FF:25-2G2: Difference between revisions

Latest revision as of 19:09, 4 June 2020

Name:	spleen, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10465
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	spleen
dev stage	adult
sex	male
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		SAMD00005695

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10465		CAGE		DRX009084		DRR009958

Accession ID Mm9

Library id		BAM		CTSS
CNhs10465		DRZ001383		DRZ002766

Accession ID Mm10

Library id		BAM		CTSS
CNhs10465		DRZ012733		DRZ014116

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

CNhs10465

0	0
1	0
10	0
100	0
1000	0
1001	0
1002	0.0171
1003	-0.0527
1004	0
1005	0.128
1006	-0.143
1007	-0.025
1008	0
1009	-0.0624
101	0.0816
1010	0
1011	0.0202
1012	0.128
1013	-0.0433
1014	-0.0874
1015	-0.234
1016	-0.466
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.079
1022	-0.185
1023	0
1024	-0.0504
1025	-0.0295
1026	0
1027	0
1028	0
1029	0.0321
103	-0.0736
1030	0.374
1031	-0.348
1032	-0.281
1033	0.0612
1034	0
1035	0
1036	0.13
1037	0
1038	-0.304
1039	-0.221
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: CNhs10465

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	2.03443e-7
MA0003.1	MA0003.1	0.844
MA0004.1	MA0004.1	0.733
MA0006.1	MA0006.1	0.253
MA0007.1	MA0007.1	0.664
MA0009.1	MA0009.1	0.653
MA0014.1	MA0014.1	0.692
MA0017.1	MA0017.1	0.313
MA0018.2	MA0018.2	0.007
MA0019.1	MA0019.1	0.184
MA0024.1	MA0024.1	0.0145
MA0025.1	MA0025.1	0.562
MA0027.1	MA0027.1	0.505
MA0028.1	MA0028.1	0.0518
MA0029.1	MA0029.1	0.824
MA0030.1	MA0030.1	0.306
MA0031.1	MA0031.1	0.921
MA0035.2	MA0035.2	4.55585e-6
MA0038.1	MA0038.1	0.0689
MA0039.2	MA0039.2	0.345
MA0040.1	MA0040.1	0.248
MA0041.1	MA0041.1	0.377
MA0042.1	MA0042.1	0.936
MA0043.1	MA0043.1	0.0129
MA0046.1	MA0046.1	3.06436e-12
MA0047.2	MA0047.2	0.497
MA0048.1	MA0048.1	0.596
MA0050.1	MA0050.1	1.84537e-14
MA0051.1	MA0051.1	1.09493e-8
MA0052.1	MA0052.1	3.98578e-5
MA0055.1	MA0055.1	0.599
MA0057.1	MA0057.1	0.729
MA0058.1	MA0058.1	0.838
MA0059.1	MA0059.1	0.471
MA0060.1	MA0060.1	0.893
MA0061.1	MA0061.1	4.59346e-5
MA0062.2	MA0062.2	2.70737e-7
MA0065.2	MA0065.2	0.36
MA0066.1	MA0066.1	0.177
MA0067.1	MA0067.1	0.787
MA0068.1	MA0068.1	0.696
MA0069.1	MA0069.1	0.436
MA0070.1	MA0070.1	0.535
MA0071.1	MA0071.1	0.839
MA0072.1	MA0072.1	0.464
MA0073.1	MA0073.1	0.889
MA0074.1	MA0074.1	0.615
MA0076.1	MA0076.1	0.0971
MA0077.1	MA0077.1	0.197
MA0078.1	MA0078.1	0.838
MA0079.2	MA0079.2	0.0685
MA0080.2	MA0080.2	3.45622e-14
MA0081.1	MA0081.1	0.00717
MA0083.1	MA0083.1	0.154
MA0084.1	MA0084.1	0.287
MA0087.1	MA0087.1	0.0877
MA0088.1	MA0088.1	0.254
MA0090.1	MA0090.1	0.0267
MA0091.1	MA0091.1	0.221
MA0092.1	MA0092.1	0.696
MA0093.1	MA0093.1	0.831
MA0099.2	MA0099.2	0.953
MA0100.1	MA0100.1	0.18
MA0101.1	MA0101.1	3.81156e-4
MA0102.2	MA0102.2	0.317
MA0103.1	MA0103.1	0.722
MA0104.2	MA0104.2	0.826
MA0105.1	MA0105.1	5.29559e-7
MA0106.1	MA0106.1	0.622
MA0107.1	MA0107.1	1.7784e-4
MA0108.2	MA0108.2	0.00332
MA0111.1	MA0111.1	0.743
MA0112.2	MA0112.2	0.00118
MA0113.1	MA0113.1	0.24
MA0114.1	MA0114.1	0.936
MA0115.1	MA0115.1	0.992
MA0116.1	MA0116.1	0.00202
MA0117.1	MA0117.1	0.688
MA0119.1	MA0119.1	0.41
MA0122.1	MA0122.1	0.946
MA0124.1	MA0124.1	0.79
MA0125.1	MA0125.1	0.046
MA0131.1	MA0131.1	0.876
MA0135.1	MA0135.1	0.288
MA0136.1	MA0136.1	6.47913e-20
MA0137.2	MA0137.2	0.155
MA0138.2	MA0138.2	0.0118
MA0139.1	MA0139.1	0.224
MA0140.1	MA0140.1	2.2068e-27
MA0141.1	MA0141.1	0.778
MA0142.1	MA0142.1	6.0363e-5
MA0143.1	MA0143.1	0.136
MA0144.1	MA0144.1	0.322
MA0145.1	MA0145.1	0.618
MA0146.1	MA0146.1	0.186
MA0147.1	MA0147.1	0.763
MA0148.1	MA0148.1	0.66
MA0149.1	MA0149.1	0.154
MA0150.1	MA0150.1	0.0118
MA0152.1	MA0152.1	0.403
MA0153.1	MA0153.1	5.19293e-8
MA0154.1	MA0154.1	0.0011
MA0155.1	MA0155.1	0.681
MA0156.1	MA0156.1	1.00735e-16
MA0157.1	MA0157.1	0.993
MA0159.1	MA0159.1	0.0859
MA0160.1	MA0160.1	0.981
MA0162.1	MA0162.1	0.142
MA0163.1	MA0163.1	3.24261e-4
MA0164.1	MA0164.1	0.42
MA0258.1	MA0258.1	0.0622
MA0259.1	MA0259.1	0.68

