FF:820-7A2: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	thymus, neonate N20
Species:	Mouse (Mus musculus)
Library ID:	CNhs11186
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	thymus
dev stage	20 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		SAMD00004712

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11186		CAGE		DRX009123		DRR009997

Accession ID Mm9

Library id		BAM		CTSS
CNhs11186		DRZ001422		DRZ002805

Accession ID Mm10

Library id		BAM		CTSS
CNhs11186		DRZ012772		DRZ014155

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

CNhs11186

0	0
1	0
10	0
100	0
1000	-0.0355
1001	0.0981
1002	-0.0537
1003	-0.0838
1004	0
1005	0.143
1006	-0.14
1007	0.0617
1008	0.111
1009	-0.0886
101	0.0894
1010	0
1011	0.0404
1012	0.536
1013	-0.157
1014	-0.0874
1015	0.0156
1016	-0.483
1017	0
1018	0.0773
1019	0
102	0.0773
1020	0
1021	0.0286
1022	-0.27
1023	0
1024	-0.135
1025	-0.0611
1026	0
1027	0
1028	0
1029	0.356
103	-0.0788
1030	0.0404
1031	-0.738
1032	-0.469
1033	0.0449
1034	0
1035	0
1036	0.0906
1037	0
1038	-0.257
1039	-0.177
104	0
1040	-0.0865
1041	0.0404

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: CNhs11186

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	4.92799e-4
MA0003.1	MA0003.1	0.428
MA0004.1	MA0004.1	0.392
MA0006.1	MA0006.1	0.794
MA0007.1	MA0007.1	0.519
MA0009.1	MA0009.1	0.454
MA0014.1	MA0014.1	0.233
MA0017.1	MA0017.1	0.921
MA0018.2	MA0018.2	0.0523
MA0019.1	MA0019.1	0.642
MA0024.1	MA0024.1	0.00468
MA0025.1	MA0025.1	0.0102
MA0027.1	MA0027.1	0.645
MA0028.1	MA0028.1	1.60227e-4
MA0029.1	MA0029.1	0.143
MA0030.1	MA0030.1	0.701
MA0031.1	MA0031.1	0.273
MA0035.2	MA0035.2	0.37
MA0038.1	MA0038.1	0.626
MA0039.2	MA0039.2	0.22
MA0040.1	MA0040.1	0.997
MA0041.1	MA0041.1	0.241
MA0042.1	MA0042.1	0.944
MA0043.1	MA0043.1	0.083
MA0046.1	MA0046.1	2.59624e-14
MA0047.2	MA0047.2	0.702
MA0048.1	MA0048.1	0.886
MA0050.1	MA0050.1	8.11051e-8
MA0051.1	MA0051.1	3.05998e-6
MA0052.1	MA0052.1	6.21576e-4
MA0055.1	MA0055.1	0.405
MA0057.1	MA0057.1	0.73
MA0058.1	MA0058.1	0.664
MA0059.1	MA0059.1	0.0588
MA0060.1	MA0060.1	0.695
MA0061.1	MA0061.1	1.17116e-5
MA0062.2	MA0062.2	1.19128e-14
MA0065.2	MA0065.2	0.45
MA0066.1	MA0066.1	0.00798
MA0067.1	MA0067.1	0.507
MA0068.1	MA0068.1	0.961
MA0069.1	MA0069.1	0.834
MA0070.1	MA0070.1	0.423
MA0071.1	MA0071.1	0.456
MA0072.1	MA0072.1	4.61998e-5
MA0073.1	MA0073.1	0.772
MA0074.1	MA0074.1	0.882
MA0076.1	MA0076.1	1.47848e-5
MA0077.1	MA0077.1	0.168
MA0078.1	MA0078.1	0.74
MA0079.2	MA0079.2	0.0323
MA0080.2	MA0080.2	1.16205e-13
MA0081.1	MA0081.1	0.0263
MA0083.1	MA0083.1	0.066
MA0084.1	MA0084.1	0.347
MA0087.1	MA0087.1	0.374
MA0088.1	MA0088.1	0.487
MA0090.1	MA0090.1	0.0355
MA0091.1	MA0091.1	0.0571
MA0092.1	MA0092.1	0.963
MA0093.1	MA0093.1	0.464
MA0099.2	MA0099.2	0.218
MA0100.1	MA0100.1	0.024
MA0101.1	MA0101.1	1.06221e-4
MA0102.2	MA0102.2	0.833
MA0103.1	MA0103.1	9.83106e-5
MA0104.2	MA0104.2	0.213
MA0105.1	MA0105.1	9.89957e-9
MA0106.1	MA0106.1	0.666
MA0107.1	MA0107.1	6.34631e-5
MA0108.2	MA0108.2	0.0112
MA0111.1	MA0111.1	0.283
MA0112.2	MA0112.2	0.0074
MA0113.1	MA0113.1	0.697
MA0114.1	MA0114.1	0.442
MA0115.1	MA0115.1	0.659
MA0116.1	MA0116.1	0.00437
MA0117.1	MA0117.1	0.81
MA0119.1	MA0119.1	0.968
MA0122.1	MA0122.1	0.845
MA0124.1	MA0124.1	0.414
MA0125.1	MA0125.1	0.228
MA0131.1	MA0131.1	0.267
MA0135.1	MA0135.1	0.167
MA0136.1	MA0136.1	1.45624e-21
MA0137.2	MA0137.2	0.103
MA0138.2	MA0138.2	6.43836e-5
MA0139.1	MA0139.1	0.2
MA0140.1	MA0140.1	0.511
MA0141.1	MA0141.1	0.54
MA0142.1	MA0142.1	0.436
MA0143.1	MA0143.1	0.326
MA0144.1	MA0144.1	0.497
MA0145.1	MA0145.1	0.459
MA0146.1	MA0146.1	0.428
MA0147.1	MA0147.1	0.109
MA0148.1	MA0148.1	0.53
MA0149.1	MA0149.1	0.0582
MA0150.1	MA0150.1	0.593
MA0152.1	MA0152.1	0.914
MA0153.1	MA0153.1	4.33631e-9
MA0154.1	MA0154.1	0.0616
MA0155.1	MA0155.1	0.976
MA0156.1	MA0156.1	3.11567e-23
MA0157.1	MA0157.1	0.484
MA0159.1	MA0159.1	0.102
MA0160.1	MA0160.1	0.511
MA0162.1	MA0162.1	0.532
MA0163.1	MA0163.1	0.00334
MA0164.1	MA0164.1	0.665
MA0258.1	MA0258.1	0.0245
MA0259.1	MA0259.1	0.831

