FF:539-13I7: Difference between revisions

Latest revision as of 19:18, 4 June 2020

Name:	placenta, adult pregnant day10
Species:	Mouse (Mus musculus)
Library ID:	CNhs10472
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	placenta
dev stage	10 days pregnant 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		SAMD00005919

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10472		CAGE		DRX009074		DRR009948

Accession ID Mm9

Library id		BAM		CTSS
CNhs10472		DRZ001373		DRZ002756

Accession ID Mm10

Library id		BAM		CTSS
CNhs10472		DRZ012723		DRZ014106

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

CNhs10472

0	0
1	0
10	0
100	0
1000	-0.0258
1001	0.0641
1002	0.0147
1003	-0.175
1004	0.129
1005	0.094
1006	-0.0595
1007	0.00944
1008	0
1009	0.0343
101	0.092
1010	0
1011	-0.016
1012	0
1013	0.177
1014	0.00644
1015	-0.115
1016	-0.234
1017	0
1018	0.316
1019	0
102	0
1020	0
1021	0
1022	-0.124
1023	0
1024	0.0916
1025	0.0916
1026	0
1027	-0.048
1028	0
1029	0.105
103	0
1030	0
1031	0.0645
1032	-0.213
1033	-0.0665
1034	0
1035	0
1036	-0.0518
1037	0
1038	-0.127
1039	-0.0886
104	0
1040	0.0719
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data

TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression Analyst: Michiel de Hoon link to dataset. data

library id: CNhs10472

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0682
MA0003.1	MA0003.1	0.08
MA0004.1	MA0004.1	0.411
MA0006.1	MA0006.1	0.0393
MA0007.1	MA0007.1	0.817
MA0009.1	MA0009.1	0.5
MA0014.1	MA0014.1	0.358
MA0017.1	MA0017.1	0.0312
MA0018.2	MA0018.2	0.924
MA0019.1	MA0019.1	0.321
MA0024.1	MA0024.1	0.53
MA0025.1	MA0025.1	0.354
MA0027.1	MA0027.1	0.00607
MA0028.1	MA0028.1	0.352
MA0029.1	MA0029.1	8.2156e-6
MA0030.1	MA0030.1	0.332
MA0031.1	MA0031.1	0.0545
MA0035.2	MA0035.2	0.0476
MA0038.1	MA0038.1	0.413
MA0039.2	MA0039.2	6.56889e-5
MA0040.1	MA0040.1	0.779
MA0041.1	MA0041.1	0.45
MA0042.1	MA0042.1	0.732
MA0043.1	MA0043.1	0.425
MA0046.1	MA0046.1	0.689
MA0047.2	MA0047.2	0.593
MA0048.1	MA0048.1	0.2
MA0050.1	MA0050.1	0.021
MA0051.1	MA0051.1	0.132
MA0052.1	MA0052.1	0.00158
MA0055.1	MA0055.1	0.0294
MA0057.1	MA0057.1	0.152
MA0058.1	MA0058.1	0.16
MA0059.1	MA0059.1	0.923
MA0060.1	MA0060.1	0.171
MA0061.1	MA0061.1	0.233
MA0062.2	MA0062.2	0.0147
MA0065.2	MA0065.2	0.0543
MA0066.1	MA0066.1	0.78
MA0067.1	MA0067.1	0.632
MA0068.1	MA0068.1	0.328
MA0069.1	MA0069.1	0.509
MA0070.1	MA0070.1	0.385
MA0071.1	MA0071.1	0.922
MA0072.1	MA0072.1	0.731
MA0073.1	MA0073.1	0.378
MA0074.1	MA0074.1	0.469
MA0076.1	MA0076.1	0.531
MA0077.1	MA0077.1	0.0728
MA0078.1	MA0078.1	0.235
MA0079.2	MA0079.2	0.00481
MA0080.2	MA0080.2	3.74983e-4
MA0081.1	MA0081.1	0.596
MA0083.1	MA0083.1	0.538
MA0084.1	MA0084.1	0.126
MA0087.1	MA0087.1	0.61
MA0088.1	MA0088.1	0.19
MA0090.1	MA0090.1	0.0482
MA0091.1	MA0091.1	0.0874
MA0092.1	MA0092.1	0.626
MA0093.1	MA0093.1	0.383
MA0099.2	MA0099.2	3.74413e-30
MA0100.1	MA0100.1	0.317
MA0101.1	MA0101.1	0.052
MA0102.2	MA0102.2	0.631
MA0103.1	MA0103.1	0.881
MA0104.2	MA0104.2	0.551
MA0105.1	MA0105.1	0.687
MA0106.1	MA0106.1	0.0756
MA0107.1	MA0107.1	0.0678
MA0108.2	MA0108.2	5.07198e-5
MA0111.1	MA0111.1	0.263
MA0112.2	MA0112.2	0.0137
MA0113.1	MA0113.1	0.854
MA0114.1	MA0114.1	0.0202
MA0115.1	MA0115.1	0.0282
MA0116.1	MA0116.1	0.92
MA0117.1	MA0117.1	0.468
MA0119.1	MA0119.1	0.0618
MA0122.1	MA0122.1	0.611
MA0124.1	MA0124.1	0.137
MA0125.1	MA0125.1	0.869
MA0131.1	MA0131.1	0.933
MA0135.1	MA0135.1	0.6
MA0136.1	MA0136.1	0.00117
MA0137.2	MA0137.2	0.0457
MA0138.2	MA0138.2	0.0795
MA0139.1	MA0139.1	0.802
MA0140.1	MA0140.1	0.926
MA0141.1	MA0141.1	0.678
MA0142.1	MA0142.1	0.0535
MA0143.1	MA0143.1	0.111
MA0144.1	MA0144.1	0.00277
MA0145.1	MA0145.1	0.0334
MA0146.1	MA0146.1	0.0674
MA0147.1	MA0147.1	0.638
MA0148.1	MA0148.1	0.0791
MA0149.1	MA0149.1	0.111
MA0150.1	MA0150.1	7.12013e-4
MA0152.1	MA0152.1	0.66
MA0153.1	MA0153.1	0.297
MA0154.1	MA0154.1	0.0696
MA0155.1	MA0155.1	0.897
MA0156.1	MA0156.1	1.95255e-4
MA0157.1	MA0157.1	0.245
MA0159.1	MA0159.1	0.0517
MA0160.1	MA0160.1	0.335
MA0162.1	MA0162.1	0.701
MA0163.1	MA0163.1	0.955
MA0164.1	MA0164.1	0.0254
MA0258.1	MA0258.1	0.182
MA0259.1	MA0259.1	0.742

