FF:89-27D5: Difference between revisions

Latest revision as of 19:21, 4 June 2020

Name:	vagina, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10502
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	vagina
dev stage	adult
sex	female
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		SAMD00005786

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10502		CAGE		DRX009130		DRR010004

Accession ID Mm9

Library id		BAM		CTSS
CNhs10502		DRZ001429		DRZ002812

Accession ID Mm10

Library id		BAM		CTSS
CNhs10502		DRZ012779		DRZ014162

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

CNhs10502

0	0
1	0
10	0
100	0
1000	0.0422
1001	0.141
1002	-0.0422
1003	0.148
1004	0.216
1005	0.0455
1006	-0.0101
1007	-0.0195
1008	0
1009	0.169
101	0.0595
1010	0
1011	-0.0459
1012	0
1013	0.0984
1014	-0.0874
1015	-0.147
1016	-0.0393
1017	0.553
1018	0.94
1019	0
102	0
1020	0
1021	0
1022	0.014
1023	0
1024	0.0761
1025	0.0549
1026	0
1027	-0.00502
1028	0.0844
1029	0.14
103	0.197
1030	0
1031	0.136
1032	0.0853
1033	0.00913
1034	0.0844
1035	0
1036	0.053
1037	0
1038	-0.0466
1039	-0.159
104	0
1040	0.137
1041	0.0844

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: CNhs10502

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0942
MA0003.1	MA0003.1	0.428
MA0004.1	MA0004.1	0.911
MA0006.1	MA0006.1	0.0367
MA0007.1	MA0007.1	0.941
MA0009.1	MA0009.1	0.184
MA0014.1	MA0014.1	0.511
MA0017.1	MA0017.1	3.86391e-4
MA0018.2	MA0018.2	0.277
MA0019.1	MA0019.1	0.167
MA0024.1	MA0024.1	5.23007e-4
MA0025.1	MA0025.1	0.467
MA0027.1	MA0027.1	0.351
MA0028.1	MA0028.1	0.0517
MA0029.1	MA0029.1	0.212
MA0030.1	MA0030.1	0.558
MA0031.1	MA0031.1	0.348
MA0035.2	MA0035.2	4.4504e-6
MA0038.1	MA0038.1	0.289
MA0039.2	MA0039.2	9.5958e-4
MA0040.1	MA0040.1	0.877
MA0041.1	MA0041.1	0.0273
MA0042.1	MA0042.1	0.031
MA0043.1	MA0043.1	0.262
MA0046.1	MA0046.1	7.44021e-7
MA0047.2	MA0047.2	0.476
MA0048.1	MA0048.1	0.994
MA0050.1	MA0050.1	0.0526
MA0051.1	MA0051.1	0.536
MA0052.1	MA0052.1	0.545
MA0055.1	MA0055.1	0.384
MA0057.1	MA0057.1	0.0655
MA0058.1	MA0058.1	0.579
MA0059.1	MA0059.1	0.398
MA0060.1	MA0060.1	6.37041e-8
MA0061.1	MA0061.1	0.533
MA0062.2	MA0062.2	0.043
MA0065.2	MA0065.2	0.719
MA0066.1	MA0066.1	0.929
MA0067.1	MA0067.1	0.288
MA0068.1	MA0068.1	0.566
MA0069.1	MA0069.1	0.561
MA0070.1	MA0070.1	0.612
MA0071.1	MA0071.1	0.0885
MA0072.1	MA0072.1	0.583
MA0073.1	MA0073.1	0.922
MA0074.1	MA0074.1	0.514
MA0076.1	MA0076.1	0.0191
MA0077.1	MA0077.1	0.21
MA0078.1	MA0078.1	0.347
MA0079.2	MA0079.2	0.0188
MA0080.2	MA0080.2	0.0131
MA0081.1	MA0081.1	0.359
MA0083.1	MA0083.1	0.0321
MA0084.1	MA0084.1	0.584
MA0087.1	MA0087.1	0.744
MA0088.1	MA0088.1	0.808
MA0090.1	MA0090.1	0.121
MA0091.1	MA0091.1	0.351
MA0092.1	MA0092.1	0.279
MA0093.1	MA0093.1	0.794
MA0099.2	MA0099.2	1.34429e-32
MA0100.1	MA0100.1	0.0932
MA0101.1	MA0101.1	0.389
MA0102.2	MA0102.2	0.132
MA0103.1	MA0103.1	1.61034e-4
MA0104.2	MA0104.2	0.0807
MA0105.1	MA0105.1	0.705
MA0106.1	MA0106.1	0.00533
MA0107.1	MA0107.1	0.103
MA0108.2	MA0108.2	1.0896e-9
MA0111.1	MA0111.1	0.378
MA0112.2	MA0112.2	0.0629
MA0113.1	MA0113.1	0.382
MA0114.1	MA0114.1	0.00126
MA0115.1	MA0115.1	4.52519e-4
MA0116.1	MA0116.1	0.672
MA0117.1	MA0117.1	0.668
MA0119.1	MA0119.1	0.644
MA0122.1	MA0122.1	0.577
MA0124.1	MA0124.1	0.366
MA0125.1	MA0125.1	0.279
MA0131.1	MA0131.1	0.278
MA0135.1	MA0135.1	0.686
MA0136.1	MA0136.1	0.042
MA0137.2	MA0137.2	0.0982
MA0138.2	MA0138.2	0.846
MA0139.1	MA0139.1	0.78
MA0140.1	MA0140.1	6.89958e-5
MA0141.1	MA0141.1	0.00218
MA0142.1	MA0142.1	0.348
MA0143.1	MA0143.1	0.035
MA0144.1	MA0144.1	0.0157
MA0145.1	MA0145.1	0.00383
MA0146.1	MA0146.1	0.441
MA0147.1	MA0147.1	0.0734
MA0148.1	MA0148.1	0.951
MA0149.1	MA0149.1	0.268
MA0150.1	MA0150.1	0.0132
MA0152.1	MA0152.1	0.839
MA0153.1	MA0153.1	2.29093e-7
MA0154.1	MA0154.1	0.169
MA0155.1	MA0155.1	0.679
MA0156.1	MA0156.1	0.203
MA0157.1	MA0157.1	0.0735
MA0159.1	MA0159.1	0.983
MA0160.1	MA0160.1	0.028
MA0162.1	MA0162.1	0.849
MA0163.1	MA0163.1	0.827
MA0164.1	MA0164.1	0.776
MA0258.1	MA0258.1	0.277
MA0259.1	MA0259.1	0.145

