FF:879-12E4: Difference between revisions

Latest revision as of 19:21, 4 June 2020

Name:	urinary bladder, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10481
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	urinary bladder
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		SAMD00005219

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10481		CAGE		DRX009127		DRR010001

Accession ID Mm9

Library id		BAM		CTSS
CNhs10481		DRZ001426		DRZ002809

Accession ID Mm10

Library id		BAM		CTSS
CNhs10481		DRZ012776		DRZ014159

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

CNhs10481

0	0
1	0
10	0
100	0
1000	0.433
1001	0.203
1002	0.0404
1003	0.137
1004	0
1005	0.0378
1006	0.131
1007	-0.0227
1008	0
1009	0.479
101	-0.0409
1010	0
1011	-0.0286
1012	0
1013	0.0764
1014	-0.0084
1015	-0.211
1016	0.00527
1017	0
1018	0.569
1019	0
102	0
1020	0
1021	0
1022	0.128
1023	0
1024	0.204
1025	0.879
1026	0
1027	0
1028	0.0767
1029	0.117
103	0.142
1030	0
1031	0.268
1032	0.158
1033	0
1034	0.211
1035	0
1036	-0.225
1037	0
1038	0.137
1039	0.103
104	0
1040	0.353
1041	0.911

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: CNhs10481

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.774
MA0003.1	MA0003.1	0.0767
MA0004.1	MA0004.1	0.239
MA0006.1	MA0006.1	0.192
MA0007.1	MA0007.1	0.517
MA0009.1	MA0009.1	0.581
MA0014.1	MA0014.1	0.373
MA0017.1	MA0017.1	0.0149
MA0018.2	MA0018.2	0.0669
MA0019.1	MA0019.1	0.344
MA0024.1	MA0024.1	1.81159e-10
MA0025.1	MA0025.1	0.709
MA0027.1	MA0027.1	0.84
MA0028.1	MA0028.1	0.00461
MA0029.1	MA0029.1	0.917
MA0030.1	MA0030.1	0.021
MA0031.1	MA0031.1	0.011
MA0035.2	MA0035.2	0.106
MA0038.1	MA0038.1	0.357
MA0039.2	MA0039.2	0.0326
MA0040.1	MA0040.1	0.142
MA0041.1	MA0041.1	0.35
MA0042.1	MA0042.1	0.459
MA0043.1	MA0043.1	0.206
MA0046.1	MA0046.1	7.31234e-4
MA0047.2	MA0047.2	1.0603e-4
MA0048.1	MA0048.1	0.0743
MA0050.1	MA0050.1	4.77429e-7
MA0051.1	MA0051.1	5.20781e-4
MA0052.1	MA0052.1	0.625
MA0055.1	MA0055.1	0.0702
MA0057.1	MA0057.1	0.544
MA0058.1	MA0058.1	0.0793
MA0059.1	MA0059.1	0.0024
MA0060.1	MA0060.1	1.09057e-8
MA0061.1	MA0061.1	0.794
MA0062.2	MA0062.2	2.46182e-4
MA0065.2	MA0065.2	0.43
MA0066.1	MA0066.1	0.405
MA0067.1	MA0067.1	0.855
MA0068.1	MA0068.1	0.108
MA0069.1	MA0069.1	0.807
MA0070.1	MA0070.1	0.757
MA0071.1	MA0071.1	0.0803
MA0072.1	MA0072.1	0.111
MA0073.1	MA0073.1	0.766
MA0074.1	MA0074.1	0.618
MA0076.1	MA0076.1	0.00273
MA0077.1	MA0077.1	0.169
MA0078.1	MA0078.1	0.22
MA0079.2	MA0079.2	0.012
MA0080.2	MA0080.2	0.593
MA0081.1	MA0081.1	0.221
MA0083.1	MA0083.1	7.88648e-22
MA0084.1	MA0084.1	0.797
MA0087.1	MA0087.1	0.678
MA0088.1	MA0088.1	0.548
MA0090.1	MA0090.1	0.00324
MA0091.1	MA0091.1	0.376
MA0092.1	MA0092.1	0.5
MA0093.1	MA0093.1	0.218
MA0099.2	MA0099.2	3.52693e-4
MA0100.1	MA0100.1	0.0142
MA0101.1	MA0101.1	0.911
MA0102.2	MA0102.2	0.888
MA0103.1	MA0103.1	0.736
MA0104.2	MA0104.2	0.0513
MA0105.1	MA0105.1	0.167
MA0106.1	MA0106.1	0.119
MA0107.1	MA0107.1	0.673
MA0108.2	MA0108.2	0.47
MA0111.1	MA0111.1	0.958
MA0112.2	MA0112.2	0.124
MA0113.1	MA0113.1	0.827
MA0114.1	MA0114.1	0.015
MA0115.1	MA0115.1	0.0715
MA0116.1	MA0116.1	0.685
MA0117.1	MA0117.1	0.898
MA0119.1	MA0119.1	0.786
MA0122.1	MA0122.1	0.472
MA0124.1	MA0124.1	0.34
MA0125.1	MA0125.1	0.586
MA0131.1	MA0131.1	0.145
MA0135.1	MA0135.1	0.277
MA0136.1	MA0136.1	0.426
MA0137.2	MA0137.2	0.767
MA0138.2	MA0138.2	0.122
MA0139.1	MA0139.1	0.425
MA0140.1	MA0140.1	3.84257e-4
MA0141.1	MA0141.1	8.35194e-5
MA0142.1	MA0142.1	0.539
MA0143.1	MA0143.1	0.498
MA0144.1	MA0144.1	0.716
MA0145.1	MA0145.1	9.31332e-4
MA0146.1	MA0146.1	0.627
MA0147.1	MA0147.1	0.0137
MA0148.1	MA0148.1	0.0012
MA0149.1	MA0149.1	0.391
MA0150.1	MA0150.1	0.202
MA0152.1	MA0152.1	0.43
MA0153.1	MA0153.1	1.53714e-7
MA0154.1	MA0154.1	0.361
MA0155.1	MA0155.1	0.268
MA0156.1	MA0156.1	0.847
MA0157.1	MA0157.1	0.00321
MA0159.1	MA0159.1	0.998
MA0160.1	MA0160.1	0.0189
MA0162.1	MA0162.1	0.844
MA0163.1	MA0163.1	0.221
MA0164.1	MA0164.1	0.919
MA0258.1	MA0258.1	0.888
MA0259.1	MA0259.1	0.0353