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: CNhs10472

Novel motif	Logo	P-value
1	1	0.603
10	10	0.693
100	100	0.718
101	101	0.134
102	102	0.133
103	103	0.552
104	104	0.732
105	105	0.405
106	106	0.0529
107	107	0.0653
108	108	0.405
109	109	0.421
11	11	0.896
110	110	0.521
111	111	0.399
112	112	0.00618
113	113	0.948
114	114	0.382
115	115	0.823
116	116	0.739
117	117	0.0766
118	118	0.756
119	119	0.101
12	12	0.877
120	120	0.964
121	121	0.192
122	122	0.631
123	123	0.0141
124	124	0.0457
125	125	0.502
126	126	0.483
127	127	0.801
128	128	0.283
129	129	0.826
13	13	0.0028
130	130	0.0439
131	131	0.921
132	132	0.704
133	133	0.437
134	134	0.283
135	135	0.147
136	136	0.0159
137	137	0.0961
138	138	0.326
139	139	0.184
14	14	0.787
140	140	0.674
141	141	0.394
142	142	0.455
143	143	0.235
144	144	0.45
145	145	0.821
146	146	0.834
147	147	0.0376
148	148	0.319
149	149	0.802
15	15	0.25
150	150	0.0885
151	151	0.957
152	152	0.00983
153	153	0.473
154	154	0.646
155	155	0.622
156	156	0.111
157	157	0.151
158	158	0.00768
159	159	0.498
160	160	0.495
161	161	0.154
162	162	0.788
163	163	0.0323
164	164	0.0201
165	165	0.838
166	166	0.735
167	167	0.0649
168	168	0.279
169	169	0.0444
17	17	0.119
18	18	0.697
19	19	0.0222
2	2	0.183
20	20	0.277
21	21	0.489
22	22	0.035
23	23	0.407
24	24	0.103
25	25	0.848
26	26	0.594
27	27	0.44
28	28	0.504
29	29	0.053
3	3	0.78
30	30	0.334
31	31	0.309
32	32	0.686
33	33	0.629
34	34	0.729
35	35	0.0281
36	36	0.473
37	37	0.0381
38	38	0.791
39	39	0.978
4	4	0.188
40	40	0.83
41	41	0.997
42	42	0.801
43	43	0.572
44	44	0.709
45	45	0.044
46	46	0.718
47	47	0.677
48	48	0.81
49	49	0.545
5	5	0.92
50	50	0.101
51	51	0.949
52	52	0.259
53	53	0.891
54	54	0.793
55	55	0.515
56	56	0.971
57	57	0.338
58	58	0.645
59	59	0.284
6	6	0.461
60	60	0.289
61	61	0.209
62	62	0.512
63	63	0.794
64	64	0.499
65	65	0.765
66	66	0.722
67	67	0.626
68	68	0.525
69	69	0.213
7	7	0.487
70	70	0.186
71	71	0.787
72	72	0.298
73	73	0.0054
74	74	0.837
75	75	0.281
76	76	0.887
77	77	0.392
78	78	0.00392
79	79	0.177
8	8	0.326
80	80	0.69
81	81	0.585
82	82	0.971
83	83	0.356
84	84	0.664
85	85	0.524
86	86	0.594
87	87	0.0803
88	88	0.537
89	89	0.619
9	9	0.61
90	90	0.198
91	91	0.195
92	92	0.713
93	93	0.619
94	94	0.0258
95	95	0.225
96	96	0.979
97	97	0.72
98	98	0.69
99	99	0.493

