FF:432-17C5: Difference between revisions

Latest revision as of 19:16, 4 June 2020

Name:	lung, embryo E15
Species:	Mouse (Mus musculus)
Library ID:	CNhs11020
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	lung
dev stage	15 days embryo
sex	mixture
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		SAMD00005866

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11020		CAGE		DRX009033		DRR009907

Accession ID Mm9

Library id		BAM		CTSS
CNhs11020		DRZ001332		DRZ002715

Accession ID Mm10

Library id		BAM		CTSS
CNhs11020		DRZ012682		DRZ014065

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

CNhs11020

0	0
1	0
10	0
100	0
1000	0
1001	0.0241
1002	0.128
1003	0.0665
1004	0
1005	-0.096
1006	-0.138
1007	0.0915
1008	0
1009	0.15
101	0.115
1010	0
1011	0
1012	0
1013	-0.17
1014	0.364
1015	0.226
1016	0.21
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.00109
1022	-0.0484
1023	0
1024	0.0956
1025	0.919
1026	0
1027	0.043
1028	0
1029	0.306
103	0.13
1030	0
1031	0.394
1032	-0.0504
1033	0.00159
1034	0
1035	0
1036	0.223
1037	0
1038	0.158
1039	-0.0991
104	0
1040	0.206
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: CNhs11020

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.0037
MA0003.1	MA0003.1	0.371
MA0004.1	MA0004.1	0.627
MA0006.1	MA0006.1	0.897
MA0007.1	MA0007.1	0.285
MA0009.1	MA0009.1	0.548
MA0014.1	MA0014.1	0.333
MA0017.1	MA0017.1	1.14548e-4
MA0018.2	MA0018.2	0.0799
MA0019.1	MA0019.1	0.529
MA0024.1	MA0024.1	4.34845e-9
MA0025.1	MA0025.1	0.163
MA0027.1	MA0027.1	0.0295
MA0028.1	MA0028.1	0.11
MA0029.1	MA0029.1	0.637
MA0030.1	MA0030.1	0.223
MA0031.1	MA0031.1	0.0104
MA0035.2	MA0035.2	0.00446
MA0038.1	MA0038.1	0.127
MA0039.2	MA0039.2	0.0318
MA0040.1	MA0040.1	0.496
MA0041.1	MA0041.1	0.202
MA0042.1	MA0042.1	0.302
MA0043.1	MA0043.1	0.94
MA0046.1	MA0046.1	2.82406e-10
MA0047.2	MA0047.2	0.708
MA0048.1	MA0048.1	9.5677e-4
MA0050.1	MA0050.1	2.12865e-4
MA0051.1	MA0051.1	4.28927e-4
MA0052.1	MA0052.1	0.0575
MA0055.1	MA0055.1	0.00148
MA0057.1	MA0057.1	0.224
MA0058.1	MA0058.1	0.548
MA0059.1	MA0059.1	0.757
MA0060.1	MA0060.1	2.31021e-5
MA0061.1	MA0061.1	0.0852
MA0062.2	MA0062.2	0.702
MA0065.2	MA0065.2	2.61974e-4
MA0066.1	MA0066.1	0.0181
MA0067.1	MA0067.1	0.136
MA0068.1	MA0068.1	0.973
MA0069.1	MA0069.1	0.615
MA0070.1	MA0070.1	0.351
MA0071.1	MA0071.1	0.0169
MA0072.1	MA0072.1	0.003
MA0073.1	MA0073.1	0.592
MA0074.1	MA0074.1	0.521
MA0076.1	MA0076.1	0.288
MA0077.1	MA0077.1	0.492
MA0078.1	MA0078.1	0.529
MA0079.2	MA0079.2	0.0703
MA0080.2	MA0080.2	4.66735e-5
MA0081.1	MA0081.1	0.575
MA0083.1	MA0083.1	0.0172
MA0084.1	MA0084.1	0.683
MA0087.1	MA0087.1	0.693
MA0088.1	MA0088.1	0.641
MA0090.1	MA0090.1	0.273
MA0091.1	MA0091.1	0.816
MA0092.1	MA0092.1	0.626
MA0093.1	MA0093.1	0.612
MA0099.2	MA0099.2	1.15773e-5
MA0100.1	MA0100.1	0.643
MA0101.1	MA0101.1	0.5
MA0102.2	MA0102.2	0.673
MA0103.1	MA0103.1	0.00388
MA0104.2	MA0104.2	0.842
MA0105.1	MA0105.1	0.038
MA0106.1	MA0106.1	0.642
MA0107.1	MA0107.1	0.309
MA0108.2	MA0108.2	0.0644
MA0111.1	MA0111.1	0.35
MA0112.2	MA0112.2	0.0052
MA0113.1	MA0113.1	0.175
MA0114.1	MA0114.1	8.2418e-5
MA0115.1	MA0115.1	0.0501
MA0116.1	MA0116.1	0.504
MA0117.1	MA0117.1	0.0293
MA0119.1	MA0119.1	0.507
MA0122.1	MA0122.1	0.365
MA0124.1	MA0124.1	0.312
MA0125.1	MA0125.1	0.943
MA0131.1	MA0131.1	0.256
MA0135.1	MA0135.1	0.178
MA0136.1	MA0136.1	3.59743e-4
MA0137.2	MA0137.2	0.049
MA0138.2	MA0138.2	3.63063e-6
MA0139.1	MA0139.1	0.413
MA0140.1	MA0140.1	0.178
MA0141.1	MA0141.1	0.00101
MA0142.1	MA0142.1	0.666
MA0143.1	MA0143.1	0.244
MA0144.1	MA0144.1	0.175
MA0145.1	MA0145.1	0.118
MA0146.1	MA0146.1	0.561
MA0147.1	MA0147.1	0.903
MA0148.1	MA0148.1	0.625
MA0149.1	MA0149.1	0.0641
MA0150.1	MA0150.1	4.94858e-5
MA0152.1	MA0152.1	0.0685
MA0153.1	MA0153.1	1.37683e-5
MA0154.1	MA0154.1	0.031
MA0155.1	MA0155.1	0.371
MA0156.1	MA0156.1	0.234
MA0157.1	MA0157.1	0.164
MA0159.1	MA0159.1	0.00614
MA0160.1	MA0160.1	0.0012
MA0162.1	MA0162.1	0.867
MA0163.1	MA0163.1	0.923
MA0164.1	MA0164.1	0.942
MA0258.1	MA0258.1	4.21311e-4
MA0259.1	MA0259.1	0.638