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: CNhs11186

Novel motif	Logo	P-value
1	1	0.167
10	10	0.012
100	100	0.827
101	101	0.663
102	102	0.56
103	103	0.181
104	104	0.8
105	105	0.754
106	106	0.601
107	107	0.958
108	108	0.303
109	109	0.371
11	11	0.139
110	110	0.0612
111	111	0.767
112	112	0.131
113	113	0.255
114	114	0.52
115	115	0.517
116	116	0.794
117	117	2.96113e-4
118	118	0.15
119	119	0.255
12	12	0.591
120	120	0.24
121	121	0.448
122	122	0.914
123	123	0.617
124	124	0.813
125	125	0.104
126	126	0.555
127	127	0.683
128	128	0.367
129	129	0.187
13	13	0.0319
130	130	0.465
131	131	0.516
132	132	0.82
133	133	0.761
134	134	0.601
135	135	0.537
136	136	0.372
137	137	0.279
138	138	0.734
139	139	0.214
14	14	0.84
140	140	0.931
141	141	0.784
142	142	0.672
143	143	0.271
144	144	0.147
145	145	0.0845
146	146	0.833
147	147	0.406
148	148	0.265
149	149	0.885
15	15	0.0884
150	150	0.298
151	151	0.127
152	152	0.107
153	153	0.186
154	154	0.0985
155	155	0.111
156	156	0.635
157	157	0.824
158	158	0.0566
159	159	0.0137
160	160	0.934
161	161	0.313
162	162	0.566
163	163	0.98
164	164	0.15
165	165	0.222
166	166	0.386
167	167	0.109
168	168	0.248
169	169	0.302
17	17	0.492
18	18	0.683
19	19	0.65
2	2	0.106
20	20	0.297
21	21	0.517
22	22	0.979
23	23	0.883
24	24	0.253
25	25	0.22
26	26	0.0371
27	27	0.41
28	28	0.145
29	29	0.0592
3	3	0.118
30	30	0.194
31	31	0.714
32	32	0.183
33	33	0.557
34	34	0.955
35	35	0.0443
36	36	0.204
37	37	0.232
38	38	0.325
39	39	0.819
4	4	0.95
40	40	0.662
41	41	0.989
42	42	0.0287
43	43	0.381
44	44	0.697
45	45	0.841
46	46	0.105
47	47	0.372
48	48	0.257
49	49	0.128
5	5	0.193
50	50	0.876
51	51	0.828
52	52	0.284
53	53	0.938
54	54	0.396
55	55	0.347
56	56	0.654
57	57	0.216
58	58	0.193
59	59	0.799
6	6	0.278
60	60	0.824
61	61	0.0435
62	62	0.0648
63	63	0.445
64	64	0.815
65	65	0.497
66	66	0.513
67	67	0.754
68	68	0.646
69	69	0.535
7	7	0.147
70	70	0.238
71	71	0.0348
72	72	0.495
73	73	0.434
74	74	0.846
75	75	0.0197
76	76	0.055
77	77	0.288
78	78	0.12
79	79	0.744
8	8	0.327
80	80	0.0937
81	81	0.947
82	82	0.757
83	83	0.939
84	84	0.246
85	85	0.989
86	86	0.177
87	87	0.13
88	88	0.282
89	89	0.612
9	9	0.302
90	90	0.0283
91	91	0.96
92	92	0.851
93	93	0.94
94	94	0.236
95	95	0.49
96	96	0.0169
97	97	0.505
98	98	0.546
99	99	0.397