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: CNhs10472

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011381 mouse placenta- adult pregnant day10 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)
0001987 (placenta)
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)
0000478 (extraembryonic structure)
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)
0000317 (mouse pregnant tissue sample)
0000320 (mouse pregnant day 10 sample)
0011381 (mouse placenta- adult pregnant day10 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:0005795 (embryonic uterus)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0003124 (chorion)
UBERON:0010316 (germ layer / neural crest)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005919
+|accession_numbers=CAGE;DRX009074;DRR009948;DRZ001373;DRZ002756;DRZ012723;DRZ014106
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001987,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:0000478,UBERON:0010317,UBERON:0003100,UBERON:0000474
 |ancestors_in_cell_lineage_facet=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:57645506..57645523,-!p1@Hand1!2.53!334.17!Hand1;;chr8:59799772..59799789,+!p1@Hand2!2.48!820.41!Hand2;;chr6:52195763..52195792,-!p2@Hoxa11!2.01!101.85!Hoxa11;;chr6:52195795..52195825,-!p1@Hoxa11!1.99!96.92!Hoxa11;;chrX:98449898..98449913,+!p2@Foxo4!1.94!265.41!Foxo4;;chr6:52190668..52190682,-!p3@Hoxa10!1.88!74.63!Hoxa10;;chr2:172375081..172375105,+!p1@Tfap2c!1.84!68.29!Tfap2c;;chr7:147129712..147129774,+!p1@Utf1!1.75!55.85!Utf1;;chrX:35464090..35464097,-!p1@Rhox12!1.75!55.38!Rhox12;;chr2:104966766..104966786,+!p1@Wt1!1.73!81.43!Wt1;;chr8:26958093..26958148,-!p2@Ash2l!1.73!52.10!Ash2l;;chr9:8900459..8900489,+!p1@Pgr!1.68!47.40!Pgr;;chrX:48499591..48499593,-!p3@Mbnl3!1.56!35.67!Mbnl3;;chr19:5447886..5447905,+!p1@Fosl1!1.56!34.97!Fosl1;;chr2:9800207..9800234,-!p1@Gata3!1.51!93.40!Gata3;;chr6:52184901..52184959,-!p2@Hoxa10!1.51!31.45!Hoxa10;;chr6:52190467..52190500,-!p1@Hoxa10!1.50!30.27!Hoxa10;;chr10:5636354..5636373,-!p2@Esr1!1.50!30.27!Esr1;;chr2:74529970..74529997,+!p1@Hoxd10!1.49!29.80!Hoxd10;;chr5:77543897..77543911,-!p2@Hopx!1.47!53.27!Hopx;;chr6:52195747..52195762,-!p3@Hoxa11!1.47!28.40!Hoxa11;;chr6:88148650..88148669,+!p1@Gata2!1.45!218.71!Gata2;;chr6:115311270..115311298,+!p1@Pparg!1.44!38.02!Pparg;;chr10:5636374..5636421,-!p1@Esr1!1.44!33.56!Esr1;;chr7:150155143..150155156,-!p1@Ascl2!1.44!26.28!Ascl2;;chr6:128250471..128250519,-!p1@Tead4!1.43!51.39!Tead4;;chr5:125523164..125523188,-!p8@Ncor2!1.38!23.00!Ncor2;;chr17:87153519..87153533,+!p5@Epas1!1.36!31.92!Epas1;;chr6:128250380..128250442,-!p2@Tead4!1.34!26.28!Tead4;;chr2:172375136..172375149,+!p2@Tfap2c!1.34!20.65!Tfap2c;;chr16:92697560..92697592,-!p2@Runx1!1.30!115.69!Runx1;;chr10:5636678..5636725