FF:577-18G3: Difference between revisions

Latest revision as of 19:18, 4 June 2020

Name:	placenta, adult pregnant day17
Species:	Mouse (Mus musculus)
Library ID:	CNhs10464
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	placenta
dev stage	17 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		SAMD00005396

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10464		CAGE		DRX009075		DRR009949

Accession ID Mm9

Library id		BAM		CTSS
CNhs10464		DRZ001374		DRZ002757

Accession ID Mm10

Library id		BAM		CTSS
CNhs10464		DRZ012724		DRZ014107

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

CNhs10464

0	0
1	0
10	0
100	0
1000	-0.0355
1001	0.00614
1002	-0.0327
1003	-0.156
1004	0
1005	0
1006	-9.149961e-4
1007	0.0104
1008	0
1009	0.156
101	-0.0736
1010	0
1011	-0.0489
1012	0
1013	0.135
1014	0.308
1015	-0.195
1016	-0.152
1017	0
1018	0.562
1019	0
102	0
1020	0
1021	0
1022	-0.162
1023	0
1024	0.0741
1025	0.356
1026	0
1027	-0.048
1028	0.0834
1029	0.168
103	0
1030	0
1031	-0.0143
1032	0.0829
1033	-0.0665
1034	0
1035	0
1036	-0.266
1037	0
1038	0.162
1039	-0.149
104	0
1040	0.143
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: CNhs10464

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.707
MA0003.1	MA0003.1	0.169
MA0004.1	MA0004.1	0.786
MA0006.1	MA0006.1	0.118
MA0007.1	MA0007.1	0.625
MA0009.1	MA0009.1	0.0217
MA0014.1	MA0014.1	0.119
MA0017.1	MA0017.1	0.0189
MA0018.2	MA0018.2	0.285
MA0019.1	MA0019.1	0.135
MA0024.1	MA0024.1	3.609e-4
MA0025.1	MA0025.1	0.325
MA0027.1	MA0027.1	0.655
MA0028.1	MA0028.1	0.0684
MA0029.1	MA0029.1	0.00252
MA0030.1	MA0030.1	0.0215
MA0031.1	MA0031.1	2.82025e-5
MA0035.2	MA0035.2	0.0159
MA0038.1	MA0038.1	0.623
MA0039.2	MA0039.2	9.16484e-5
MA0040.1	MA0040.1	0.469
MA0041.1	MA0041.1	0.21
MA0042.1	MA0042.1	0.726
MA0043.1	MA0043.1	0.682
MA0046.1	MA0046.1	0.453
MA0047.2	MA0047.2	0.144
MA0048.1	MA0048.1	0.442
MA0050.1	MA0050.1	0.298
MA0051.1	MA0051.1	0.0466
MA0052.1	MA0052.1	0.0504
MA0055.1	MA0055.1	0.0104
MA0057.1	MA0057.1	0.282
MA0058.1	MA0058.1	0.324
MA0059.1	MA0059.1	0.268
MA0060.1	MA0060.1	7.30053e-4
MA0061.1	MA0061.1	0.941
MA0062.2	MA0062.2	0.0109
MA0065.2	MA0065.2	0.00531
MA0066.1	MA0066.1	0.297
MA0067.1	MA0067.1	0.0623
MA0068.1	MA0068.1	0.876
MA0069.1	MA0069.1	0.93
MA0070.1	MA0070.1	0.619
MA0071.1	MA0071.1	0.161
MA0072.1	MA0072.1	0.731
MA0073.1	MA0073.1	0.884
MA0074.1	MA0074.1	0.905
MA0076.1	MA0076.1	0.132
MA0077.1	MA0077.1	0.136
MA0078.1	MA0078.1	0.311
MA0079.2	MA0079.2	0.00219
MA0080.2	MA0080.2	0.968
MA0081.1	MA0081.1	0.879
MA0083.1	MA0083.1	0.0104
MA0084.1	MA0084.1	0.62
MA0087.1	MA0087.1	0.889
MA0088.1	MA0088.1	0.416
MA0090.1	MA0090.1	3.76677e-4
MA0091.1	MA0091.1	0.0329
MA0092.1	MA0092.1	0.933
MA0093.1	MA0093.1	0.664
MA0099.2	MA0099.2	1.44241e-23
MA0100.1	MA0100.1	0.317
MA0101.1	MA0101.1	0.574
MA0102.2	MA0102.2	0.808
MA0103.1	MA0103.1	0.0822
MA0104.2	MA0104.2	0.14
MA0105.1	MA0105.1	0.051
MA0106.1	MA0106.1	0.383
MA0107.1	MA0107.1	0.556
MA0108.2	MA0108.2	0.00406
MA0111.1	MA0111.1	0.535
MA0112.2	MA0112.2	0.14
MA0113.1	MA0113.1	0.637
MA0114.1	MA0114.1	0.00245
MA0115.1	MA0115.1	6.31628e-4
MA0116.1	MA0116.1	0.351
MA0117.1	MA0117.1	0.0272
MA0119.1	MA0119.1	0.00947
MA0122.1	MA0122.1	0.424
MA0124.1	MA0124.1	0.154
MA0125.1	MA0125.1	0.95
MA0131.1	MA0131.1	0.773
MA0135.1	MA0135.1	0.74
MA0136.1	MA0136.1	0.559
MA0137.2	MA0137.2	0.00157
MA0138.2	MA0138.2	0.388
MA0139.1	MA0139.1	0.993
MA0140.1	MA0140.1	0.673
MA0141.1	MA0141.1	0.478
MA0142.1	MA0142.1	0.137
MA0143.1	MA0143.1	0.326
MA0144.1	MA0144.1	0.0111
MA0145.1	MA0145.1	0.0718
MA0146.1	MA0146.1	0.0105
MA0147.1	MA0147.1	0.101
MA0148.1	MA0148.1	0.707
MA0149.1	MA0149.1	0.554
MA0150.1	MA0150.1	0.00145
MA0152.1	MA0152.1	0.207
MA0153.1	MA0153.1	0.891
MA0154.1	MA0154.1	0.186
MA0155.1	MA0155.1	0.704
MA0156.1	MA0156.1	0.243
MA0157.1	MA0157.1	0.00329
MA0159.1	MA0159.1	0.1
MA0160.1	MA0160.1	0.182
MA0162.1	MA0162.1	0.981
MA0163.1	MA0163.1	0.454
MA0164.1	MA0164.1	0.0322
MA0258.1	MA0258.1	0.352
MA0259.1	MA0259.1	0.492