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: CNhs10502

Novel motif	Logo	P-value
1	1	0.778
10	10	0.667
100	100	0.364
101	101	0.778
102	102	0.263
103	103	0.408
104	104	0.235
105	105	0.23
106	106	6.44931e-4
107	107	0.0115
108	108	0.762
109	109	0.291
11	11	0.955
110	110	0.557
111	111	0.502
112	112	0.506
113	113	0.83
114	114	0.817
115	115	0.185
116	116	0.335
117	117	0.458
118	118	0.128
119	119	0.0135
12	12	0.514
120	120	0.838
121	121	0.267
122	122	0.237
123	123	0.568
124	124	0.712
125	125	0.553
126	126	0.268
127	127	0.585
128	128	0.00317
129	129	0.595
13	13	0.0461
130	130	0.496
131	131	0.26
132	132	0.722
133	133	0.275
134	134	0.831
135	135	0.555
136	136	0.123
137	137	0.14
138	138	0.0163
139	139	0.198
14	14	0.412
140	140	0.0484
141	141	0.483
142	142	0.839
143	143	0.804
144	144	0.659
145	145	0.247
146	146	0.157
147	147	0.186
148	148	0.492
149	149	0.272
15	15	0.703
150	150	0.349
151	151	0.403
152	152	0.00378
153	153	0.154
154	154	0.643
155	155	0.879
156	156	0.887
157	157	0.187
158	158	0.409
159	159	0.239
160	160	0.37
161	161	0.829
162	162	0.783
163	163	0.396
164	164	0.763
165	165	0.308
166	166	0.493
167	167	0.192
168	168	0.944
169	169	0.0432
17	17	0.0131
18	18	0.893
19	19	0.0655
2	2	0.164
20	20	0.531
21	21	0.00895
22	22	0.399
23	23	0.0723
24	24	0.0538
25	25	0.182
26	26	0.0405
27	27	0.987
28	28	0.543
29	29	0.924
3	3	0.641
30	30	0.061
31	31	0.965
32	32	0.846
33	33	0.922
34	34	0.937
35	35	0.167
36	36	0.179
37	37	0.159
38	38	0.786
39	39	0.375
4	4	0.79
40	40	0.374
41	41	0.348
42	42	0.437
43	43	0.262
44	44	0.316
45	45	0.12
46	46	0.22
47	47	0.868
48	48	0.937
49	49	0.372
5	5	0.827
50	50	0.518
51	51	0.59
52	52	0.101
53	53	0.174
54	54	0.376
55	55	0.82
56	56	0.553
57	57	0.702
58	58	0.481
59	59	0.196
6	6	0.18
60	60	0.126
61	61	0.258
62	62	0.786
63	63	0.298
64	64	0.582
65	65	0.676
66	66	0.575
67	67	0.698
68	68	0.373
69	69	0.893
7	7	0.769
70	70	0.0709
71	71	0.386
72	72	0.609
73	73	0.0122
74	74	0.83
75	75	0.566
76	76	0.108
77	77	0.0171
78	78	0.0632
79	79	0.833
8	8	0.717
80	80	0.0814
81	81	0.153
82	82	0.549
83	83	0.211
84	84	0.446
85	85	0.109
86	86	0.287
87	87	0.187
88	88	0.82
89	89	0.893
9	9	0.153
90	90	0.609
91	91	0.784
92	92	0.262
93	93	0.249
94	94	0.931
95	95	0.643
96	96	0.499
97	97	0.25
98	98	0.99
99	99	0.223

