FF:595-22B6: Difference between revisions

Latest revision as of 19:18, 4 June 2020

Name:	mammary gland, adult lactating day02
Species:	Mouse (Mus musculus)
Library ID:	CNhs10480
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	mammary gland
dev stage	2 days lactation 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		SAMD00005704

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10480		CAGE		DRX009044		DRR009918

Accession ID Mm9

Library id		BAM		CTSS
CNhs10480		DRZ001343		DRZ002726

Accession ID Mm10

Library id		BAM		CTSS
CNhs10480		DRZ012693		DRZ014076

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

CNhs10480

0	0
1	0
10	0
100	0
1000	0.2
1001	0.0326
1002	-0.0577
1003	0.16
1004	0
1005	0
1006	0
1007	-0.00387
1008	0
1009	0.0377
101	1.64964e-4
1010	0
1011	-3.231029e-4
1012	0
1013	0.555
1014	-0.0874
1015	-0.221
1016	-0.206
1017	0
1018	0.181
1019	1.954
102	0
1020	0
1021	0.0648
1022	0.394
1023	0
1024	0.0865
1025	0
1026	0
1027	0
1028	0
1029	-0.0455
103	0
1030	0
1031	-0.424
1032	0.0723
1033	0
1034	0
1035	0
1036	-0.0646
1037	0
1038	-0.14
1039	0.122
104	0
1040	-0.121
1041	1.015

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: CNhs10480

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00288
MA0003.1	MA0003.1	0.293
MA0004.1	MA0004.1	0.751
MA0006.1	MA0006.1	0.127
MA0007.1	MA0007.1	0.274
MA0009.1	MA0009.1	0.433
MA0014.1	MA0014.1	0.393
MA0017.1	MA0017.1	0.219
MA0018.2	MA0018.2	0.0268
MA0019.1	MA0019.1	0.822
MA0024.1	MA0024.1	0.0162
MA0025.1	MA0025.1	0.3
MA0027.1	MA0027.1	0.406
MA0028.1	MA0028.1	0.758
MA0029.1	MA0029.1	0.243
MA0030.1	MA0030.1	0.0433
MA0031.1	MA0031.1	0.711
MA0035.2	MA0035.2	0.0137
MA0038.1	MA0038.1	0.58
MA0039.2	MA0039.2	0.00679
MA0040.1	MA0040.1	0.0183
MA0041.1	MA0041.1	0.225
MA0042.1	MA0042.1	0.132
MA0043.1	MA0043.1	0.0897
MA0046.1	MA0046.1	1.22044e-12
MA0047.2	MA0047.2	0.807
MA0048.1	MA0048.1	0.952
MA0050.1	MA0050.1	6.18869e-4
MA0051.1	MA0051.1	3.86315e-4
MA0052.1	MA0052.1	0.634
MA0055.1	MA0055.1	0.505
MA0057.1	MA0057.1	0.158
MA0058.1	MA0058.1	0.591
MA0059.1	MA0059.1	0.23
MA0060.1	MA0060.1	0.204
MA0061.1	MA0061.1	0.264
MA0062.2	MA0062.2	0.488
MA0065.2	MA0065.2	0.00183
MA0066.1	MA0066.1	0.588
MA0067.1	MA0067.1	0.654
MA0068.1	MA0068.1	0.705
MA0069.1	MA0069.1	0.379
MA0070.1	MA0070.1	0.465
MA0071.1	MA0071.1	0.961
MA0072.1	MA0072.1	0.667
MA0073.1	MA0073.1	0.79
MA0074.1	MA0074.1	0.646
MA0076.1	MA0076.1	0.741
MA0077.1	MA0077.1	0.241
MA0078.1	MA0078.1	0.489
MA0079.2	MA0079.2	0.972
MA0080.2	MA0080.2	9.24739e-4
MA0081.1	MA0081.1	0.123
MA0083.1	MA0083.1	0.814
MA0084.1	MA0084.1	0.71
MA0087.1	MA0087.1	0.399
MA0088.1	MA0088.1	0.396
MA0090.1	MA0090.1	0.985
MA0091.1	MA0091.1	0.382
MA0092.1	MA0092.1	0.261
MA0093.1	MA0093.1	0.659
MA0099.2	MA0099.2	0.319
MA0100.1	MA0100.1	0.215
MA0101.1	MA0101.1	0.205
MA0102.2	MA0102.2	0.321
MA0103.1	MA0103.1	1.51835e-4
MA0104.2	MA0104.2	0.951
MA0105.1	MA0105.1	0.376
MA0106.1	MA0106.1	0.296
MA0107.1	MA0107.1	0.119
MA0108.2	MA0108.2	0.0942
MA0111.1	MA0111.1	0.614
MA0112.2	MA0112.2	1.14672e-4
MA0113.1	MA0113.1	0.0406
MA0114.1	MA0114.1	0.104
MA0115.1	MA0115.1	0.548
MA0116.1	MA0116.1	0.0993
MA0117.1	MA0117.1	0.341
MA0119.1	MA0119.1	0.143
MA0122.1	MA0122.1	0.9
MA0124.1	MA0124.1	0.226
MA0125.1	MA0125.1	0.0989
MA0131.1	MA0131.1	0.459
MA0135.1	MA0135.1	0.833
MA0136.1	MA0136.1	0.0145
MA0137.2	MA0137.2	8.6792e-5
MA0138.2	MA0138.2	0.578
MA0139.1	MA0139.1	0.372
MA0140.1	MA0140.1	0.0349
MA0141.1	MA0141.1	0.521
MA0142.1	MA0142.1	0.487
MA0143.1	MA0143.1	0.212
MA0144.1	MA0144.1	1.20247e-4
MA0145.1	MA0145.1	0.0563
MA0146.1	MA0146.1	0.0101
MA0147.1	MA0147.1	0.692
MA0148.1	MA0148.1	0.691
MA0149.1	MA0149.1	0.186
MA0150.1	MA0150.1	0.0863
MA0152.1	MA0152.1	0.218
MA0153.1	MA0153.1	6.99199e-7
MA0154.1	MA0154.1	0.0509
MA0155.1	MA0155.1	0.596
MA0156.1	MA0156.1	0.0184
MA0157.1	MA0157.1	0.152
MA0159.1	MA0159.1	0.0385
MA0160.1	MA0160.1	0.538
MA0162.1	MA0162.1	0.248
MA0163.1	MA0163.1	0.0489
MA0164.1	MA0164.1	0.273
MA0258.1	MA0258.1	0.0149
MA0259.1	MA0259.1	0.688