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: CNhs11020

Novel motif	Logo	P-value
1	1	0.248
10	10	0.715
100	100	0.763
101	101	0.739
102	102	0.933
103	103	0.702
104	104	0.64
105	105	0.662
106	106	0.189
107	107	0.644
108	108	0.69
109	109	0.148
11	11	0.126
110	110	0.824
111	111	0.0697
112	112	0.129
113	113	0.567
114	114	0.0305
115	115	0.531
116	116	0.997
117	117	0.822
118	118	0.724
119	119	0.0718
12	12	0.534
120	120	0.148
121	121	0.74
122	122	0.735
123	123	0.166
124	124	0.846
125	125	0.595
126	126	0.826
127	127	0.451
128	128	0.147
129	129	0.0676
13	13	0.108
130	130	0.0253
131	131	0.314
132	132	0.924
133	133	0.659
134	134	0.459
135	135	0.819
136	136	0.962
137	137	0.887
138	138	0.762
139	139	0.00833
14	14	0.322
140	140	0.473
141	141	0.46
142	142	0.865
143	143	0.676
144	144	0.707
145	145	0.968
146	146	0.101
147	147	0.314
148	148	0.243
149	149	0.338
15	15	0.138
150	150	0.766
151	151	0.0483
152	152	0.177
153	153	0.362
154	154	0.722
155	155	0.887
156	156	0.335
157	157	0.958
158	158	0.845
159	159	0.0208
160	160	0.239
161	161	0.997
162	162	0.824
163	163	0.0366
164	164	0.716
165	165	0.214
166	166	0.158
167	167	0.927
168	168	0.456
169	169	0.372
17	17	0.15
18	18	0.0752
19	19	0.708
2	2	0.378
20	20	0.476
21	21	0.408
22	22	0.495
23	23	0.0602
24	24	0.668
25	25	0.234
26	26	0.0531
27	27	0.18
28	28	0.234
29	29	0.616
3	3	0.283
30	30	0.475
31	31	0.219
32	32	0.0944
33	33	0.933
34	34	0.679
35	35	0.155
36	36	0.528
37	37	0.352
38	38	0.544
39	39	0.578
4	4	0.633
40	40	0.396
41	41	0.224
42	42	0.604
43	43	0.266
44	44	0.0222
45	45	0.198
46	46	0.52
47	47	0.261
48	48	0.145
49	49	0.191
5	5	0.461
50	50	0.539
51	51	0.654
52	52	0.569
53	53	0.655
54	54	0.24
55	55	0.544
56	56	0.355
57	57	0.968
58	58	0.282
59	59	0.251
6	6	0.755
60	60	0.307
61	61	0.862
62	62	0.0599
63	63	0.358
64	64	0.309
65	65	0.164
66	66	0.77
67	67	0.419
68	68	0.155
69	69	0.731
7	7	0.876
70	70	7.17346e-4
71	71	0.544
72	72	0.132
73	73	0.0954
74	74	0.646
75	75	0.366
76	76	0.322
77	77	0.164
78	78	0.462
79	79	0.87
8	8	0.462
80	80	0.147
81	81	0.113
82	82	0.13
83	83	0.912
84	84	0.248
85	85	0.036
86	86	0.406
87	87	0.00466
88	88	0.354
89	89	0.245
9	9	0.749
90	90	0.0383
91	91	0.69
92	92	0.065
93	93	0.979
94	94	0.774
95	95	0.366
96	96	0.387
97	97	0.187
98	98	0.204
99	99	0.993