,-!p6@Esr1!1.30!18.77!Esr1;;chr17:87153505..87153516,+!p6@Epas1!1.28!24.88!Epas1;;chr11:94981424..94981439,+!p1@Dlx3!1.25!19.01!Dlx3;;chr19:5447692..5447711,+!p2@Fosl1!1.25!16.90!Fosl1;;chr5:148118639..148118715,-!p1@Cdx2!1.25!16.90!Cdx2;;chr17:87153462..87153473,+!p3@Epas1!1.24!61.25!Epas1;;chr17:48025139..48025166,-!p8@Foxp4!1.23!18.77!Foxp4;;chrX:133654344..133654358,-!p2@Esx1!1.21!15.25!Esx1;;chr10:80555320..80555378,-!p1@Creb3l3!1.20!17.37!Creb3l3;;chr2:105003277..105003280,+!p5@Wt1!1.20!14.78!Wt1;;chr10:127095407..127095440,+!p3@Stat6!1.18!17.37!Stat6;;chr6:128250521..128250543,-!p3@Tead4!1.16!21.12!Tead4;;chr2:172376528..172376543,+!p3@Tfap2c!1.16!13.38!Tfap2c;;chr10:44178375..44178390,-!p2@Prdm1!1.15!17.84!Prdm1;;chr11:57645586..57645597,-!p2@Hand1!1.14!12.91!Hand1;;chr2:104966874..104966907,+!p2@Wt1!1.11!11.97!Wt1;;chr17:28409136..28409150,+!p3@Ppard!1.10!11.50!Ppard;;chr15:79178060..79178074,+!p2@Maff!1.09!14.78!Maff;;chr9:119893782..119893802,-!p1@Csrnp1!1.09!11.26!Csrnp1;;chr1:137155026..137155042,-!p1@Elf3!1.08!65.24!Elf3;;chr17:87153440..87153451,+!p4@Epas1!1.08!22.76!Epas1;;chr2:104966933..104966966,+!p3@Wt1!1.08!11.03!Wt1;;chr6:52664406..52664434,+!p3@Tax1bp1!1.06!12.67!Tax1bp1;;chr2:105003138..105003155,+!p13@Wt1!1.06!10.56!Wt1;;chr2:74529998..74530020,+!p2@Hoxd10!1.06!10.56!Hoxd10;;chr17:87153028..87153049,+!p2@Epas1!1.05!213.55!Epas1;;chr17:87153240..87153254,+!p1@Epas1!1.05!202.99!Epas1;;chr2:133377954..133377973,+!p1@Bmp2!1.05!33.56!Bmp2;;chr6:72185553..72185612,-!p2@Atoh8!1.04!19.48!Atoh8;;chr18:76219118..76219155,+!p1@Zbtb7c!1.04!17.84!Zbtb7c;;chr6:52664439..52664461,+!p4@Tax1bp1!1.04!10.09!Tax1bp1;;chr17:47922678..47922688,+!p10@Tfeb!1.04!9.86!Tfeb;;chr6:52184880..52184893,-!p6@Hoxa10!1.03!9.62!Hoxa10;;chr6:108610766..108610781,+!p2@Bhlhe40!1.00!16.43!Bhlhe40;;chr5:144951153..144951203,+!p1@Bhlha15!1.00!13.14!Bhlha15;;chr2:74517742..74517758,+!p2@Hoxd11!1.00!8.92!Hoxd11;;chr2:74549968..74549996,+!p1@Hoxd3!0.99!11.03!Hoxd3;;chr19:19185671..19185693,-!p1@Rorb!0.98!20.65!Rorb;;chr15:81606702..81606709,+!p7@Zc3h7b!0.98!8.45!Zc3h7b;;chr4:107107224..107107259,+!p2@Glis1!0.98!8.45!Glis1;;chr10:79390075..79390115,+!p2@Arid3a!0.97!29.10!Arid3a;;chr10:44178493..44178520,-!p3@Prdm1!0.97!11.73!Prdm1;;chr6:52190656..52190667,-!p7@Hoxa10!0.96!8.21!Hoxa10;;chr9:8900409..8900425,+!p2@Pgr!0.96!8.21!Pgr;;chr2:173044380..173044432,-!p1@Zbp1!0.95!19.48!Zbp1;;chr19:59533221..59533271,+!p1@Emx2!0.95!9.86!Emx2;;chr6:86619104..86619119,-!p1@Mxd1!0.94!65.47!Mxd1;;chr2:104966662..104966673,+!p4@Wt1!0.94!7.74!Wt1;;chr10:44178521..44178557,-!p1@Prdm1!0.93!13.61!Prdm1;;chr2:169458799..169458832,+!p5@Tshz2!0.93!12.67!Tshz2;;chr14:99697871..99697934,+!p1@Klf5!0.92!151.13!Klf5;;chr6:88143711..88143717,+!p2@Gata2!0.92!11.97!Gata2;;chr6:52190858