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: CNhs10480

Novel motif	Logo	P-value
1	1	0.202
10	10	0.0878
100	100	0.791
101	101	0.915
102	102	0.434
103	103	0.0713
104	104	0.739
105	105	0.374
106	106	0.0163
107	107	0.199
108	108	0.385
109	109	0.0188
11	11	0.0507
110	110	0.0978
111	111	0.0235
112	112	0.166
113	113	0.976
114	114	0.36
115	115	0.14
116	116	0.405
117	117	0.126
118	118	0.976
119	119	0.0348
12	12	0.451
120	120	0.665
121	121	0.638
122	122	0.0874
123	123	0.441
124	124	0.666
125	125	0.0566
126	126	0.641
127	127	0.253
128	128	0.0114
129	129	0.137
13	13	2.7623e-5
130	130	0.839
131	131	0.142
132	132	0.752
133	133	0.362
134	134	0.38
135	135	0.119
136	136	0.685
137	137	0.0959
138	138	0.652
139	139	0.0759
14	14	0.617
140	140	0.593
141	141	0.222
142	142	0.406
143	143	0.696
144	144	0.0532
145	145	0.0302
146	146	0.285
147	147	0.331
148	148	0.461
149	149	0.148
15	15	0.182
150	150	0.151
151	151	0.141
152	152	0.0303
153	153	0.469
154	154	0.865
155	155	0.814
156	156	0.349
157	157	0.388
158	158	0.302
159	159	0.557
160	160	0.283
161	161	0.52
162	162	0.525
163	163	0.403
164	164	0.153
165	165	0.23
166	166	0.791
167	167	0.414
168	168	0.735
169	169	0.00115
17	17	0.0251
18	18	0.915
19	19	0.105
2	2	0.425
20	20	0.435
21	21	0.792
22	22	0.139
23	23	0.33
24	24	0.0169
25	25	0.539
26	26	0.0321
27	27	0.597
28	28	0.477
29	29	0.221
3	3	0.17
30	30	0.871
31	31	0.736
32	32	0.714
33	33	0.366
34	34	0.93
35	35	0.815
36	36	0.303
37	37	0.041
38	38	0.15
39	39	0.178
4	4	0.955
40	40	0.466
41	41	0.954
42	42	0.184
43	43	0.183
44	44	0.228
45	45	0.759
46	46	0.126
47	47	0.0886
48	48	0.128
49	49	0.214
5	5	0.133
50	50	0.633
51	51	0.65
52	52	0.184
53	53	0.993
54	54	0.869
55	55	0.352
56	56	0.331
57	57	0.415
58	58	0.242
59	59	0.429
6	6	0.345
60	60	0.0585
61	61	0.167
62	62	0.135
63	63	0.0252
64	64	0.612
65	65	0.189
66	66	0.927
67	67	0.933
68	68	0.025
69	69	0.626
7	7	0.0458
70	70	0.00253
71	71	0.0487
72	72	0.304
73	73	0.0253
74	74	0.981
75	75	0.187
76	76	0.735
77	77	0.282
78	78	0.0143
79	79	0.937
8	8	0.283
80	80	0.616
81	81	0.41
82	82	0.569
83	83	0.84
84	84	0.794
85	85	0.0616
86	86	0.205
87	87	0.153
88	88	0.219
89	89	0.15
9	9	0.846
90	90	0.904
91	91	0.317
92	92	0.198
93	93	0.835
94	94	0.958
95	95	0.272
96	96	0.827
97	97	0.915
98	98	0.145
99	99	0.351