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: CNhs10502

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011438 mouse vagina- 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)
0000996 (vagina)
0003134 (female reproductive organ)
0000479 (tissue)
0005156 (reproductive structure)
0004119 (endoderm-derived structure)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0003975 (internal female genitalia)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011438 (mouse vagina- 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:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000161,UBERON:0000162,UBERON:0000163,UBERON:0000164,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000990,UBERON:0000996,UBERON:0001007,UBERON:0001046,UBERON:0001062,UBERON:0001353,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003064,UBERON:0003100,UBERON:0003104,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004122,UBERON:0004175,UBERON:0004185,UBERON:0004921,UBERON:0005156,UBERON:0005423,UBERON:0006866,UBERON:0007023,UBERON:0007026,UBERON:0009142
+|DRA_sample_Accession=CAGE@SAMD00005786
+|accession_numbers=CAGE;DRX009130;DRR010004;DRZ001429;DRZ002812;DRZ012779;DRZ014162
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000996,UBERON:0003134,UBERON:0000479,UBERON:0005156,UBERON:0004119,UBERON:0000062,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003133,UBERON:0003975,UBERON:0004175,UBERON:0010317,UBERON:0003100,UBERON:0000474
 |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:0011438
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:103143336..103143367,-!p1@Ehf!2.49!489.40!Ehf;;chr16:25801993..25802014,+!p1@Trp63!2.13!133.12!Trp63;;chr12:75002389..75002406,+!p4@Hif1a!2.13!132.48!Hif1a;;chr13:55932591..55932622,-!p1@Pitx1!2.10!149.20!Pitx1;;chr11:121380640..121380655,-!p1@Zfp750!2.09!199.36!Zfp750;;chr10:5636354..5636373,-!p2@Esr1!2.09!121.76!Esr1;;chr2:103143315..103143328,-!p2@Ehf!2.08!118.97!Ehf;;chr4:135129538..135129558,-!p1@Grhl3!2.01!149.63!Grhl3;;chr11:121380594..121380609,-!p2@Zfp750!1.97!156.06!Zfp750;;chr10:5636374..5636421,-!p1@Esr1!1.95!109.11!Esr1;;chr5:77543897..77543911,-!p2@Hopx!1.91!148.13!Hopx;;chr1:137155026..137155042,-!p1@Elf3!1.86!395.30!Elf3;;chr9:8900459..8900489,+!p1@Pgr!1.82!65.38!Pgr;;chr19:5560600..5560617,-!p1@Ovol1!1.74!65.81!Ovol1;;chr12:75002335..75002352,+!p7@Hif1a!1.73!53.16!Hif1a;;chr13:53568104..53568156,-!p1@Msx2!1.68!68.60!Msx2;;chr9:8900409..8900425,+!p2@Pgr!1.66!45.23!Pgr;;chr12:74147689..74147711,-!p1@Six1!1.62!86.39!Six1;;chr11:121380611..121380625,-!p3@Zfp750!1.62!49.30!Zfp750;;chr12:75002357..75002378,+!p6@Hif1a!1.61!39.66!Hif1a;;chr6:86619104..86619119,-!p1@Mxd1!1.59!292.61!Mxd1;;chr11:78200071..78200100,-!p1@Foxn1!1.58!36.66!Foxn1;;chr9:8899828..8899855,+!p3@Pgr!1.51!31.30!Pgr;;chr11:94981424..94981439,+!p1@Dlx3!1.50!34.73!Dlx3;;chr6:6832076..6832092,-!p1@Dlx5!1.49!34.94!Dlx5;;chr13:40829137..40829205,-!p1@Tfap2a!1.49!33.66!Tfap2a;;chr2:160192