FF:752-24D1: Difference between revisions

Latest revision as of 19:20, 4 June 2020

Name:	spleen, neonate N10
Species:	Mouse (Mus musculus)
Library ID:	CNhs11116
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	spleen
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		SAMD00005884

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11116		CAGE		DRX009087		DRR009961

Accession ID Mm9

Library id		BAM		CTSS
CNhs11116		DRZ001386		DRZ002769

Accession ID Mm10

Library id		BAM		CTSS
CNhs11116		DRZ012736		DRZ014119

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

CNhs11116

0	0
1	0
10	0
100	0
1000	0
1001	0.0119
1002	0.00471
1003	-0.0927
1004	0
1005	0.075
1006	-0.143
1007	0.0174
1008	0
1009	-0.185
101	0.103
1010	0
1011	-0.103
1012	0.244
1013	-0.0779
1014	-0.0196
1015	-0.164
1016	-0.465
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.075
1022	-0.165
1023	0
1024	0.049
1025	0
1026	0
1027	0
1028	0
1029	0.266
103	-0.00877
1030	0.46
1031	-0.188
1032	-0.177
1033	0.00845
1034	0
1035	0
1036	0.411
1037	0
1038	-0.255
1039	-0.173
104	0
1040	-0.0915
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: CNhs11116

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00953
MA0003.1	MA0003.1	0.608
MA0004.1	MA0004.1	0.937
MA0006.1	MA0006.1	0.374
MA0007.1	MA0007.1	0.785
MA0009.1	MA0009.1	0.413
MA0014.1	MA0014.1	0.991
MA0017.1	MA0017.1	0.226
MA0018.2	MA0018.2	9.60074e-4
MA0019.1	MA0019.1	0.499
MA0024.1	MA0024.1	5.21844e-7
MA0025.1	MA0025.1	0.0555
MA0027.1	MA0027.1	0.636
MA0028.1	MA0028.1	0.0434
MA0029.1	MA0029.1	0.964
MA0030.1	MA0030.1	0.253
MA0031.1	MA0031.1	0.502
MA0035.2	MA0035.2	4.92642e-13
MA0038.1	MA0038.1	0.0469
MA0039.2	MA0039.2	0.718
MA0040.1	MA0040.1	0.885
MA0041.1	MA0041.1	0.3
MA0042.1	MA0042.1	0.843
MA0043.1	MA0043.1	5.52888e-4
MA0046.1	MA0046.1	7.46664e-11
MA0047.2	MA0047.2	0.834
MA0048.1	MA0048.1	0.102
MA0050.1	MA0050.1	1.27315e-5
MA0051.1	MA0051.1	0.00112
MA0052.1	MA0052.1	3.91262e-6
MA0055.1	MA0055.1	0.188
MA0057.1	MA0057.1	0.71
MA0058.1	MA0058.1	0.964
MA0059.1	MA0059.1	0.182
MA0060.1	MA0060.1	0.267
MA0061.1	MA0061.1	0.0101
MA0062.2	MA0062.2	3.30613e-4
MA0065.2	MA0065.2	0.29
MA0066.1	MA0066.1	0.199
MA0067.1	MA0067.1	0.574
MA0068.1	MA0068.1	0.793
MA0069.1	MA0069.1	0.497
MA0070.1	MA0070.1	0.157
MA0071.1	MA0071.1	0.724
MA0072.1	MA0072.1	0.771
MA0073.1	MA0073.1	0.868
MA0074.1	MA0074.1	0.731
MA0076.1	MA0076.1	0.0992
MA0077.1	MA0077.1	0.0814
MA0078.1	MA0078.1	0.508
MA0079.2	MA0079.2	0.0329
MA0080.2	MA0080.2	7.53797e-10
MA0081.1	MA0081.1	0.0843
MA0083.1	MA0083.1	0.143
MA0084.1	MA0084.1	0.193
MA0087.1	MA0087.1	0.0967
MA0088.1	MA0088.1	0.108
MA0090.1	MA0090.1	0.0563
MA0091.1	MA0091.1	0.0211
MA0092.1	MA0092.1	0.635
MA0093.1	MA0093.1	0.989
MA0099.2	MA0099.2	0.629
MA0100.1	MA0100.1	0.0573
MA0101.1	MA0101.1	0.0404
MA0102.2	MA0102.2	0.917
MA0103.1	MA0103.1	0.642
MA0104.2	MA0104.2	0.638
MA0105.1	MA0105.1	1.0843e-5
MA0106.1	MA0106.1	0.314
MA0107.1	MA0107.1	0.0738
MA0108.2	MA0108.2	9.42747e-4
MA0111.1	MA0111.1	0.668
MA0112.2	MA0112.2	0.00124
MA0113.1	MA0113.1	0.496
MA0114.1	MA0114.1	0.722
MA0115.1	MA0115.1	0.591
MA0116.1	MA0116.1	4.71306e-4
MA0117.1	MA0117.1	0.973
MA0119.1	MA0119.1	0.107
MA0122.1	MA0122.1	0.773
MA0124.1	MA0124.1	0.88
MA0125.1	MA0125.1	0.0657
MA0131.1	MA0131.1	0.755
MA0135.1	MA0135.1	0.076
MA0136.1	MA0136.1	4.14394e-10
MA0137.2	MA0137.2	0.754
MA0138.2	MA0138.2	0.00512
MA0139.1	MA0139.1	0.13
MA0140.1	MA0140.1	1.01847e-45
MA0141.1	MA0141.1	0.266
MA0142.1	MA0142.1	0.36
MA0143.1	MA0143.1	0.254
MA0144.1	MA0144.1	0.785
MA0145.1	MA0145.1	0.966
MA0146.1	MA0146.1	0.474
MA0147.1	MA0147.1	0.547
MA0148.1	MA0148.1	0.657
MA0149.1	MA0149.1	0.0235
MA0150.1	MA0150.1	0.0303
MA0152.1	MA0152.1	0.891
MA0153.1	MA0153.1	1.30421e-6
MA0154.1	MA0154.1	0.00593
MA0155.1	MA0155.1	0.688
MA0156.1	MA0156.1	6.46543e-8
MA0157.1	MA0157.1	0.423
MA0159.1	MA0159.1	0.272
MA0160.1	MA0160.1	0.965
MA0162.1	MA0162.1	0.186
MA0163.1	MA0163.1	4.8273e-5
MA0164.1	MA0164.1	0.456
MA0258.1	MA0258.1	0.115
MA0259.1	MA0259.1	0.857

