FF:748-24E4: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	thymus, neonate N10
Species:	Mouse (Mus musculus)
Library ID:	CNhs11194
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	thymus
dev stage	10 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		SAMD00005475

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11194		CAGE		DRX009122		DRR009996

Accession ID Mm9

Library id		BAM		CTSS
CNhs11194		DRZ001421		DRZ002804

Accession ID Mm10

Library id		BAM		CTSS
CNhs11194		DRZ012771		DRZ014154

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

CNhs11194

0	0
1	0
10	0
100	0
1000	0
1001	0.129
1002	-0.0259
1003	-0.112
1004	0
1005	0
1006	-0.172
1007	0.0849
1008	0.0417
1009	-0.12
101	0.112
1010	0
1011	0.0798
1012	0.547
1013	-0.163
1014	-0.0874
1015	0.0751
1016	-0.459
1017	0
1018	0
1019	0
102	0.0417
1020	0
1021	0.177
1022	-0.22
1023	0
1024	-0.0529
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	0.527
103	-0.0678
1030	0.0417
1031	-0.684
1032	-0.521
1033	0.0419
1034	0
1035	0
1036	0.142
1037	0
1038	-0.36
1039	-0.166
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: CNhs11194

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0108
MA0003.1	MA0003.1	0.255
MA0004.1	MA0004.1	0.338
MA0006.1	MA0006.1	0.989
MA0007.1	MA0007.1	0.515
MA0009.1	MA0009.1	0.458
MA0014.1	MA0014.1	0.297
MA0017.1	MA0017.1	0.903
MA0018.2	MA0018.2	0.0318
MA0019.1	MA0019.1	0.367
MA0024.1	MA0024.1	3.83111e-4
MA0025.1	MA0025.1	0.00824
MA0027.1	MA0027.1	0.724
MA0028.1	MA0028.1	1.77824e-5
MA0029.1	MA0029.1	0.152
MA0030.1	MA0030.1	0.648
MA0031.1	MA0031.1	0.276
MA0035.2	MA0035.2	0.424
MA0038.1	MA0038.1	0.414
MA0039.2	MA0039.2	0.17
MA0040.1	MA0040.1	0.915
MA0041.1	MA0041.1	0.246
MA0042.1	MA0042.1	0.94
MA0043.1	MA0043.1	0.0731
MA0046.1	MA0046.1	1.08319e-14
MA0047.2	MA0047.2	0.455
MA0048.1	MA0048.1	0.556
MA0050.1	MA0050.1	1.49803e-5
MA0051.1	MA0051.1	4.46721e-5
MA0052.1	MA0052.1	3.58696e-4
MA0055.1	MA0055.1	0.945
MA0057.1	MA0057.1	0.749
MA0058.1	MA0058.1	0.514
MA0059.1	MA0059.1	0.0153
MA0060.1	MA0060.1	0.386
MA0061.1	MA0061.1	3.50978e-4
MA0062.2	MA0062.2	2.89415e-14
MA0065.2	MA0065.2	0.367
MA0066.1	MA0066.1	0.0091
MA0067.1	MA0067.1	0.599
MA0068.1	MA0068.1	0.965
MA0069.1	MA0069.1	0.769
MA0070.1	MA0070.1	0.436
MA0071.1	MA0071.1	0.254
MA0072.1	MA0072.1	7.94811e-6
MA0073.1	MA0073.1	0.776
MA0074.1	MA0074.1	0.974
MA0076.1	MA0076.1	1.35018e-6
MA0077.1	MA0077.1	0.187
MA0078.1	MA0078.1	0.889
MA0079.2	MA0079.2	0.0252
MA0080.2	MA0080.2	1.08083e-12
MA0081.1	MA0081.1	0.0458
MA0083.1	MA0083.1	0.0269
MA0084.1	MA0084.1	0.479
MA0087.1	MA0087.1	0.403
MA0088.1	MA0088.1	0.324
MA0090.1	MA0090.1	0.0646
MA0091.1	MA0091.1	0.0407
MA0092.1	MA0092.1	0.842
MA0093.1	MA0093.1	0.385
MA0099.2	MA0099.2	0.136
MA0100.1	MA0100.1	0.0174
MA0101.1	MA0101.1	8.15918e-4
MA0102.2	MA0102.2	0.462
MA0103.1	MA0103.1	2.92081e-4
MA0104.2	MA0104.2	0.126
MA0105.1	MA0105.1	3.00991e-7
MA0106.1	MA0106.1	0.653
MA0107.1	MA0107.1	0.00144
MA0108.2	MA0108.2	6.81634e-4
MA0111.1	MA0111.1	0.248
MA0112.2	MA0112.2	0.0106
MA0113.1	MA0113.1	0.682
MA0114.1	MA0114.1	0.627
MA0115.1	MA0115.1	0.84
MA0116.1	MA0116.1	0.00157
MA0117.1	MA0117.1	0.778
MA0119.1	MA0119.1	0.964
MA0122.1	MA0122.1	0.906
MA0124.1	MA0124.1	0.363
MA0125.1	MA0125.1	0.442
MA0131.1	MA0131.1	0.155
MA0135.1	MA0135.1	0.128
MA0136.1	MA0136.1	9.91674e-20
MA0137.2	MA0137.2	0.0971
MA0138.2	MA0138.2	2.5952e-5
MA0139.1	MA0139.1	0.197
MA0140.1	MA0140.1	0.768
MA0141.1	MA0141.1	0.807
MA0142.1	MA0142.1	0.655
MA0143.1	MA0143.1	0.392
MA0144.1	MA0144.1	0.515
MA0145.1	MA0145.1	0.342
MA0146.1	MA0146.1	0.526
MA0147.1	MA0147.1	0.0579
MA0148.1	MA0148.1	0.52
MA0149.1	MA0149.1	0.0218
MA0150.1	MA0150.1	0.504
MA0152.1	MA0152.1	0.795
MA0153.1	MA0153.1	2.05904e-8
MA0154.1	MA0154.1	0.112
MA0155.1	MA0155.1	0.975
MA0156.1	MA0156.1	1.79994e-21
MA0157.1	MA0157.1	0.43
MA0159.1	MA0159.1	0.108
MA0160.1	MA0160.1	0.495
MA0162.1	MA0162.1	0.551
MA0163.1	MA0163.1	0.0015
MA0164.1	MA0164.1	0.788
MA0258.1	MA0258.1	0.0428
MA0259.1	MA0259.1	0.615