793..160192809,-!p1@Mafb!1.46!401.51!Mafb;;chr7:19946556..19946611,+!p1@Ppp1r13l!1.46!105.25!Ppp1r13l;;chr2:103264245..103264268,+!p2@Elf5!1.46!27.65!Elf5;;chr13:55932624..55932641,-!p2@Pitx1!1.46!27.65!Pitx1;;chr13:31650185..31650201,+!p1@Foxq1!1.45!91.75!Foxq1;;chr17:27865882..27865901,-!p1@Spdef!1.44!26.37!Spdef;;chr2:172375081..172375105,+!p1@Tfap2c!1.41!24.44!Tfap2c;;chr13:40826961..40827001,-!p4@Tfap2a!1.37!22.51!Tfap2a;;chr4:124805061..124805087,-!p1@Zc3h12a!1.32!59.81!Zc3h12a;;chr13:55937467..55937516,-!p3@Pitx1!1.32!19.72!Pitx1;;chr12:25257265..25257294,+!p2@Grhl1!1.31!19.51!Grhl1;;chr4:55545337..55545357,-!p1@Klf4!1.30!274.18!Klf4;;chr13:55937432..55937460,-!p4@Pitx1!1.30!18.86!Pitx1;;chr10:44178521..44178557,-!p1@Prdm1!1.28!32.16!Prdm1;;chr19:59533221..59533271,+!p1@Emx2!1.25!20.58!Emx2;;chr5:77543935..77543947,-!p4@Hopx!1.25!16.72!Hopx;;chr1:194979361..194979373,+!p2@Irf6!1.24!22.08!Irf6;;chr11:121381087..121381108,-!p4@Zfp750!1.24!16.51!Zfp750;;chr14:64562503..64562524,+!p1@Sox7!1.23!91.32!Sox7;;chr11:5761979..5761992,+!p2@Aebp1!1.23!32.37!Aebp1;;chr4:135129447..135129467,-!p2@Grhl3!1.23!19.29!Grhl3;;chr4:89354729..89354776,+!p1@Dmrta1!1.23!16.08!Dmrta1;;chr11:83664365..83664383,+!p1@Hnf1b!1.23!15.86!Hnf1b;;chr11:69468531..69468557,+!p1@Sox15!1.22!15.65!Sox15;;chr17:27866019..27866031,-!p2@Spdef!1.22!15.43!Spdef;;chr11:96143666..96143725,+!p1@Hoxb8!1.20!17.15!Hoxb8;;chr12:25257176..25257190,+!p3@Grhl1!1.20!16.72!Grhl1;;chr12:75002306..75002311,+!p10@Hif1a!1.20!14.79!Hif1a;;chr19:5560570..5560582,-!p2@Ovol1!1.17!13.93!Ovol1;;chr1:194979315..194979359,+!p1@Irf6!1.16!80.60!Irf6;;chr6:52190467..52190500,-!p1@Hoxa10!1.16!13.51!Hoxa10;;chr6:6831950..6831985,-!p2@Dlx5!1.15!14.58!Dlx5;;chr9:31720843..31720888,-!p1@Barx2!1.15!14.58!Barx2;;chr14:99697871..99697934,+!p1@Klf5!1.14!251.88!Klf5;;chr12:25257141..25257173,+!p1@Grhl1!1.14!26.58!Grhl1;;chr1:69732511..69732540,-!p2@Ikzf2!1.10!15.22!Ikzf2;;chr2:103264213..103264233,+!p1@Elf5!1.09!11.36!Elf5;;chr9:8900490..8900502,+!p4@Pgr!1.07!10.72!Pgr;;chr11:5761889..5761969,+!p1@Aebp1!1.06!441.60!Aebp1;;chr10:5636336..5636347,-!p9@Esr1!1.06!10.50!Esr1;;chr16:92826249..92826325,-!p1@Runx1!1.05!25.30!Runx1;;chr10:5636678..5636725,-!p6@Esr1!1.04!10.08!Esr1;;chr11:96153767..96153822,+!p1@Hoxb6!1.03!15.22!Hoxb6;;chr13:31650026..31650045,+!p2@Foxq1!1.02!16.29!Foxq1;;chr10:44178493..44178520,-!p3@Prdm1!1.02!13.51!Prdm1;;chr7:20162663..20162678,+!p1@Zfp296!1.02!12.65!Zfp296;;chr19:44831390..44831414,+!p1@Pax2!1.02!9.43!Pax2;;chr16:92697560..92697592,-!p2@Runx1!1.01!58.95!Runx1;;chr6:145814003..145814056,-!p1@Bhlhe41!1.01!27.22!Bhlhe41;;chr4:55545051..55545110,-!p2@Klf4!1.01!11.58!Klf4;;chr15:102087880..102087927,-!p2@Rarg!1.00!21.22!Rarg;;chr15:50721640..50721654,-!p7@Trps1!0.98!13.72!Trps1;;chr6:52195795..52195825,-!p1@Hoxa11!0.97!8.36!Hoxa11;;chr11:98636531..98636559,-!p1@Nr1d1!0.96!47.59!Nr1d1;;chr12:75002422..75002429,+!p11@Hif1a!0.96!8.15!Hif1a;;chr10:44178375..44178390,-!