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: CNhs10464

Novel motif	Logo	P-value
1	1	0.496
10	10	0.779
100	100	0.678
101	101	0.803
102	102	0.174
103	103	0.809
104	104	0.77
105	105	0.935
106	106	0.426
107	107	0.294
108	108	0.972
109	109	0.672
11	11	0.84
110	110	0.682
111	111	0.365
112	112	0.144
113	113	0.565
114	114	0.758
115	115	0.839
116	116	0.362
117	117	0.174
118	118	0.919
119	119	0.29
12	12	0.585
120	120	0.149
121	121	0.264
122	122	0.74
123	123	0.0315
124	124	0.242
125	125	0.226
126	126	0.665
127	127	0.915
128	128	0.432
129	129	0.931
13	13	0.0147
130	130	0.0471
131	131	0.751
132	132	0.755
133	133	0.873
134	134	0.539
135	135	0.0795
136	136	9.28448e-4
137	137	0.416
138	138	0.017
139	139	0.153
14	14	0.943
140	140	0.132
141	141	0.864
142	142	0.63
143	143	0.979
144	144	0.626
145	145	0.889
146	146	0.614
147	147	0.286
148	148	0.507
149	149	0.878
15	15	0.8
150	150	0.103
151	151	0.321
152	152	0.0113
153	153	0.692
154	154	0.491
155	155	0.258
156	156	0.00505
157	157	0.359
158	158	0.0596
159	159	0.825
160	160	0.464
161	161	0.00682
162	162	0.737
163	163	0.207
164	164	0.141
165	165	0.907
166	166	0.0171
167	167	0.0888
168	168	0.215
169	169	0.079
17	17	0.108
18	18	0.969
19	19	0.0198
2	2	0.512
20	20	0.263
21	21	1
22	22	0.0365
23	23	0.0828
24	24	0.25
25	25	0.899
26	26	0.566
27	27	0.195
28	28	0.552
29	29	0.57
3	3	0.829
30	30	0.538
31	31	0.332
32	32	0.592
33	33	0.774
34	34	0.913
35	35	0.00474
36	36	0.15
37	37	0.0986
38	38	0.618
39	39	0.517
4	4	0.0417
40	40	0.637
41	41	0.609
42	42	0.812
43	43	0.948
44	44	0.841
45	45	0.124
46	46	0.619
47	47	0.506
48	48	0.612
49	49	0.63
5	5	0.629
50	50	0.245
51	51	0.905
52	52	0.453
53	53	0.72
54	54	0.633
55	55	0.291
56	56	0.942
57	57	0.191
58	58	0.609
59	59	0.775
6	6	0.996
60	60	0.233
61	61	0.299
62	62	0.546
63	63	0.455
64	64	0.372
65	65	0.698
66	66	0.829
67	67	0.469
68	68	0.188
69	69	0.223
7	7	0.569
70	70	0.119
71	71	0.253
72	72	0.574
73	73	0.00626
74	74	0.776
75	75	0.475
76	76	0.349
77	77	0.699
78	78	0.00868
79	79	0.291
8	8	0.0628
80	80	0.517
81	81	0.319
82	82	0.917
83	83	0.615
84	84	0.547
85	85	0.673
86	86	0.59
87	87	0.00236
88	88	0.326
89	89	0.825
9	9	0.719
90	90	0.0909
91	91	0.615
92	92	0.383
93	93	0.132
94	94	0.0126
95	95	0.203
96	96	0.878
97	97	0.499
98	98	0.383
99	99	0.213