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: CNhs10481

Novel motif	Logo	P-value
1	1	0.496
10	10	0.099
100	100	0.0923
101	101	0.604
102	102	0.835
103	103	0.582
104	104	0.322
105	105	0.237
106	106	0.0289
107	107	0.0978
108	108	0.745
109	109	0.838
11	11	0.53
110	110	0.82
111	111	0.599
112	112	0.4
113	113	0.531
114	114	0.601
115	115	0.65
116	116	0.209
117	117	0.0233
118	118	0.0762
119	119	0.394
12	12	0.487
120	120	0.942
121	121	0.889
122	122	0.709
123	123	0.295
124	124	0.156
125	125	0.398
126	126	0.591
127	127	0.318
128	128	0.0649
129	129	0.181
13	13	0.751
130	130	0.199
131	131	0.854
132	132	0.777
133	133	0.637
134	134	0.22
135	135	0.915
136	136	0.693
137	137	0.872
138	138	0.0191
139	139	0.308
14	14	0.442
140	140	0.0565
141	141	0.262
142	142	0.994
143	143	0.527
144	144	0.844
145	145	0.629
146	146	0.104
147	147	0.776
148	148	0.866
149	149	0.0426
15	15	0.96
150	150	0.375
151	151	0.339
152	152	0.00965
153	153	0.755
154	154	0.631
155	155	0.278
156	156	0.0259
157	157	0.771
158	158	0.425
159	159	0.894
160	160	0.536
161	161	0.911
162	162	0.795
163	163	0.0517
164	164	0.672
165	165	0.704
166	166	0.00113
167	167	0.122
168	168	0.102
169	169	0.0756
17	17	0.175
18	18	0.281
19	19	0.122
2	2	0.018
20	20	0.0386
21	21	0.6
22	22	0.329
23	23	0.135
24	24	0.364
25	25	0.0584
26	26	0.594
27	27	0.467
28	28	0.691
29	29	0.107
3	3	0.414
30	30	0.355
31	31	0.754
32	32	0.508
33	33	0.429
34	34	0.596
35	35	0.198
36	36	0.0445
37	37	0.469
38	38	0.889
39	39	0.155
4	4	0.295
40	40	0.255
41	41	0.0757
42	42	0.354
43	43	0.65
44	44	0.304
45	45	0.0475
46	46	0.616
47	47	0.88
48	48	0.938
49	49	0.888
5	5	0.838
50	50	0.49
51	51	0.712
52	52	0.0594
53	53	0.105
54	54	0.682
55	55	0.973
56	56	0.901
57	57	0.349
58	58	0.946
59	59	0.383
6	6	0.485
60	60	0.056
61	61	0.851
62	62	0.556
63	63	0.55
64	64	0.685
65	65	0.827
66	66	0.83
67	67	0.609
68	68	0.0175
69	69	0.948
7	7	0.754
70	70	0.136
71	71	0.377
72	72	0.23
73	73	0.118
74	74	0.532
75	75	0.14
76	76	0.0341
77	77	0.382
78	78	0.821
79	79	0.914
8	8	0.128
80	80	0.652
81	81	0.174
82	82	0.224
83	83	0.89
84	84	0.618
85	85	0.463
86	86	0.645
87	87	0.632
88	88	0.602
89	89	0.232
9	9	0.231
90	90	0.046
91	91	0.871
92	92	0.308
93	93	0.0212
94	94	0.0855
95	95	0.544
96	96	0.686
97	97	0.216
98	98	0.952
99	99	0.602