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: CNhs10480

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011390 mouse mammary gland- adult lactating day02 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)
0001911 (mammary gland)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002365 (exocrine gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0002330 (exocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000324 (mouse lactating sample)
0011390 (mouse mammary gland- adult lactating day02 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:0006601 (presumptive ectoderm)
UBERON:0008425 (mammary ridge)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0000483,UBERON:0002530,UBERON:0001911,UBERON:0000479,UBERON:0004121,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005153,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0002365,UBERON:0005085,UBERON:0001048,UBERON:0006598,UBERON:0005157,UBERON:0002532,UBERON:0000924,UBERON:0003100,UBERON:0002330,UBERON:0000076,UBERON:0006601,UBERON:0005333,UBERON:0008425,UBERON:0005311
+|DRA_sample_Accession=CAGE@SAMD00005704
+|accession_numbers=CAGE;DRX009044;DRR009918;DRZ001343;DRZ002726;DRZ012693;DRZ014076
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001911,UBERON:0000479,UBERON:0004121,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002365,UBERON:0002530,UBERON:0010317,UBERON:0003100,UBERON:0002330
 |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:0000324,FF:0011390
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:103264213..103264233,+!p1@Elf5!3.03!1065.16!Elf5;;chr2:103264245..103264268,+!p2@Elf5!2.66!460.29!Elf5;;chr13:72766250..72766273,+!p1@Irx2!2.49!467.67!Irx2;;chr2:103264277..103264292,+!p3@Elf5!2.40!248.83!Elf5;;chr5:144951153..144951203,+!p1@Bhlha15!1.95!125.40!Bhlha15;;chr13:72766279..72766296,+!p2@Irx2!1.87!107.20!Irx2;;chr2:103143336..103143367,-!p1@Ehf!1.84!107.20!Ehf;;chr11:5420655..5420659,+!p3@Xbp1!1.78!59.01!Xbp1;;chr13:72101178..72101203,-!p1@Irx1!1.73!79.67!Irx1;;chr15:97738692..97738747,-!p1@Vdr!1.71!262.11!Vdr;;chr15:78994907..78994926,-!p1@Sox10!1.66!111.63!Sox10;;chr2:9800207..9800234,-!p1@Gata3!1.59!112.12!Gata3;;chr2:172375081..172375105,+!p1@Tfap2c!1.58!37.37!Tfap2c;;chr13:72766234..72766243,+!p3@Irx2!1.57!36.39!Irx2;;chr15:97741053..97741072,-!p2@Vdr!1.55!34.42!Vdr;;chr13:72101161..72101177,-!p2@Irx1!1.51!42.78!Irx1;;chr11:90250944..90250982,-!p2@Hlf!1.48!47.70!Hlf;;chr11:5420954..5420969,+!p2@Xbp1!1.39!282.76!Xbp1;;chr13:40826961..40827001,-!p4@Tfap2a!1.35!21.64!Tfap2a;;chr11:100720767..100720797,+!p4@Stat5a!1.33!20.16!Stat5a;;chr11:90250894..90250916,-!p5@Hlf!1.33!20.16!Hlf;;chr11:34108085..34108092,-!p1@Foxi1!1.32!19.67!Foxi1;;chr11:60023912..60023930,-!p1@Srebf1!1.29!437.67!Srebf1;;chr7:87170879..87170914,+!p2@Zfp710!1.18!32.95!Zfp710;;chr8:94881733..94881790,+!p1@Irx5!1.18!27.54!Irx5;;chr13:40829137..40829205,-!p1@Tfap2a!1.14!14.26!Tfap2a;;chr17:14011485..14011507,+!p2@Mllt4!1.14!12.79!Mllt4;;chr12:25257141..25257173,+!p1@Grhl1!1.11!24.59!Grhl1;;chr11:90252223..90252240,-!p1@Hlf!1.10!96.39!Hlf;;chr8:94325321..94325366,-!p1@Irx3!1.10!28.52!Irx3;;chr9:69137716