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: CNhs11020

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011348 mouse lung- embryo E15 sample

part_of relathionship
UBERON:0000310 breast

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)
0000922 (embryo)
0002048 (lung)
0000310 (breast)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0001443 (chest)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000298 (mouse embryonic day 15 sample)
0011348 (mouse lung- embryo E15 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:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002048,UBERON:0000310,UBERON:0002100,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005153,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0009569,UBERON:0005291,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0003104,UBERON:0000464,UBERON:0001048,UBERON:0000925,UBERON:0005181,UBERON:0006598,UBERON:0004185,UBERON:0005157,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0001443,UBERON:0007026,UBERON:0001041,UBERON:0002224,UBERON:0000915,UBERON:0009142,UBERON:0008947,UBERON:0003258,UBERON:0005597,UBERON:0006595,UBERON:0006603,UBERON:0000118
+|DRA_sample_Accession=CAGE@SAMD00005866
+|accession_numbers=CAGE;DRX009033;DRR009907;DRZ001332;DRZ002715;DRZ012682;DRZ014065
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002048,UBERON:0000310,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0001443,UBERON:0002224,UBERON:0000915
 |ancestors_in_cell_lineage_facet=
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000298,FF:0011348
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr11:85699862..85699920,+!p1@Tbx4!1.91!79.78!Tbx4;;chr10:22539932..22539956,-!p1@Tcf21!1.76!146.83!Tcf21;;chr8:123608252..123608268,+!p1@Foxf1a!1.54!49.40!Foxf1a;;chr2:180069370..180069409,-!p1@Gata5!1.54!39.72!Gata5;;chr6:14851440..14851497,+!p2@Foxp2!1.40!57.20!Foxp2;;chr12:57636220..57636236,-!p3@Nkx2-1!1.34!20.71!Nkx2-1;;chr11:85646303..85646329,+!p1@Tbx2!1.27!115.43!Tbx2;;chr12:57636240..57636256,-!p4@Nkx2-1!1.27!17.82!Nkx2-1;;chr12:57636178..57636194,-!p2@Nkx2-1!1.25!16.80!Nkx2-1;;chr13:31717548..31717596,+!p1@Foxf2!1.24!32.59!Foxf2;;chr13:72101161..72101177,-!p2@Irx1!1.22!21.39!Irx1;;chr6:52154386..52154407,-!p2@Hoxa5!1.21!19.18!Hoxa5;;chr13:72766250..72766273,+!p1@Irx2!1.18!22.07!Irx2;;chr2:147871627..147871641,-!p1@Foxa2!1.17!13.75!Foxa2;;chr11:85646263..85646278,+!p2@Tbx2!1.15!33.10!Tbx2;;chr13:72766279..72766296,+!p2@Irx2!1.13!18.67!Irx2;;chr12:37835141..37835194,+!p1@Meox2!1.12!38