FF:49-24D7: Difference between revisions

Revision as of 11:10, 28 November 2014

Name:	adrenal gland, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10508
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/6J
tissue	adrenal gland
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		SAMD00005456

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10508		CAGE		DRX008927		DRR009801

Accession ID Mm9

Library id		BAM		CTSS
CNhs10508		DRZ001226		DRZ002609

Download raw sequence, BAM & CTSS

Mm9

BAM	CTSS
[{{{mm9bam}}} download]	[{{{mm9ctss}}} donwload]

Mm10

BAM	CTSS
[{{{mm10bam}}} download]	[{{{mm10ctss}}} 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

CNhs10508

0	0
1	0.0601
10	0
100	0
1000	0.0993
1001	0.0498
1002	0.0227
1003	-0.0503
1004	0
1005	0.0311
1006	0.162
1007	-0.0614
1008	0
1009	0.37
101	-0.0018
1010	0
1011	0.00281
1012	0
1013	0.234
1014	-0.0874
1015	-0.116
1016	0.0359
1017	0
1018	0
1019	0
102	0
1020	0
1021	0
1022	0.283
1023	0
1024	0.0881
1025	0
1026	0
1027	0
1028	0
1029	0.0219
103	-0.0736
1030	0
1031	-0.037
1032	0.0482
1033	0.0599
1034	0
1035	0
1036	-0.213
1037	0
1038	0.12
1039	0.317
104	0
1040	0.105
1041	0.802

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: CNhs10508

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.11
MA0003.1	MA0003.1	0.212
MA0004.1	MA0004.1	0.318
MA0006.1	MA0006.1	0.736
MA0007.1	MA0007.1	0.567
MA0009.1	MA0009.1	0.212
MA0014.1	MA0014.1	0.351
MA0017.1	MA0017.1	0.808
MA0018.2	MA0018.2	0.101
MA0019.1	MA0019.1	0.924
MA0024.1	MA0024.1	1.35738e-9
MA0025.1	MA0025.1	0.0324
MA0027.1	MA0027.1	0.93
MA0028.1	MA0028.1	0.0918
MA0029.1	MA0029.1	0.00713
MA0030.1	MA0030.1	0.389
MA0031.1	MA0031.1	0.21
MA0035.2	MA0035.2	0.496
MA0038.1	MA0038.1	0.611
MA0039.2	MA0039.2	0.164
MA0040.1	MA0040.1	0.324
MA0041.1	MA0041.1	0.323
MA0042.1	MA0042.1	0.889
MA0043.1	MA0043.1	0.409
MA0046.1	MA0046.1	4.43873e-4
MA0047.2	MA0047.2	0.364
MA0048.1	MA0048.1	0.0465
MA0050.1	MA0050.1	3.13063e-9
MA0051.1	MA0051.1	4.90219e-6
MA0052.1	MA0052.1	0.0487