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: CNhs11194

Novel motif	Logo	P-value
1	1	0.141
10	10	0.0104
100	100	0.591
101	101	0.808
102	102	0.573
103	103	0.123
104	104	0.869
105	105	0.72
106	106	0.703
107	107	0.978
108	108	0.251
109	109	0.27
11	11	0.115
110	110	0.052
111	111	0.656
112	112	0.157
113	113	0.46
114	114	0.495
115	115	0.452
116	116	0.861
117	117	5.36424e-4
118	118	0.2
119	119	0.189
12	12	0.622
120	120	0.368
121	121	0.483
122	122	0.674
123	123	0.617
124	124	0.842
125	125	0.0675
126	126	0.533
127	127	0.688
128	128	0.527
129	129	0.12
13	13	0.0146
130	130	0.334
131	131	0.431
132	132	0.811
133	133	0.874
134	134	0.553
135	135	0.352
136	136	0.271
137	137	0.49
138	138	0.618
139	139	0.28
14	14	0.796
140	140	0.99
141	141	0.86
142	142	0.467
143	143	0.33
144	144	0.201
145	145	0.093
146	146	0.867
147	147	0.413
148	148	0.202
149	149	0.628
15	15	0.114
150	150	0.341
151	151	0.256
152	152	0.0568
153	153	0.182
154	154	0.0626
155	155	0.0955
156	156	0.00347
157	157	0.747
158	158	0.0529
159	159	0.0178
160	160	0.966
161	161	0.277
162	162	0.599
163	163	0.951
164	164	0.121
165	165	0.451
166	166	0.375
167	167	0.123
168	168	0.289
169	169	0.462
17	17	0.527
18	18	0.699
19	19	0.747
2	2	0.0737
20	20	0.207
21	21	0.558
22	22	0.884
23	23	0.931
24	24	0.251
25	25	0.228
26	26	0.0287
27	27	0.629
28	28	0.201
29	29	0.03
3	3	0.116
30	30	0.102
31	31	0.606
32	32	0.211
33	33	0.389
34	34	0.963
35	35	0.0461
36	36	0.113
37	37	0.215
38	38	0.232
39	39	0.984
4	4	0.779
40	40	0.535
41	41	0.975
42	42	0.0336
43	43	0.352
44	44	0.839
45	45	0.666
46	46	0.107
47	47	0.336
48	48	0.2
49	49	0.107
5	5	0.307
50	50	0.801
51	51	0.904
52	52	0.191
53	53	0.81
54	54	0.304
55	55	0.465
56	56	0.818
57	57	0.16
58	58	0.235
59	59	0.628
6	6	0.223
60	60	0.914
61	61	0.067
62	62	0.102
63	63	0.567
64	64	0.69
65	65	0.478
66	66	0.544
67	67	0.765
68	68	0.467
69	69	0.518
7	7	0.141
70	70	0.293
71	71	0.0276
72	72	0.592
73	73	0.533
74	74	0.777
75	75	0.0205
76	76	0.0332
77	77	0.261
78	78	0.136
79	79	0.716
8	8	0.268
80	80	0.132
81	81	0.998
82	82	0.742
83	83	0.911
84	84	0.129
85	85	0.854
86	86	0.283
87	87	0.0359
88	88	0.304
89	89	0.514
9	9	0.361
90	90	0.0308
91	91	0.881
92	92	0.978
93	93	0.832
94	94	0.268
95	95	0.383
96	96	0.0104
97	97	0.516
98	98	0.471
99	99	0.477