..69137744,+!p1@Rora!1.08!69.34!Rora;;chr13:72101141..72101158,-!p3@Irx1!1.08!13.77!Irx1;;chr2:103143315..103143328,-!p2@Ehf!1.07!10.82!Ehf;;chr4:119406412..119406439,+!p2@Hivep3!1.06!20.65!Hivep3;;chr12:25257265..25257294,+!p2@Grhl1!1.05!10.33!Grhl1;;chr15:50721515..50721540,-!p3@Trps1!1.03!29.01!Trps1;;chr15:50721211..50721234,-!p6@Trps1!1.01!15.24!Trps1;;chr2:173044380..173044432,-!p1@Zbp1!1.00!21.64!Zbp1;;chr8:112603658..112603674,+!p2@Zfp612!1.00!16.72!Zfp612;;chr11:11586218..11586285,+!p1@Ikzf1!0.99!28.52!Ikzf1;;chr9:31720843..31720888,-!p1@Barx2!0.99!9.84!Barx2;;chr2:103264977..103264986,+!p6@Elf5!0.99!8.85!Elf5;;chr11:100720806..100720820,+!p6@Stat5a!0.97!8.36!Stat5a;;chr4:119406389..119406411,+!p1@Hivep3!0.96!40.82!Hivep3;;chr15:97741033..97741048,-!p3@Vdr!0.95!7.87!Vdr;;chr1:39250584..39250643,+!p1@Npas2!0.93!39.34!Npas2;;chr15:50721640..50721654,-!p7@Trps1!0.90!11.31!Trps1;;chr13:40825465..40825469,-!p2@Tfap2a!0.90!6.88!Tfap2a;;chr4:149943593..149943605,+!p5@Rere!0.89!12.29!Rere;;chr9:69137672..69137702,+!p2@Rora!0.87!29.01!Rora;;chr11:90251852..90251855,-!p4@Hlf!0.87!7.87!Hlf;;chr11:100721761..100721851,+!p1@Stat5a!0.85!47.21!Stat5a;;chr8:94325814..94325839,-!p2@Irx3!0.85!13.28!Irx3;;chr9:51021788..51021802,+!p1@Pou2af1!0.85!7.38!Pou2af1;;chr15:50721503..50721514,-!p15@Trps1!0.84!7.38!Trps1;;chr15:50714356..50714368,-!p14@Trps1!0.84!5.90!Trps1;;chr6:115372058..115372085,+!p3@Pparg!0.84!5.90!Pparg;;chr10:5734677..5734702,-!p4@Esr1!0.84!5.90!Esr1;;chr1:38721792..38721845,-!p1@Aff3!0.83!7.38!Aff3;;chr13:44825008..44825066,+!p5@Jarid2!0.81!11.31!Jarid2;;chr11:90250999..90251013,-!p8@Hlf!0.81!5.41!Hlf;;chr1:36364590..36364608,+!p1@Arid5a!0.79!57.54!Arid5a;;chr6:133986088..133986122,+!p4@Etv6!0.79!23.60!Etv6;;chr17:28369739..28369774,+!p2@Ppard!0.79!17.21!Ppard;;chr12:25257176..25257190,+!p3@Grhl1!0.79!5.90!Grhl1;;chr7:148452314..148452329,-!p1@Irf7!0.78!37.87!Irf7;;chr6:72849280..72849297,-!p6@Kcmf1!0.78!10.33!Kcmf1;;chr7:51787434..51787448,-!p1@Spib!0.78!7.38!Spib;;chr16:25801993..25802014,+!p1@Trp63!0.77!4.92!Trp63;;chr2:172375136..172375149,+!p2@Tfap2c!0.77!4.92!Tfap2c;;chr2:103264952..103264963,+!p7@Elf5!0.77!4.92!Elf5;;chr18:39648811..39648818,-!p4@Nr3c1!0.76!8.85!Nr3c1;;chr14:79915425..79915501,+!p1@Elf1!0.74!44.75!Elf1;;chr19:55816770..55816793,+!p2@Tcf7l2!0.74!43.28!Tcf7l2;;chr15:50721239..50721260,-!p9@Trps1!0.73!7.87!Trps1;;chr15:50721588..50721610,-!p1@Trps1!0.72!48.19!Trps1;;chr10:5734525..5734569,-!p3@Esr1!0.72!7.38!Esr1;;chr13:30841099..30841116,+!p1@Irf4!0.71!6.88!Irf4;;chr13:37918486..37918575,+!p2@Rreb1!0.70!28.52!Rreb1;;chr10:128082840..128082872,-!p1@Ikzf4!0.70!4.92!Ikzf4;;chr4:82151653..82151706,-!p2@Nfib!0.69!125.89!Nfib;;chr19:5560600..5560617,-!p1@Ovol1!0.69!4.92!Ovol1;;chr13:40824310..40824314,-!p6@Tfap2a!0.69!3.93!Tfap2a;;chr15:102828658..102828678,+!p1@Hoxc6!0.69!3.93!Hoxc6;;chr10:5636354..5636373,-!p2@Esr1!0.69!3.93!Esr1;;chr19:55816414..55816425,+!p4@Tcf7l2!0.68!22.62!Tcf7l2;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.68!16.72!Ppp1r13l;;chr11:11585678..11585745,+!p5@Ikzf1!0.68!5.90!Ikzf1;;chr2:74549968..74549996,+!p1@Hoxd3!0.68!4.92!Hoxd3;