..52190873,-!p4@Hoxa10!0.92!7.27!Hoxa10;;chr2:9800094..9800108,-!p3@Gata3!0.92!7.27!Gata3;;chr4:134676555..134676575,+!p2@Runx3!0.92!7.27!Runx3;;chr6:52176164..52176195,-!p1@Hoxa9!0.90!8.68!Hoxa9;;chr1:57029281..57029326,-!p1@Satb2!0.89!10.79!Satb2;;chrX:48559194..48559210,-!p4@Mbnl3!0.89!8.68!Mbnl3;;chrX:133654245..133654253,-!p3@Esx1!0.88!6.57!Esx1;;chr10:44178474..44178487,-!p4@Prdm1!0.87!9.39!Prdm1;;chr7:148452314..148452329,-!p1@Irf7!0.86!46.00!Irf7;;chr2:44965856..44965896,-!p5@Zeb2!0.85!24.88!Zeb2;;chr12:75009172..75009223,+!p3@Hif1a!0.85!15.49!Hif1a;;chr15:79178013..79178028,+!p3@Maff!0.85!8.21!Maff;;chr9:8899828..8899855,+!p3@Pgr!0.85!6.10!Pgr;;chr11:69468531..69468557,+!p1@Sox15!0.84!5.87!Sox15;;chr11:96829969..96829987,-!p2@Sp2!0.84!5.87!Sp2;;chr12:3891810..3891829,+!p2@Dnmt3a!0.83!9.15!Dnmt3a;;chr7:19946556..19946611,+!p1@Ppp1r13l!0.82!23.70!Ppp1r13l;;chr5:125523411..125523420,-!p24@Ncor2!0.82!5.63!Ncor2;;chr2:74536026..74536039,+!p1@Hoxd9!0.82!5.63!Hoxd9;;chr5:77524175..77524186,-!p8@Hopx!0.81!5.40!Hopx;;chr2:167363692..167363710,+!p1@Snai1!0.80!69.46!Snai1;;chr1:4483679..4483695,-!p1@Sox17!0.80!26.99!Sox17;;chr5:77524231..77524245,-!p3@Hopx!0.80!13.85!Hopx;;chr18:3281750..3281776,-!p2@Crem!0.80!11.26!Crem;;chr15:79178029..79178044,+!p4@Maff!0.79!6.57!Maff;;chr7:147129777..147129814,+!p2@Utf1!0.79!5.16!Utf1;;chr16:92697354..92697362,-!p3@Runx1!0.78!7.98!Runx1;;chr6:115311308..115311317,+!p10@Pparg!0.77!4.93!Pparg;;chr9:118387969..118387984,+!p2@Eomes!0.77!4.93!Eomes;;chr9:8900563..8900574,+!p5@Pgr!0.77!4.93!Pgr;;chr9:8900490..8900502,+!p4@Pgr!0.77!4.93!Pgr;;chr9:24578720..24578735,-!p1@Tbx20!0.76!4.69!Tbx20;;chr9:48644037..48644067,-!p2@Zbtb16!0.75!12.44!Zbtb16;;chr6:145813905..145813932,-!p2@Bhlhe41!0.75!9.39!Bhlhe41;;chr4:107107175..107107204,+!p1@Glis1!0.75!5.63!Glis1;;chr13:53568104..53568156,-!p1@Msx2!0.74!7.04!Msx2;;chr1:52176315..52176343,+!p1@Stat1!0.73!69.70!Stat1;;chr15:79177964..79177986,+!p1@Maff!0.73!16.43!Maff;;chr13:44825008..44825066,+!p5@Jarid2!0.73!9.15!Jarid2;;chrX:137135036..137135064,-!p4@Tsc22d3!0.73!9.15!Tsc22d3;;chr9:96653072..96653154,-!p1@Zbtb38!0.72!12.44!Zbtb38;;chr2:32219200..32219213,+!p5@Ciz1!0.72!5.63!Ciz1;;chr13:40829137..40829205,-!p1@Tfap2a!0.72!4.93!Tfap2a;;chr18:76219161..76219176,+!p4@Zbtb7c!0.71!5.63!Zbtb7c;;chr7:56136362..56136400,-!p1@E2f8!0.70!29.33!E2f8;;chr18:36441119..36441158,+!p2@Pura!0.70!10.79!Pura;;chr17:28409059..28409076,+!p6@Ppard!0.70!3.99!Ppard;;chr2:74550015..74550057,+!p2@Hoxd3!0.70!3.99!Hoxd3;;chr16:17233653..17233683,+!p1@Hic2!0.69!28.16!Hic2;;chr2:173044357..173044377,-!p2@Zbp1!0.69!5.87!Zbp1;;chr10:67599319..67599360,-!p2@Arid5b!0.68!48.11!Arid5b;;chr2:74520343..74520383,+!p4@Hoxd11!0.68!3.75!Hoxd11;;chr2:104966465..104966479,+!p6@Wt1!0.68!3.75!Wt1;;chr5:31271