p2@Prdm1!0.95!10.93!Prdm1;;chr6:51382677..51382783,+!p1@Nfe2l3!0.94!20.36!Nfe2l3;;chr5:32438894..32438908,+!p2@Fosl2!0.94!16.51!Fosl2;;chr6:52195763..52195792,-!p2@Hoxa11!0.94!7.72!Hoxa11;;chr18:76219118..76219155,+!p1@Zbtb7c!0.93!13.51!Zbtb7c;;chr15:79178060..79178074,+!p2@Maff!0.93!10.08!Maff;;chr10:22539932..22539956,-!p1@Tcf21!0.92!20.15!Tcf21;;chr15:103170516..103170531,-!p2@Zfp385a!0.92!18.01!Zfp385a;;chr3:30408603..30408668,-!p1@Mecom!0.92!17.58!Mecom;;chr2:115890469..115890485,-!p7@Meis2!0.92!12.00!Meis2;;chr4:89354785..89354801,+!p2@Dmrta1!0.92!7.29!Dmrta1;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.91!21.22!Tfcp2l1;;chr12:25257114..25257131,+!p4@Grhl1!0.90!9.22!Grhl1;;chr8:87502608..87502623,-!p1@Junb!0.89!114.47!Junb;;chr15:103170533..103170556,-!p1@Zfp385a!0.89!26.15!Zfp385a;;chr6:108610766..108610781,+!p2@Bhlhe40!0.89!12.43!Bhlhe40;;chr10:44178474..44178487,-!p4@Prdm1!0.87!9.43!Prdm1;;chr9:8900563..8900574,+!p5@Pgr!0.87!6.43!Pgr;;chr13:40825465..40825469,-!p2@Tfap2a!0.87!6.43!Tfap2a;;chr16:55822241..55822258,-!p1@Nfkbiz!0.86!207.29!Nfkbiz;;chr15:37162834..37162849,+!p2@Grhl2!0.86!7.50!Grhl2;;chr5:32438831..32438878,+!p1@Fosl2!0.85!67.10!Fosl2;;chr5:76733981..76734018,-!p3@Clock!0.85!13.51!Clock;;chr15:37162796..37162828,+!p1@Grhl2!0.85!10.50!Grhl2;;chr5:31271028..31271040,+!p1@Tcf23!0.85!6.00!Tcf23;;chr1:194979383..194979393,+!p3@Irf6!0.85!6.00!Irf6;;chr19:59532915..59532940,+!p5@Emx2!0.85!6.00!Emx2;;chr15:35225845..35225867,+!p1@Osr2!0.84!15.65!Osr2;;chr5:92391466..92391471,+!p2@Thap6!0.83!8.57!Thap6;;chr11:96147952..96147967,+!p1@Hoxb7!0.83!7.29!Hoxb7;;chr6:6831928..6831949,-!p3@Dlx5!0.83!5.79!Dlx5;;chr6:6813269..6813272,+!p2@Dlx6!0.83!5.79!Dlx6;;chr12:74147860..74147888,-!p2@Six1!0.83!5.79!Six1;;chr2:74517742..74517758,+!p2@Hoxd11!0.83!5.79!Hoxd11;;chr11:96145450..96145517,+!p2@Hoxb7!0.82!8.79!Hoxb7;;chr2:24331085..24331100,-!p1@Pax8!0.82!5.57!Pax8;;chr13:53568081..53568094,-!p3@Msx2!0.82!5.57!Msx2;;chr17:48025139..48025166,-!p8@Foxp4!0.81!6.43!Foxp4;;chr13:31898729..31898761,+!p1@Foxc1!0.80!13.93!Foxc1;;chr13:53568191..53568219,-!p2@Msx2!0.80!5.36!Msx2;;chr6:6812988..6813002,+!p3@Dlx6!0.80!5.36!Dlx6;;chr6:6812962..6812979,+!p1@Dlx6!0.80!5.36!Dlx6;;chr19:59534008..59534046,+!p7@Emx2!0.80!5.36!Emx2;;chr2:103264277..103264292,+!p3@Elf5!0.79!5.14!Elf5;;chr11:121381115..121381124,-!p5@Zfp750!0.79!5.14!Zfp750;;chr6:6831986..6832007,-!p4@Dlx5!0.79!5.14!Dlx5;;chr15:50721588..50721610,-!p1@Trps1!0.78!55.31!Trps1;;chr4:148178529..148178548,+!p3@Casz1!0.78!12.65!Casz1;;chr5:65194752..65194769,+!p1@Klf3!0.77!178.57!Klf3;;chr19:19185671..19185693,-!p1@Rorb!0.77!12.65!Rorb;;chr16:25802129..25802142,+!p3@Trp63!0.77!4.93!Trp63;;chr18:76219161..76219176,+!p4@Zbtb7c!0.76!6.43!Zbtb7c;;chr6:52184901..52184959,-!p2@Hoxa10!0.76!4.72!Hoxa10;;chr11:96143843..96143868,+!p3@Hoxb8!0.76!4.72!Hoxb8;;chr15:97738692..97738747,-!p1@Vdr!0.75!28.08!Vdr;;chr16:14705961..14705978,+!p2@Snai2!0.75!23.79!Snai2;;chr2:115890953..115