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: CNhs11116

Novel motif	Logo	P-value
1	1	0.0784
10	10	0.0244
100	100	0.571
101	101	0.97
102	102	0.723
103	103	0.0102
104	104	0.865
105	105	0.723
106	106	0.243
107	107	0.466
108	108	0.362
109	109	0.061
11	11	0.191
110	110	0.0698
111	111	0.0197
112	112	0.0423
113	113	0.995
114	114	0.453
115	115	0.528
116	116	0.793
117	117	0.00148
118	118	0.112
119	119	0.201
12	12	0.809
120	120	0.873
121	121	0.189
122	122	0.59
123	123	0.165
124	124	0.881
125	125	0.0208
126	126	0.242
127	127	0.444
128	128	0.161
129	129	0.197
13	13	0.00325
130	130	0.277
131	131	0.938
132	132	0.168
133	133	0.443
134	134	0.0639
135	135	0.928
136	136	0.818
137	137	0.0126
138	138	0.626
139	139	0.461
14	14	0.762
140	140	0.202
141	141	0.747
142	142	0.0666
143	143	0.453
144	144	0.646
145	145	0.00674
146	146	0.851
147	147	0.746
148	148	0.123
149	149	0.692
15	15	0.0463
150	150	0.166
151	151	0.326
152	152	0.469
153	153	0.593
154	154	0.244
155	155	0.0992
156	156	0.771
157	157	0.563
158	158	0.0494
159	159	0.0975
160	160	0.434
161	161	0.0804
162	162	0.982
163	163	0.716
164	164	0.0224
165	165	0.353
166	166	0.381
167	167	0.0746
168	168	0.486
169	169	0.0637
17	17	0.432
18	18	0.238
19	19	0.257
2	2	0.321
20	20	0.0745
21	21	0.421
22	22	0.638
23	23	0.892
24	24	0.435
25	25	0.361
26	26	8.08329e-4
27	27	0.85
28	28	0.287
29	29	0.016
3	3	0.0378
30	30	0.387
31	31	0.891
32	32	0.551
33	33	0.197
34	34	0.971
35	35	0.693
36	36	0.044
37	37	0.153
38	38	0.488
39	39	0.656
4	4	0.846
40	40	0.251
41	41	0.697
42	42	0.0532
43	43	0.0976
44	44	0.917
45	45	0.68
46	46	0.135
47	47	0.185
48	48	0.254
49	49	0.0583
5	5	0.0998
50	50	0.958
51	51	0.819
52	52	0.842
53	53	0.98
54	54	0.97
55	55	0.282
56	56	0.594
57	57	0.0651
58	58	0.315
59	59	0.494
6	6	0.382
60	60	0.394
61	61	0.438
62	62	0.15
63	63	0.41
64	64	0.576
65	65	0.539
66	66	0.782
67	67	0.429
68	68	0.689
69	69	0.279
7	7	0.0433
70	70	0.345
71	71	0.0173
72	72	0.409
73	73	0.445
74	74	0.712
75	75	0.0449
76	76	0.251
77	77	0.77
78	78	0.0426
79	79	0.989
8	8	0.0209
80	80	0.0596
81	81	0.437
82	82	0.599
83	83	0.485
84	84	0.0574
85	85	0.391
86	86	0.79
87	87	0.352
88	88	0.724
89	89	0.633
9	9	0.421
90	90	0.0241
91	91	0.127
92	92	0.461
93	93	0.451
94	94	0.119
95	95	0.193
96	96	0.00692
97	97	0.859
98	98	0.26
99	99	0.971