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: CNhs10464

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011384 mouse placenta- adult pregnant day17 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)
0000321 (mouse pregnant day 17 sample)
0011384 (mouse placenta- adult pregnant day17 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
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0001987,UBERON:0005795,UBERON:0000995,UBERON:0003134,UBERON:0000926,UBERON:0000479,UBERON:0005156,UBERON:0000064,UBERON:0000077,UBERON:0000062,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0000990,UBERON:0002050,UBERON:0004923,UBERON:0005423,UBERON:0005631,UBERON:0000467,UBERON:0001062,UBERON:0000478,UBERON:0005291,UBERON:0003133,UBERON:0003975,UBERON:0004175,UBERON:0000925,UBERON:0006598,UBERON:0000158,UBERON:0002532,UBERON:0003124,UBERON:0003100,UBERON:0000474,UBERON:0003081,UBERON:0006595,UBERON:0006603,UBERON:0004872,UBERON:0004340
+|DRA_sample_Accession=CAGE@SAMD00005396
+|accession_numbers=CAGE;DRX009075;DRR009949;DRZ001374;DRZ002757;DRZ012724;DRZ014107
+|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=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000998,FF:0000004,FF:0000317,FF:0000321,FF:0011384
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:57645506..57645523,-!p1@Hand1!2.45!280.04!Hand1;;chrX:98449898..98449913,+!p2@Foxo4!2.40!764.08!Foxo4;;chr8:26958093..26958148,-!p2@Ash2l!1.98!95.32!Ash2l;;chr6:115311270..115311298,+!p1@Pparg!1.91!113.75!Pparg;;chrX:35464090..35464097,-!p1@Rhox12!1.91!81.13!Rhox12;;chr2:172375081..172375105,+!p1@Tfap2c!1.83!67.15!Tfap2c;;chrX:48499591..48499593,-!p3@Mbnl3!1.80!61.85!Mbnl3;;chr11:94981424..94981439,+!p1@Dlx3!1.73!58.89!Dlx3;;chr6:128250380..128250442,-!p2@Tead4!1.69!59.95!Tead4;;chr5:148118639..148118715,-!p1@Cdx2!1.69!48.09!Cdx2;;chrX:133654344..133654358,-!p2@Esx1!1.59!38.34!Esx1;;chr5:125523164..125523188,-!p8@Ncor2!1.56!34.95!Ncor2;;chrX:137135036..137135064,-!p4@Tsc22d3!1.55!66.52!Tsc22d3;;chr9:119893782..119893802,-!p1@Csrnp1!1.50!30.29!Csrnp1;;chrX:133654245..133654253,-!p3@Esx1!1.42!25.21!Esx1;;chr8:59799772..59799789,+!p1@Hand2!1.39!66.30!Hand2;;chr5:144951153..144951203,+!p1@Bhlha15!1.38!33.26!Bhlha15;;chr6:128250471..128250519,-!p1@Tead4!1.35!42.15!Tead4;;chr1:137155026..137155042,-!p1@Elf3!1.34!117.99!Elf3;;chr7:6649134..6649167,-!p1@Zim1!1.34!109.31!Zim1;;chr2:9800207..9800234,-!p1@Gata3!1.31!57.62!Gata3;;chr17:87153505..87153516,+!p6@Epas1!1.30!26.06!Epas1;;chr17:87153519..87153533,+!p5@Epas1!1.28!26.48!Epas1;;chr17:87153462..87153473,+!p3@Epas1!1.24!60.58!Epas1;;chr6:52190668..52190682,-!p3@Hoxa10!1.24!16.52!Hoxa10;;chr3:127336052..127336058,+!p1@Neurog2!1.24!16.52!Neurog2;;chr6:128250521..128250543,-!p3@Tead4!1.23!25.21!Tead4;;chr6:52195795..52195825,-!p1@Hoxa11!1.23!15.89!Hoxa11;;chr12:3891810..3891829,+!p2@Dnmt3a!1.22!24.36!Dnmt3a;;chr6:52195763..52195792,-!p2@Hoxa11!1.22!15.68!Hoxa11;;chr6:88148650..88148669,+!p1@Gata2!1.21!124.35!Gata2;;chr13:53568