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: CNhs10465

Novel motif	Logo	P-value
1	1	0.176
10	10	0.0389
100	100	0.922
101	101	0.84
102	102	0.61
103	103	0.037
104	104	0.99
105	105	0.899
106	106	0.0977
107	107	0.552
108	108	0.593
109	109	0.0864
11	11	0.119
110	110	0.0773
111	111	0.0768
112	112	0.0241
113	113	0.427
114	114	0.313
115	115	0.889
116	116	0.776
117	117	0.00171
118	118	0.104
119	119	0.116
12	12	0.806
120	120	0.789
121	121	0.144
122	122	0.848
123	123	0.316
124	124	0.841
125	125	0.0538
126	126	0.215
127	127	0.372
128	128	0.139
129	129	0.221
13	13	0.0453
130	130	0.34
131	131	0.911
132	132	0.189
133	133	0.941
134	134	0.3
135	135	0.93
136	136	0.513
137	137	0.044
138	138	0.919
139	139	0.538
14	14	0.637
140	140	0.693
141	141	0.288
142	142	0.28
143	143	0.0872
144	144	0.792
145	145	0.0353
146	146	0.739
147	147	0.688
148	148	0.0746
149	149	0.661
15	15	0.0223
150	150	0.135
151	151	0.125
152	152	0.812
153	153	0.433
154	154	0.799
155	155	0.132
156	156	0.0692
157	157	0.843
158	158	0.0519
159	159	0.396
160	160	0.542
161	161	0.0445
162	162	0.431
163	163	0.441
164	164	0.0544
165	165	0.163
166	166	0.396
167	167	0.446
168	168	0.448
169	169	0.0199
17	17	0.336
18	18	0.128
19	19	0.306
2	2	0.495
20	20	0.142
21	21	0.27
22	22	0.382
23	23	0.605
24	24	0.168
25	25	0.269
26	26	0.00456
27	27	0.419
28	28	0.167
29	29	0.0409
3	3	0.038
30	30	0.471
31	31	0.661
32	32	0.609
33	33	0.198
34	34	0.66
35	35	0.456
36	36	0.105
37	37	0.159
38	38	0.241
39	39	0.743
4	4	0.998
40	40	0.212
41	41	0.838
42	42	0.0603
43	43	0.0614
44	44	0.264
45	45	0.882
46	46	0.132
47	47	0.126
48	48	0.19
49	49	0.0878
5	5	0.111
50	50	0.871
51	51	0.829
52	52	0.757
53	53	0.857
54	54	0.999
55	55	0.144
56	56	0.429
57	57	0.416
58	58	0.199
59	59	0.155
6	6	0.511
60	60	0.256
61	61	0.233
62	62	0.0687
63	63	0.314
64	64	0.487
65	65	0.201
66	66	0.722
67	67	0.522
68	68	0.174
69	69	0.746
7	7	0.0712
70	70	0.175
71	71	0.034
72	72	0.256
73	73	0.179
74	74	0.687
75	75	0.0269
76	76	0.226
77	77	0.747
78	78	0.027
79	79	0.764
8	8	0.0293
80	80	0.00288
81	81	0.398
82	82	0.457
83	83	0.127
84	84	0.515
85	85	0.152
86	86	0.414
87	87	0.387
88	88	0.577
89	89	0.744
9	9	0.424
90	90	0.0852
91	91	0.28
92	92	0.456
93	93	0.164
94	94	0.101
95	95	0.116
96	96	0.108
97	97	0.871
98	98	0.108
99	99	0.693