MA0055.1	MA0055.1	5.2659e-4
MA0057.1	MA0057.1	0.689
MA0058.1	MA0058.1	0.443
MA0059.1	MA0059.1	0.0384
MA0060.1	MA0060.1	3.56831e-7
MA0061.1	MA0061.1	0.89
MA0062.2	MA0062.2	0.356
MA0065.2	MA0065.2	0.364
MA0066.1	MA0066.1	0.264
MA0067.1	MA0067.1	0.526
MA0068.1	MA0068.1	0.6
MA0069.1	MA0069.1	0.499
MA0070.1	MA0070.1	0.0127
MA0071.1	MA0071.1	0.188
MA0072.1	MA0072.1	0.118
MA0073.1	MA0073.1	0.748
MA0074.1	MA0074.1	0.604
MA0076.1	MA0076.1	0.19
MA0077.1	MA0077.1	0.17
MA0078.1	MA0078.1	0.0387
MA0079.2	MA0079.2	0.0126
MA0080.2	MA0080.2	0.0246
MA0081.1	MA0081.1	0.252
MA0083.1	MA0083.1	0.972
MA0084.1	MA0084.1	0.247
MA0087.1	MA0087.1	0.453
MA0088.1	MA0088.1	0.775
MA0090.1	MA0090.1	0.601
MA0091.1	MA0091.1	0.204
MA0092.1	MA0092.1	0.513
MA0093.1	MA0093.1	0.464
MA0099.2	MA0099.2	0.0169
MA0100.1	MA0100.1	0.11
MA0101.1	MA0101.1	0.861
MA0102.2	MA0102.2	0.319
MA0103.1	MA0103.1	3.00646e-5
MA0104.2	MA0104.2	0.0939
MA0105.1	MA0105.1	0.0319
MA0106.1	MA0106.1	0.236
MA0107.1	MA0107.1	0.673
MA0108.2	MA0108.2	4.56712e-4
MA0111.1	MA0111.1	0.899
MA0112.2	MA0112.2	0.43
MA0113.1	MA0113.1	0.61
MA0114.1	MA0114.1	0.865
MA0115.1	MA0115.1	0.329
MA0116.1	MA0116.1	0.757
MA0117.1	MA0117.1	0.144
MA0119.1	MA0119.1	0.705
MA0122.1	MA0122.1	0.322
MA0124.1	MA0124.1	0.344
MA0125.1	MA0125.1	0.53
MA0131.1	MA0131.1	0.153
MA0135.1	MA0135.1	0.142
MA0136.1	MA0136.1	0.108
MA0137.2	MA0137.2	0.744
MA0138.2	MA0138.2	0.0184
MA0139.1	MA0139.1	0.705
MA0140.1	MA0140.1	0.419
MA0141.1	MA0141.1	0.184
MA0142.1	MA0142.1	0.601
MA0143.1	MA0143.1	0.436
MA0144.1	MA0144.1	0.894
MA0145.1	MA0145.1	0.164
MA0146.1	MA0146.1	0.156
MA0147.1	MA0147.1	0.0403
MA0148.1	MA0148.1	0.927
MA0149.1	MA0149.1	0.787
MA0150.1	MA0150.1	0.00806
MA0152.1	MA0152.1	0.948
MA0153.1	MA0153.1	8.69554e-8
MA0154.1	MA0154.1	0.28
MA0155.1	MA0155.1	0.724
MA0156.1	MA0156.1	0.0268
MA0157.1	MA0157.1	0.195
MA0159.1	MA0159.1	0.299
MA0160.1	MA0160.1	0.145
MA0162.1	MA0162.1	0.404
MA0163.1	MA0163.1	0.0495
MA0164.1	MA0164.1	0.754
MA0258.1	MA0258.1	0.469
MA0259.1	MA0259.1	0.0418