;chr19:55816300..55816332,+!p1@Tcf7l2!0.67!198.18!Tcf7l2;;chr18:75979866..75979890,+!p3@Zbtb7c!0.67!8.36!Zbtb7c;;chr11:106128936..106128955,-!p4@Smarcd2!0.67!4.43!Smarcd2;;chr15:50721942..50721987,-!p13@Trps1!0.67!4.43!Trps1;;chr6:90412582..90412601,+!p1@Klf15!0.66!19.18!Klf15;;chr5:135582751..135582788,+!p1@Mlxipl!0.66!16.23!Mlxipl;;chr2:151969288..151969294,+!p1@Tcf15!0.66!5.90!Tcf15;;chr7:20162663..20162678,+!p1@Zfp296!0.66!4.92!Zfp296;;chr17:87153240..87153254,+!p1@Epas1!0.65!80.16!Epas1;;chr3:94176733..94176794,+!p1@Rorc!0.65!31.47!Rorc;;chr1:19199021..19199048,+!p8@Tfap2b!0.65!3.44!Tfap2b;;chr8:94881639..94881650,+!p5@Irx5!0.65!3.44!Irx5;;chr8:94881686..94881700,+!p4@Irx5!0.65!3.44!Irx5;;chr9:31720903..31720918,-!p2@Barx2!0.65!3.44!Barx2;;chr5:104121453..104121479,+!p4@Aff1!0.64!17.70!Aff1;;chr12:37835141..37835194,+!p1@Meox2!0.64!11.80!Meox2;;chr10:5636374..5636421,-!p1@Esr1!0.64!4.43!Esr1;;chr11:5420973..5420992,+!p1@Xbp1!0.63!406.20!Xbp1;;chr6:133985839..133985915,+!p1@Etv6!0.63!65.90!Etv6;;chr4:148275237..148275311,+!p2@Casz1!0.63!15.74!Casz1;;chr3:89197057..89197114,-!p1@Zbtb7b!0.63!12.79!Zbtb7b;;chr6:51382677..51382783,+!p1@Nfe2l3!0.63!9.34!Nfe2l3;;chr15:37162796..37162828,+!p1@Grhl2!0.63!5.90!Grhl2;;chr12:113916993..113917009,+!p2@Zbtb42!0.62!5.90!Zbtb42;;chr2:173044357..173044377,-!p2@Zbp1!0.62!4.92!Zbp1;;chr2:91864661..91864686,-!p1@Creb3l1!0.61!80.16!Creb3l1;;chr7:35904304..35904320,+!p1@Cebpa!0.61!76.22!Cebpa;;chr19:25746898..25746910,+!p1@Dmrt2!0.61!4.92!Dmrt2;;chr6:90412556..90412581,+!p3@Klf15!0.60!7.38!Klf15;;chr6:90412608..90412630,+!p2@Klf15!0.60!6.88!Klf15;;chr4:44723520..44723544,-!p2@Pax5!0.60!2.95!Pax5;;chr2:74536026..74536039,+!p1@Hoxd9!0.60!2.95!Hoxd9;;chr2:9809357..9809371,-!p2@Gata3!0.60!2.95!Gata3;;chr11:100721640..100721658,+!p2@Stat5a!0.60!2.95!Stat5a;;chr11:60034039..60034050,-!p4@Srebf1!0.60!2.95!Srebf1;;chr15:37163124..37163153,+!p3@Grhl2!0.60!2.95!Grhl2;;chr1:137155026..137155042,-!p1@Elf3!0.58!19.67!Elf3;;chr6:99216488..99216534,-!p2@Foxp1!0.58!9.34!Foxp1;;chr13:31898729..31898761,+!p1@Foxc1!0.58!7.87!Foxc1;;chr8:94325847..94325869,-!p3@Irx3!0.58!4.92!Irx3;;chr14:22808697..22808715,-!p4@Zfp503!0.58!3.44!Zfp503;;chr1:52176406..52176433,+!p2@Stat1!0.57!7.87!Stat1;;chr11:121380640..121380655,-!p1@Zfp750!0.57!4.92!Zfp750;;chr6:52664406..52664434,+!p3@Tax1bp1!0.57!3.44!Tax1bp1;;chr16:55822241..55822258,-!p1@Nfkbiz!0.56!102.29!Nfkbiz;;chr11:60034052..60034134,-!p2@Srebf1!0.56!77.21!Srebf1;;chr1:194979315..194979359,+!p1@Irf6!0.55!19.18!Irf6;;chr16:92826249..92826325,-!p1@Runx1!0.55!7.38!Runx1;;chr16:15887371..15887385,+!p1@Cebpd!0.54!107.20!Cebpd;;chr7:20408047..20408125,-!p1@Bcl3!0.54!35.90!Bcl3;;chr17:87153440..87153451,+!p4@Epas1!0.54!5.90!Epas1;;chr11:60036258..60036276,-!p3@Srebf1!0.54!4.92!Srebf1;;chr8:94325486..94325510,-!p4@Irx3!0.54!3.44!Irx3;;chr11:98636373..98636387,-!p5@Nr1d1!0.54!2.95!Nr1d1;;chr11:98407234..98407259,-!p2@Ikzf3!0.54!2.46!Ikzf3;;chr11:90252071..90252093,-!p7@Hlf!0.54!2.46!Hlf;;chr10:5734660..5734670,-!p7@Esr1!0.54!2.46!Esr1;;chr1:169548377..169548430,+!p1@Rxrg!0.54!2.46!Rxrg;;chr2:172376261..172376267,+!p4@Tfap2c!0.54!2.46!Tfap