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: CNhs10481

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011437 mouse urinary bladder- 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)
0001255 (urinary bladder)
0002100 (trunk)
0000479 (tissue)
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)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0002323 (body cavity)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0001556 (lower urinary tract)
0001008 (renal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011437 (mouse urinary bladder- 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:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0001255,UBERON:0002100,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0006554,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0000161,UBERON:0000162,UBERON:0005423,UBERON:0002553,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0003103,UBERON:0005291,UBERON:0003102,UBERON:0002323,UBERON:0000489,UBERON:0005177,UBERON:0003104,UBERON:0000464,UBERON:0004458,UBERON:0005256,UBERON:0000925,UBERON:0006598,UBERON:0003886,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0001556,UBERON:0001008,UBERON:0004122,UBERON:0001353,UBERON:0000163,UBERON:0007026,UBERON:0006866,UBERON:0009142,UBERON:0001046,UBERON:0000164,UBERON:0003064,UBERON:0006595,UBERON:0006603,UBERON:0000931
+|DRA_sample_Accession=CAGE@SAMD00005219
+|accession_numbers=CAGE;DRX009127;DRR010001;DRZ001426;DRZ002809;DRZ012776;DRZ014159
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001255,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0002323,UBERON:0000489,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0001556,UBERON:0001008
 |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:0011437
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:31650185..31650201,+!p1@Foxq1!2.03!357.79!Foxq1;;chr4:135129538..135129558,-!p1@Grhl3!1.86!106.83!Grhl3;;chr16:25801993..25802014,+!p1@Trp63!1.85!69.16!Trp63;;chr2:103143336..103143367,-!p1@Ehf!1.81!101.04!Ehf;;chr6:52190467..52190500,-!p1@Hoxa10!1.81!64.14!Hoxa10;;chr13:55932591..55932622,-!p1@Pitx1!1.80!73.61!Pitx1;;chr2:9800207..9800234,-!p1@Gata3!1.75!160.54!Gata3;;chr12:58646974..58647003,-!p1@Foxa1!1.74!70.71!Foxa1;;chr10:22539932..22539956,-!p1@Tcf21!1.72!133.69!Tcf21;;chr13:53568104..53568156,-!p1@Msx2!1.60!57.18!Msx2;;chr2:180069370..180069409,-!p1@Gata5!1.54!39.60!Gata5;;chr11:69468531..69468557,+!p1@Sox15!1.53!32.84!Sox15;;chr5:77543897..77543911,-!p2@Hopx!1.51!59.50!Hopx;;chr9:24578720..24578735,-!p1@Tbx20!1.51!31.49!Tbx20;;chr1:137155026..137155042,-!p1@Elf3!1.47!160.35!Elf3;;chr11:121380640..121380655,-!p1@Zfp750!1.41!40.57!Zfp750;;chr2:9809451..9809469,-!p6@Gata3!1.38!22.80!Gata3;;chr8:123608252..123608268,+!p1@Foxf1a!1.36!32.46!Foxf1a;;chr2:74517742..74517758,+!p2@Hoxd11!1.35!21.25!Hoxd11;;chr11:98636531..98636559,-!p1@Nr1d1!1.33!112.24!Nr1d1;;chr11:121380594..121380609,-!p2@Zfp750!1.33!34.77!Zfp750;;chr6:52195795..52195825,-!p1@Hoxa11!1.33!20.28!Hoxa11;;chr6:52176164..52176195,-!p1@Hoxa9!1.31!24.15!Hoxa9;;chr2:103143315..103143328,-!p2@Ehf!1.31!19