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: CNhs10465

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011306 mouse spleen- adult 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)
0007023 (adult organism)
0002106 (spleen)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002323 (body cavity)
0005177 (trunk region element)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011306 (mouse spleen- adult 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:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002095,UBERON:0002100,UBERON:0002106,UBERON:0002193,UBERON:0002323,UBERON:0002390,UBERON:0002405,UBERON:0002417,UBERON:0002532,UBERON:0002553,UBERON:0003081,UBERON:0003104,UBERON:0003281,UBERON:0004119,UBERON:0004120,UBERON:0004177,UBERON:0004185,UBERON:0004457,UBERON:0004458,UBERON:0004782,UBERON:0004854,UBERON:0004872,UBERON:0004921,UBERON:0004923,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0005602,UBERON:0006293,UBERON:0007023,UBERON:0007026,UBERON:0009034,UBERON:0009142
+|DRA_sample_Accession=CAGE@SAMD00005695
+|accession_numbers=CAGE;DRX009084;DRR009958;DRZ001383;DRZ002766;DRZ012733;DRZ014116
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0002106,UBERON:0002100,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002323,UBERON:0005177,UBERON:0004177,UBERON:0005057,UBERON:0005172,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0005173,UBERON:0002390,UBERON:0002417,UBERON:0002193,UBERON:0000916,UBERON:0002405
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000998,FF:0000004,FF:0011306
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:87425854..87425891,+!p1@Klf1!2.28!188.47!Klf1;;chr15:103085660..103085681,-!p1@Nfe2!2.17!214.10!Nfe2;;chr2:28477452..28477483,-!p1@Gfi1b!2.00!121.66!Gfi1b;;chr7:122989594..122989626,-!p1@Sox6!2.00!99.28!Sox6;;chr9:51021788..51021802,+!p1@Pou2af1!1.93!98.76!Pou2af1;;chrX:7544943..7545001,-!p1@Gata1!1.89!77.23!Gata1;;chr7:51787434..51787448,-!p1@Spib!1.88!106.79!Spib;;chr10:88145766..88145770,-!p1@Spic!1.88!95.69!Spic;;chr4:114732112..114732158,+!p1@Tal1!1.86!151.56!Tal1;;chr7:122989632..122989668,-!p2@Sox6!1.75!55.70!Sox6;;chr4:44723559..44723593,-!p1@Pax5!1.74!54.00!Pax5;;chr11:11584970..11585030,+!p2@Ikzf1!1.71!70.74!Ikzf1;;chr9:96159147..96159204,+!p2@Tfdp2!1.69!87.66!Tfdp2;;chr1:38721792..38721845,-!p1@Aff3!1.66!55.87!Aff3;;chr15:103082088..103082136,-!p2@Nfe2!1.66!44.60!Nfe2;;chr15:103085690..103085710,-!p3@Nfe2!1.57!39.47!Nfe2;;chr13:30841099..30841116,+!p1@Irf4!1.52!49.55!Irf4;;chr6:99216488..99216534,-!p2@Foxp1!1.50!84.07!Foxp1;;chr4:44723520..44723544,-!p2@Pax5!1.46!27.68!Pax5;;chr11:98407264..98407295,-!p1@Ikzf3!1.43!26.14!Ikzf