2c;;chr6:115372099..115372121,+!p5@Pparg!0.54!2.46!Pparg;;chr5:144951136..144951139,+!p2@Bhlha15!0.54!2.46!Bhlha15;;chr4:44723633..44723646,-!p3@Pax5!0.54!2.46!Pax5;;chr4:44723559..44723593,-!p1@Pax5!0.54!2.46!Pax5;;chr15:37162834..37162849,+!p2@Grhl2!0.53!2.95!Grhl2;;chr1:52065508..52065522,+!p2@Stat4!0.53!2.95!Stat4;;chr18:39649430..39649522,-!p2@Nr3c1!0.52!29.01!Nr3c1;;chr3:95238432..95238455,+!p2@Arnt!0.52!16.72!Arnt;;chr8:112603610..112603656,+!p1@Zfp612!0.52!13.28!Zfp612;;chr3:99057269..99057306,+!p1@Tbx15!0.52!2.95!Tbx15;;chr3:130815703..130815721,+!p2@Lef1!0.52!2.95!Lef1;;chr12:37835203..37835218,+!p3@Meox2!0.52!2.95!Meox2;;chr12:86939657..86939685,+!p6@Jdp2!0.52!2.95!Jdp2;;chr12:25780945..25780961,-!p1@Id2!0.51!495.21!Id2;;chr11:100948597..100948637,+!p1@Mlx!0.51!69.34!Mlx;;chr9:63605740..63605771,-!p1@Smad3!0.51!42.29!Smad3;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.51!7.87!Tfcp2l1;;chr15:50720601..50720630,-!p2@Trps1!0.51!6.39!Trps1;;chr8:94325273..94325288,-!p5@Irx3!0.51!2.95!Irx3;;chr16:92697560..92697592,-!p2@Runx1!0.50!17.70!Runx1;;chr19:55816546..55816556,+!p3@Tcf7l2!0.50!10.33!Tcf7l2;;chr4:82151583..82151594,-!p6@Nfib!0.50!4.92!Nfib;;chr5:92391466..92391471,+!p2@Thap6!0.50!3.44!Thap6;;chr19:23215509..23215523,+!p4@Klf9!0.50!2.95!Klf9;;chr15:50721616..50721632,-!p4@Trps1!0.49!6.88!Trps1;;chr11:100683839..100683890,-!p2@Stat5b!0.49!5.90!Stat5b;;chr6:133985790..133985801,+!p8@Etv6!0.49!2.95!Etv6;;chr10:80889867..80889924,-!p1@Nfic!0.48!76.72!Nfic;;chr14:56223010..56223067,+!p1@Irf9!0.48!21.15!Irf9;;chr4:97444012..97444045,+!p4@Nfia!0.48!20.16!Nfia;;chr17:15701263..15701277,-!p2@Prdm9!0.48!5.90!Prdm9;;chr6:146744595..146744613,+!p2@Arntl2!0.48!3.93!Arntl2;;chr8:74474953..74475029,+!p1@Zfp961!0.47!43.77!Zfp961;;chr11:98636531..98636559,-!p1@Nr1d1!0.47!14.75!Nr1d1;;chr6:29476690..29476724,+!p1@Irf5!0.47!11.80!Irf5;;chr3:89197216..89197258,-!p3@Zbtb7b!0.47!4.92!Zbtb7b;;chr11:121380594..121380609,-!p2@Zfp750!0.47!3.93!Zfp750;;chr11:100721732..100721742,+!p3@Stat5a!0.47!1.97!Stat5a;;chr11:90249521..90249551,-!p3@Hlf!0.47!1.97!Hlf;;chr11:9025196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5;;chr6:28348078..28348109,-!p5@Zfp800!0.17!0.49!Zfp800;;chr13:67627072..67627115,-!p1@Zfp58!0.16!24.59!Zfp87;;chr9:19426523..19426584,+!p1@Zfp317!0.16!18.69!Zfp317;;chr7:134488857..134488914,-!p1@Zfp768!0.16!16.72!Zfp768;;chr9:22112085..22112138,-!p1@Zfp810!0.16!15.74!Zfp810;;chr5:108697916..108697943,+!p2@Dr1!0.16!14.75!Dr1;;chr17:24806629..24806672,+!p1@Zfp598!0.16!13.77!Zfp598;;chr6:72849946..72849979,-!p2@Kcmf1!0.16!6.88!Kcmf1;;chr2:168415815..168415872,-!p1@Nfatc2!0.16!6.39!Nfatc2;;chrX:7339938..7339963,+!p1@Tfe3!0.16!5.90!Tfe3;;chr10:127707562..127707597,+!p2@Stat2!0.16!5.90!Stat2;;chr10:114821572..114821618,-!p3@Thap2!0.16!4.92!Thap2;;chr17:15701286..15701323,-!p1@Prdm9!0.16!4.43!Prdm9;;chr16:42907554..42907591,+!p5@Zbtb20!0.16!2.46!Zbtb20;;chr2:169458496..169458516,+!p6@Tshz2!0.16!1.97!Tshz2;;chr5:76733981..76734018,-!p3@Clock!0.16!1.97!Clock;;chr13:5860740..5860747,+!p4@Klf6!0.16!1.97!Klf6;;chr12:72117645..72117677,+!p3@Arid4a!0.16!1.97!Arid4a;;chr11:102180407..102180