.32!Ehf;;chr8:59799772..59799789,+!p1@Hand2!1.28!51.20!Hand2;;chr6:52195763..52195792,-!p2@Hoxa11!1.28!17.97!Hoxa11;;chr2:9809357..9809371,-!p2@Gata3!1.24!16.23!Gata3;;chr3:128916868..128916890,+!p1@Pitx2!1.22!21.25!Pitx2;;chr6:51382677..51382783,+!p1@Nfe2l3!1.21!38.83!Nfe2l3;;chr11:96153767..96153822,+!p1@Hoxb6!1.20!22.99!Hoxb6;;chr11:96145450..96145517,+!p2@Hoxb7!1.19!21.64!Hoxb7;;chr11:121380611..121380625,-!p3@Zfp750!1.18!17.39!Zfp750;;chr2:133377954..133377973,+!p1@Bmp2!1.12!39.22!Bmp2;;chr12:9581262..9581282,+!p1@Osr1!1.11!140.45!Osr1;;chr13:48356475..48356492,+!p1@Id4!1.07!234.15!Id4;;chr6:52184901..52184959,-!p2@Hoxa10!1.07!10.82!Hoxa10;;chr14:99697871..99697934,+!p1@Klf5!1.06!207.49!Klf5;;chr11:85646303..85646329,+!p1@Tbx2!1.04!67.62!Tbx2;;chr5:120120667..120120685,+!p3@Tbx3!1.04!19.51!Tbx3;;chr13:55937467..55937516,-!p3@Pitx1!1.04!10.05!Pitx1;;chr6:88148650..88148669,+!p1@Gata2!1.02!80.56!Gata2;;chr4:122673187..122673201,+!p2@Mycl1!1.00!16.03!Mycl1;;chr11:98636508..98636524,-!p3@Nr1d1!1.00!11.20!Nr1d1;;chr2:74549968..74549996,+!p1@Hoxd3!0.98!10.82!Hoxd3;;chr6:88143711..88143717,+!p2@Gata2!0.97!13.72!Gata2;;chr4:135129447..135129467,-!p2@Grhl3!0.97!10.05!Grhl3;;chr11:85646427..85646451,+!p4@Tbx2!0.96!14.49!Tbx2;;chr2:74542918..74542971,+!p1@Hoxd8!0.95!12.17!Hoxd8;;chr2:9809402..9809422,-!p5@Gata3!0.95!7.92!Gata3;;chr13:55937432..55937460,-!p4@Pitx1!0.95!7.92!Pitx1;;chr5:120285144..120285160,+!p1@Tbx5!0.95!7.92!Tbx5;;chr13:55932624..55932641,-!p2@Pitx1!0.94!7.73!Pitx1;;chr3:30408603..30408668,-!p1@Mecom!0.93!17.97!Mecom;;chr2:44965856..44965896,-!p5@Zeb2!0.92!29.36!Zeb2;;chr16:43363190..43363242,+!p2@Zbtb20!0.92!23.38!Zbtb20;;chr7:119822957..119822980,+!p2@Tead1!0.91!35.93!Tead1;;chr11:85646469..85646488,+!p5@Tbx2!0.91!11.01!Tbx2;;chr11:85646263..85646278,+!p2@Tbx2!0.90!18.55!Tbx2;;chr15:98126545..98126588,-!p1@Zfp641!0.89!15.26!Zfp641;;chr6:52163319..52163342,-!p1@Hoxa3!0.88!9.85!Hoxa3;;chr2:103264213..103264233,+!p1@Elf5!0.88!6.57!Elf5;;chr14:69808725..69808748,+!p1@Nkx3-1!0.88!6.57!Nkx3-1;;chr11:85699862..85699920,+!p1@Tbx4!0.88!6.57!Tbx4;;chr5:104121453..104121479,+!p4@Aff1!0.87!30.72!Aff1;;chr11:5761979..5761992,+!p2@Aebp1!0.87!13.52!Aebp1;;chr13:31717548..31717596,+!p1@Foxf2!0.87!13.14!Foxf2;;chr5:120121446..120121461,+!p2@Tbx3!0.86!21.44!Tbx3;;chr11:69468501..69468515,+!p2@Sox15!0.86!6.18!Sox15;;chr3:30408674..30408716,-!p2@Mecom!0.85!10.24!Mecom;;chr11:5761889..5761969,+!p1@Aebp1!0.84!266.60!Aebp1;;chr7:20162663..20162678,+!p1@Zfp296!0.84!7.92!Zfp296;;chr2:9809374..9809396,-!p4@Gata3!0.84!5.99!Gata3;;chr6:52210774..52210787,-!p1@Hoxa13!0.84!5.99!Hoxa13;;chr18:11052606..11052633,+!p4@Gata6!0.83!15.26!Gata6;;chr2:103264245..103264268,+!p2@Elf5!0.83!5.80!Elf5;;chr6:15135215..15135244,+!p11@Foxp2!0.83!5.80!Foxp2;;chr2:74549945..74549965,+!p4@Hoxd3!0.83!5.80!Hoxd3;;chr4:48058129..48058179,+!p2@Nr4a3!0.82!11.20!Nr4a3;;chr15:37162834..37162849,+!p2@Grhl2!0.82!6.76!Grhl2;;chr10:107769168..107769215,+!p1@Pawr!0.81!60.08!Pawr;;chr7:52960555..52960662,+!p1@Dbp!0.81!50.04!Dbp;;chr10:107769750..107769799,+!p2@Pawr!0.81!12.36!Pawr;;chr7:38554763..38