890974,-!p6@Meis2!0.75!7.29!Meis2;;chr4:55545152..55545194,-!p3@Klf4!0.75!5.57!Klf4;;chr7:20408047..20408125,-!p1@Bcl3!0.74!56.81!Bcl3;;chr6:88148650..88148669,+!p1@Gata2!0.74!41.80!Gata2;;chr6:52210774..52210787,-!p1@Hoxa13!0.74!4.50!Hoxa13;;chr1:189432881..189432903,+!p2@Esrrg!0.74!4.50!Esrrg;;chr12:25257298..25257323,+!p5@Grhl1!0.74!4.50!Grhl1;;chr10:67599319..67599360,-!p2@Arid5b!0.73!54.02!Arid5b;;chr7:89137163..89137200,-!p1@Bnc1!0.73!5.36!Bnc1;;chr12:56593574..56593592,-!p1@Nfkbia!0.72!247.81!Nfkbia;;chr19:59534052..59534083,+!p8@Emx2!0.72!4.29!Emx2;;chr6:52190668..52190682,-!p3@Hoxa10!0.72!4.29!Hoxa10;;chr4:148178459..148178482,+!p4@Casz1!0.72!4.29!Casz1;;chr12:109242266..109242295,-!p1@Bcl11b!0.71!39.02!Bcl11b;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.71!7.50!Hoxb2;;chr14:79915502..79915514,+!p4@Elf1!0.71!6.65!Elf1;;chr7:19946535..19946550,+!p3@Ppp1r13l!0.71!6.65!Ppp1r13l;;chr15:79178013..79178028,+!p3@Maff!0.71!5.57!Maff;;chr10:5734677..5734702,-!p4@Esr1!0.71!4.07!Esr1;;chr11:96880072..96880079,+!p1@Sp6!0.71!4.07!Sp6;;chr11:18918917..18918944,-!p1@Meis1!0.70!58.74!Meis1;;chr12:86940338..86940357,+!p1@Jdp2!0.70!45.02!Jdp2;;chr4:148275237..148275311,+!p2@Casz1!0.70!18.44!Casz1;;chr1:165243792..165243808,-!p1@Prrx1!0.70!15.65!Prrx1;;chr10:5734525..5734569,-!p3@Esr1!0.70!7.07!Esr1;;chr5:32438395..32438406,+!p3@Fosl2!0.70!6.43!Fosl2;;chr11:96143962..96144035,+!p2@Hoxb8!0.69!3.86!Hoxb8;;chr6:108610610..108610676,+!p1@Bhlhe40!0.68!215.44!Bhlhe40;;chr2:115891381..115891392,-!p5@Meis2!0.68!8.15!Meis2;;chr11:85646427..85646451,+!p4@Tbx2!0.68!7.07!Tbx2;;chr6:108610513..108610528,+!p3@Bhlhe40!0.68!6.22!Bhlhe40;;chr16:14705925..14705951,+!p1@Snai2!0.67!29.37!Snai2;;chr15:50720601..50720630,-!p2@Trps1!0.67!9.65!Trps1;;chr13:55932739..55932756,-!p5@Pitx1!0.67!3.64!Pitx1;;chr12:74147842..74147856,-!p3@Six1!0.67!3.64!Six1;;chr13:40827030..40827039,-!p12@Tfap2a!0.67!3.64!Tfap2a;;chr13:40824310..40824314,-!p6@Tfap2a!0.67!3.64!Tfap2a;;chr6:97757008..97757061,+!p1@Mitf!0.66!17.36!Mitf;;chr5:65213356..65213412,+!p6@Klf3!0.66!8.36!Klf3;;chr14:22807216..22807231,-!p3@Zfp503!0.66!6.65!Zfp503;;chr7:52960555..52960662,+!p1@Dbp!0.65!34.30!Dbp;;chr11:16908650..16908690,-!p1@Plek!0.65!24.65!Plek;;chr10:80600749..80600766,+!p2@Zbtb7a!0.65!21.01!Zbtb7a;;chr17:32506357..32506377,-!p3@Wiz!0.65!7.93!Wiz;;chr13:31898637..31898653,+!p2@Foxc1!0.65!6.65!Foxc1;;chr15:37163124..37163153,+!p3@Grhl2!0.65!3.43!Grhl2;;chrX:95345005..95345053,+!p1@Ar!0.65!3.43!Ar;;chr11:83664334..83664353,+!p2@Hnf1b!0.65!3.43!Hnf1b;;chr15:36937137..36937157,-!p2@Gm10193,p2@Zfp706!0.64!121.33!Zfp706;;chr6:146744595..146744613,+!p2@Arntl2!0.64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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:89-27D5
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011438
+|is_a=EFO:0002091;;FF:0011438
+|is_obsolete=
+|library_id=CNhs10502
+|library_id_phase_based=2:CNhs10502
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;89