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: CNhs11186

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011426 mouse thymus- neonate N20 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)
0002370 (thymus)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011426 (mouse thymus- neonate N20 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:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|DRA_sample_Accession=CAGE@DRS008986
+|DRA_sample_Accession=CAGE@SAMD00004712
+|accession_numbers=CAGE;DRX009123;DRR009997;DRZ001422;DRZ002805;DRZ012772;DRZ014155
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
 |ancestors_in_cell_lineage_facet=
@@ Line 8: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:52096066..52096081,-!p2@Tcf7!2.86!867.08!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.56!478.91!Satb1;;chr17:51971932..51971958,-!p2@Satb1!2.31!274.64!Satb1;;chr11:52095821..52095836,-!p3@Tcf7!2.18!149.89!Tcf7;;chr1:38721792..38721845,-!p1@Aff3!2.09!150.86!Aff3;;chr3:94181376..94181403,+!p2@Rorc!2.00!98.43!Rorc;;chr11:52096804..52096896,-!p1@Tcf7!1.99!739.51!Tcf7;;chr3:130815703..130815721,+!p2@Lef1!1.94!102.43!Lef1;;chr12:109242266..109242295,-!p1@Bcl11b!1.91!626.36!Bcl11b;;chr17:51965903..51965926,-!p5@Satb1!1.75!55.75!Satb1;;chr16:92826249..92826325,-!p1@Runx1!1.73!124.84!Runx1;;chr11:52095797..52095809,-!p5@Tcf7!1.70!49.61!Tcf7;;chr11:11590117..11590138,+!p4@Ikzf1!1.69!47.66!Ikzf1;;chr4:102787521..102787588,+!p4@Mier1!1.67!80.89!Mier1;;chr3:94181427..94181449,+!p3@Rorc!1.66!44.73!Rorc;;chr11:11590140..11590187,+!p3@Ikzf1!1.62!48.53!Ikzf1;;chr10:20880731..20880775,-!p2@Myb!1.60!80.21!Myb;;chr11:98407264..98407295,-!p1@Ikzf3!1.58!36.94!Ikzf3;;chr2:9800207..9800234,-!p1@Gata3!1.57!105.94!Gata3;;chr10:20880629..20880683,-!p1@Myb!1.56!97.65!Myb;;chr17:51971991..51972003,-!p4@Satb1!1.54!33.33!Satb1;;chr2:147190749..147190769,+!p1@Pax1!1.52!31.97!Pax1;;chr11:98407234..98407259,-!p2@Ikzf3!1.51!31.28!Ikzf3;;chr10:20880698..20880717,-!p3@Myb!1.48!45.22!Myb;;chr11:11584970..11585030,+!p2@Ikzf1!1.45!38.79!Ikzf1;;chr14:79915425..79915501,+!p1@Elf1!1.44!224.25!Elf1;;chr12:109241728..109241781,-!p2@Bcl11b!1.44!28.17!Bcl11b;;chr3:130813200..130813252,+!p1@Lef1!1.42!109.25!Lef1;;chr8:108583550..108583595,+!p2@Nfatc3!1.40!106.81!Nfatc3;;chr4:6917606..6917681,-!p1@Tox!1.39!96.58!Tox;;chr17:51972530..51972571,-!p7@Satb1!1.39!23.49!Satb1;;chr3:94181331..94181345,+!p4@Rorc!1.39!23.29!Rorc;;chr11:11586218..11586285,+!p1@Ikzf1!1.38!72.12!Ikzf1;;chr2:173044380..173044432,-!p1@Zbp1!1.37!52.04!Zbp1;;chr11:11585912..11585950,+!p6@Ikzf1!1.37!28.75!Ikzf1;;chr17:51972438..51972463,-!p8@Satb1!1.36!22.03!Satb1;;chr17:51965928..51965960,-!p10@Satb1!1.35!21.64!Satb1;;chr4:135728311..135728342,+!p3@E2f2!1.35!21.64!E2f2;;chr11:11585678..11585745,+!p5@Ikzf1!1.30!27.58!Ikzf1;;chr3:94181355..94181373,+!p5@Rorc!1.29!18.71!Rorc;;chr7:51787434..51787448,-!p1@Spib!1.28!25.73!Spib;;chr9:32503590..32503680,+!p1@Ets1!1.