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: CNhs11116

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011417 mouse spleen- 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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011417 (mouse spleen- 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:0004872 (splanchnic layer of lateral plate 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:0002106,UBERON:0000945,UBERON:0002100,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004457,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004923,UBERON:0004921,UBERON:0005423,UBERON:0002553,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0009569,UBERON:0005291,UBERON:0010039,UBERON:0002323,UBERON:0005177,UBERON:0000042,UBERON:0003104,UBERON:0004177,UBERON:0005057,UBERON:0005172,UBERON:0000464,UBERON:0004458,UBERON:0001048,UBERON:0000925,UBERON:0004854,UBERON:0009034,UBERON:0006598,UBERON:0003886,UBERON:0002095,UBERON:0004782,UBERON:0004185,UBERON:0005173,UBERON:0003281,UBERON:0002532,UBERON:0001555,UBERON:0005409,UBERON:0002390,UBERON:0002417,UBERON:0007026,UBERON:0001041,UBERON:0002193,UBERON:0000916,UBERON:0002405,UBERON:0003887,UBERON:0009664,UBERON:0009142,UBERON:0003081,UBERON:0002296,UBERON:0005602,UBERON:0001179,UBERON:0006595,UBERON:0006603,UBERON:0004872,UBERON:0006293,UBERON:0003061
+|DRA_sample_Accession=CAGE@SAMD00005884
+|accession_numbers=CAGE;DRX009087;DRR009961;DRZ001386;DRZ002769;DRZ012736;DRZ014119
+|ancestors_in_anatomy_facet=UBERON:0000468,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:0000004,FF:0000303,FF:0000305,FF:0011417
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr8:87425854..87425891,+!p1@Klf1!2.33!210.41!Klf1;;chr7:122989594..122989626,-!p1@Sox6!2.25!174.99!Sox6;;chr15:103085660..103085681,-!p1@Nfe2!2.19!224.91!Nfe2;;chr2:28477452..28477483,-!p1@Gfi1b!2.18!183.28!Gfi1b;;chr7:122989632..122989668,-!p2@Sox6!2.16!144.86!Sox6;;chr9:96159147..96159204,+!p2@Tfdp2!2.05!201.18!Tfdp2;;chrX:7544943..7545001,-!p1@Gata1!2.00!100.02!Gata1;;chr4:114732112..114732158,+!p1@Tal1!1.94!180.65!Tal1;;chr15:103082088..103082136,-!p2@Nfe2!1.75!55.19!Nfe2;;chr11:11584970..11585030,+!p2@Ikzf1!1.73!74.97!Ikzf1;;chr15:103085690..103085710,-!p3@Nfe2!1.71!55.00!Nfe2;;chr10:88145766..88145770,-!p1@Spic!1.67!58.58!Spic;;chr7:51787434..51787448,-!p1@Spib!1.66!63.10!Spib;;chr9:96159116..96159130,+!p6@Tfdp2!1.64!52.55!Tfdp2;;chr9:96159225..96159249,+!p5@Tfdp2!1.52!35.98!Tfdp2;;chr4:87452200..87452229,-!p2@Mllt3!1.49!61.78!Mllt3;;chr4:135728581..135728668,+!p1@E2f2!1.48!133.93!E2f2;;chr9:96159133..96159145,+!p9@Tfdp2!1.44!26.37!Tfdp2;;chr16:92826249..92826325,-!p1@Runx1!1.42!61.03!Runx1;;chr1:38721792..38721845,-!p1@Aff3!1.41!30.89!Aff3;;chr4:44723559..44723593,-!p1@Pax5!1.38!22.98!Pax5;;chr8:87225670..87225697,+!p2@Lyl1!1.36!62.35!Lyl1;;chr4:44723520..44723544,-!p2@Pax5!1.33!20.53!Pax5;;chr10:79884592..79884621,-!p5@Tcf3!1.33!20.16!Tcf3;;chr9:96159210..96159221,+!p10@Tfdp2!1.31!19.21!Tfdp2;;chr4:87452180..87452196,-!p3@Mllt3!1.30!36.92!Mllt3;;chr9:51021788..51021802,+!