554780,-!p1@Zfp536!0.81!10.43!Zfp536;;chr3:128917187..128917223,+!p2@Pitx2!0.81!6.38!Pitx2;;chr11:83664365..83664383,+!p1@Hnf1b!0.81!5.41!Hnf1b;;chr6:52190840..52190853,-!p5@Hoxa10!0.81!5.41!Hoxa10;;chr19:5560600..5560617,-!p1@Ovol1!0.80!6.57!Ovol1;;chr9:48644037..48644067,-!p2@Zbtb16!0.79!13.72!Zbtb16;;chr6:52210816..52210831,-!p2@Hoxa13!0.79!5.22!Hoxa13;;chr6:52190668..52190682,-!p3@Hoxa10!0.78!5.02!Hoxa10;;chr12:25257265..25257294,+!p2@Grhl1!0.78!5.02!Grhl1;;chr18:11052642..11052659,+!p1@Gata6!0.77!26.85!Gata6;;chr13:53568081..53568094,-!p3@Msx2!0.77!4.83!Msx2;;chr8:79426176..79426275,+!p1@Nr3c2!0.76!26.08!Nr3c2;;chr5:144951153..144951203,+!p1@Bhlha15!0.76!7.15!Bhlha15;;chr11:98636400..98636418,-!p4@Nr1d1!0.76!6.38!Nr1d1;;chr16:92697560..92697592,-!p2@Runx1!0.75!32.26!Runx1;;chr4:148275237..148275311,+!p2@Casz1!0.75!21.06!Casz1;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.75!19.71!Ppp1r13l;;chr13:64253718..64253763,-!p2@Zfp367!0.75!12.94!Zfp367;;chr4:119486912..119486954,+!p3@Hivep3!0.75!8.50!Hivep3;;chr8:90328310..90328362,-!p3@Zfp423!0.75!5.41!Zfp423;;chr5:77543935..77543947,-!p4@Hopx!0.75!4.64!Hopx;;chr11:85646341..85646352,+!p3@Tbx2!0.74!9.47!Tbx2;;chr11:96055613..96055628,+!p1@Hoxb13!0.74!4.44!Hoxb13;;chr6:52176144..52176161,-!p2@Hoxa9!0.74!4.44!Hoxa9;;chr2:74549915..74549930,+!p6@Hoxd3!0.74!4.44!Hoxd3;;chr16:30065419..30065437,+!p1@Hes1!0.73!259.26!Hes1;;chr12:25257141..25257173,+!p1@Grhl1!0.72!9.47!Grhl1;;chr6:52190858..52190873,-!p4@Hoxa10!0.72!4.25!Hoxa10;;chr7:38554745..38554756,-!p7@Zfp536!0.72!4.25!Zfp536;;chr14:52634536..52634572,-!p4@Zfp219!0.71!13.52!Zfp219;;chr18:36441119..36441158,+!p2@Pura!0.71!11.01!Pura;;chr4:148178529..148178548,+!p3@Casz1!0.71!10.63!Casz1;;chr4:84320893..84320910,-!p1@Bnc2!0.71!9.85!Bnc2;;chr16:43363968..43364001,+!p7@Zbtb20!0.70!7.92!Zbtb20;;chr9:63514630..63514652,-!p8@Smad3!0.70!4.06!Smad3;;chr2:180069423..180069434,-!p2@Gata5!0.70!4.06!Gata5;;chr2:74550178..74550214,+!p5@Hoxd3!0.69!4.44!Hoxd3;;chr2:74517725..74517738,+!p5@Hoxd11!0.69!3.86!Hoxd11;;chr15:102828658..102828678,+!p1@Hoxc6!0.69!3.86!Hoxc6;;chr5:77544170..77544181,-!p6@Hopx!0.69!3.86!Hopx;;chr6:115311030..115311065,+!p4@Pparg!0.68!5.80!Pparg;;chr10:107769229..107769238,+!p3@Pawr!0.68!5.60!Pawr;;chr17:46693107..46693137,-!p1@Srf!0.67!40.96!Srf;;chr6:145814003..145814056,-!p1@Bhlhe41!0.67!11.78!Bhlhe41;;chr12:9581284..9581303,+!p2@Osr1!0.67!7.73!Osr1;;chr2:172375081..172375105,+!p1@Tfap2c!0.67!3.67!Tfap2c;;chr11:60023912..60023930,-!p1@Srebf1!0.66!101.23!Srebf1;;chr7:77511234..77511302,-!p2@Nr2f2!0.66!27.63!Nr2f2;;chr5:104121391..104121450,+!p3@Aff1!0.66!21.25!Aff1;;chr4:148178559..148178603,+!p1@Casz1!0.66!11.59!Casz1;;chr1:69732511..69732540,-!p2@Ikzf2!0.66!4.83!Ikzf2;;chr2:75542527..75542590,-!p1@Nfe2l2!0.65!363.39!Nfe2l2;;chr6:115310872..115310899,+!p2@Pparg!0.65!6.57!Pparg;;chr11:96143666..96143725,+!p1@Hoxb8!0.65!4.06!Hoxb8;;chr5:120285130..120285141,+!p3@Tbx5!0.65!3.48!Tbx5;;chr12:75002389..75002406,+!p4@Hif1a!0.65!3.48!Hif1a;;chr2:74517609..74517621,+!p3@Hoxd11!0.65!3.48!Hoxd11;;chr3:128902837..128902861,+!p3@Pitx2!0.65!3.48!Pitx2