3;;chr4:135728581..135728668,+!p1@E2f2!1.41!113.97!E2f2;;chr11:11586218..11586285,+!p1@Ikzf1!1.36!68.18!Ikzf1;;chr16:92826249..92826325,-!p1@Runx1!1.35!51.60!Runx1;;chr7:25917492..25917512,-!p1@Pou2f2!1.30!31.61!Pou2f2;;chr9:96159225..96159249,+!p5@Tfdp2!1.30!21.19!Tfdp2;;chr11:98407234..98407259,-!p2@Ikzf3!1.30!18.80!Ikzf3;;chr4:87452200..87452229,-!p2@Mllt3!1.29!39.13!Mllt3;;chr8:87225670..87225697,+!p2@Lyl1!1.26!50.07!Lyl1;;chr2:91034924..91034946,-!p2@Nr1h3!1.26!21.19!Nr1h3;;chr11:16908650..16908690,-!p1@Plek!1.25!101.33!Plek;;chr9:96159116..96159130,+!p6@Tfdp2!1.22!19.31!Tfdp2;;chr4:63064364..63064384,-!p1@Akna!1.21!43.74!Akna;;chr4:44723633..44723646,-!p3@Pax5!1.21!15.04!Pax5;;chr10:79884592..79884621,-!p5@Tcf3!1.21!15.04!Tcf3;;chr10:22539932..22539956,-!p1@Tcf21!1.20!39.13!Tcf21;;chr4:114729957..114730012,+!p3@Tal1!1.19!14.52!Tal1;;chr8:123260252..123260264,+!p1@Irf8!1.13!88.34!Irf8;;chr2:173044380..173044432,-!p1@Zbp1!1.13!29.90!Zbp1;;chr9:96159133..96159145,+!p9@Tfdp2!1.13!12.64!Tfdp2;;chr4:135728181..135728203,+!p2@E2f2!1.12!16.06!E2f2;;chr8:87225702..87225726,+!p3@Lyl1!1.11!23.92!Lyl1;;chr3:130815703..130815721,+!p2@Lef1!1.11!14.52!Lef1;;chr4:134708451..134708469,+!p1@Runx3!1.10!20.33!Runx3;;chr11:11585912..11585950,+!p6@Ikzf1!1.08!14.01!Ikzf1;;chr5:134720044..134720103,-!p6@Gtf2i!1.08!10.94!Gtf2i;;chr11:98407370..98407395,-!p3@Ikzf3!1.07!10.76!Ikzf3;;chr4:87452180..87452196,-!p3@Mllt3!1.05!20.50!Mllt3;;chr1:52065508..52065522,+!p2@Stat4!1.05!11.96!Stat4;;chr8:124806048..124806094,+!p1@Zfpm1!1.03!90.39!Zfpm1;;chr11:5420655..5420659,+!p3@Xbp1!1.03!9.74!Xbp1;;chr2:90936901..90936945,+!p1@Sfpi1!1.02!50.24!Sfpi1;;chr11:120491440..120491474,-!p3@Mafg!1.00!13.33!Mafg;;chr15:103085802..103085817,-!p4@Nfe2!1.00!11.45!Nfe2;;chr4:135728473..135728494,+!p5@E2f2!1.00!9.06!E2f2;;chr6:86619104..86619119,-!p1@Mxd1!0.99!73.47!Mxd1;;chr8:87225329..87225396,+!p1@Lyl1!0.99!33.83!Lyl1;;chr2:166868994..166869023,-!p7@Znfx1!0.99!8.89!Znfx1;;chr11:52096066..52096081,-!p2@Tcf7!0.98!10.42!Tcf7;;chr4:44723835..44723849,-!p4@Pax5!0.98!8.54!Pax5;;chr19:45225149..45225186,+!p1@Tlx1!0.98!8.54!Tlx1;;chr11:23977565..23977612,+!p5@Bcl11a!0.97!18.62!Bcl11a;;chr4:134708909..134708939,+!p3@Runx3!0.97!8.37!Runx3;;chr11:11585678..11585745,+!p5@Ikzf1!0.96!11.96!Ikzf1;;chr6:29476690..29476724,+!p1@Irf5!0.95!37.93!Irf5;;chr13:112476264..112476282,+!p3@Mier3!0.95!11.28!Mier3;;chr8:124806017..124806040,+!p2@Zfpm1!0.93!86.29!Zfpm1;;chr7:148452314..148452329,-!p1@Irf7!0.93!54.51!Irf7;;chr7:56136362..56136400,-!p1@E2f8!0.93!50.58!E2f8;;chr11:96976641..96976646,-!p1@Tbx21!0.93!7.52!Tbx21;;chr1:52176406..52176433,+!p2@Stat1!0.92!18.45!Stat1;;chr17:45692676..