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: CNhs11194

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011413 mouse thymus- neonate N10 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)
0000305 (mouse neonate N10 sample)
0011413 (mouse thymus- neonate N10 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002370,UBERON:0000483,UBERON:0002530,UBERON:0006562,UBERON:0000974,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0002368,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0003929,UBERON:0000072,UBERON:0004807,UBERON:0003104,UBERON:0004177,UBERON:0005057,UBERON:0005058,UBERON:0001048,UBERON:0000925,UBERON:0003408,UBERON:0006598,UBERON:0003351,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0002390,UBERON:0007026,UBERON:0001041,UBERON:0000949,UBERON:0001557,UBERON:0001042,UBERON:0002193,UBERON:0002405,UBERON:0009113,UBERON:0008814,UBERON:0009142,UBERON:0003081,UBERON:0003295,UBERON:0009722,UBERON:0006595,UBERON:0006603,UBERON:0009145,UBERON:0005562,UBERON:0003061,UBERON:0007690
+|DRA_sample_Accession=CAGE@SAMD00005475
+|accession_numbers=CAGE;DRX009122;DRR009996;DRZ001421;DRZ002804;DRZ012771;DRZ014154
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000305,FF:0011413
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:52096066..52096081,-!p2@Tcf7!2.75!680.48!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.50!413.69!Satb1;;chr17:51971932..51971958,-!p2@Satb1!2.24!233.51!Satb1;;chr11:52095821..52095836,-!p3@Tcf7!2.15!140.96!Tcf7;;chr3:94181376..94181403,+!p2@Rorc!2.04!109.40!Rorc;;chr1:38721792..38721845,-!p1@Aff3!2.01!126.44!Aff3;;chr11:52096804..52096896,-!p1@Tcf7!1.92!632.79!Tcf7;;chr12:109242266..109242295,-!p1@Bcl11b!1.89!607.58!Bcl11b;;chr3:130815703..130815721,+!p2@Lef1!1.85!83.99!Lef1;;chr3:94181427..94181449,+!p3@Rorc!1.72!51.62!Rorc;;chr16:92826249..92826325,-!p1@Runx1!1.69!115.04!Runx1;;chr4:102787521..102787588,+!p4@Mier1!1.66!79.05!Mier1;;chr11:11590117..11590138,+!p4@Ikzf1!1.61!40.13!Ikzf1;;chr11:52095797..52095809,-!p5@Tcf7!1.61!39.73!Tcf7;;chr17:51965903..51965926,-!p5@Satb1!1.59!37.91!Satb1;;chr11:98407264..98407295,-!p1@Ikzf3!1.58!37.20!Ikzf3;;chr17:51971991..51972003,-!p4@Satb1!1.57!35.99!Satb1;;chr11:11590140..11590187,+!p3@Ikzf1!1.56!42.35!Ikzf1;;chr10:20880731..20880775,-!p2@Myb!1.55!70.98!Myb;;chr2:147190749..147190769,+!p1@Pax1!1.55!34.38!Pax1;;chr10:20880629..20880683,-!p1@Myb!1.51!87.21!Myb;;chr2:9800207..9800234,-!p1@Gata3!1.46!81.77!Gata3;;chr11:11584970..11585030,+!p2@Ikzf1!1.44!37.20!Ikzf1;;chr10:20880698..20880717,-!p3@Myb!1.43!40.23!Myb;;chr11:98407234..98407259,-!p2@Ikzf3!1.42!25.41!Ikzf3;;chr17:51972530..51972571,-!p7@Satb1!1.42!25.41!Satb1;;chr3:130813200..130813252,+!p1@Lef1!1.41!106.57!Lef1;;chr3:94181331..94181345,+!p4@Rorc!1.40!24.40!Rorc;;chr12:109241728..109241781,-!p2@Bcl11b!1.38!24.50!Bcl11b;;chr3:94181355..94181373,+!p5@Rorc!1.37!22.48!Rorc;;chr14:79915425..79915501,+!p1@Elf1!1.35!184.71!Elf1;;chr4:135728311..135728342,+!p3@E2f2!1.35!21.58!E2f2;;chr17:51972438..51972463,-!p8@Satb1!1.31!19.46!Satb1;;chr4:6917606..6917681,-!p1@Tox!1.30!77.94!Tox;;chr11:11585912..11585950,+!p6@Ikzf1!1.29!23.39!Ikzf1;;chr17:51965928..51965960,-!p10@Satb1!1.29!18.65!Satb1;;chr8:108583550..108583595,+!p2@Nfatc3!1.27!78.54!Nfatc3;;chr11:11585678..11585745,+!p5@Ikzf1!1.26!24.70!Ikzf1;;chr11:11586218..11586285,+!p1@Ikzf1!1.25!52.33!Ikzf1;;chr17:51972400..51972428,-!p11@Satb1!1.23!16.03!Satb1;;chr12:109241852..109241873,-!p4@Bcl11b!1.21!18.35!Bcl11b;;chr1:52065454..52065495,+!p1@Stat4!1.20!24.60!Stat4;;chr17:48025139..48025166,-!p8@Foxp4!1.20!17.64!Foxp4;;chr17:51972603..51972624,-!p9@Satb1!1.20!14.82!Satb1;;chr11:52096750..52096772,-!p4@Tcf7!1.19!22.28!Tcf7;;chr11:98826178..98826197,+!p7@Rara!1.19!14.42!Rara;;chr11:98407340..98407359,-!p4@Ikzf3!1.19!14.42!Ikzf3;;chr3:94181461..94181472,+!p6@Rorc!1.17!13.71!Rorc;;chr11:98407370..98407395,-!p3@Ikzf3!1.16!13.61!Ikzf3;;chr5:108155007..108155034,-!p1@Gfi1!1.16!13.41!Gfi1;;chr5:104182963..104182982,+!p5@Aff1!1.15!27.63!Aff1;;chr17:51951634..51951651,-!p6@Satb1!1.15!25.11!Satb1;;chr9:32503590..32503680,+!p1@Ets1!1.14!463.70!Ets1;;chr2:173044380..173044432,-!p1@Zbp1!1.14!30.25!Zbp1;;chr8:124984566..124984595,-!p1@Snai3!1.14!19.56!Snai3;;chr11:98407142..98407159,-!p5@Ikzf3!1.14!12.80!Ikzf3;;chr17:51972575..51972595,-!p13@Satb1!1.11!11.90!Satb1;;chr17:51952856..51952876,-!p12@Satb1!1.11!11.80!Satb1;;chr17:51965860..51965876,-!p14@Satb1!1.09!11.39!Satb1;;chr11:100800901..100800921,-!p4@Stat3!1.08!13.01!Stat3;;chr10:20881160..20881175,-!p4@Myb!1.08!11.09!Myb;;chr4:135728282..135728310,+!p4@E2f2!1.07!12.30!E2f2;;chr11:52096732..52096741,-!p6@Tcf7!1.06!10.49!Tcf7;;chr2:147190725..147190747,+!p2@Pax1!1.04!10.08!Pax1;;chr3:130813254..130813263,+!p4@Lef1!1.04!9.98!Lef1;;chr4:63064364..63064384,-!p1@Akna!1.03!28.53!Akna;;chr16:23988711..23988727,-!p1@Bcl6!1.02!114.54!Bcl6;;chr3:94181408..94181419,+!p7@Rorc!1.01!9.18!Rorc;;chr7:51787434..51787448,-!p1@Spib!1.00!13.21!Spib;;chr6:99216488..99216534,-!p2@Foxp1!0.97!24.10!Foxp1;;chr9:71958979..71959032,-!p4@Tcf12!0.97!10.79!Tcf12;;chr11:98407121..98407133,-!p10@Ikzf3!0.97!8.37!Ikzf3;;chr11:11590085..11590106,+!p7@Ikzf1!0.96!8.17!Ikzf1;;chr1:133904862..133904893,+!p6@Elk4!0.95!16.54!Elk4;;chr1:69732354..69732402,-!p1@Ikzf2!0.95!9.07!Ikzf2;;chr4:102792039..102792052,+!p7@Mier1!0.93!10.69!Mier1;;chr10:88145766..88145770,-!p1@Spic!0.93!9.88!Spic;;chr17:45692642..