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: CNhs10508

Novel motif	Logo	P-value
1	1	0.118
10	10	0.126
100	100	0.113
101	101	0.108
102	102	0.606
103	103	0.97
104	104	0.728
105	105	0.693
106	106	0.688
107	107	0.715
108	108	0.203
109	109	0.711
11	11	0.821
110	110	0.905
111	111	0.792
112	112	0.218
113	113	0.0547
114	114	0.364
115	115	0.0687
116	116	0.0779
117	117	0.0155
118	118	0.985
119	119	0.114
12	12	0.884
120	120	0.0084
121	121	0.12
122	122	0.251
123	123	0.248
124	124	0.0199
125	125	0.456
126	126	0.0658
127	127	0.147
128	128	0.445
129	129	0.269
13	13	0.0351
130	130	0.275
131	131	0.194
132	132	0.539
133	133	0.855
134	134	0.888
135	135	0.0913
136	136	0.502
137	137	0.562
138	138	0.159
139	139	0.131
14	14	0.118
140	140	0.212
141	141	0.398
142	142	0.526
143	143	0.853
144	144	0.976
145	145	0.16
146	146	0.274
147	147	0.69
148	148	0.926
149	149	0.00273
15	15	0.369
150	150	0.981
151	151	0.226
152	152	0.0087
153	153	0.673
154	154	0.489
155	155	0.765
156	156	3.6108e-4
157	157	0.229
158	158	0.478
159	159	0.731
160	160	0.601
161	161	0.246
162	162	0.867
163	163	0.206
164	164	0.939
165	165	0.692
166	166	0.336
167	167	0.0721
168	168	0.68
169	169	0.174
17	17	0.95
18	18	0.788
19	19	0.378
2	2	0.0382
20	20	0.0338
21	21	0.591
22	22	0.104
23	23	0.611
24	24	0.281
25	25	0.75
26	26	0.0177
27	27	0.397
28	28	0.95
29	29	0.0604
3	3	0.976
30	30	0.493
31	31	0.685
32	32	0.266
33	33	0.0989
34	34	0.795
35	35	0.779
36	36	0.191
37	37	0.847
38	38	0.272
39	39	0.681
4	4	0.24
40	40	0.613
41	41	0.00744
42	42	0.795
43	43	0.736
44	44	0.626
45	45	0.512
46	46	0.164
47	47	0.908
48	48	0.657
49	49	0.904
5	5	0.823
50	50	0.983
51	51	0.827
52	52	0.918
53	53	0.147
54	54	0.928
55	55	0.0326
56	56	0.381
57	57	0.138
58	58	0.794
59	59	0.888
6	6	0.765
60	60	0.928
61	61	0.418
62	62	0.581
63	63	0.844
64	64	0.932
65	65	0.746
66	66	0.277
67	67	0.416
68	68	0.924
69	69	0.476
7	7	0.257
70	70	0.82
71	71	0.00782
72	72	0.39
73	73	0.156
74	74	0.582
75	75	0.332
76	76	0.532
77	77	0.637
78	78	0.897
79	79	0.319
8	8	0.423
80	80	0.553
81	81	0.123
82	82	0.0167
83	83	0.0202
84	84	0.119
85	85	0.802
86	86	0.841
87	87	0.348
88	88	0.513
89	89	0.85
9	9	0.918
90	90	0.251
91	91	0.00151
92	92	0.634
93	93	0.657
94	94	0.287
95	95	0.613
96	96	0.867
97	97	0.132
98	98	0.68
99	99	0.731