028..31271040,+!p1@Tcf23!0.68!3.75!Tcf23;;chr4:43575544..43575565,+!p2@Creb3!0.66!24.17!Creb3;;chr4:87678709..87678726,-!p4@Mllt3!0.66!12.44!Mllt3;;chr18:3281725..3281740,-!p3@Crem!0.66!4.69!Crem;;chr2:38206744..38206766,+!p1@Lhx2!0.66!4.46!Lhx2;;chr2:163372884..163372904,+!p1@Hnf4a!0.66!3.52!Hnf4a;;chr11:83664365..83664383,+!p1@Hnf1b!0.66!3.52!Hnf1b;;chr12:86814833..86814846,+!p1@Fos!0.65!95.51!Fos;;chr6:108610513..108610528,+!p3@Bhlhe40!0.65!5.63!Bhlhe40;;chr1:74634786..74634804,-!p5@Zfp142!0.65!4.93!Zfp142;;chr5:125538737..125538781,-!p2@Ncor2!0.64!13.85!Ncor2;;chr5:107003725..107003746,-!p5@Zfp644!0.64!4.69!Zfp644;;chr3:54559463..54559493,+!p3@Smad9!0.63!6.57!Smad9;;chr11:96153767..96153822,+!p1@Hoxb6!0.63!5.40!Hoxb6;;chr6:108610610..108610676,+!p1@Bhlhe40!0.62!187.50!Bhlhe40;;chr5:32438831..32438878,+!p1@Fosl2!0.62!38.49!Fosl2;;chr13:55932591..55932622,-!p1@Pitx1!0.62!3.99!Pitx1;;chr7:6238191..6238224,+!p1@Zfp667!0.61!22.06!Zfp667;;chr8:94325321..94325366,-!p1@Irx3!0.61!8.45!Irx3;;chr8:44392345..44392363,-!p1@Zfp42!0.61!3.05!Zfp42;;chr5:77524199..77524210,-!p10@Hopx!0.61!3.05!Hopx;;chr12:86940338..86940357,+!p1@Jdp2!0.60!35.44!Jdp2;;chr1:170362242..170362256,-!p3@Pbx1!0.60!25.81!Pbx1;;chr14:63864056..63864102,-!p1@Gata4!0.60!5.63!Gata4;;chr14:79880971..79880992,+!p2@Elf1!0.59!44.59!Elf1;;chr11:74981654..74981658,-!p1@Hic1!0.59!13.61!Hic1;;chr16:43363152..43363186,+!p3@Zbtb20!0.59!7.51!Zbtb20;;chr7:19608891..19608895,-!p1@Foxa3!0.59!3.99!Foxa3;;chr16:55822241..55822258,-!p1@Nfkbiz!0.58!108.18!Nfkbiz;;chr13:5860776..5860796,+!p1@Klf6!0.58!82.60!Klf6;;chr5:120121446..120121461,+!p2@Tbx3!0.58!11.03!Tbx3;;chr16:43363190..43363242,+!p2@Zbtb20!0.58!10.09!Zbtb20;;chr5:77695241..77695257,+!p10@Rest!0.58!3.29!Rest;;chr2:74549945..74549965,+!p4@Hoxd3!0.58!2.82!Hoxd3;;chr2:103264213..103264233,+!p1@Elf5!0.58!2.82!Elf5;;chr15:82742573..82742620,-!p2@Tcf20!0.58!2.82!Tcf20;;chr17:68663935..68663949,+!p@chr17:68663935..68663949,+!0.58!2.82!L3mbtl4;;chr9:118387300..118387317,+!p1@Eomes!0.58!2.82!Eomes;;chr2:169458192..169458247,+!p1@Tshz2!0.57!30.04!Tshz2;;chr5:120121020..120121049,+!p1@Tbx3!0.57!20.18!Tbx3;;chr16:50429979..50429997,-!p4@Bbx!0.57!4.69!Bbx;;chr11:5761889..5761969,+!p1@Aebp1!0.56!138.46!Aebp1;;chr16:50432467..50432522,-!p1@Bbx!0.56!64.77!Bbx;;chr9:36954842..36954908,-!p1@Pknox2!0.56!38.49!Pknox2;;chr17:84105510..84105540,+!p2@Mta3!0.56!17.13!Mta3;;chrX:7339938..7339963,+!p1@Tfe3!0.56!16.19!Tfe3;;chr3:54559496..54559511,+!p1@Smad9!0.56!6.81!Smad9;;chr11:98636400..98636418,-!p4@Nr1d1!0.56!3.75!Nr1d1;;chr15:37162834..37162849,+!p2@Grhl2!0.56!3.29!Grhl2;;chr5:77524250..77524300,-!p1@Hopx!0.55!64.53!Hopx;;chr4:149943593..149943605,+!p5@Rere!0.55!5.16!Rere;;chr2:745433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633152,+!p4@Tef!0.13!1.17!Tef;;chr5:3648045..3648074,-!p2@Gatad1!0.13!1.17!Gatad1;;chr7:119822940..119822945,+!p6@Tead1!0.13!0.70!Tead1;;chr5:125538905..125538910,-!p4@Ncor2!0.13!0.70!Ncor2;;chr5:53981578..53981590,+!p4@Rbpj!0.13!0.70!Rbpj;;chr17:71200967..71200983,-!p8@Tgif1!0.13!0.70!Tgif1;;chr16:95923586..95923598,+!p5@Ets2!0.13!0.70!Ets2;;chr2:91489942..91489953,-!p3@Zfp408!0.13!0.70!Zfp408;;chr3:19957878..19957885,+!p2@Hltf!0.13!0.70!Hltf;;chr2:75542527..75542590,-!p1@Nfe2l2!0.12!106.78!Nfe2l2;;chr17:34729193..34729274,+!p1@Pbx2!0.12!56.09!Pbx2;;chr15:102301149..102301221,+!p2@Pcbp2!0.12!43.88!Pcbp2;;chr11:96691218..96691265,-!p2@Nfe2l1!0.12!32.85!Nfe2l1;;chr19:5424906..5425026,-!p1@Drap1!0.12!31.92!Drap1;;chr8:86590723..86590781,+!p1@Rfx1!0.12!21.36!Rfx1;;chr17:48549054..48549091,-!p1@Nfya!0.12!20.65!Nfya;;chr15:81494344..81494388,+!p1@L3mbtl2!0.12!13.14!L3mbtl2;;chr15:102076870..102076941,-!p1@Rarg!0.12!12.20!Rarg;;chr18:80348206..80348256,-!p1@Adnp2!0.12!9.39!Adnp2;;chr10:114821444..114821491,-!p1@Thap2!0.12!8.68!Thap2;;chr8:107694661..107694713,+!p2@Cbfb!0.12!7.27!Cbfb;;chr8:72520015..72520053,-!p2@Gatad2a!0.12!7.27!Gatad2a;;chr4:120498356..120498401,-!p2@Nfyc!0.12!5.87!Nfyc;;chr18:69504195..69504213,+!p4@Tcf4!0.12!4.69!Tcf4;;chr3:94641302..94641341,+!p3@Pogz!0.12!3.99!Pogz;;chr12:110031310..110031342,+!p4@Yy1!0.12!3.99!Yy1;;chr8:118230894..118230918,-!p5@Maf!0.12!2.58!Maf;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.12!2.58!Tfcp2l1;;chr12:34642682..34642753,+!p2@Twist1!0.12!2.35!Twist1;;chr2:56976543..56976558,-!p2@Nr4a2!0.12!1.88!Nr4a2;;chr1:170361730..170361769,-!p7@Pbx1!0.12!1.88!Pbx1;;chr16:3884438..3884470,-!p2@Zfp597!0.12!1.88!Zfp597;;chr16:8672256..8672279,-!p1@Carhsp1,p1@Gm9791!0.12!1.88!Carhsp1;;chr8:72520121..72520135,-!p12@Gatad2a!0.12!1.64!Gatad2a;;chr8:4613211..4613224,+!p3@Zfp958!0.12!1.64!Zfp958;;chr10:119913792..119913820,-!p5@Hmga2!0.12!1.17!Hmga2;;chr6:72185210..72185228,-!p3@Atoh8!0.12!1.17!Atoh8;;chr11:4604619..4604634,+!p2@Zmat5!0.12!0.70!Zmat5;;chrX:48559029..48559051,-!p7@Mbnl3!0.12!0.70!Mbnl3;;chr4:135842093..135842105,+!p6@Zfp46!0.12!0.70!Zfp46;;chr4:61869573..61869595,-!p2@Zfp37!0.12!0.70!Zfp37;;chr3:29912079..29912096,-!p10@Mecom!0.12!0.47!Mecom;;chr3:34548946..34548972,+!p2@Sox2!0.12!0.47!Sox2;;chr10:127080230..127080241,+!p6@Stat6!0.12!0.47!Stat6;;chr5:38611816..38611827,+!p4@Lyar!0.12!0.47!Lyar;;chr6:128312812..128312821,+!p5@Foxm1!0.12!0.47!Foxm1;;chr1:170362027..170362036,-!p15@Pbx1!0.12!0.47!Pbx1;;chr12:78063165..78063227,-!p1@Max!0.11!97.86!Max;;chr14:52899256..52899305,+!p1@Tox4!0.11!29.33!Tox4;;chr11:100948597..100948637,+!p1@Mlx!0.11!27.22!Mlx;;chr5:77694479..77694574,+!p1@Rest!0.11!24.41!Rest;;chr7:26006436..26006488,+!p1@Zfp526!0.11!12.67!Zfp526;;chr4:102791976..102792008,+!p2@Mier1!0.11!12