104..53568156,-!p1@Msx2!1.19!21.40!Msx2;;chrX:48559194..48559210,-!p4@Mbnl3!1.18!17.79!Mbnl3;;chr6:145813905..145813932,-!p2@Bhlhe41!1.15!25.21!Bhlhe41;;chr7:19946556..19946611,+!p1@Ppp1r13l!1.11!46.81!Ppp1r13l;;chr13:40829137..40829205,-!p1@Tfap2a!1.10!12.92!Tfap2a;;chr17:87153240..87153254,+!p1@Epas1!1.08!217.55!Epas1;;chr13:55932591..55932622,-!p1@Pitx1!1.07!12.92!Pitx1;;chr4:43575544..43575565,+!p2@Creb3!1.06!61.64!Creb3;;chr10:79390075..79390115,+!p2@Arid3a!1.06!35.80!Arid3a;;chr9:8900459..8900489,+!p1@Pgr!1.05!10.17!Pgr;;chr10:5636354..5636373,-!p2@Esr1!1.03!9.74!Esr1;;chr6:52190467..52190500,-!p1@Hoxa10!1.02!9.53!Hoxa10;;chr7:148452314..148452329,-!p1@Irf7!1.01!66.09!Irf7;;chr6:115311308..115311317,+!p10@Pparg!1.01!9.32!Pparg;;chr9:77899745..77899755,+!p1@Gcm1!1.01!9.32!Gcm1;;chr17:87153440..87153451,+!p4@Epas1!1.00!18.64!Epas1;;chr5:77543897..77543911,-!p2@Hopx!1.00!17.37!Hopx;;chr11:57645586..57645597,-!p2@Hand1!1.00!9.11!Hand1;;chr2:172375136..172375149,+!p2@Tfap2c!1.00!8.90!Tfap2c;;chr6:52184901..52184959,-!p2@Hoxa10!0.99!8.69!Hoxa10;;chr16:17233653..17233683,+!p1@Hic2!0.98!56.35!Hic2;;chr2:91864661..91864686,-!p1@Creb3l1!0.97!184.93!Creb3l1;;chr1:193007123..193007139,-!p1@Atf3!0.97!47.87!Atf3;;chr2:38206744..38206766,+!p1@Lhx2!0.97!10.17!Lhx2;;chr2:24331116..24331125,-!p2@Pax8!0.97!8.26!Pax8;;chr10:12810631..12810649,+!p1@Plagl1!0.96!218.61!Plagl1;;chr9:24578720..24578735,-!p1@Tbx20!0.96!8.05!Tbx20;;chr10:5636374..5636421,-!p1@Esr1!0.94!9.74!Esr1;;chr2:24331085..24331100,-!p1@Pax8!0.93!7.41!Pax8;;chr8:24780125..24780143,+!p1@Zmat4!0.92!10.80!Zmat4;;chr17:87153028..87153049,+!p2@Epas1!0.91!151.46!Epas1;;chr16:95923651..95923701,+!p3@Ets2!0.91!11.65!Ets2;;chr15:79178013..79178028,+!p3@Maff!0.90!9.32!Maff;;chrX:55284180..55284195,+!p2@Zic3!0.90!6.99!Zic3;;chr18:36441119..36441158,+!p2@Pura!0.88!16.52!Pura;;chr2:172376528..172376543,+!p3@Tfap2c!0.88!6.57!Tfap2c;;chr2:167363692..167363710,+!p1@Snai1!0.87!83.25!Snai1;;chrX:133654667..133654672,-!p1@Esx1!0.87!6.35!Esx1;;chr8:94325321..94325366,-!p1@Irx3!0.86!15.89!Irx3;;chr19:5447886..5447905,+!p1@Fosl1!0.85!6.14!Fosl1;;chr17:34730333..34730362,+!p2@Pbx2!0.83!24.15!Pbx2;;chr6:145814003..145814056,-!p1@Bhlhe41!0.83!17.58!Bhlhe41;;chr4:107107175..107107204,+!p1@Glis1!0.83!6.99!Glis1;;chr5:148118614..148118625,-!p4@Cdx2!0.83!5.72!Cdx2;;chr2:167514456..167514473,+!p1@Cebpb!0.82!266.91!Cebpb;;chr16:50432467..50432522,-!p1@Bbx!0.82!117.14!Bbx;;chr7:6683123..6683142,-!p1@Peg3!0.81!304.40!Peg3;;chr7:6238191..6238224,+!p1@Zfp667!0.81!35.16!Zfp667;;chr2:9800094..9800108,-!p3@Gata3!0.81!5.51!Gata3;;chr5:125523411..125523420,-!p24@Ncor2!0.81!5.51!Ncor2;;chr15:79177964..79177986,+!p1@Maff!0.80!19.70!Maff;;chr2:104966766..104966786,+!p1@Wt1!0.80!8.69!Wt1;;chr13:5860776..5860796,+!p1@Klf6!0.79!135.36!Klf6;;chr5:145992626..145992652,+!p2@Zfp655!0.78!38.55!Zfp655;;chr19:41557591..41557634,+!p3@Lcor!0.78!13.77!Lcor;;chr7:19946535..19946550,+!p3@Ppp1r13l!0.78!7.84!Ppp1r13l;;chr15:79178060..79178074,+!p2@