;;chr2:74543397..74543435,+!p2@Hoxd8!0.65!3.48!Hoxd8;;chr11:98636575..98636607,-!p2@Nr1d1!0.64!13.91!Nr1d1;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!0.64!6.95!Zbtb38;;chr13:31650026..31650045,+!p2@Foxq1!0.64!6.18!Foxq1;;chr18:53623836..53623839,+!p1@Prdm6!0.64!4.06!Prdm6;;chr18:11052485..11052508,+!p2@Gata6!0.63!10.43!Gata6;;chr2:104966766..104966786,+!p1@Wt1!0.63!5.60!Wt1;;chr16:25802129..25802142,+!p3@Trp63!0.63!3.28!Trp63;;chr17:14011485..14011507,+!p2@Mllt4!0.63!3.28!Mllt4;;chr11:83664334..83664353,+!p2@Hnf1b!0.63!3.28!Hnf1b;;chr16:42907676..42907797,+!p1@Zbtb20!0.62!49.46!Zbtb20;;chr2:169458192..169458247,+!p1@Tshz2!0.62!33.61!Tshz2;;chr6:14851287..14851342,+!p1@Foxp2!0.62!11.98!Foxp2;;chr15:102087880..102087927,-!p2@Rarg!0.62!8.31!Rarg;;chr5:120121020..120121049,+!p1@Tbx3!0.61!22.41!Tbx3;;chr15:50721515..50721540,-!p3@Trps1!0.61!10.43!Trps1;;chr2:173044380..173044432,-!p1@Zbp1!0.61!8.31!Zbp1;;chr15:37162796..37162828,+!p1@Grhl2!0.61!5.60!Grhl2;;chr1:69732682..69732719,-!p4@Ikzf2!0.61!3.86!Ikzf2;;chr12:58647114..58647128,-!p2@Foxa1!0.61!3.09!Foxa1;;chr13:53568191..53568219,-!p2@Msx2!0.61!3.09!Msx2;;chr2:9811653..9811662,-!p8@Gata3!0.61!3.09!Gata3;;chr4:135840573..135840601,+!p1@Zfp46!0.60!28.40!Zfp46;;chr12:113916993..113917009,+!p2@Zbtb42!0.60!5.60!Zbtb42;;chr17:28487692..28487765,-!p1@Tead3!0.59!70.32!Tead3;;chr10:67599319..67599360,-!p2@Arid5b!0.59!38.83!Arid5b;;chr5:32438831..32438878,+!p1@Fosl2!0.59!35.93!Fosl2;;chr6:48395426..48395504,-!p2@Zfp467!0.59!32.65!Zfp467;;chr1:170362242..170362256,-!p3@Pbx1!0.59!25.11!Pbx1;;chr1:194979315..194979359,+!p1@Irf6!0.59!21.06!Irf6;;chr9:69137672..69137702,+!p2@Rora!0.59!14.68!Rora;;chr17:56970339..56970428,-!p1@Rfx2!0.59!10.63!Rfx2;;chr7:119822915..119822936,+!p5@Tead1!0.59!5.22!Tead1;;chr16:92697354..92697362,-!p3@Runx1!0.59!4.83!Runx1;;chr12:9581317..9581333,+!p3@Osr1!0.59!4.83!Osr1;;chr15:37163124..37163153,+!p3@Grhl2!0.59!2.90!Grhl2;;chr11:98407164..98407177,-!p8@Ikzf3!0.59!2.90!Ikzf3;;chr2:9809579..9809627,-!p7@Gata3!0.59!2.90!Gata3;;chr5:120120834..120120845,+!p8@Tbx3!0.59!2.90!Tbx3;;chr6:83020355..83020371,-!p1@Tlx2!0.59!2.90!Tlx2;;chr5:120285161..120285176,+!p2@Tbx5!0.59!2.90!Tbx5;;chr7:108966820..108966835,+!p1@Phox2a!0.59!2.90!Phox2a;;chr12:36219645..36219730,-!p1@Ahr!0.58!33.42!Ahr;;chr14:18493386..18493464,+!p1@Thrb!0.58!12.75!Thrb;;chr5:125538737..125538781,-!p2@Ncor2!0.58!11.98!Ncor2;;chr13:31898729..31898761,+!p1@Foxc1!0.58!7.92!Foxc1;;chr5:120121169..120121171,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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:879-12E4
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011437
+|is_a=EFO:0002091;;FF:0011437
+|is_obsolete=
+|library_id=CNhs10481
+|library_id_phase_based=2:CNhs10481
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;879
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;879