.20!Mier1;;chr10:80813050..80813114,-!p2@Hmg20b!0.11!11.97!Hmg20b;;chr7:13483149..13483234,+!p1@Zscan22!0.11!10.56!Zscan22;;chr19:40969182..40969226,+!p1@Zfp518a!0.11!8.92!Zfp518a;;chr16:14705961..14705978,+!p2@Snai2!0.11!4.69!Snai2;;chr13:37918773..37918818,+!p3@Rreb1!0.11!4.22!Rreb1;;chr9:21420596..21420607,+!p4@Smarca4!0.11!3.99!Smarca4;;chr2:126501274..126501308,-!p2@Gabpb1!0.11!3.99!Gabpb1;;chr19:8876976..8877011,+!p1@Zbtb3!0.11!3.05!Zbtb3;;chr4:124805061..124805087,-!p1@Zc3h12a!0.11!2.82!Zc3h12a;;chr4:63064364..63064384,-!p1@Akna!0.11!2.58!Akna;;chr17:45570631..45570658,-!p4@Cdc5l!0.11!2.58!Cdc5l;;chr7:119822828..119822839,+!p4@Tead1!0.11!2.58!Tead1;;chr5:147760339..147760350,+!p3@Gtf3a!0.11!2.58!Gtf3a;;chr17:48061631..48061648,-!p7@Foxp4!0.11!2.35!Foxp4;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011381
 |is_obsolete=
+|library_id=CNhs10472
+|library_id_phase_based=2:CNhs10472
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;539
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;539
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day10.CNhs10472.539-13I7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day10.CNhs10472.539-13I7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day10.CNhs10472.539-13I7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day10.CNhs10472.539-13I7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day10.CNhs10472.539-13I7.mm9.nobarcode.rdna.fa.gz
 |name=placenta, adult pregnant day10
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10472,LSID646,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.0259582339318102,0,0,0,0,0,0.221897739083223,0,0.0187053245808008,0,0,1.88190561280693,0,0,1.13584069725309,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.00437132257655015,0,0,0,0,0,0.0050187118358587,-0.0055155949673491,0.0531044487596988,-0.459592366253748,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0.0915514965999916,0,0.101117763746749,2.40918469820999,0,0,0,-0.0428469550828748,0,0.0836448718808979,0,0,0,0.0440805394183626,0.0710112806546206,-0.0665395461710909,-0.0425732007712371,0,0,0,0.122988405977457,0,0,-0.0558333688661133,-0.0685071042366006,-0.0142996296973108,0.0127199017600841,0,0,0,0,0,0.167123311310189,-0.0893284091371433,-0.202131473481791,-0.154066279691058,0.000359078354286724,0,0,0,0
 |rna_box=13
 |rna_catalog_number=
@@ Line 61: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 81: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:539-13I7;search_select_hide=table117:539-13I7
 }}

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FF:539-13I7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:18, 4 June 2020

CNhs10472

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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