45692695,+!p2@Nfkbie!0.92!15.21!Nfkbie;;chr9:96159210..96159221,+!p10@Tfdp2!0.92!7.35!Tfdp2;;chr14:79915425..79915501,+!p1@Elf1!0.91!65.44!Elf1;;chr1:52065454..52065495,+!p1@Stat4!0.91!12.13!Stat4;;chr5:65203599..65203617,+!p8@Klf3!0.91!12.13!Klf3;;chr2:173044357..173044377,-!p2@Zbp1!0.90!10.25!Zbp1;;chr2:38570011..38570034,-!p1@Nr5a1!0.90!7.01!Nr5a1;;chr11:100683839..100683890,-!p2@Stat5b!0.89!16.57!Stat5b;;chr2:90936947..90936977,+!p2@Sfpi1!0.89!13.84!Sfpi1;;chr4:114730254..114730276,+!p2@Tal1!0.89!8.71!Tal1;;chr5:65203575..65203589,+!p11@Klf3!0.88!8.03!Klf3;;chr4:87452236..87452249,-!p9@Mllt3!0.88!6.66!Mllt3;;chr10:20880629..20880683,-!p1@Myb!0.87!19.31!Myb;;chr5:144951153..144951203,+!p1@Bhlha15!0.87!9.57!Bhlha15;;chr7:122989676..122989687,-!p8@Sox6!0.87!6.49!Sox6;;chr10:20880731..20880775,-!p2@Myb!0.86!13.67!Myb;;chr5:104183477..104183548,+!p6@Aff1!0.86!12.64!Aff1;;chr1:52176315..52176343,+!p1@Stat1!0.84!90.39!Stat1;;chr5:138187583..138187602,+!p6@Tsc22d4!0.84!11.45!Tsc22d4;;chr11:11590140..11590187,+!p3@Ikzf1!0.84!7.18!Ikzf1;;chrX:7156792..7156811,+!p1@Foxp3!0.84!5.98!Foxp3;;chr11:44430812..44430838,+!p1@Ebf1!0.83!60.32!Ebf1;;chr1:87546583..87546595,+!p1@Sp100!0.82!8.20!Sp100;;chr11:98407340..98407359,-!p4@Ikzf3!0.82!5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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0004872,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:25-2G2
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011306
+|is_a=EFO:0002091;;FF:0011306
+|is_obsolete=
+|library_id=CNhs10465
+|library_id_phase_based=2:CNhs10465
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;25
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;25
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spleen%252c%2520adult.CNhs10465.25-2G2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spleen%252c%2520adult.CNhs10465.25-2G2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spleen%252c%2520adult.CNhs10465.25-2G2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spleen%252c%2520adult.CNhs10465.25-2G2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spleen%252c%2520adult.CNhs10465.25-2G2.mm9.nobarcode.rdna.fa.gz
 |name=spleen, adult
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10465,LSID646,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0835410936585095,0,0.034101416720665,0.0685090053637401,0.179727725901961,0,-0.058965863610408,0,0.0342545026818701,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.0642244135189994,0,0.0898638629509805,0,0,0,0.0685090053637401,0,0,0,0,0,0,0,0.295965345163263,0,0,0,0.0685090053637401,0,0.194154540277381,-0.0486979113270117,0.359753086866429