26!614.76!Ets1;;chr17:51972400..51972428,-!p11@Satb1!1.25!16.96!Satb1;;chr11:98407142..98407159,-!p5@Ikzf3!1.25!16.67!Ikzf3;;chr11:52096750..52096772,-!p4@Tcf7!1.24!25.34!Tcf7;;chr17:51972603..51972624,-!p9@Satb1!1.23!16.08!Satb1;;chr11:98407370..98407395,-!p3@Ikzf3!1.22!15.59!Ikzf3;;chr1:52065454..52065495,+!p1@Stat4!1.21!25.05!Stat4;;chr5:104182963..104182982,+!p5@Aff1!1.20!31.48!Aff1;;chr4:63064364..63064384,-!p1@Akna!1.17!40.35!Akna;;chr17:51952856..51952876,-!p12@Satb1!1.17!13.74!Satb1;;chr12:109241852..109241873,-!p4@Bcl11b!1.16!15.98!Bcl11b;;chr17:51951634..51951651,-!p6@Satb1!1.14!24.95!Satb1;;chr1:69732354..69732402,-!p1@Ikzf2!1.14!14.52!Ikzf2;;chr11:52096732..52096741,-!p6@Tcf7!1.14!12.96!Tcf7;;chr10:13685980..13686007,+!p6@Hivep2!1.13!15.69!Hivep2;;chr17:51972575..51972595,-!p13@Satb1!1.13!12.38!Satb1;;chr11:100800901..100800921,-!p4@Stat3!1.11!13.94!Stat3;;chr11:98407340..98407359,-!p4@Ikzf3!1.11!11.89!Ikzf3;;chr11:98826178..98826197,+!p7@Rara!1.10!11.60!Rara;;chr4:135728282..135728310,+!p4@E2f2!1.09!12.77!E2f2;;chr10:13686012..13686028,+!p8@Hivep2!1.09!11.31!Hivep2;;chr5:108155007..108155034,-!p1@Gfi1!1.09!11.21!Gfi1;;chr17:51965860..51965876,-!p14@Satb1!1.08!11.11!Satb1;;chr11:100683839..100683890,-!p2@Stat5b!1.07!25.53!Stat5b;;chr16:23988711..23988727,-!p1@Bcl6!1.06!123.87!Bcl6;;chr6:99216488..99216534,-!p2@Foxp1!1.06!29.82!Foxp1;;chr8:124984566..124984595,-!p1@Snai3!1.05!15.79!Snai3;;chr17:48025139..48025166,-!p8@Foxp4!1.04!11.89!Foxp4;;chr11:11590085..11590106,+!p7@Ikzf1!1.04!10.04!Ikzf1;;chr10:67000609..67000625,+!p1@Egr2!1.03!22.51!Egr2;;chr9:71958979..71959032,-!p4@Tcf12!1.03!12.47!Tcf12;;chr3:94181408..94181419,+!p7@Rorc!1.03!9.75!Rorc;;chr3:94181461..94181472,+!p6@Rorc!1.03!9.65!Rorc;;chr17:45692642..45692663,+!p1@Nfkbie!1.01!30.11!Nfkbie;;chr2:147190725..147190747,+!p2@Pax1!1.01!9.26!Pax1;;chr10:86956396..86956411,-!p1@Ascl1!1.00!14.23!Ascl1;;chr4:102792039..102792052,+!p7@Mier1!1.00!12.67!Mier1;;chr10:20881160..20881175,-!p4@Myb!0.99!8.87!Myb;;chr11:98407210..98407221,-!p7@Ikzf3!0.99!8.77!Ikzf3;;chr10:88145766..88145770,-!p1@Spic!0.98!11.40!Spic;;chr3:130815472..130815497,+!p6@Lef1!0.98!8.48!Lef1;;chr16:25801993..25802014,+!p1@Trp63!0.98!8.48!Trp63;;chr19:25746898..25746910,+!p1@Dmrt2!0.96!12.38!Dmrt2;;chr2:173044357..173044377,-!p2@Zbp1!0.96!11.79!Zbp1;;chr4:135728181..135728203,+!p2@E2f2!0.96!10.72!E2f2;;chr3:130813254..130813263,+!p4@Lef1!0.95!7.89!Lef1;;chr11:98407121..98407133,-!p10@Ikzf3!0.95!7.89!Ikzf3;;chr4:102787381..102787397,+!p9@Mier1!0.93!8.87!Mier1;;chr11:98407305..98407321,-!p6@Ikzf3!0.93!7.60!Ikzf3;;chr10:13686074..13686090,+!p9@Hivep2!0.92!8.38!Hivep2;;chr1:52176315..52176343,+!p1@Stat1!0.91!107.69!Stat1;;chr5:138186979..138187025,+!p4@Tsc22d4!0.91!27.48!Tsc22d4;;chr11:52074095..52074127,-!p8@Tcf7!0.91!7.11!Tcf7;;chr1:133904862..133904893,+!p6@Elk4!0.90!14.91!Elk4;;chr11:52070502..52070527,-!p7@Tcf7!0.90!6.92!Tcf7;;chrX:7156792..7156811,+!p1@Foxp3!0.89!6.82!Foxp3;;chr10:77506405..77506441,-!p1@Aire!0.89!6.72!Aire;;chr4:134676555..134676575,+!p2@Runx3!0.88!6.63!Runx3;;chr11:106134241..106134320,-!p2@Smarcd2!0.87!77.48!Smarcd2;;chr14:65568469..65568511,-!p2@Hmbox1!0.87!21.83!Hmbox1;;chr13:30841099..30841116,+!p1@Irf4!0.87!10.33!Irf4;;chr1:87546583..87546595,+!p1@Sp100!0.87!9.26!Sp100;;chr11:98407164..98407177,-!p8@Ikzf3!0.87!6.33!Ikzf3;;chr1:133904901..133904934,+!p3@Elk4!0.86!19.20!Elk4;;chr7:148514080..148514108,-!p4@Deaf1!0.86!13.74!Deaf1;;chr12:77470718..77470752,-!p4@Zbtb25!0.86!9.06!Zbtb25;;chr10:77506352..77506356,-!p2@Aire!0.86!6.24!Aire;;chr15:100430414..100430470,-!p1@Pou6f1!0.85!19.98!Pou6f1;;chr12:74147689..74147711,-!p1@Six1!0.85!14.03!Six1;;chr5:108155037..108155060,-!p2@Gfi1!0.85!6.14!Gfi1;;chr2:147190772..147190783,+!p3@Pax1!0.85!6.14!Pax1;;chr12:109241804..109241823,-!p5@Bcl11b!0.85!6.04!Bcl11b;;chr9:32348943..32349001,-!p1@Fli1!0.84!51.85!Fli1;;chr5:104183477..104183548,+!p6@Aff1!0.83!11.99!Aff1;;chr17:51972017..51972022,-!p17@Satb1!0.83!5.75!Satb1;;chr12:57796615..57796687,+!p1@Pax9!0.82!5.65!Pax9;;chr9:32349051..32349061,-!p5@Fli1!0.82!5.65!Fli1;;chr11:98338697..98338709,-!p9@Ikzf3!0.82!5.56!Ikzf3;;chr11:11590188..11590200,+!p8@Ikzf1!0.82!5.56!Ikzf1;;chrX:45807489..45807502,-!p2@Elf4!0.81!18.13!Elf4;;chr17:45692676..45692695,+!p2@Nfkbie!0.81!11.69!Nfkbie;;chr4:134708451..134708469,+!p1@Runx3!0.81!10.14!Runx3;;chr11:78200071..78200100,-!p1@Foxn1!0.81!5.46!Foxn1;;chr15:100430393..100430410,-!p3@Pou6f1!0.81!5.46!Pou6f1;;chr16:95924005..95924042,+!p2@Ets2!0.80!104.18!Ets2;;chr9:71959562..71959624,-!p3@Tcf12!0.80!19.59!Tcf12;;chr5:138187583..138187602,+!p6@Tsc22d4!0.80!10.23!Tsc22d4;;chr10:30375579..30375616,-!p3@Ncoa7!0.79!13.06!Ncoa7;;chr7:31206743..31206761,+!p1@Nfkbid!0.79!7.21!Nfkbid;;chr10:20881176..20881191,-!p6@Myb!0.79!5.17!Myb;;chr12:3891810..3891829,+!p2@Dnmt3a!0.78!8.09!Dnmt3a;;chr11:52096305..52096328,-!p11@Tcf7!0.78!5.07!Tcf7;;chr11:98407087..98407102,-!p11@Ikzf3!0.78!5.07!Ikzf3;;chr15:101097270..101097290,+!p1@Nr4a1!0.77!54.77!Nr4a1;;chr11:100721761..100721851,+!p1@Stat5a!0.77!39.67!Stat5a;;chr3:130813736..130813752,+!p3@Lef1!0.77!7.02!Lef1;;chr11:52070563..52070589,-!p9@Tcf7!0.77!4.87!Tcf7;;chr18:80904854..80904919,-!p2@Nfatc1!0.76!61.79!Nfatc1;;chr11:62272010..62272050,-!p2@Ncor1!0.76!16.57!Ncor1;;chr9:72122748..72122757,+!p4@Zfp280d!0.76!5.75!Zfp280d;;chr16:95924055..95924077,+!p1@Ets2!0.75!282.43!Ets2;;chr4:102792009..102792021,+!p6@Mier1!0.75!8.28!Mier1;;chr2:91077082..91077122,-!p1@Ddb2!0.74!31.09!Ddb2;;chr7:134169810..134169824,-!p7@Maz!0.74!18.81!Maz;;chr4:102792072..102792091,+!p5@Mier1!0.74!12.86!Mier1;;chr1:64579555..64579570,+!p3@Creb1!0.73!22.71!Creb1;;chr1:87495371..87495397,-!p1@Sp110!0.73!4.39!Sp110;;chr7:148452314..148452329,-!p1@Irf7!0.72!33.23!Irf7;;chr2:168415815..168415872,-!p1@Nfatc2!0.72!25.73!Nfatc2;;chr11:11590205..11590216,+!p9@Ikzf1!0.72!4.29!Ikzf1;;chr11:100711801..100711910,-!p1@Stat5b!0.71!64.52!Stat5b;;chr7:87