Maff!0.78!6.78!Maff;;chr6:30908793..30908815,-!p1@Klf14!0.78!5.08!Klf14;;chr12:86940338..86940357,+!p1@Jdp2!0.77!52.53!Jdp2;;chr16:92697560..92697592,-!p2@Runx1!0.77!33.47!Runx1;;chr17:84105510..84105540,+!p2@Mta3!0.77!28.17!Mta3;;chr16:25801993..25802014,+!p1@Trp63!0.77!4.87!Trp63;;chr16:95924055..95924077,+!p1@Ets2!0.75!279.19!Ets2;;chrX:98449805..98449834,+!p3@Foxo4!0.75!13.77!Foxo4;;chr6:52195747..52195762,-!p3@Hoxa11!0.75!4.66!Hoxa11;;chr13:40825465..40825469,-!p2@Tfap2a!0.75!4.66!Tfap2a;;chr6:52184880..52184893,-!p6@Hoxa10!0.74!4.45!Hoxa10;;chr10:127080230..127080241,+!p6@Stat6!0.73!5.08!Stat6;;chr8:123608252..123608268,+!p1@Foxf1a!0.72!6.57!Foxf1a;;chr13:53568191..53568219,-!p2@Msx2!0.72!4.24!Msx2;;chr18:84581781..84581790,-!p8@Zfp407!0.72!4.24!Zfp407;;chr6:83661226..83661282,+!p1@Vax2!0.72!4.24!Vax2;;chr4:107107224..107107259,+!p2@Glis1!0.72!4.24!Glis1;;chr13:44825008..44825066,+!p5@Jarid2!0.71!8.69!Jarid2;;chr10:127095407..127095440,+!p3@Stat6!0.71!5.30!Stat6;;chr17:84105477..84105509,+!p3@Mta3!0.70!17.79!Mta3;;chr13:31650185..31650201,+!p1@Foxq1!0.70!15.46!Foxq1;;chr15:79178029..79178044,+!p4@Maff!0.70!5.08!Maff;;chr2:74536026..74536039,+!p1@Hoxd9!0.70!4.02!Hoxd9;;chr11:100553754..100553787,-!p1@Zfp385c!0.70!4.02!Zfp385c;;chr11:96829969..96829987,-!p2@Sp2!0.70!4.02!Sp2;;chr2:147871627..147871641,-!p1@Foxa2!0.70!4.02!Foxa2;;chr14:76904313..76904328,+!p1@Tsc22d1!0.69!861.73!Tsc22d1;;chr9:57684520..57684612,-!p1@Arid3b!0.69!39.19!Arid3b;;chr7:119822915..119822936,+!p5@Tead1!0.69!6.78!Tead1;;chr10:44178375..44178390,-!p2@Prdm1!0.69!5.51!Prdm1;;chr16:95923586..95923598,+!p5@Ets2!0.69!5.08!Ets2;;chr4:55545051..55545110,-!p2@Klf4!0.69!5.08!Klf4;;chr6:52664406..52664434,+!p3@Tax1bp1!0.69!4.87!Tax1bp1;;chr5:145992579..145992623,+!p1@Zfp655!0.68!133.24!Zfp655;;chr4:124334894..124334899,+!p1@Pou3f1!0.68!5.08!Pou3f1;;chr2:74529970..74529997,+!p1@Hoxd10!0.68!3.81!Hoxd10;;chr11:83664365..83664383,+!p1@Hnf1b!0.68!3.81!Hnf1b;;chr13:40826961..40827001,-!p4@Tfap2a!0.68!3.81!Tfap2a;;chrX:35419715..35419724,+!p1@Rhox10!0.68!3.81!Rhox10;;chr5:125523193..125523196,-!p23@Ncor2!0.68!3.81!Ncor2;;chr16:50429979..50429997,-!p4@Bbx!0.67!6.14!Bbx;;chr15:37162834..37162849,+!p2@Grhl2!0.67!4.45!Grhl2;;chr1:4483679..4483695,-!p1@Sox17!0.66!19.28!Sox17;;chr15:37162796..37162828,+!p1@Grhl2!0.66!6.35!Grhl2;;chr4:129118044..129118067,-!p1@Zbtb8b!0.66!4.66!Zbtb8b;;chr10:88969376..88969395,-!p1@Nr1h4!0.66!3.60!Nr1h4;;chr7:150155143..150155156,-!p1@Ascl2!0.66!3.60!Ascl2;;chr6:52664439..52664461,+!p4@Tax1bp1!0.66!3.60!Tax1bp1;;chr4:43575485..43575542,+!p1@Creb3!0.65!114.39!Creb3;;chr6:145813964..145813994,-!p3@Bhlhe41!0.65!4.66!Bhlhe41;;chr10:126727842..126727859,+!p1@Ddit3!0.64!113.54!Ddit3;;chr14:79881330..79881415,+!p3@Elf1!0.64!12.71!Elf1;;chr13:55932624..55932641,-!p2@Pitx1!0.64!3.39!Pitx1;;chr11:85699862..85699920,+!p1@Tbx4!0.64!3.39!Tbx4;;chr2:105003277..105003280,+!p5@Wt1!0.64!3.39!Wt1;;chr17:47922678..47922688,+!p10@Tfeb!0.64!3.39!Tfeb;;chr7:31065553..31065603,