0,0,0.0891552085376298,0.0709294268737839,0.218010362146814,0,0,0.355578477054666,0.532583551226426,0
 |rna_box=122
 |rna_catalog_number=custom
@@ Line 58: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=N/A
 |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=table111:11636-122C7;search_select_hide=table117:11636-122C7
 }}

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FF:11636-122C7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:12, 4 June 2020

CNhs12108

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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