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: CNhs10508

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011373 mouse adrenal gland - 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)
0002369 (adrenal gland)
0002100 (trunk)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0005172 (abdomen element)
0002530 (gland)
0006858 (adrenal/interrenal gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011373 (mouse adrenal gland - 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:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:38570011..38570034,-!p1@Nr5a1!2.26!181.99!Nr5a1;;chr18:3281725..3281740,-!p3@Crem!1.87!91.29!Crem;;chr11:96143666..96143725,+!p1@Hoxb8!1.84!77.93!Hoxb8;;chr7:108966820..108966835,+!p1@Phox2a!1.73!52.25!Phox2a;;chr15:101097270..101097290,+!p1@Nr4a1!1.65!427.96!Nr4a1;;chr8:59799772..59799789,+!p1@Hand2!1.65!120.24!Hand2;;chr11:96132637..96132652,+!p1@Hoxb9!1.64!42.90!Hoxb9;;chr5:120120667..120120685,+!p3@Tbx3!1.59!70.96!Tbx3;;chr5:120130377..120130432,+!p10@Tbx3!1.49!29.99!Tbx3;;chr15:102828658..102828678,+!p1@Hoxc6!1.49!29.99!Hoxc6;;chr4:133109285..133109308,+!p1@Nr0b2!1.41!24.79!Nr0b2;;chr9:24578720..24578735,-!p1@Tbx20!1.37!22.56!Tbx20;;chr11:98636531..98636559,-!p1@Nr1d1!1.36!120.98!Nr1d1;;chr19:37509324..37509337,+!p1@Hhex!1.34!143.25!Hhex;;chr11:96153767..96153822,+!p1@Hoxb6!1.32!30.88!Hoxb6;;chr7:116154364..116154444,+!p1@Tub!1.26!29.39!Tub;;chr7:52960555..52960662,+!p1@Dbp!1.24!135.82!Dbp;;chr10:88996336..88996380,-!p2@Nr1h4!1.23!19.89!Nr1h4;;chr18:3281750..3281776,-!p2@Crem!1.22!31.17!Crem;;chr11:57645506..57645523,-!p1@Hand1!1.22!15.59!Hand1;;chr11:98636508..98636524,-!p3@Nr1d1!1.20!18.26!Nr1d1;;chr9:96653072..96653154,-!p1@Zbtb38!1.17!36.96!Zbtb38;;chr4:48058129..48058179,+!p2@Nr4a3!1.15!24.64!Nr4a3;;chr4:48058047..48058062,+!p1@Nr4a3!1.14!19.45!Nr4a3;;chr6:83020355..83020371,-!p1@Tlx2!1.13!12.47!Tlx2;;chr16:43363190..43363242,+!p2@Zbtb20!1.11!36.22!Zbtb20;;chr2:38567715..38567730,-!p2@Nr5a1!1.11!12.02!Nr5a1;;chr11:96147952..96147967,+!p1@Hoxb7!1.08!13.81!Hoxb7;;chr11:96132767..96132796,+!p2@Hoxb9!1.08!11.13!Hoxb9;;chr11:5761889..5761969,+!p1@Aebp1!1.06!435.23!Aebp1;;chr18:11052485..11052508,+!p2@Gata6!1.06!30.13!Gata6;;chr6:88143711..88143717,+!p2@Gata2!1.03!15.73!Gata2;;chr5:120120834..120120845,+!p8@Tbx3!1.03!9.65!Tbx3;;chr11:96160426..96160443,+!p2@Hoxb6!1.03!9.65!Hoxb6;;chr5:120130275..120130296,+!p11@Tbx3!1.02!9.50!Tbx3;;chr10:88996295..88996335,-!p3@Nr1h4!1.01!10.98!Nr1h4;;chr11:5761979..5761992,+!p2@Aebp1!1.00!18.41!Aebp1;;chr2:9800207..9800234,-!p1@Gata3!0.99!27.31!Gata3;;chr7:52960700..52960719,+!p2@Dbp!0.98!10.54!Dbp;;chr5:120121446..120121461,+!p2@Tbx3!0.97!28.20!Tbx3;;chr10:22539932..22539956,-!p1@Tcf21!0.97!22.86!Tcf21;;chr2:115890953..115890974,-!p6@Meis2!0.95!12.17!Meis2;;chr11:96145450..96145517,+!p2@Hoxb7!0.95!12.02!Hoxb7;;chr2:34227446..34227511,-!p1@Pbx3!0.94!18.26!Pbx3;;chr4:48058016..48058032,+!p3@Nr4a3!0.90!12.17!Nr4a3;;chr2:56967334..56967366,-!p1@Nr4a2!0.89!14.40!Nr4a2;;chr11:96143962..96144035,+!p2@Hoxb8!0.89!6.68!Hoxb8;;chrX:45245679..45245702,-!p1@Smarca1!0.88!31.17!Smarca1;;chr2:74542918..74542971,+!p1@Hoxd8!0.88!10.24!Hoxd8;;chr5:67490474..67490494,-!p2@Phox2b!0.88!6.53!Phox2b;;chr11:96160360..96160397,+!p3@Hoxb6!0.87!6.38!Hoxb6;;chr5:135582751..135582788,+!p1@Mlxipl!0.86!26.57!Mlxipl;;chr15:102839948..102839975,+!p3@Hoxc6!0.86!6.23!Hoxc6;;chr14:19071466..19071550,-!p1@Nr1d2!0.85!44.24!Nr1d2;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