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;89
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/vagina%252c%2520adult.CNhs10502.89-27D5.mm9.nobarcode.rdna.fa.gz
 |name=vagina, adult
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10502,LSID648,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.145248123132783,0,0,0,0,0.0208867538010007,0.147808025287109,0,0,0,0,1.12097142618561e-05,0,0,0,0,0,0,-0.107542900771771,0,0,0,0,0,0.154952218286625,0,0,0,0,0,0.0101143672889883,0,0.348674371204667,0,0,0,0,0,0.097530210978616,-0.0407460403531483,0.0501968191114865,-0.667854755644601,-0.114916419723726,0,0,0,0,0,0,0,0,0,0,0,0.0843504501108034,0.202917082783196,0,0,0,0,0.0415034950279286,0,0.0696569650212278,0,0.0843504501108034,0,0.0256119201407331,-0.0949853038488843,0.275670318350908,0.0055825160585482,0,0.0379775419985211,0,0.0369680894652996,0.154952218286625,0,0,0.0167895805773672,-0.0698274417942446,0.190091035506729,0,0,0,0,0,0,-0.0411337708825408,-0.174621166856102,-0.0578655779147686,0.0180356625981624,0,0,0,0
 |rna_box=27
 |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=vagina
 |top_motifs=FOS_FOS{B,L1}_JUN{B,D}:3.72379793502;BACH2:3.00945984319;ZNF148:2.96122818057;T:2.88257809221;TP53:2.57567971151;NFE2:2.08074094126;FOSL2:1.99449518834;FOXO1,3,4:1.95773722075;CDC5L:1.85185517245;TBP:1.70237632932;TFCP2:1.69423038652;SPZ1:1.63843892599;HAND1,2:1.47751951371;SNAI1..3:1.45347379108;TBX4,5:1.36149571197;ZEB1:1.27636194336;HMX1:1.26865995947;NFE2L2:1.2434511072;FOXN1:1.20854312995;CEBPA,B_DDIT3:1.1806239888;SP1:1.15776580977;NFE2L1:1.11854327654;MYOD1:1.08970853525;HOX{A4,D4}:1.08481284416;TFAP2{A,C}:1.0559253416;HLF:1.04954718409;NKX2-2,8:1.01118624589;SMAD1..7,9:0.992512966741;GLI1..3:0.976705359561;GCM1,2:0.953776929398;EP300:0.918766658093;EBF1:0.911677531071;NFATC1..3:0.897969005729;BPTF:0.86759112709;PITX1..3:0.862107504506;NKX3-2:0.824830864377;FOX{D1,D2}:0.820613960535;PAX5:0.809570076865;NANOG:0.783235718152;SRF:0.775352527037;TEAD1:0.736695943454;ATF6:0.683104702608;ATF2:0.659620811177;GTF2A1,2:0.643523226186;GTF2I:0.630647821713;STAT5{A,B}:0.60821866546;XCPE1{core}:0.604974045711;VSX1,2:0.598519836862;IRF7:0.572391945086;NFKB1_REL_RELA:0.503205459623;ETS1,2:0.493768833605;IKZF2:0.480037501601;MAFB:0.472037222708;MAZ:0.457580333678;CRX:0.452675812708;MYBL2:0.439200894294;ELF1,2,4:0.437729861002;RXRA_VDR{dimer}:0.421715892565;PDX1:0.406790603533;LEF1_TCF7_TCF7L1,2:0.400270075918;ADNP_IRX_SIX_ZHX:0.385323642117;POU5F1:0.358610989827;TEF:0.358235025362;HSF1,2:0.349596865346;SREBF1,2:0.33527043043;TFAP4:0.324865233751;SOX5:0.317769910664;DMAP1_NCOR{1,2}_SMARC:0.299454264024;NKX2-1,4:0.292663481185;FOXM1:0.285830146443;AIRE:0.265879087117;TOPORS:0.264812507736;RUNX1..3:0.264540375239;STAT2,4,6:0.262397675836;ATF4:0.250816855147;TLX1..3_NFIC{dimer}:0.246316838856;HOX{A5,B5}:0.226987401506;FOXP1:0.219623850923;ZNF238:0.216473234617;IRF1,2:0.213827468065;SPIB:0.20224868471;