p1@Pou2af1!1.29!22.04!Pou2af1;;chr7:122989676..122989687,-!p8@Sox6!1.29!18.46!Sox6;;chr6:99216488..99216534,-!p2@Foxp1!1.26!48.22!Foxp1;;chr4:114729957..114730012,+!p3@Tal1!1.24!16.20!Tal1;;chr4:135728181..135728203,+!p2@E2f2!1.23!21.29!E2f2;;chr11:16908650..16908690,-!p1@Plek!1.22!94.00!Plek;;chr4:135728473..135728494,+!p5@E2f2!1.21!15.07!E2f2;;chr19:45225149..45225186,+!p1@Tlx1!1.17!13.94!Tlx1;;chr11:98407264..98407295,-!p1@Ikzf3!1.17!13.75!Ikzf3;;chr7:56136362..56136400,-!p1@E2f8!1.14!81.94!E2f8;;chr10:22539932..22539956,-!p1@Tcf21!1.14!34.28!Tcf21;;chr8:87225702..87225726,+!p3@Lyl1!1.14!26.18!Lyl1;;chr5:65203599..65203617,+!p8@Klf3!1.14!21.10!Klf3;;chr11:11586218..11586285,+!p1@Ikzf1!1.12!38.99!Ikzf1;;chr13:112476264..112476282,+!p3@Mier3!1.11!16.76!Mier3;;chr8:124806048..124806094,+!p1@Zfpm1!1.10!105.11!Zfpm1;;chr11:11585912..11585950,+!p6@Ikzf1!1.10!14.69!Ikzf1;;chr2:166868994..166869023,-!p7@Znfx1!1.08!10.93!Znfx1;;chr11:120491440..120491474,-!p3@Mafg!1.07!16.01!Mafg;;chr5:104183477..104183548,+!p6@Aff1!1.05!20.34!Aff1;;chr15:103085802..103085817,-!p4@Nfe2!1.04!12.62!Nfe2;;chr4:44723633..44723646,-!p3@Pax5!1.03!9.80!Pax5;;chr13:30841099..30841116,+!p1@Irf4!1.02!14.88!Irf4;;chr14:47896467..47896523,-!p1@Wdhd1!1.00!110.01!Wdhd1;;chr2:162880387..162880413,+!p1@Mybl2!1.00!58.02!Mybl2;;chr9:96159427..96159432,+!p11@Tfdp2!0.99!10.55!Tfdp2;;chr4:87452236..87452249,-!p9@Mllt3!0.99!8.66!Mllt3;;chr10:20880731..20880775,-!p2@Myb!0.98!18.27!Myb;;chr2:162880327..162880385,+!p2@Mybl2!0.96!55.19!Mybl2;;chr4:114730254..114730276,+!p2@Tal1!0.96!10.55!Tal1;;chr5:65203575..65203589,+!p11@Klf3!0.96!9.98!Klf3;;chr11:101413151..101413207,-!p1@Brca1!0.95!79.11!Brca1;;chr11:98407234..98407259,-!p2@Ikzf3!0.95!7.91!Ikzf3;;chr6:86619104..86619119,-!p1@Mxd1!0.94!65.55!Mxd1;;chr4:114730015..114730042,+!p7@Tal1!0.92!7.35!Tal1;;chr19:43686789..43686811,+!p1@Nkx2-3!0.90!6.97!Nkx2-3;;chr2:38570011..38570034,-!p1@Nr5a1!0.90!6.97!Nr5a1;;chr13:55431084..55431137,-!p1@Mxd3!0.89!55.76!Mxd3;;chr10:20880629..20880683,-!p1@Myb!0.88!19.78!Myb;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.87!10.36!Ncoa4;;chr8:124806017..124806040,+!p2@Zfpm1!0.86!72.33!Zfpm1;;chr8:87225329..87225396,+!p1@Lyl1!0.86!24.86!Lyl1;;chr10:20880698..20880717,-!p3@Myb!0.86!10.17!Myb;;chr6:86619130..86619158,-!p2@Mxd1!0.85!93.62!Mxd1;;chr7:56136349..56136360,-!p5@E2f8!0.84!7.53!E2f8;;chr7:25917492..25917512,-!p1@Pou2f2!0.82!9.80!Pou2f2;;chr13:112476296..112476308,+!p4@Mier3!0.82!6.40!Mier3;;chr1:87546583..87546595,+!p1@Sp100!0.81!8.10!Sp100;;chr10:80598968..80599012,+!p5@Zbtb7a!0.81!7.35!Zbtb7a;;chr6:83301243..83301258,+!p2@Bola3!0.81!5.46!Bola3;;chr4:135728282..135728310,+!p4@E2f2!0.80!6.03!E2f2;;chr8:123260252..123260264,+!p1@Irf8!0.79!39.37!Irf8;;chr2:162880418..162880429,+!p4@Mybl2!0.79!6.78!Mybl2;;chr7:56137011..56137041,-!p2@E2f8!0.78!10.36!E2f8;;chr4:114732159..114732166,+!p6@Tal1!0.77!4.90!Tal1;;chr7:148452314..148452329,-!p1@Irf7!0.76!36.36!Irf7;;chr15:103083928..103083932,-!p10@Nfe2!0.76!4.71!Nfe2;;chr14:79915425..79915501,+!p1@Elf1!0.75!45.21!Elf1;;chr