,-0.804483640575865,-0.142199700646776,0,0,0,0,0,0,0,0,0,0,0.0685090053637401,0,0.0616633898001348,0,0,0,0,0,0,0,0,0,0,-0.0284874588465605,0.197383407175164,0.110101697278922,-0.0698404715885695,0,0,-0.0729583017401753,-0.0325131384176686,0.404463883488154,0,-0.0324019513999773,0.00893153929383845,0.166342285146326,-0.0103225894761673,0,0,0,0,0,0,0.0705588186773153,-0.147714480048756,0.0729659836445492,0,0,0,0,0
 |rna_box=2
 |rna_catalog_number=
@@ Line 57: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=spleen
 |top_motifs=POU2F1..3:3.62407095786;GATA6:2.86104288161;SPIB:2.05504252185;POU5F1:2.05470493332;IRF1,2:1.84455481406;ETS1,2:1.63328612255;SPI1:1.63197198047;ELF1,2,4:1.5499153442;RUNX1..3:1.54830526623;E2F1..5:1.32837208236;ALX4:1.29516417472;AIRE:1.28481533722;NFKB1_REL_RELA:1.24508444399;DMAP1_NCOR{1,2}_SMARC:1.22048502417;IRF7:1.18448057059;STAT5{A,B}:1.10833398782;TBX4,5:1.08378417352;POU1F1:1.04316626264;NFE2L2:0.896712725665;PBX1:0.801589333881;MYB:0.793480192188;ZBTB16:0.78072932435;CEBPA,B_DDIT3:0.759980838839;OCT4_SOX2{dimer}:0.686357664378;PITX1..3:0.673596980345;RXRA_VDR{dimer}:0.659729869656;FOXO1,3,4:0.626420189913;PAX1,9:0.620368404157;NFATC1..3:0.534735469993;HOX{A5,B5}:0.480025945342;PPARG:0.47389794312;NFY{A,B,C}:0.462775756268;YY1:0.431935743562;STAT2,4,6:0.42427941541;ARID5B:0.419507034495;ZNF148:0.408496303043;STAT1,3:0.406997880888;TEF:0.396953506251;FOXP3:0.353616308547;NR6A1:0.345722978107;SREBF1,2:0.316546049812;ZNF423:0.254567096457;NFE2:0.198432936709;FOXM1:0.198191099334;FOX{I1,J2}:0.112132142275;GFI1:0.0796452801977;BACH2:0.048733660115;FOXP1:0.0374409841886;HOXA9_MEIS1:0.0199311979786;TFDP1:0.00455721680337;EBF1:-0.0118373671755;ELK1,4_GABP{A,B1}:-0.0122413434111;NKX2-2,8:-0.0284922607954;TLX2:-0.0300824120393;ATF5_CREB3:-0.0485085305035;bHLH_family:-0.0519164644486;ATF4:-0.0787462239249;PRDM1:-0.0789082311267;NFE2L1:-0.0986714862508;FOXQ1:-0.104297373033;PAX2:-0.128580699716;IKZF2:-0.132267337721;NFIL3:-0.207498526647;CDX1,2,4:-0.214865628539;BPTF:-0.222369404459;EP300:-0.26234541941;NFIX:-0.27019376079;FOX{F1,F2,J1}:-0.281821829693;HLF:-0.343160519022;LMO2:-0.346113940753;SRF:-0.355818740574;NKX3-2:-0.378430494774;ZNF143:-0.400822392384;PDX1:-0.413554474374;SOX17:-0.419095054555;TAL1_TCF{3,4,12}:-0.440503834467;NR1H4:-0.452808477155;ALX1:-0.462320425214;MYFfamily:-0.466197711068;GATA4:-0.468942550416;SMAD1..7,9:-0.499728409757;TBP:-0.505320744141;MTF1:-0.525230466803;HAND1,2:-0.529429357778;HMGA1,2:-0.530333905463;EVI1:-0.551334034994;ZEB1:-0.555291364641;NKX3-1:-0.56528866608;HSF1,2:-0.565518709199;PAX4:-0.566085284693;NHLH1,2:-0.573424866698;SPZ1:-0.573745316521;NRF1:-0.586868