MYFfamily:0.19452769454;PRDM1:0.159853135601;TLX2:0.156826950615;SPI1:0.141672590117;ESR1:0.112478233534;NR3C1:0.0695093871286;NKX2-3_NKX2-5:0.0516460961893;HIF1A:0.0509268244924;KLF4:0.0242503541157;HIC1:0.0230159041017;TGIF1:0.020161950267;bHLH_family:-0.00781823044193;MZF1:-0.0374284187263;GZF1:-0.0418279297337;POU2F1..3:-0.0496086798957;REST:-0.0502309932113;HBP1_HMGB_SSRP1_UBTF:-0.0794194560709;NKX3-1:-0.0969318626228;NFIL3:-0.129136895844;DBP:-0.149281963837;GFI1:-0.156772112266;SOX2:-0.168638136093;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.175106148105;RREB1:-0.176663764601;NKX6-1,2:-0.185166898283;ELK1,4_GABP{A,B1}:-0.190932377079;ALX4:-0.199953487208;MED-1{core}:-0.240535258356;NHLH1,2:-0.24902679474;ZNF384:-0.262575710127;LHX3,4:-0.267244611091;EGR1..3:-0.282322006264;MTE{core}:-0.283430664404;AHR_ARNT_ARNT2:-0.300897301488;PAX4:-0.305078843723;ZBTB6:-0.323182092399;TFDP1:-0.326429827408;ZNF423:-0.345959545808;ATF5_CREB3:-0.346120405519;LMO2:-0.349853781426;PATZ1:-0.359002296914;MTF1:-0.385458912864;RFX2..5_RFXANK_RFXAP:-0.395984011051;HMGA1,2:-0.399782456943;MEF2{A,B,C,D}:-0.403959270008;STAT1,3:-0.411950686698;TFAP2B:-0.422641642703;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.430402323228;PAX2:-0.435126349288;IKZF1:-0.435865842876;GFI1B:-0.442039041651;ZBTB16:-0.444045918545;BREu{core}:-0.449403780487;JUN:-0.449437741831;PRRX1,2:-0.456861570399;HNF1A:-0.460410657886;SOX17:-0.479253768605;CREB1:-0.488016926758;ZIC1..3:-0.503843166091;HNF4A_NR2F1,2:-0.53060527415;E2F1..5:-0.541260247657;ONECUT1,2:-0.548308964294;POU1F1:-0.564864572321;NR1H4:-0.570919013701;PAX8:-0.59805902594;ZNF143:-0.610721510726;POU6F1:-0.650989127747;TAL1_TCF{3,4,12}:-0.651264093911;NFIX:-0.656630932314;SOX{8,9,10}:-0.666583873657;MYB:-0.671548860533;FOX{F1,F2,J1}:-0.679506188716;RFX1:-0.720646008946;GATA4:-0.748218657738;POU3F1..4:-0.751019903338;FOXL1:-0.808672760566;ZFP161:-0.815189342626;RBPJ:-0.827250727852;UFEwm:-0.851498892446;AR:-0.85499955057;NRF1:-0.879362398965;HES1:-0.881717082988;GATA6:-0.885407983991;RXR{A,B,G}:-0.911594547695;PPARG:-0.932887367584;NR6A1:-0.956844120132;EN1,2:-0.958686515603;OCT4_SOX2{dimer}:-0.958808655073;ARID5B:-0.983296709417;FOX{I1,J2}:-1.00345596591;PAX1,9:-1.01661824826;FOXA2:-1.04658654466;CUX2:-1.0581432018;ALX1:-1.09548732728;CDX1,2,4:-1.10317004139;RORA:-1.1859222055;ESRRA:-1.2808406667;FOXQ1:-1.32852855003;NANOG{mouse}:-1.39967007414;PAX6:-1.50502940035;FOXD3:-1.53603605696;HOXA9_MEIS1:-1.53618356117;YY1:-1.59356438022;EVI1:-1.59421444384;NFY{A,B,C}:-1.70890399369;FOXP3:-1.7282108791;NR5A1,2:-1.82602020978;PBX1:-1.84869748245
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:89-27D5;search_select_hide=table117:89-27D5
 }}

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FF:89-27D5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:21, 4 June 2020

CNhs10502

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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