4:44723835..44723849,-!p4@Pax5!0.74!4.52!Pax5;;chr4:63064364..63064384,-!p1@Akna!0.73!13.94!Akna;;chr19:53384910..53384937,+!p3@Mxi1!0.73!13.37!Mxi1;;chr17:26978409..26978442,-!p1@Nkx2-5!0.73!4.33!Nkx2-5;;chr3:135271185..135271254,-!p4@Nfkb1!0.71!8.10!Nfkb1;;chr7:56136402..56136420,-!p3@E2f8!0.70!7.91!E2f8;;chr11:52096066..52096081,-!p2@Tcf7!0.70!5.09!Tcf7;;chr11:23980664..23980706,+!p2@Bcl11a!0.69!18.84!Bcl11a;;chr11:11585678..11585745,+!p5@Ikzf1!0.69!6.03!Ikzf1;;chr1:52065508..52065522,+!p2@Stat4!0.69!4.71!Stat4;;chr2:90936901..90936945,+!p1@Sfpi1!0.68!22.60!Sfpi1;;chr17:56970339..56970428,-!p1@Rfx2!0.68!13.19!Rfx2;;chr19:45225276..45225304,+!p2@Tlx1!0.68!3.77!Tlx1;;chr6:83301229..83301242,+!p3@Bola3!0.68!3.77!Bola3;;chr15:103085864..103085876,-!p5@Nfe2!0.68!3.77!Nfe2;;chr2:166888058..166888105,-!p2@Znfx1!0.67!13.19!Znfx1;;chr2:91034924..91034946,-!p2@Nr1h3!0.66!4.52!Nr1h3;;chr3:130815703..130815721,+!p2@Lef1!0.66!4.52!Lef1;;chr5:42155788..42155800,-!p1@Nkx3-2!0.66!3.58!Nkx3-2;;chr12:84828663..84828679,-!p1@Dpf3!0.65!31.27!Dpf3;;chr10:30522690..30522752,-!p2@Ncoa7!0.65!24.49!Ncoa7;;chr6:29476690..29476724,+!p1@Irf5!0.65!18.27!Irf5;;chr10:41995430..41995458,-!p3@Foxo3!0.64!9.98!Foxo3;;chr11:3189171..3189197,+!p4@Patz1!0.64!7.16!Patz1;;chr4:134708451..134708469,+!p1@Runx3!0.64!6.40!Runx3;;chr1:181733959..181733977,-!p4@Ahctf1!0.64!4.52!Ahctf1;;chr11:98407370..98407395,-!p3@Ikzf3!0.64!3.39!Ikzf3;;chr15:103083245..103083260,-!p7@Nfe2!0.64!3.39!Nfe2;;chr18:70727922..70728052,+!p1@Mbd2!0.63!139.39!Mbd2;;chr8:107821563..107821642,+!p1@E2f4!0.63!110.01!E2f4;;chr11:102180696..102180760,-!p2@Ubtf!0.63!19.21!Ubtf;;chr5:65194752..65194769,+!p1@Klf3!0.62!128.66!Klf3;;chr11:98407340..98407359,-!p4@Ikzf3!0.62!3.20!Ikzf3;;chr9:96159665..96159680,+!p3@Tfdp2!0.61!16.39!Tfdp2;;chr17:56970481..56970551,-!p2@Rfx2!0.61!10.93!Rfx2;;chr5:65213356..65213412,+!p6@Klf3!0.61!7.35!Klf3;;chr11:23978111..23978134,+!p3@Bcl11a!0.61!7.16!Bcl11a;;chrX:103070746..103070764,-!p5@Atrx!0.61!5.09!Atrx;;chr5:34163023..34163090,+!p2@Whsc1!0.60!22.98!Whsc1;;chr2:44965593..44965624,-!p3@Zeb2!0.60!20.16!Zeb2;;chr2:90922554..90922575,+!p4@Sfpi1!0.60!6.03!Sfpi1;;chr11:11590140..11590187,+!p3@Ikzf1!0.60!3.77!Ikzf1;;chr15:103083199..103083215,-!p8@Nfe2!0.60!3.01!Nfe2;;chr5:104183219..104183236,+!p2@Aff1!0.59!23.92!Aff1;;chr5:104183579..104183600,+!p9@Aff1!0.59!3.39!Aff1;;chr9:20757282..20757325,-!p2@Dnmt1!0.58!81.00!Dnmt1;;chr11:23978022..23978076,+!p1@Bcl11a!0.58!74.97!Bcl11a;;chr2:72817320..72817399,-!p2@Sp3!0.58!29.57!Sp3;;chr18:74375772..74375799,+!p2@Cxxc1!0.58!9.61!Cxxc1;;chr10:30522881..30522960,-!p1@Ncoa7!0.57!40.31!Ncoa7;;chr6:47545052..47545064,-!p2@Ezh2!0.57!6.03!Ezh2;;chr17:48015645..48015689,-!p9@Foxp4!0.57!3.77!Foxp4;;chr8:124806111..124806122,+!p3@Zfpm1!0.57!3.58!Zfpm1;;chr13:30077847..30077906,-!p1@E2f3!0.56!25.43!E2f3;;chr7:31377960..31377973,-!p3@Zbtb32!0.56!2.64!Zbtb32;;chrX:7544928..7544938,-!p2@Gata1!0.56!2.64!Gata1;;chr7:122989672..122989673,-!p20@Sox6!0.56!2.64!Sox6;;chr11:96976641..96976646,-!p1@Tbx21!0.56!2.64!Tbx21;;chr1:38721779