419,-!p6@Ubtf!0.16!1.97!Ubtf;;chr10:107769229..107769238,+!p3@Pawr!0.16!0.98!Pawr;;chr1:165243653..165243664,-!p4@Prrx1!0.16!0.98!Prrx1;;chr4:63071717..63071736,-!p4@Akna!0.16!0.98!Akna;;chr13:37870253..37870272,+!p13@Rreb1!0.16!0.98!Rreb1;;chr14:104867201..104867258,-!p1@Pou4f1!0.16!0.98!Pou4f1;;chr12:77470718..77470752,-!p4@Zbtb25!0.16!0.98!Zbtb25;;chr14:67853457..67853482,+!p2@Ebf2!0.16!0.98!Ebf2;;chr7:52963269..52963305,+!p4@Dbp!0.16!0.98!Dbp;;chr7:19895384..19895399,-!p2@Fosb!0.16!0.98!Fosb;;chr17:13897509..13897607,+!p1@Mllt4!0.15!36.88!Mllt4;;chr5:25004592..25004630,-!p2@Mll3!0.15!25.08!Mll3;;chr9:30838206..30838285,+!p2@Zbtb44!0.15!15.74!Zbtb44;;chr2:32218712..32218782,+!p2@Ciz1!0.15!12.29!Ciz1;;chr10:107769168..107769215,+!p1@Pawr!0.15!12.29!Pawr;;chr7:17200019..17200060,-!p4@Grlf1!0.15!4.92!Grlf1;;chr7:6336020..6336068,+!p1@Zfp28!0.15!4.92!Zfp28;;chr14:79881330..79881415,+!p3@Elf1!0.15!3.44!Elf1;;chr15:57526206..57526241,+!p2@Zhx2!0.15!3.44!Zhx2;;chr11:53164533..53164548,+!p4@Aff4!0.15!2.95!Aff4;;chr5:65194789..65194800,+!p7@Klf3!0.15!2.46!Klf3;;chr9:63605691..63605705,-!p3@Smad3!0.15!2.46!Smad3;;chr3:152059025..152059046,+!p4@Gm8261,p4@Zzz3!0.15!2.46!Zzz3;;chr11:23977565..23977612,+!p5@Bcl11a!0.15!1.97!Bcl11a;;chr15:102076652..102076679,-!p4@Rarg!0.15!1.48!Rarg;;chr7:135020469..135020485,+!p4@Zfp646!0.15!1.48!Zfp646;;chr5:110539135..110539159,+!p4@Zfp605!0.15!0.98!Zfp605;;chr6:115311030..115311065,+!p4@Pparg!0.15!0.98!Pparg;;chr19:53385060..53385069,+!p6@Mxi1!0.15!0.98!Mxi1;;chr13:96094769..96094829,+!p4@Zbed3!0.15!0.98!Zbed3;;chr12:109241728..109241781,-!p2@Bcl11b!0.15!0.49!Bcl11b;;chr7:51809271..51809325,-!p1@Nr1h2!0.14!69.34!Nr1h2;;chr8:47825107..47825145,+!p1@Irf2!0.14!49.67!Irf2;;chr7:71083748..71083819,-!p1@Klf13!0.14!41.31!Klf13;;chr11:100800671..100800770,-!p1@Stat3!0.14!39.83!Stat3;;chr12:110031495..110031585,+!p1@Yy1!0.14!31.96!Yy1;;chr9:113840256..113840306,+!p1@Ubp1!0.14!26.56!Ubp1;;chr6:118429255..118429336,-!p1@Zfp9!0.14!19.67!Zfp9;;chr7:148513456..148513506,-!p1@Deaf1!0.14!18.69!Deaf1;;chr1:181476358..181476391,-!p1@Tfb2m!0.14!18.69!Tfb2m;;chr8:72498160..72498214,-!p1@Gatad2a!0.14!15.74!Gatad2a;;chr17:84105551..84105600,+!p1@Mta3!0.14!13.28!Mta3;;chr14:31832311..31832343,+!p1@Pbrm1!0.14!11.31!Pbrm1;;chr12:84828663..84828679,-!p1@Dpf3!0.14!8.85!Dpf3;;chr2:83484634..83484647,+!p4@Zc3h15!0.14!7.87!Zc3h15;;chr8:79426176..79426275,+!p1@Nr3c2!0.14!5.41!Nr3c2;;chr8:124900576..124900601,+!p2@Zc3h18!0.14!4.92!Zc3h18;;chr3:95021663..95021687,-!p3@Gabpb2!0.14!3.44!Gabpb2;;chr1:52176378..52176401,+!p3@Stat1!0.14!2.95!Stat1;;chr1:181476392..181476407,-!p2@Tfb2m!0.14!2.46!Tfb2m;;chr6:35083731..35083742,-!p2@Cnot4!0.14!2.46!Cnot4;;chr7:134550321..134550345,-!p2@Zfp764!0.14!1.97!Zfp764;;chr2:56976543..56976558,-!p2@Nr4a2!0.14!1.97!Nr4a2;;chr14:55711114..55711159,-!p2@Zfhx2!0.14!1.97!Zfhx2;;chr1:4486481..4486501,-!p2@Sox17!0.14!0.98!Sox17;;chr6:52163319..52163342,-!p1@Hoxa3!0.14!0.98!Hoxa3;;chr16:3872255..3872283,-!p4@Zfp597!0.14!0.98!Zfp597;;chr8:111228161..111228183,+!p@chr8:111228161..111228183,+!0.14!0.98!Zfhx3;;chr10:22451765..22451795,-!p6@Tbpl1!0.14!0.98!Tbpl1;;chr11:62271274..62271337,-!p4@Ncor1!0.14!0.98!Ncor1;;chr1:138846047..138846074,-!p5@Nr5a2!0.14!0.49!Nr5a2;;chr15:36937029..36937108,-!p1@Gm10193,p1@Zfp706!0.13!149.99!Zfp706;;chr2:168055853..168055886,-!p1@Adnp,p1@Dpm1!0.13!82.12!Adnp;;chr11:121121297..121121369,+!p1@Foxk2!0.13!70.81!Foxk2;;chr12:117285924..117286018,+!p1@Zfp386!0.13!34.42!Zfp386;;chr7:52253030..52253070,+!p1@Irf3!0.13!26.56!Irf3;;chr7:13420322..13420401,+!p1@Zfp110!0.13!23.60!Zfp110;;chr3:19957802..19957857,+!p1@Hltf!0.13!21.15!Hltf;;chr2:160192793..160192809,-!p1@Mafb!0.13!17.70!Mafb;;chr11:83943084..83943122,-!p1@Tada2a!0.13!17.70!Tada2a;;chr8:27268658..27268724,+!p1@Thap1!0.13!13.77!Thap1;;chr8:123260252..123260264,+!p1@Irf8!0.13!7.87!Irf8;;chr11:100800771..100800798,-!p2@Stat3!0.13!7.38!Stat3;;chr2:162880387..162880413,+!p1@Mybl2!0.13!6.88!Mybl2;;chr18:83084030..83084056,+!p1@Zfp516!0.13!5.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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0008425,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011390
 |is_obsolete=
+|library_id=CNhs10480
+|library_id_phase_based=2:CNhs10480
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;595
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;595
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/mammary%2520gland%252c%2520adult%2520lactating%2520day02.CNhs10480.595-22B6.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/mammary%2520gland%252c%2520adult%2520lactating%2520day02.CNhs10480.595-22B6.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/mammary%2520gland%252c%2520adult%2520lactating%2520day02.CNhs10480.595-22B6.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/mammary%2520gland%252c%2520adult%2520lactating%2520day02.CNhs10480.595-22B6.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/mammary%2520gland%252c%2520adult%2520lactating%2520day02.CNhs10480.595-22B6.mm9.nobarcode.rdna.fa.gz
 |name=mammary gland, adult lactating day02
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10480,LSID647,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0309236311712353,0,0,0.173700201812769,0,0.0252957680405283,0.273786692599345,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.105545104140655,0,0,2.14512653097121,0,0,0,0,0,0,0,0,0,0,0.495694015036884,0,0,0,0,0,-0.060603497984211,-0.0791492285386178,-0.210955233681459,-0.59058478455025,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,0.327621034364136,0,0,0,0,0,0,0,0,0,0,0.120570631752371,0.228277475603925,-0.158091042771083,0.0446242532411756,0,0,-0.0717734142081996,0.0120475462521433,0,0,0,-0.05470110331406,0.176233860923757,0.0948686069728618,0,0,0,0,0,0,-0.0628849933665826,-0.0917514740315233,-0.269803002231399,0,0,0,0,0
 |rna_box=22
 |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: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:595-22B6;search_select_hide=table117:595-22B6
 }}

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FF:595-22B6: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:18, 4 June 2020

CNhs10480

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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