.85!10.69!Hoxb2;;chr5:125538737..125538781,-!p2@Ncor2!0.84!22.27!Ncor2;;chr18:11052456..11052477,+!p3@Gata6!0.84!19.59!Gata6;;chr1:52176315..52176343,+!p1@Stat1!0.80!83.42!Stat1;;chr15:102820964..102821006,+!p1@Hoxc8!0.80!5.34!Hoxc8;;chr15:102828642..102828653,+!p2@Hoxc6!0.80!5.34!Hoxc6;;chr16:42907676..42907797,+!p1@Zbtb20!0.79!72.44!Zbtb20;;chr15:102865131..102865151,+!p2@Hoxc4!0.79!5.94!Hoxc4;;chr5:120120708..120120713,+!p12@Tbx3!0.79!5.20!Tbx3;;chr2:44965856..44965896,-!p5@Zeb2!0.78!21.23!Zeb2;;chr2:34227273..34227292,-!p4@Pbx3!0.78!5.49!Pbx3;;chr11:96143843..96143868,+!p3@Hoxb8!0.78!5.05!Hoxb8;;chr11:96690797..96690813,-!p1@Nfe2l1!0.77!103.46!Nfe2l1;;chr16:42907554..42907591,+!p5@Zbtb20!0.77!13.06!Zbtb20;;chr7:77511403..77511450,-!p3@Nr2f2!0.76!10.69!Nr2f2;;chr8:111227518..111227550,+!p@chr8:111227518..111227550,+!0.76!8.76!Zfhx3;;chr11:98636400..98636418,-!p4@Nr1d1!0.76!6.38!Nr1d1;;chr1:19202352..19202354,+!p2@Tfap2b!0.76!4.75!Tfap2b;;chr15:76287876..76287894,+!p1@Scx!0.75!27.91!Scx;;chr14:33412570..33412586,+!p1@Prrxl1!0.75!4.60!Prrxl1;;chr9:69137716..69137744,+!p1@Rora!0.74!31.62!Rora;;chr16:43363152..43363186,+!p3@Zbtb20!0.74!10.98!Zbtb20;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.74!8.31!Zfhx3;;chr6:52167513..52167549,-!p2@Hoxa7!0.74!6.68!Hoxa7;;chr7:52960730..52960762,+!p3@Dbp!0.74!5.94!Dbp;;chr2:74549968..74549996,+!p1@Hoxd3!0.74!5.79!Hoxd3;;chr5:67490284..67490302,-!p1@Phox2b!0.74!4.45!Phox2b;;chr10:88996274..88996286,-!p4@Nr1h4!0.74!4.45!Nr1h4;;chr6:88148650..88148669,+!p1@Gata2!0.73!40.38!Gata2;;chr4:94718861..94718872,-!p2@Jun!0.72!35.92!Jun;;chr15:102865088..102865107,+!p1@Hoxc4!0.72!5.94!Hoxc4;;chr15:102839976..102839989,+!p4@Hoxc6!0.72!4.30!Hoxc6;;chr10:129717274..129717298,-!p1@Neurod4!0.72!4.30!Neurod4;;chr8:109817400..109817417,+!p1@Nfat5!0.71!99.31!Nfat5;;chr15:35225845..35225867,+!p1@Osr2!0.71!11.43!Osr2;;chr9:48644037..48644067,-!p2@Zbtb16!0.71!11.28!Zbtb16;;chr2:173044380..173044432,-!p1@Zbp1!0.71!10.84!Zbp1;;chr7:19895354..19895369,-!p1@Fosb!0.71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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs10508
-|library_id_phase_based=1:CNhs10508
+|library_id_phase_based=2:CNhs10508
 |name=adrenal gland, adult
 |namespace=FANTOM5
@@ Line 51: / Line 51: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10508,LSID648,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0.0601091194109999,0,0.0697128539903382,0.125434928380337,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.049207324636011,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0864261836612438,0,0,0,0.0601091194109999,0,0.00184661424875375,0.0191946655463514,-0.0982568009196536,0.406764345460973,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0.528283328328409,0.241100675518586,0.0468956778560972,0,0,0,0,-0.0428469550828748,0,0.0392811494250319,0,0,0,0.0475182644990573,-0.034038867230932,0.63398355677566,-0.00653814929135355,0.202425254301389,0.0634128640266047,0,0.0775878403842942,0.0601091194109999,0,0.0077421420536071,0.16779793546931,-0.107619465261827,-0.0187224754289076,0,0,0,0,0.0300545597055,0,-0.0797682383444224,-0.25794531413401,-0.133369419201212,0,0,0,0,0

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FF:49-24D7: Difference between revisions

From FANTOM5_SSTAR

Revision as of 11:10, 28 November 2014

CNhs10508

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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