..38721790,-!p6@Aff3!0.56!2.64!Aff3;;chr10:80040030..80040072,-!p1@Klf16!0.55!63.86!Klf16;;chr11:58717675..58717719,-!p1@Zfp39!0.55!22.42!Zfp39;;chr5:65194720..65194738,+!p2@Klf3!0.55!16.95!Klf3;;chr12:85534957..85535017,-!p2@C130039O16Rik!0.55!15.63!C130039O16Rik;;chr10:30523091..30523182,-!p4@Ncoa7!0.55!10.55!Ncoa7;;chr14:79881330..79881415,+!p3@Elf1!0.55!10.36!Elf1;;chr4:126703093..126703158,+!p3@Sfpq!0.55!8.66!Sfpq;;chr4:126700722..126700753,+!p4@Sfpq!0.55!7.35!Sfpq;;chr6:28211956..28211967,-!p2@Zfp800!0.55!6.22!Zfp800;;chr6:16848347..16848391,-!p1@Tfec!0.55!3.58!Tfec;;chr4:102791976..102792008,+!p2@Mier1!0.54!33.91!Mier1;;chr9:32348943..32349001,-!p1@Fli1!0.54!25.62!Fli1;;chr11:23977565..23977612,+!p5@Bcl11a!0.54!6.22!Bcl11a;;chr2:104966766..104966786,+!p1@Wt1!0.54!4.33!Wt1;;chr1:38721767..38721778,-!p5@Aff3!0.54!2.45!Aff3;;chr2:90936947..90936977,+!p2@Sfpi1!0.53!5.46!Sfpi1;;chr13:59924433..59924504,-!p1@Zcchc6!0.52!66.49!Zcchc6;;chr6:29997979..29998049,+!p1@Nrf1!0.52!54.63!Nrf1;;chr3:95021853..95021911,-!p1@Gabpb2!0.52!22.98!Gabpb2;;chr3:95238432..95238455,+!p2@Arnt!0.52!16.76!Arnt;;chr1:52065454..52065495,+!p1@Stat4!0.52!4.33!Stat4;;chr16:8672238..8672254,-!p2@Carhsp1,p2@Gm9791!0.52!3.58!Carhsp1;;chr6:47544966..47545046,-!p1@Ezh2!0.51!61.22!Ezh2;;chr13:64254457..64254497,-!p1@Zfp367!0.51!12.62!Zfp367;;chr4:63071779..63071791,-!p3@Akna!0.51!3.58!Akna;;chr13:59923965..59924003,-!p2@Zcchc6!0.51!2.83!Zcchc6;;chr4:135728311..135728342,+!p3@E2f2!0.51!2.26!E2f2;;chr16:92826338..92826347,-!p6@Runx1!0.51!2.26!Runx1;;chr19:53384985..53385042,+!p1@Mxi1!0.50!88.16!Mxi1;;chr10:126727842..126727859,+!p1@Ddit3!0.50!82.69!Ddit3;;chr3:95021612..95021650,-!p2@Gabpb2!0.50!14.32!Gabpb2;;chrX:103070960..103070973,-!p7@Atrx!0.50!3.20!Atrx;;chr6:83299445..83299490,+!p1@Bola3!0.49!117.92!Bola3;;chr14:56223010..56223067,+!p1@Irf9!0.49!21.47!Irf9;;chr6:115803317..115803361,-!p2@Mbd4!0.49!6.40!Mbd4;;chr7:87170879..87170914,+!p2@Zfp710!0.49!5.84!Zfp710;;chr7:148514080..148514108,-!p4@Deaf1!0.49!5.27!Deaf1;;chr17:45692676..45692695,+!p2@Nfkbie!0.49!5.09!Nfkbie;;chr13:64254502..64254515,-!p3@Zfp367!0.49!3.58!Zfp367;;chr1:87546602..87546617,+!p2@Sp100!0.49!2.64!Sp100;;chr14:32978944..32978953,+!p8@Gm6768,p8@Ncoa4!0.49!2.07!Ncoa4;;chr4:87452167..87452178,-!p8@Mllt3!0.49!2.07!Mllt3;;chr4:13678514..13678539,+!p14@Runx1t1!0.49!2.07!Runx1t1;;chr3:95021663..95021687,-!p3@Gabpb2!0.48!8.85!Gabpb2;;chr4:135736690..135736705,+!p6@E2f2!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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0004872,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011417
 |is_obsolete=
+|library_id=CNhs11116
+|library_id_phase_based=2:CNhs11116
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;752
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;752