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/urinary%2520bladder%252c%2520adult.CNhs10481.879-12E4.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/urinary%2520bladder%252c%2520adult.CNhs10481.879-12E4.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/urinary%2520bladder%252c%2520adult.CNhs10481.879-12E4.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/urinary%2520bladder%252c%2520adult.CNhs10481.879-12E4.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/urinary%2520bladder%252c%2520adult.CNhs10481.879-12E4.mm9.nobarcode.rdna.fa.gz
 |name=urinary bladder, adult
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10481,LSID647,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0679532649830915,0,0,0,0,0,-0.123064976552954,0,0.00223787301245392,0,0,-0.00762978323090903,0,0,0,0,0,0,0.00664519106141434,0,0,0,0.0767094571656325,0.0767094571656325,0.248649546054984,0,0,0,0,0,0,0,0.177444318154863,0,0,0,0,0,0.0617880574407109,0,-0.031876788693374,-0.190692043852763,-0.193159180844719,0,0,0,0,0,0,0,0,0,0,0.334280313231288,0.0767094571656325,0.428856361025334,0,0,0,0,0,0,0.0383547285828163,0,0,0.000421210678805739,-0.0508720369424898,0.0608470653075561,-0.08138158560545,0.077039341765658,0,0,0.0145182333342513,0,0.198538541943989,0,0.012820280478402,0.0707974371873785,-0.0750024888694859,-0.00212213767427494,0,0,0,0,0,0,-0.105942237559495,-0.374460517305552,-0.0520759771984484,0,0,0,0,0
 |rna_box=12
 |rna_catalog_number=
@@ Line 54: / Line 73: @@
 |rna_rin=
 |rna_sample_type=
-|rna_tube_id=12E4
+|rna_tube_id=1.20E+05
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=urinary bladder
 |top_motifs=SRF:2.50773966126;NFATC1..3:2.0324759249;GZF1:1.93384469144;FOXQ1:1.79914768426;TP53:1.70466983265;ATF6:1.64817649506;TFAP2{A,C}:1.59779873059;NFE2L2:1.58497142975;ZNF148:1.57147150314;TFCP2:1.4907990236;FOX{I1,J2}:1.4018536455;ZNF423:1.39433670163;BACH2:1.29251858379;TEAD1:1.25997164866;HAND1,2:1.25464003395;TFAP4:1.24512115589;SPZ1:1.19020862841;SP1:1.18972901845;GTF2A1,2:1.18936953652;CDC5L:1.15769211156;MYBL2:1.01664626408;TLX1..3_NFIC{dimer}:1.00513311059;SNAI1..3:0.998278055561;HMX1:0.993661085205;FOXO1,3,4:0.943493824789;FOS_FOS{B,L1}_JUN{B,D}:0.910568219974;GCM1,2:0.886620742834;TOPORS:0.869581832356;SMAD1..7,9:0.866997375302;IRF1,2:0.865661125274;XCPE1{core}:0.844614049798;FOSL2:0.82123483254;SOX5:0.802349150792;SREBF1,2:0.78488757899;GTF2I:0.743264747603;ZEB1:0.741420458261;NFE2:0.716065853418;ZIC1..3:0.657558974394;VSX1,2:0.648742977148;ESR1:0.64441502046;AR:0.636725847222;HIC1:0.632291974096;IRF7:0.631560219944;MAZ:0.631379487504;PRDM1:0.614466786824;FOX{D1,D2}:0.611525219841;TFAP2B:0.592510299321;POU2F1..3:0.590452107237;GLI1..3:0.574701816731;EBF1:0.548236638027;IKZF1:0.534707471679;PAX5:0.524783620835;ZNF238:0.516211417258;NHLH1,2:0.50856562341;FOXN1:0.48951446349;CDX1,2,4:0.44765889557;ATF2:0.431334997413;TBX4,5:0.427624986902;RXRA_VDR{dimer}:0.422767549516;NKX2-1,4:0.405023275614;RREB1:0.400836750033;TEF:0.381957677145;EP300:0.359734809552;BPTF:0.350255221888;PAX8:0.307228450757;PAX1,9:0.2960185623;STAT2,4,6:0.278725048233;RFX2..5_RFXANK_RFXAP:0.243321620152;ETS1,2:0.243077291532;EGR1..3:0.216674005444;MTF1:0.211262330871;NKX3-1:0.209122378665;MTE{core}:0.206705354571;PATZ1:0.197673896386;NR3C1:0.184150233422;MAFB:0.169525027814;DMAP1_NCOR{1,2