45692663,+!p1@Nfkbie!0.92!24.10!Nfkbie;;chr10:13685980..13686007,+!p6@Hivep2!0.91!8.97!Hivep2;;chr10:20881176..20881191,-!p6@Myb!0.91!7.16!Myb;;chr5:138186979..138187025,+!p4@Tsc22d4!0.90!26.82!Tsc22d4;;chr5:104183477..104183548,+!p6@Aff1!0.90!14.01!Aff1;;chr19:25746898..25746910,+!p1@Dmrt2!0.90!10.49!Dmrt2;;chr3:130815472..130815497,+!p6@Lef1!0.90!6.96!Lef1;;chr4:102787381..102787397,+!p9@Mier1!0.88!7.86!Mier1;;chr16:25801993..25802014,+!p1@Trp63!0.88!6.65!Trp63;;chr11:98407305..98407321,-!p6@Ikzf3!0.88!6.65!Ikzf3;;chr11:98407087..98407102,-!p11@Ikzf3!0.88!6.55!Ikzf3;;chr1:87495371..87495397,-!p1@Sp110!0.87!6.35!Sp110;;chr12:109241804..109241823,-!p5@Bcl11b!0.85!6.15!Bcl11b;;chr11:52070502..52070527,-!p7@Tcf7!0.85!6.15!Tcf7;;chr11:98338697..98338709,-!p9@Ikzf3!0.85!6.05!Ikzf3;;chr10:77506405..77506441,-!p1@Aire!0.85!6.05!Aire;;chr14:65568469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fp384;;chr12:109242296..109242307,-!p3@Bcl11b!0.61!4.84!Bcl11b;;chr3:95021612..95021650,-!p2@Gabpb2!0.60!18.25!Gabpb2;;chr9:72380594..72380635,+!p3@Rfx7!0.60!5.75!Rfx7;;chr17:51951383..51951409,-!p19@Satb1!0.60!3.02!Satb1;;chr6:47544966..47545046,-!p1@Ezh2!0.59!74.71!Ezh2;;chr8:108583462..108583523,+!p1@Nfatc3!0.59!65.54!Nfatc3;;chr4:102791976..102792008,+!p2@Mier1!0.59!38.82!Mier1;;chr15:101097270..101097290,+!p1@Nr4a1!0.59!36.20!Nr4a1;;chr7:148452314..148452329,-!p1@Irf7!0.59!24.40!Irf7;;chr19:28085586..28085622,-!p3@Rfx3!0.59!14.82!Rfx3;;chrX:98449898..98449913,+!p2@Foxo4!0.59!10.99!Foxo4;;chrX:48559055..48559077,-!p6@Mbnl3!0.59!3.93!Mbnl3;;chr9:51021788..51021802,+!p1@Pou2af1!0.59!3.53!Pou2af1;;chr11:98826125..98826141,+!p12@Rara!0.59!2.92!Rara;;chr5:104182999..104183006,+!p18@Aff1!0.59!2.92!Aff1;;chr4:134676555..134676575,+!p2@Runx3!0.59!2.92!Runx3;;chr9:72122773..72122820,+!p1@Zfp280d!0.58!91.85!Zfp280d;;chr7:134170081..134170122,-!p2@Maz!0.58!63.02!Maz;;chr7:56136362..56136400,-!p1@E2f8!0.58!22.18!E2f8;;chr5:104121391..104121450,+!p3@Aff1!0.58!17.64!Aff1;;chr6:29998062..29998078,+!p2@Nrf1!0.58!16.13!Nrf1;;chr1:133904946..133904974,+!p7@Elk4!0.58!4.74!Elk4;;chr12:109241897..109241915,-!p6@Bcl11b!0.58!2.82!Bcl11b;;chr1:133904183..133904211,+!p1@Elk4!0.57!28.84!Elk4;;chrX:48559079..48559108,-!p2@Mbnl3!0.57!7.26!Mbnl3;;chr10:92773708..92773734,-!p3@Elk3!0.57!6.05!Elk3;;chr8:74405624..74405679,+!p3@Zfp709!0.57!5.24!Zfp709;;chr5:34530519..34530545,-!p4@Mxd4!0.57!4.64!Mxd4;;chr11:3191741..3191769,+!p5@Patz1!0.57!3.63!Patz1;;chr1:181733959..181733977,-!p4@Ahctf1!0.57!3.63!Ahctf1;;chr10:20862857..20862868,-!p7@Myb!0.57!2.72!Myb;;chr7:4947724..4947743,-!p3@Zfp579!0.56!6.86!Zfp579;;chr9:72122708..72122720,+!p3@Zfp280d!0.56!5.44!Zfp280d;;chr16:92697354..92697362,-!p3@Runx1!0.56!4.44!Runx1;;chr9:21420812..21420815,+!p6@Smarca4!0.56!4.34!Smarca4;;chr4:102787067..102787080,+!p10@Mier1!0.56!3.53!Mier1;;chr16:95923586..95923598,+!p5@Ets2!0.56!3.53!Ets2;;chr17:51952893..51952904,-!p26@Satb1!0.56!2.62!Satb1;;chr17:51966014..51966025,-!p34@Satb1!0.56!2.62!Satb1;;chr5:137043112..137043157,-!p1@Cux1!0.55!297.13!Cux1;;chr12:77471524..77471607,+!p1@Zbtb1!0.55!40.94!Zbtb1;;chr4:133276801..133276891,-!p3@Arid1a!0.55!33.37!Arid1a;;chr2:72818459..72818528,-!p3@Sp3!0.55!23.19!Sp3;;chr15:96118197..96118200,+!p3@Arid2!0.55!4.84!Arid2;;chr14:79915521..79915539,+!p5@Elf1!0.55!3.23!Elf1;;chr3:130815382..130815401,+!p14@Lef1!0.55!2.52!Lef1;;chr8:125921689..125921725,+!p3@Tcf25!0.55!2.52!Tcf25;;chr8:72676653..72676668,+!p4@2310045N01Rik,p4@Mef2b!0.55!2.52!Mef2b;;chr10:82226833..82226864,-!p3@Nfyb!0.54!15.83!Nfyb;;chr4:124805061..124805087,-!p1@Zc3h12a!0.54!9.18!Zc3h12a;;chr7:4947697..4947718,-!p2@Zfp579!0.54!8.87!Zfp579;;chr6:47545052..47545064,-!p2@Ezh2!0.54!5.65!Ezh2;;chrX:103070960..103070973,-!p7@Atrx!0.54!3.53!Atrx;;chr4:108151497..108151514,+!p3@Zcchc11!0.53!5.55!Zcchc11;;chr16:95923651..95923701,+!p3@Ets2!0.53!4.34!Ets2;;chr4:48058047..48058062,+!p1@Nr4a3!0.53!4.03!Nr4a3;;chr19:9016729..9016740,+!p6@Mta2!0.53!3.02!Mta2;;chr2:9800094..9800108,-!p3@Gata3!0.53!2.42!Gata3;;chr3:130813586..130813604,+!p7@Lef1!0.52!2.32!Lef1;;chr11:98407448..98407455,-!p12@Ikzf3!0.52!2.32!Ikzf3;;chr17:14011485..14011507,+!p2@Mllt4!0.52!2.32!Mllt4;;chr5:108494715..108494757,+!p1@Mtf2!0.51!43.96!Mtf2;;chr5:104183219..104183236,+!p2@Aff1!0.51!19.76!Aff1;;chr6:47785797..47785823,+!p2@Zfp398!0.51!12.50!Zfp398;;chr2:165818215..165818226,+!p4@Ncoa3!0.51!4.94!Ncoa3;;chrX:103070839..103070856,-!p4@Atrx!0.51!3.83!Atrx;;chr3:130813557..130813582,+!p5@Lef1!0.51!2.62!Lef1;;chr5:104183579..104183600,+!p9@Aff1!0.51!2.62!Aff1;;chr3:130813268..130813275,+!p12@Lef1!0.51!2.22!Lef1;;chr4:6917763..6917782,-!p6@Tox!0.51!2.22!Tox;;chr1:38721767..38721778,-!p5@Aff3!0.51!2.22!Aff3;;chr6:99216360..99216372,-!p8@Foxp1!0.51!2.22!Foxp1;;chr12:109241791..109241802,-!p7@Bcl11b!0.51!2.22!Bcl11b;;chr9:20757246..20757278,-!p1@Dnmt1!0.50!83.48!Dnmt1;;chr18:5591866..5591900,+!p1@Zeb1!0.50!70.28!Zeb1;;chr17:88840082..88840127,+!p1@Foxn2!0.50!19.96!Foxn2;;chr19:26681929..26681987,+!p4@Smarca2!0.50!15.83!Smarca2;;chr6:51382677..51382783,+!p1@Nfe2l3!0.50!6.65!Nfe2l3;;chr5:77695390..77695414,+!p2@Rest!0.50!2.92!Rest;;chr11:53583544..53583559,+!p1@Irf1!0.49!46.58!Irf1;;chr5:34163023..34163090,+!p2@Whsc1!0.49!17.75!Whsc1;;chr2:168415815..168415872,-!p1@Nfatc2!0.49!14.92!Nfatc2;;chr11:102179074..102179099,-!p4@Ubtf!0.49!7.86!Ubtf;;chr7:16986617..16986632,+!p2@Zc3h4!0.49!7.36!Zc3h4;;chr4:126700650..