+!p@chr7:31065553..31065603,+!0.64!3.39!Thap8;;chr7:119822957..119822980,+!p2@Tead1!0.63!18.64!Tead1;;chr8:94325814..94325839,-!p2@Irx3!0.63!7.63!Irx3;;chr6:115311030..115311065,+!p4@Pparg!0.62!4.87!Pparg;;chr11:96880072..96880079,+!p1@Sp6!0.62!3.18!Sp6;;chr8:26958153..26958170,-!p5@Ash2l!0.62!3.18!Ash2l;;chr19:5447692..5447711,+!p2@Fosl1!0.62!3.18!Fosl1;;chr7:20408047..20408125,-!p1@Bcl3!0.61!42.37!Bcl3;;chr10:67599319..67599360,-!p2@Arid5b!0.61!40.46!Arid5b;;chr5:140267476..140267493,+!p1@Mafk!0.61!20.55!Mafk;;chr10:92773708..92773734,-!p3@Elk3!0.60!6.57!Elk3;;chr2:105003138..105003155,+!p13@Wt1!0.60!2.97!Wt1;;chrX:58146612..58146615,-!p1@Sox3!0.60!2.97!Sox3;;chr6:53523358..53523388,+!p1@Creb5!0.59!42.15!Creb5;;chr18:75527009..75527027,+!p1@Smad7!0.58!72.45!Smad7;;chr10:44178521..44178557,-!p1@Prdm1!0.58!5.51!Prdm1;;chr2:32219200..32219213,+!p5@Ciz1!0.58!3.81!Ciz1;;chr12:100631123..100631206,-!p3@Foxn3!0.57!18.85!Foxn3;;chr11:96690779..96690790,-!p3@Nfe2l1!0.57!7.63!Nfe2l1;;chr14:63864056..63864102,-!p1@Gata4!0.57!5.30!Gata4;;chr11:95170996..95171026,-!p3@Myst2!0.57!2.75!Myst2;;chr5:144951136..144951139,+!p2@Bhlha15!0.57!2.75!Bhlha15;;chr14:79880971..79880992,+!p2@Elf1!0.56!41.94!Elf1;;chr9:69137716..69137744,+!p1@Rora!0.56!20.55!Rora;;chr3:87945895..87945946,+!p2@Mef2d!0.56!10.17!Mef2d;;chr11:53164533..53164548,+!p4@Aff4!0.56!9.11!Aff4;;chr9:96653072..96653154,-!p1@Zbtb38!0.56!8.26!Zbtb38;;chr8:94325847..94325869,-!p3@Irx3!0.56!4.66!Irx3;;chr19:59533221..59533271,+!p1@Emx2!0.56!3.39!Emx2;;chr15:36937137..36937157,-!p2@Gm10193,p2@Zfp706!0.55!97.87!Zfp706;;chr11:96690797..96690813,-!p1@Nfe2l1!0.55!62.07!Nfe2l1;;chr7:71083428..71083518,-!p3@Klf13!0.55!24.15!Klf13;;chr7:17647736..17647772,-!p1@Hif3a!0.55!11.02!Hif3a;;chr17:71202822..71202877,-!p3@Tgif1!0.55!8.90!Tgif1;;chr15:82742573..82742620,-!p2@Tcf20!0.55!2.54!Tcf20;;chr15:102828658..102828678,+!p1@Hoxc6!0.55!2.54!Hoxc6;;chr11:69468531..69468557,+!p1@Sox15!0.55!2.54!Sox15;;chr2:72817045..72817123,-!p1@Sp3!0.54!102.74!Sp3;;chr13:5860749..5860772,+!p2@Klf6!0.54!30.72!Klf6;;chr7:119822940..119822945,+!p6@Tead1!0.54!3.39!Tead1;;chr6:37392095..37392154,-!p1@Creb3l2!0.53!96.60!Creb3l2;;chr8:125778192..125778217,+!p2@Zfp276!0.52!7.84!Zfp276;;chr11:95170871..95170900,-!p2@Myst2!0.52!7.41!Myst2;;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+|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0005795,UBERON:0004872,UBERON:0003124,UBERON:0010316
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:577-18G3
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011384
+|is_a=EFO:0002091;;FF:0011384
+|is_obsolete=
+|library_id=CNhs10464
+|library_id_phase_based=2:CNhs10464
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;577
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;577