}_SMARC:0.158758398693;FOXP1:0.157541716878;CRX:0.149453351102;POU5F1:0.148003529645;T:0.145356236513;ELF1,2,4:0.142008819078;GFI1B:0.133326275804;ALX4:0.132626603208;AHR_ARNT_ARNT2:0.128936292274;DBP:0.127257594154;RBPJ:0.113675127271;IKZF2:0.10758225835;PDX1:0.086400149034;STAT1,3:0.0822350937545;NANOG:0.0651135089978;MYFfamily:0.0588572031463;ATF4:0.0289603679443;REST:0.0161834868239;ZNF384:0.00535981913952;HIF1A:0.000694380856407;SPIB:-0.00618579759096;MYOD1:-0.04117191581;NFE2L1:-0.0456432524361;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0496265792047;NKX2-3_NKX2-5:-0.0574243352071;LHX3,4:-0.0732773684682;MEF2{A,B,C,D}:-0.0748737705831;GATA4:-0.0816506605274;FOX{F1,F2,J1}:-0.0844198412959;ZFP161:-0.0860836788217;TGIF1:-0.0913882832281;SPI1:-0.108729102001;RUNX1..3:-0.120488242567;BREu{core}:-0.128551387901;TBP:-0.136321995796;MZF1:-0.150565516313;MED-1{core}:-0.157728360883;JUN:-0.160606148972;HMGA1,2:-0.165354830171;NFIL3:-0.167899711982;NFKB1_REL_RELA:-0.177862904457;HSF1,2:-0.18825859743;KLF4:-0.19198331963;ADNP_IRX_SIX_ZHX:-0.19343091908;NKX2-2,8:-0.202683993318;HNF1A:-0.251760816251;GATA6:-0.264560885339;SOX2:-0.27560916273;HBP1_HMGB_SSRP1_UBTF:-0.282460626244;FOXL1:-0.288362147343;HLF:-0.302970477008;RORA:-0.308826010037;RXR{A,B,G}:-0.314161778437;HNF4A_NR2F1,2:-0.320679042094;ATF5_CREB3:-0.329608636206;UFEwm:-0.331254503276;NR1H4:-0.33753553809;STAT5{A,B}:-0.34954571653;LMO2:-0.36200462838;PRRX1,2:-0.371483836873;CEBPA,B_DDIT3:-0.380813047765;ESRRA:-0.383396070819;NKX3-2:-0.406114966126;RFX1:-0.420824767332;ELK1,4_GABP{A,B1}:-0.456051139809;ZBTB6:-0.502380972836;FOXA2:-0.505033189495;ONECUT1,2:-0.529264127294;TAL1_TCF{3,4,12}:-0.535774229648;LEF1_TCF7_TCF7L1,2:-0.556792952553;ZNF143:-0.610725326048;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.632262926419;SOX17:-0.642320387636;FOXM1:-0.651679231742;PBX1:-0.677282218655;NFIX:-0.685151357412;HES1:-0.708334690506;TFDP1:-0.759884364452;MYB:-0.797333698821;bHLH_family:-0.798053885448;NR6A1:-0.810454607297;PAX4:-0.815883739065;TLX2:-0.831861155696;NR5A1,2:-0.858941394209;FOXP3:-0.868756479692;SOX{8,9,10}:-0.884630362961;ALX1:-0.887592032483;OCT4_SOX2{dimer}:-0.89558956713;CUX2:-0.897959288979;CREB1:-0.909239871669;FOXD3:-0.939060164822;YY1:-0.955116373309;NRF1:-0.968629361792;PAX2:-0.9890808106;GFI1:-0.997777356075;ZBTB16:-1.11318074406;PPARG:-1.19415652936;POU3F1..4:-1.22068349244;ARID5B:-1.25755321052;POU1F1:-1.30961363164;HOXA9_MEIS1:-1.31982916019;NFY{A,B,C}:-1.32867057984;EVI1:-1.33573958945;POU6F1:-1.3393467214;E2F1..5:-1.37046469695;PITX1..3:-1.37390175889;HOX{A5,B5}:-1.41412992579;HOX{A4,D4}:-1.46695216743;AIRE:-1.49733845606;NKX6-1,2:-1.51055991103;NANOG{mouse}:-1.57058116953;EN1,2:-2.05243816219;PAX6:-2.1027689405
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:879-12E4;search_select_hide=table117:879-12E4
 }}

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FF:879-12E4: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:21, 4 June 2020

CNhs10481

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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