126700678,+!p5@Sfpq!0.49!4.94!Sfpq;;chr7:56137011..56137041,-!p2@E2f8!0.49!4.84!E2f8;;chr13:37870281..37870293,+!p10@Rreb1!0.49!3.93!Rreb1;;chr5:138187466..138187477,+!p11@Tsc22d4!0.49!2.82!Tsc22d4;;chr4:134708909..134708939,+!p3@Runx3!0.49!2.12!Runx3;;chr17:51951370..51951382,-!p27@Satb1!0.49!2.12!Satb1;;chr2:17986272..17986332,+!p2@Mllt10!0.48!28.23!Mllt10;;chr8:109620410..109620462,-!p1@Terf2!0.48!26.11!Terf2;;chr5:137043177..137043190,-!p2@Cux1!0.48!22.48!Cux1;;chr17:45570660..45570694,-!p1@Cdc5l!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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011413
 |is_obsolete=
+|library_id=CNhs11194
+|library_id_phase_based=2:CNhs11194
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;748
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;748
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N10.CNhs11194.748-24E4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N10.CNhs11194.748-24E4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N10.CNhs11194.748-24E4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N10.CNhs11194.748-24E4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N10.CNhs11194.748-24E4.mm9.nobarcode.rdna.fa.gz
 |name=thymus, neonate N10
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11194,LSID746,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0640799830119125,0.041718751492076,0.0224822203216395,0.0797788474440915,0.889601648991376,0.0161562821986656,0.252209353856276,0.0367207325059176,0.0588199543753377,0,0,0.0304313412152928,0,0,0,0,0,0,0.423595003283195,0,0.0398894237220457,0,0,0.041718751492076,0,0,0,0,0,0,0.0735759961581185,0,0.427050922604159,0,0,0,0,0,0.21419813746755,-0.0244430615325461,0.0566640924202622,-0.727347081396039,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,0.048765034048394,0,0,0,0,0,0,0.0693472026335275,0,0.0797788474440915,0,0.119676505215192,0.271768770157962,0.0473723884977647,0.0934486511026822,0.041718751492076,0.0797788474440915,-0.0760168881589905,0,0.041718751492076,0,0,-0.130988540332765,-0.271820172518173,0.354785472902234,0.000840722233390595,0,0,0,0,0,-0.122469471105573,-0.0979132027284013,-0.196227006073281,0.0161711540901388,0,0,0,0.0370998594177474
 |rna_box=24
 |rna_catalog_number=
@@ Line 56: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=24E4
+|rna_tube_id=2.40E+05
 |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=table111:748-24E4;search_select_hide=table117:748-24E4
 }}

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FF:748-24E4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs11194

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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