171047..87171078,+!p1@Zfp710!0.71!15.20!Zfp710;;chr18:74375772..74375799,+!p2@Cxxc1!0.71!13.45!Cxxc1;;chr16:92826338..92826347,-!p6@Runx1!0.71!4.09!Runx1;;chr5:134720044..134720103,-!p6@Gtf2i!0.71!4.09!Gtf2i;;chr7:71083748..71083819,-!p1@Klf13!0.70!154.18!Klf13;;chr9:57684520..57684612,-!p1@Arid3b!0.70!40.06!Arid3b;;chr8:72520015..72520053,-!p2@Gatad2a!0.70!30.50!Gatad2a;;chr2:91077034..91077078,-!p2@Ddb2!0.70!9.65!Ddb2;;chr7:71083729..71083742,-!p4@Klf13!0.70!7.50!Klf13;;chr12:109242296..109242307,-!p3@Bcl11b!0.70!6.14!Bcl11b;;chr1:52065508..52065522,+!p2@Stat4!0.70!4.87!Stat4;;chr1:87546602..87546617,+!p2@Sp100!0.70!4.87!Sp100;;chr10:20862857..20862868,-!p7@Myb!0.70!4.00!Myb;;chr11:52070478..52070500,-!p10@Tcf7!0.70!4.00!Tcf7;;chr5:138187341..138187406,+!p3@Tsc22d4!0.69!47.56!Tsc22d4;;chr8:108160490..108160512,+!p2@Ctcf!0.69!36.64!Ctcf;;chr19:26681929..26681987,+!p4@Smarca2!0.69!24.75!Smarca2;;chr11:3190303..3190351,+!p3@Patz1!0.69!8.28!Patz1;;chr9:51021788..51021802,+!p1@Pou2af1!0.69!4.78!Pou2af1;;chr4:133276801..133276891,-!p3@Arid1a!0.68!45.42!Arid1a;;chr15:61816932..61816952,+!p2@Myc!0.68!36.06!Myc;;chrX:45947746..45947762,-!p2@Zfp280c!0.68!8.67!Zfp280c;;chr5:138187411..138187422,+!p8@Tsc22d4!0.68!6.24!Tsc22d4;;chr4:102791976..102792008,+!p2@Mier1!0.67!47.07!Mier1;;chr19:28085586..28085622,-!p3@Rfx3!0.67!18.13!Rfx3;;chr9:72380594..72380635,+!p3@Rfx7!0.67!6.92!Rfx7;;chr5:108494765..108494786,+!p2@Mtf2!0.67!5.17!Mtf2;;chr6:99216375..99216395,-!p5@Foxp1!0.67!3.70!Foxp1;;chr7:134169762..134169795,-!p3@Maz!0.66!37.52!Maz;;chr10:13685585..13685645,+!p2@Hivep2!0.66!14.03!Hivep2;;chr4:133276698..133276743,-!p6@Arid1a!0.65!11.01!Arid1a;;chr10:92773708..92773734,-!p3@Elk3!0.65!7.50!Elk3;;chr4:48058047..48058062,+!p1@Nr4a3!0.65!5.65!Nr4a3;;chr1:133904946..133904974,+!p7@Elk4!0.65!5.65!Elk4;;chr9:21420744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207;;chr18:60720384..60720450,+!p1@Rbm22!0.25!82.45!Rbm22;;chr5:22940253..22940289,+!p1@Mll5!0.25!81.77!Mll5;;chr17:15636872..15636923,+!p1@Tbp!0.25!61.20!Tbp;;chr8:13338760..13338817,+!p1@Tfdp1!0.25!55.75!Tfdp1;;chr9:20264394..20264448,-!p1@Zfp26!0.25!28.56!Zfp26;;chr15:102034070..102034124,+!p1@Zfp740!0.25!26.61!Zfp740;;chr13:44826937..44826952,+!p2@Jarid2!0.25!22.42!Jarid2;;chrX:20639107..20639188,-!p1@Zfp182!0.25!20.08!Zfp182;;chr10:20032304..20032324,+!p2@Bclaf1!0.25!14.52!Bclaf1;;chr1:64579364..64579389,+!p2@Creb1!0.25!14.03!Creb1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.25!10.92!Tsc22d3;;chr15:76709732..76709764,+!p1@Zfp7!0.25!7.02!Zfp7;;chr17:84105477..84105509,+!p3@Mta3!0.25!5.65!Mta3;;chr7:28764153..28764173,-!p2@Zfp780b!0.25!4.78!Zfp780b;;chr10:79896690..79896746,-!p4@Tcf3!0.25!4.78!Tcf3;;chr11:80196900..80196917,+!p3@Zfp207!0.25!4.58!Zfp207;;chr3:87945895..87945946,+!p2@Mef2d!0.25!4.39!Mef2d;;chr17:71200558..71200572,-!p4@Tgif1!0.25!3.22!Tgif1;;chr6:140572352..140572382,+!p3@Aebp2!0.25!2.73!Aebp2;;chr5:147760297..147760304,+!p4@Gtf3a!