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spleen%252c%2520neonate%2520N10.CNhs11116.752-24D1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/spleen%252c%2520neonate%2520N10.CNhs11116.752-24D1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spleen%252c%2520neonate%2520N10.CNhs11116.752-24D1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spleen%252c%2520neonate%2520N10.CNhs11116.752-24D1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/spleen%252c%2520neonate%2520N10.CNhs11116.752-24D1.mm9.nobarcode.rdna.fa.gz
 |name=spleen, neonate N10
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11116,LSID734,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.0803200384612925,0,0.0511385902339572,0.0749511157581746,0.328422570374201,0,0.301830964291271,0,0.106901036464273,0,0,-0.0843392403965415,0,0,0,0,0,0,0.295535356947324,0,0.0694254785851855,0,0,0,0,0,0,0,0,0,0,0,0.321984658780589,0,0,0,0,0,0.18486243650484,-0.185783426657699,0.417694908880487,-0.740312078399944,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0.0749511157581746,0,0.0728454096069307,0,0,0,0,0,0,0,0,0.194543581824615,0,0.123619930984516,0.416278130886787,0.130122911160585,0.0779206414868675,0,0.15073475888222,-0.0939543678030287,0,0.623483308864934,0,-0.0324399722447379,-0.0658492437509446,-0.196769614565115,0.249590975534293,0,0,0,0,0,0,-0.0228539682250623,0.179844167604911,-0.0259037141535167,0.0749511157581746,0,0,0,0
 |rna_box=24
 |rna_catalog_number=
@@ Line 59: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 79: / Line 97: @@
 |top_motifs=GATA6:3.75131202458;AIRE:2.79432485125;POU1F1:2.78555684162;ZBTB16:2.50804320975;PITX1..3:2.31380341589;E2F1..5:2.16707065539;STAT5{A,B}:1.75165622782;SPIB:1.74844543957;FOXP1:1.64650823078;ALX4:1.41478740433;TEF:1.38233269673;NFE2L2:1.34815085152;ARID5B:1.21530255648;IRF1,2:1.21512949936;CDX1,2,4:1.12418930032;PAX1,9:1.11096508555;ELF1,2,4:1.07550477613;POU5F1:1.06933500966;NFY{A,B,C}:1.04670917529;NR6A1:1.02414661143;FOX{I1,J2}:0.98328574938;MYB:0.97761359841;SPI1:0.945221450535;POU2F1..3:0.929506099303;ETS1,2:0.894164998355;GFI1:0.893947605962;PBX1:0.822606125217;ZNF423:0.800693167477;NKX2-2,8:0.798498272733;DMAP1_NCOR{1,2}_SMARC:0.79686625495;IKZF2:0.715376656648;NFE2:0.704144906195;FOXO1,3,4:0.678179251986;CEBPA,B_DDIT3:0.669434551229;EVI1:0.6179554806;YY1:0.617746878444;RUNX1..3:0.608040878212;NKX3-1:0.589768981881;NKX6-1,2:0.522903274394;PPARG:0.46204651176;HOX{A5,B5}:0.458029771592;FOXP3:0.433340468928;IRF7:0.429299697502;PAX4:0.353099386545;OCT4_SOX2{dimer}:0.335296058691;ZNF384:0.305672980506;BPTF:0.287300167149;TAL1_TCF{3,4,12}:0.193584606352;NFKB1_REL_RELA:0.183250162406;TFDP1:0.165538920863;FOXM1:0.0994150972603;ELK1,4_GABP{A,B1}:0.0438066656698;STAT1,3:0.0186569361233;RXRA_VDR{dimer}:0.0127715389608;FOXD3:0.0127638998158;PDX1:-0.0011277786831;HOXA9_MEIS1:-0.0421359048683;ZNF143:-0.0815338910866;PRDM1:-0.082724620176;HES1:-0.110815895622;SOX{8,9,10}:-0.123076735863;NKX3-2:-0.137290354077;ZNF148:-0.142763256806;NR3C1:-0.15076963911;ATF5_CREB3:-0.173497876746;TBX4,5:-0.245799178702;GATA4:-0.247760401281;NFATC1..3:-0.253925107651;GLI1..3:-0.261386006595;TOPORS:-0.267482142744;UFEwm:-0.272223177418;SRF:-0.293926097699;NRF1:-0.335745175153;ALX1:-0.343180217282;FOX{D1,D2}:-0.353969926583;BACH2:-0.354347560