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day17.CNhs10464.577-18G3.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day17.CNhs10464.577-18G3.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day17.CNhs10464.577-18G3.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day17.CNhs10464.577-18G3.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/placenta%252c%2520adult%2520pregnant%2520day17.CNhs10464.577-18G3.mm9.nobarcode.rdna.fa.gz
 |name=placenta, adult pregnant day17
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10464,LSID646,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0.0123291635764751,0,0,0,-0.00392500877943558,0,0.0448550198638651,0,0,1.53328927733785,0,0,0.266544079535733,0,0,0,-0.108450909063967,0,0,0,0,0,0,0,0,0,0,0,0,0.0360693504677301,0.0624916975348053,0,0,0,0.153407546465022,0,0.0990653624990877,0,0.19576472698848,0.220995083143744,-0.186426196191743,0,0,0,0,0,0,0,0,0,0,0,0,0.087401998901582,2.52539599993395,0,0,0,0,0,0,0,0,0,0.0392280514125778,-0.0441065778036531,-0.0746486009524746,-0.0089486284138055,0,0.135640941990593,0.00155139993234354,0.171908717940459,0,0,0,-0.0703088570909237,-0.0734507223776035,-0.0788315948399074,0,0,0,0,0,0,-0.00396614092322711,4.88989793101524e-06,0.0385850857635145,0,0,0.083442441818608,0,0
 |rna_box=18
 |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=placenta
 |top_motifs=BACH2:2.0706562031;NANOG{mouse}:2.00380492106;HIF1A:1.96782130006;SREBF1,2:1.94978140942;XCPE1{core}:1.88155687584;SP1:1.82199729501;PAX2:1.7898267939;FOSL2:1.76542663014;ATF6:1.56803110277;FOS_FOS{B,L1}_JUN{B,D}:1.56315655972;FOXO1,3,4:1.32937251527;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.31624608688;PAX1,9:1.19329740747;ZNF148:1.17412804671;TEAD1:1.06126445072;HAND1,2:1.00396053927;RXRA_VDR{dimer}:0.979566286883;GZF1:0.976733420724;FOX{F1,F2,J1}:0.898710956231;ALX4:0.892871707698;NFE2:0.892260880754;FOX{D1,D2}:0.86822035269;SPZ1:0.707942714515;ATF2:0.703109785829;CEBPA,B_DDIT3:0.673012584028;NFE2L2:0.667408724894;STAT2,4,6:0.627065456182;ATF4:0.624091522266;GFI1B:0.623860354715;IRF1,2:0.598831457126;IKZF2:0.590596862988;TBX4,5:0.587070627815;EBF1:0.557111183229;TFCP2:0.554077269719;ZEB1:0.541342099927;NFE2L1:0.511651572946;ELK1,4_GABP{A,B1}:0.496529099104;FOXP3:0.486382130664;NFATC1..3:0.485263199336;TFAP2{A,C}:0.479723937474;ELF1,2,4:0.473534413314;MAZ:0.460815293114;SNAI1..3:0.460123876697;TP53:0.422511172017;FOXM1:0.406191162957;ZNF143:0.39355920707;CREB1:0.386743131437;EN1,2:0.380402914769;TBP:0.349448237661;HLF:0.340818483055;HOXA9_MEIS1:0.336943327893;IKZF1:0.329980648712;GCM1,2:0.281686291758;FOXN1:0.266511796566;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.266249942224;GLI1..3:0.264322559052;MAFB:0.259327353907;SRF:0.257430403161;SMAD1..7,9:0.239656829839;ETS1,2:0.228549360671;NKX3-2:0.219246368141;SOX5:0.212137271709;EP300:0.202994458535;MTE{core}:0.198658149379;FOXA2:0.163276671909;ESR1:0.156325031061;PITX1..3:0.121092838048;HNF1A:0.117271322653;SPIB:0.114630717079;ALX1:0.110704990594;HNF4A_NR2F1,2:0.0819663373838;EVI1:0.074798945315;TFAP2B:0.0729662535546;ZIC1..3:0.072848358834;FOXP1:-0.00133123625334;BPTF:-0.012986271532;FOX{I1,J2}:-0.0253878354379;PAX4:-0.0278830612608;HMX1:-0.0311172886559;SPI1:-0.0508121475136;NHLH1,2:-0.0531481992667;GTF2A1,2:-0.0762411255213;EGR1..3:-0.0939503612171;NFKB1_REL_RELA:-0.0945541526911;PATZ1:-0.152051167764;AIRE:-0.163372791191;PAX5:-0.181921786365;POU3F1..4:-0.214947195187;RREB1:-0.225899211603;ZNF238:-0.23744164095;ZNF423:-0.241054639412;STAT1,3:-0.249280255972;AR:-0.270653596713;HMGA1,2:-0.280488927752;CDC5L:-0.281101574867;JUN:-0.300849283597;LEF1_TCF7_TCF7L1,2:-0.325574089749;ESRRA:-0.328440137065;ATF5_CREB3:-0.339011628254;GATA6:-0.34494366036;TOPORS:-0.345264155513;REST:-0.375599788782;RXR{A,B,G}:-0.380137203177;ZBTB16:-0.383004501826;TGIF1:-0.384206502395;ZBTB6:-0.394124269753;GTF2I:-0.403938534389;TFDP1:-0.413206169769;bHLH_family:-0.41556033661;MYFfamily:-0.452226718832;NRF1:-0.472299717372;NKX3-1:-0.475140689864;UFEwm:-0.476209846746;NKX2-3_NKX2-5:-0.47774964235;ARID5B:-0.479165954848;GATA4:-0.483908439527;VSX1,2:-0.51083224374;MEF2{A,B,C,D}:-0.518878446488;MTF1:-0.523638993982;PDX1:-0.565597553928;RUNX1..3:-0.566675904306;MED-1{core}:-0.568099623585;CDX1,2,4:-0.608495697935;ZFP161:-0.617106126344;RFX2..5_RFXANK_RFXAP:-0.625755259385;NFIL3:-0.643339222658;PRRX1,2:-0.644365173611;MYB:-0.647644018215;TLX1..3_NFIC{dimer}:-0.650509542524;MYBL2:-0.659180464886;T:-0.664920957622;RFX1:-0.676449453256;NANOG:-0.677047994968;FOXD3:-0.696624962224;SOX2:-0.713332992053;FOXQ1:-0.721292577549;PPARG:-0.749095826268;CRX:-0.764588890289;MZF1:-0.791088965208;MYOD1:-0.791293459819;TFAP4:-0.792909378693;ONECUT1,2:-0.821109537267;BREu{core}:-0.825524040594;HBP1_HMGB_SSRP1_UBTF:-0.826356014064;NKX2-2,8:-0.828710661743;NKX6-1,2:-0.848723960468;KLF4:-0.863266692991;NFY{A,B,C}:-0.864512418714;PAX6:-0.876062264844;FOXL1:-0.885730570872;HIC1:-0.888652658539;LHX3,4:-0.89555803256;TAL1_TCF{3,4,12}:-0.90136634535;HSF1,2:-0.913952811958;PAX8:-0.927812525993;CUX2:-0.939039629815;IRF7:-0.957319648237;AHR_ARNT_ARNT2:-0.991148024315;RORA:-1.01672161556;SOX17:-1.02226848774;E2F1..5:-1.03214211077;DBP:-1.05326115048;POU2F1..3:-1.07619740074;NKX2-1,4:-1.10606807861;PRDM1:-1.12977048244;GFI1:-1.14138056771;HES1:-1.19820769011;DMAP1_NCOR{1,2}_SMARC:-1.22106593311;ZNF384:-1.24114105911;OCT4_SOX2{dimer}:-1.25188112757;HOX{A4,D4}:-1.27239957524;NFIX:-1.2799205104;TEF:-1.31382840572;POU6F1:-1.32180614087;NR5A1,2:-1.32504506072;LMO2:-1.36641717928;NR6A1:-1.39112718715;ADNP_IRX_SIX_ZHX:-1.44071904349;NR1H4:-1.51281125329;POU5F1:-1.566776516;STAT5{A,B}:-1.63627561255;SOX{8,9,10}:-1.66645106399;HOX{A5,B5}:-1.82535038475;TLX2:-2.02901972663;POU1F1:-2.06865965466;YY1:-2.07499543413;PBX1:-2.12847034827;RBPJ:-2.17181093905;NR3C1:-2.46818383943
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:577-18G3;search_select_hide=table117:577-18G3
 }}

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FF:577-18G3: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:18, 4 June 2020

CNhs10464

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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