0.25!2.14!Gtf3a;;chr7:56136402..56136420,-!p3@E2f8!0.25!2.14!E2f8;;chr15:100058358..100058374,+!p2@Gm1862,p4@Atf1!0.25!2.14!Atf1;;chr10:82226709..82226720,-!p6@Nfyb!0.25!1.85!Nfyb;;chr11:121380640..121380655,-!p1@Zfp750!0.25!1.85!Zfp750;;chr8:81552528..81552553,+!p6@Zfp827!0.25!1.75!Zfp827;;chr16:92697354..92697362,-!p3@Runx1!0.25!1.66!Runx1;;chr7:135020660..135020688,+!p3@Zfp646!0.25!1.46!Zfp646;;chr3:100773602..100773607,-!p2@Ttf2!0.25!1.17!Ttf2;;chr5:104182725..104182737,+!p17@Aff1!0.25!0.78!Aff1;;chr6:120314480..120314487,+!p6@Kdm5a!0.25!0.78!Kdm5a;;chr2:168032254..168032259,-!p6@Adnp!0.25!0.78!Adnp;;chr11:23670827..23670846,-!p3@Rel!0.25!0.78!Rel;;chr9:43013917..43013968,-!p1@Pou2f3!0.25!0.78!Pou2f3;;chr6:35083688..35083730,-!p1@Cnot4!0.24!79.53!Cnot4;;chr19:4397052..4397098,-!p1@Kdm2a!0.24!40.64!Kdm2a;;chr10:33670996..33671069,-!p1@Zufsp!0.24!30.41!Zufsp;;chr4:102787007..102787050,+!p1@Mier1!0.24!25.14!Mier1;;chr15:100058266..100058287,+!p1@Atf1!0.24!24.07!Atf1;;chr17:25152711..25152736,-!p1@Cramp1l!0.24!15.20!Cramp1l;;chr3:94641350..94641380,+!p1@Pogz!0.24!15.11!Pogz;;chr4:142802594..142802631,-!p1@Prdm2!0.24!14.91!Prdm2;;chr14:31832345..31832364,+!p2@Pbrm1!0.24!13.45!Pbrm1;;chr7:52960555..52960662,+!p1@Dbp!0.24!12.67!Dbp;;chr2:128793119..128793179,+!p1@Zc3h6!0.24!12.38!Zc3h6;;chr3:94641624..94641645,+!p2@Pogz!0.24!10.04!Pogz;;chr19:46380172..46380231,+!p2@Nfkb2!0.24!10.04!Nfkb2;;chr7:50834947..50835010,+!p2@Zfp719!0.24!7.60!Zfp719;;chr2:90936901..90936945,+!p1@Sfpi1!0.24!7.60!Sfpi1;;chr5:145962698..145962742,-!p1@Zkscan14!0.24!6.53!Zkscan14;;chr19:7342725..7342784,+!p1@Rcor2!0.24!5.75!Rcor2;;chr18:39649534..39649569,-!p3@Nr3c1!0.24!4.39!Nr3c1;;chr3:90097275..90097302,+!p2@Gatad2b!0.24!2.83!Gatad2b;;chr6:47827547..47827568,+!p4@Zfp282!0.24!2.83!Zfp282;;chr5:22939771..22939797,+!p4@Mll5!0.24!2.53!Mll5;;chr13:96095124..96095144,+!p3@Zbed3!0.24!2.34!Zbed3;;chr12:85559762..85559778,-!p5@C130039O16Rik!0.24!1.75!C130039O16Rik;;chr7:56136974..56136989,-!p4@E2f8!0.24!1.75!E2f8;;chr17:46520492..46520515,+!p4@Zfp318!0.24!1.46!Zfp318;;chr3:87329568..87329589,+!p2@Etv3!0.24!1.36!Etv3;;chr19:9018049..9018054,+!p5@Mta2!0.24!1.27!Mta2;;chr5:104182943..104182954,+!p12@Aff1!0.24!1.17!Aff1;;chr5:65213459..65213485,+!p12@Klf3!0.24!1.17!Klf3;;chr4:128483422..128483430,-!p6@Zfp362!0.24!1.07!Zfp362;;chr10:128082840..128082872,-!p1@Ikzf4!0.24!1.07!Ikzf4;;chr3:30993641..30993651,+!p7@Skil!0.24!0.97!Skil;;chrX:98624993..98625047,+!p1@Nono!0.23!261.58!Nono;;chr16:11176363..11176458,-!p1@Zc3h7a!0.23!75.33!Zc3h7a;;chr19:5424906..5425026,-!p1@Drap1!0.23!41.32!Drap1;;chr2:32218524..32218662,+!p1@Ciz1!0.23!34.60!Ciz1;;chr5:77694479..77694574,+!p1@Rest!0.23!32.36!Rest;;chr2:73730676..73730692,-!p1@Atf2,p1@LOC100047997!0.23!31.19!Atf2;;chr2:166888107..166888224,-!p1@Znfx1!0.23!21.54!Znfx1;;chr17:21145885..21145977,+!p1@Zfp160!0.23!20.56!Zfp160;;chr4:133310237..133310293,-!p2@Arid1a!0.23!19.00!Arid1a;;chr7:20408047..20408125,-!p1@Bcl3!0.23!16.96!Bcl3;;chr11:65620712..65620729,+!p1@Zkscan6!0.23!12.28!Zkscan6;;chr14:56223010..56223067,+!p1@Irf9!0.23!11.40!Irf9;;chr12:110031227..110031254,+!p3@Yy1!0.23!8.09!Yy1;;chr8:72520162..72520197,-!p4@Gatad2a!0.23!7.31!Gatad2a;;chr4:3865501..3865548,-!p1@Plag1!0.23!7.11!Plag1;;chr17:25152743..25152766,-!p2@Cramp1l!0.23!5.65!Cramp1l;;chr9:63605978..63605997,-!p2@Smad3!0.23!5.26!Smad3;;chr17:34169293..34169320,+!p3@Rxrb!0.23!4.00!Rxrb;;chr3:95021799..95021840,-!p4@Gabpb2!0.23!3.90!Gabpb2;;chr15:102301130..102301147,+!p3@Pcbp2!0.23!3.90!Pcbp2;;chr7:30875418..30875454,-!p2@Zfp566,p2@Zfp82!0.23!3.51!Zfp566;;chr11:23670750..23670789,-!p2@Rel!0.23!2.14!Rel;;chr13:117099847..117099907,-!p1@Isl1!0.23!2.05!Isl1;;chr18:80904923..80904933,-!p3@Nfatc1!0.23!1.27!Nfatc1;;chr7:52071034..52071052,-!p2@Atf5!0.23!1.27!Atf5;;chr5:22939909..22939948,+!p6@Mll5!0.23!1.17!Mll5;;chr16:55973994..55974005,+!p8@Rpl24,p8@Zbtb11!0.23!1.07!Zbtb11;;chr16:55838757..55838774,-!p2@Nfkbiz!0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@@ Line 42: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011426
 |is_obsolete=
-|library_ids=CNhs11186
+|library_id=CNhs11186
+|library_id_phase_based=2:CNhs11186
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;820
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;820
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm9.nobarcode.rdna.fa.gz
 |name=thymus, neonate N20
 |namespace=FANTOM5
@@ Line 48: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11186,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0189505293385716,0,0,0.0403878614760544,0.536109652550868,0,0.185216342956487,0,0.0611673224888595,0,0,-0.0843392403965415,0.0193339705341823,0,0,0,0,0,0.263210444242556,0,0.0386686448537371,0,0,0.0403878614760544,0,0,0,0,0,0,0.0386686448537371,0,0.361143792553327,0,0,0,0,0,0.168877031712697,0,0.153449179214342,-0.943823505001772,-0.229480776534297,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.0403878614760544,0,0.0733662466726585,0.0403878614760544,0.111388092060353,0,0.110710792459578,0.237604200708037,0.0418689734833877,0.0210739170101211,0,0.0403878614760544,-0.0528845320799982,0,0.0403878614760544,0,-0.00585935164408627,-0.0844410103036743,-0.345577098179449,0.171506187721214,0.0151262290979539,0,0,0,0,0,-0.117278872750909,-0.168503541963143,-0.114128948073988,0.0110225021948333,0,0,0,0.0096935057929159
@@ Line 85: / Line 97: @@
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 |xref=
-}} {{DRAAccessionNumbers
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:820-7A2;search_select_hide=table117:820-7A2
-|DRA_sample_Accession=CAGE@DRS008986
-|accession_numbers=DRX009123;DRR009997;DRZ001422;DRZ002805;CAGE
-|library_id=CNhs11186
 }}

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From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs11186

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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