575;NKX2-1,4:-0.358241472179;TLX2:-0.366078807623;SOX17:-0.378218893041;LMO2:-0.383742788155;CRX:-0.384382760039;TBP:-0.402780097854;HMGA1,2:-0.406930543443;FOXA2:-0.415980602168;FOX{F1,F2,J1}:-0.417852462863;KLF4:-0.421855092751;STAT2,4,6:-0.433931907652;FOXQ1:-0.438845165206;NANOG{mouse}:-0.4521143139;PRRX1,2:-0.453829163903;HLF:-0.472298466224;PAX8:-0.491167895819;FOXL1:-0.527433400996;EBF1:-0.532593249589;bHLH_family:-0.573280194308;BREu{core}:-0.575316359299;PAX6:-0.592470950006;ATF4:-0.598131186788;RREB1:-0.60683972073;NFIX:-0.613996518338;PAX2:-0.630366262928;HNF4A_NR2F1,2:-0.632176106772;GZF1:-0.646348475029;MEF2{A,B,C,D}:-0.651180084034;EN1,2:-0.65194395294;TLX1..3_NFIC{dimer}:-0.656234449825;NR1H4:-0.661665199715;SREBF1,2:-0.662853795415;NFE2L1:-0.663708679041;TEAD1:-0.678186470263;MYBL2:-0.686669277371;HNF1A:-0.706125961128;CDC5L:-0.734961477875;XCPE1{core}:-0.735147666769;AHR_ARNT_ARNT2:-0.745864337473;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.765837466724;ZIC1..3:-0.768207182165;TGIF1:-0.777033040419;MYOD1:-0.784693977416;SPZ1:-0.78655613705;MYFfamily:-0.789419005936;ZFP161:-0.795017349292;CREB1:-0.795360139049;TFAP4:-0.799269385899;NFIL3:-0.828681781656;RFX1:-0.854450534576;SNAI1..3:-0.854714380766;EGR1..3:-0.866673050966;IKZF1:-0.868966540288;RFX2..5_RFXANK_RFXAP:-0.878967998792;MZF1:-0.883961995053;NR5A1,2:-0.893703832171;POU6F1:-0.895086787527;EP300:-0.899447626031;SMAD1..7,9:-0.902672486517;ZNF238:-0.924438784332;NHLH1,2:-0.925149211859;FOS_FOS{B,L1}_JUN{B,D}:-0.943580176519;DBP:-0.947768983382;CUX2:-0.964039129721;ATF2:-0.993262933197;SOX2:-0.996765809113;SOX5:-1.00577372863;GCM1,2:-1.0188092993;HBP1_HMGB_SSRP1_UBTF:-1.04198652144;HOX{A4,D4}:-1.04693113969;NANOG:-1.06822893182;MTF1:-1.06854046805;RORA:-1.07613511044;ZEB1:-1.09715450193;MED-1{core}:-1.1040160756;MAFB:-1.11014989448;RXR{A,B,G}:-1.11833462362;HAND1,2:-1.12373231406;REST:-1.12900552731;GTF2I:-1.14706378408;T:-1.15042743641;POU3F1..4:-1.16821973091;HSF1,2:-1.17116264679;ESRRA:-1.19329233729;MTE{core}:-1.23090173658;RBPJ:-1.23635677207;ONECUT1,2:-1.2399758463;PATZ1:-1.24726425673;MAZ:-1.26650278317;VSX1,2:-1.28584227592;GTF2A1,2:-1.29325569775;JUN:-1.32483736736;FOXN1:-1.35921206355;ZBTB6:-1.36068276658;NKX2-3_NKX2-5:-1.38992276165;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.40279729475;SP1:-1.42723783773;LHX3,4:-1.42783329024;TFAP2{A,C}:-1.49106560461;ADNP_IRX_SIX_ZHX:-1.51826741023;TFAP2B:-1.52034866309;GFI1B:-1.55305979341;LEF1_TCF7_TCF7L1,2:-1.58085877682;PAX5:-1.59619549886;HIC1:-1.6171971619;ESR1:-1.62945533567;TP53:-1.68233484191;TFCP2:-1.79397858811;AR:-1.90857818667;HMX1:-1.94169425345;HIF1A:-2.02494884668;ATF6:-2.2382927544;FOSL2:-2.29969462186
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:752-24D1;search_select_hide=table117:752-24D1
 }}

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FF:752-24D1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:20, 4 June 2020

CNhs11116

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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