154344;SNAI1..3:-0.613000772649;HES1:-0.620751950687;FOS_FOS{B,L1}_JUN{B,D}:-0.628712989424;FOXA2:-0.634401413603;SOX{8,9,10}:-0.6357085861;HNF4A_NR2F1,2:-0.640805709197;NANOG{mouse}:-0.64868951077;FOX{D1,D2}:-0.653729744056;MAFB:-0.655569708309;CRX:-0.660774664874;ZFP161:-0.677309673407;MEF2{A,B,C,D}:-0.6846125643;TGIF1:-0.687011209063;ZNF384:-0.693128642527;BREu{core}:-0.699563995134;PRRX1,2:-0.705327265605;NKX2-1,4:-0.709048802294;MYOD1:-0.71061583379;AHR_ARNT_ARNT2:-0.757421846645;PAX8:-0.764187311059;CREB1:-0.771169979441;TFAP4:-0.772585376084;RREB1:-0.774573969486;IKZF1:-0.779311896011;EGR1..3:-0.781811624105;HNF1A:-0.791279322905;FOXL1:-0.843682951557;GLI1..3:-0.847526939763;GCM1,2:-0.85384261025;POU6F1:-0.866495317977;ATF2:-0.871367647736;MYBL2:-0.872549286294;RFX2..5_RFXANK_RFXAP:-0.8761795051;RFX1:-0.879017657535;MZF1:-0.887271919044;ESR1:-0.898358059519;PAX6:-0.899239294883;NR3C1:-0.916684209494;TLX1..3_NFIC{dimer}:-0.921110216492;UFEwm:-0.921796777436;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.933344025336;GZF1:-0.952050939741;LHX3,4:-0.956215261209;ATF6:-0.959011163942;TEAD1:-0.966371139983;TOPORS:-0.970602334546;KLF4:-0.984003382397;ZBTB6:-1.01205546593;TFAP2{A,C}:-1.01643364946;TP53:-1.01863228677;NKX6-1,2:-1.02071146393;NR5A1,2:-1.02995281462;RORA:-1.04362436162;SP1:-1.04712484041;JUN:-1.05682267099;XCPE1{core}:-1.05794890799;REST:-1.06459854683;MTE{core}:-1.0655662162;MED-1{core}:-1.06575816411;FOXD3:-1.08615260769;SOX2:-1.09187840735;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.10208737495;PATZ1:-1.11363170579;EN1,2:-1.14399759757;GTF2I:-1.16406404497;NANOG:-1.1642404745;TFAP2B:-1.16644532685;ESRRA:-1.16940117037;ZNF238:-1.1900804199;CDC5L:-1.25260304186;ZIC1..3:-1.25272883686;ADNP_IRX_SIX_ZHX:-1.25920937249;VSX1,2:-1.27827165596;CUX2:-1.28523213304;HOX{A4,D4}:-1.29038077046;NKX2-3_NKX2-5:-1.29524565584;MAZ:-1.33146281297;HBP1_HMGB_SSRP1_UBTF:-1.351881024;RXR{A,B,G}:-1.35953565843;HIF1A:-1.36398514243;HIC1:-1.36649629209;HMX1:-1.37058751128;GTF2A1,2:-1.41246039915;PAX5:-1.44896331732;SOX5:-1.45359172655;TFCP2:-1.47036516821;T:-1.49045026356;GFI1B:-1.49323275195;POU3F1..4:-1.57610908912;ONECUT1,2:-1.58420446572;LEF1_TCF7_TCF7L1,2:-1.6012519521;RBPJ:-1.60226666556;FOXN1:-1.61796933914;FOSL2:-1.75264167421;AR:-1.79182739867;DBP:-1.8773925049
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:25-2G2;search_select_hide=table117:25-2G2
 }}

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FF:25-2G2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:09, 4 June 2020

CNhs10465

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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