.02!Meox2;;chr12:37835120..37835133,+!p2@Meox2!1.12!17.48!Meox2;;chr9:24578720..24578735,-!p1@Tbx20!1.10!11.71!Tbx20;;chr6:52154414..52154462,-!p1@Hoxa5!1.09!15.62!Hoxa5;;chr11:85703483..85703508,+!p2@Tbx4!1.09!11.37!Tbx4;;chr16:14705961..14705978,+!p2@Snai2!1.08!51.43!Snai2;;chr12:58646974..58647003,-!p1@Foxa1!1.08!14.94!Foxa1;;chr6:14851287..14851342,+!p1@Foxp2!1.07!35.82!Foxp2;;chr3:30408603..30408668,-!p1@Mecom!1.07!24.78!Mecom;;chr12:57636034..57636087,-!p1@Nkx2-1!1.07!10.69!Nkx2-1;;chr2:103264213..103264233,+!p1@Elf5!1.05!10.18!Elf5;;chr6:14853484..14853504,+!p14@Foxp2!1.03!9.68!Foxp2;;chr16:14705925..14705951,+!p1@Snai2!1.01!66.20!Snai2;;chr6:14851212..14851226,+!p12@Foxp2!1.01!9.34!Foxp2;;chr7:17647736..17647772,-!p1@Hif3a!0.99!31.74!Hif3a;;chr12:57637732..57637777,-!p5@Nkx2-1!0.99!8.83!Nkx2-1;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.98!14.94!Hoxb2;;chr6:14851250..14851277,+!p4@Foxp2!0.98!11.20!Foxp2;;chr6:14851403..14851422,+!p8@Foxp2!0.98!8.49!Foxp2;;chr3:30408674..30408716,-!p2@Mecom!0.97!13.75!Mecom;;chr11:96164821..96164865,+!p1@Hoxb5!0.95!7.98!Hoxb5;;chr10:126778916..126778974,-!p1@Gli1!0.94!17.82!Gli1;;chr11:96164905..96164919,+!p2@Hoxb5!0.94!7.64!Hoxb5;;chr6:14851344..14851364,+!p6@Foxp2!0.92!9.00!Foxp2;;chr2:167363692..167363710,+!p1@Snai1!0.91!90.47!Snai1;;chr11:18918434..18918489,-!p3@Meis1!0.91!11.54!Meis1;;chr8:94325814..94325839,-!p2@Irx3!0.90!14.94!Irx3;;chr12:3891810..3891829,+!p2@Dnmt3a!0.90!11.03!Dnmt3a;;chr5:120285144..120285160,+!p1@Tbx5!0.87!6.45!Tbx5;;chr11:85646341..85646352,+!p3@Tbx2!0.85!12.39!Tbx2;;chr8:94325847..94325869,-!p3@Irx3!0.85!10.01!Irx3;;chr11:83664365..83664383,+!p1@Hnf1b!0.84!5.94!Hnf1b;;chr16:22439654..22439676,-!p2@Etv5!0.83!36.33!Etv5;;chr3:34548909..34548927,+!p1@Sox2!0.83!10.01!Sox2;;chr18:53623836..53623839,+!p1@Prdm6!0.83!6.79!Prdm6;;chr11:96180069..96180089,+!p3@Hoxb4!0.83!5.77!Hoxb4;;chr11:96180045..96180059,+!p1@Hoxb4!0.82!8.15!Hoxb4;;chr6:14851377..14851396,+!p10@Foxp2!0.82!5.60!Foxp2;;chr8:94881733..94881790,+!p1@Irx5!0.80!10.86!Irx5;;chr13:72101178..72101203,-!p1@Irx1!0.80!8.66!Irx1;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.80!6.79!Hoxb2;;chr12:57637882..57637924,-!p6@Nkx2-1!0.80!5.26!Nkx2-1;;chr10:12810631..12810649,+!p1@Plagl1!0.79!148.19!Plagl1;;chr16:22439681..22439698,-!p1@Etv5!0.79!97.77!Etv5;;chr8:94325321..94325366,-!p1@Irx3!0.78!12.90!Irx3;;chr8:94325486..94325510,-!p4@Irx3!0.78!6.79!Irx3;;chr6:14851547..14851571,+!p7@Foxp2!0.78!6.11!Foxp2;;chr11:85703335..85703350,+!p4@Tbx4!0.78!5.09!Tbx4;;chr2:103264245..103264268,+!p2@Elf5!0.76!4.75!Elf5;;chr2:44968721..44968734,-!p6@Zeb2!0.75!19.18!Zeb2;;chr9:71743854..71743909,-!p1@Tcf12!0.74!39.21!Tcf12;;chr11:101755669..101755686,-!p1@Meox1!0.74!8.49!Meox1;;chr12:3891753..3891801,+!p4@Dnmt3a!0.74!7.81!Dnmt3a;;chr18:11052642..11052659,+!p1@Gata6!0.73!24.27!Gata6;;chr11:85646469..85646488,+!p5@Tbx2!0.73!6.79!Tbx2;;chr11:18918406..18918431,-!p6@Meis1!0.73!6.11!Meis1;;chrX:48559194..48559210,-!p4@Mbnl3!0.73!5.60!Mbnl3;;chr13:31717597..31717613,+!p2@Foxf2!0.73!4.41!Foxf2;;chr12:28027561..28027591,-!p1@Sox11!0.72!31.40!Sox11;;chrX:45245679..45245702,-!p1@Smarca1!0.72!20.88!Smarca1;;chr13:72101141..72101158,-!p3@Irx1!0.72!5.43!Irx1;;chr7:52471143..52471186,+!p1@Tead2!0.71!49.57!Tead2;;chr5:120120667..120120685,+!p3@Tbx3!0.71!8.49!Tbx3;;chr12:37835203..37835218,+!p3@Meox2!0.71!5.09!Meox2;;chr4:82151274..82151290,-!p3@Nfib!0.70!74.52!Nfib;;chr14:22807107..22807119,-!p2@Zfp503!0.69!19.18!Zfp503;;chr12:37835248..37835260,+!p4@Meox2!0.69!3.90!Meox2;;chr11:52096804..52096896,-!p1@Tcf7!0.67!33.95!Tcf7;;chr13:15555670..15555771,+!p2@Gli3!0.66!10.01!Gli3;;chr6:52114821..52114828,-!p1@Hoxa2!0.66!5.77!Hoxa2;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.66!4.92!Hoxb2;;chr1:4483679..4483695,-!p1@Sox17!0.65!18.84!Sox17;;chr14:63864056..63864102,-!p1@Gata4!0.65!6.45!Gata4;;chr2:180069423..180069434,-!p2@Gata5!0.63!3.23!Gata5;;chr1:120879128..120879183,-!p3@Gli2!0.62!6.62!Gli2;;chr11:85646427..85646451,+!p4@Tbx2!0.62!6.11!Tbx2;;chr11:70043257..70043263,-!p1@Bcl6b!0.62!5.94!Bcl6b;;chr8:111227518..111227550,+!p@chr8:111227518..111227550,+!0.62!5.94!Zfhx3;;chr4:82151178..82151262,-!p1@Nfib!0.61!150.39!Nfib;;chr10:119913310..119913366,-!p1@Hmga2!0.61!28.86!Hmga2;;chr2:44968737..44968758,-!p2@Zeb2!0.61!21.05!Zeb2;;chr19:19185671..19185693,-!p1@Rorb!0.61!8.32!Rorb;;chr6:14851605..14851614,+!p17@Foxp2!0.61!3.06!Foxp2;;chr12:57637700..57637717,-!p9@Nkx2-1!0.61!3.06!Nkx2-1;;chr14:22807083..22807104,-!p1@Zfp503!0.60!62.98!Zfp503;;chr11:18918917..18918944,-!p1@Meis1!0.60!46.17!Meis1;;chr13:30077847..30077906,-!p1@E2f3!0.60!28.01!E2f3;;chr18:65741358..65741415,+!p1@Zfp532!0.60!15.11!Zfp532;;chr5:120121446..120121461,+!p2@Tbx3!0.60!11.54!Tbx3;;chr4:13670571..13670625,+!p1@Runx1t1!0.60!9.34!Runx1t1;;chr18:65741935..65741964,+!p2@Zfp532!0.60!9.34!Zfp532;;chr2:70313168..70313184,+!p1@Sp5!0.59!4.75!Sp5;;chr7:17642053..17642066,-!p2@Hif3a!0.59!4.41!Hif3a;;chr6:52141694..52141715,-!p1@Hoxa4!0.59!3.90!Hoxa4;;chr11:96160426..96160443,+!p2@Hoxb6!0.59!2.89!Hoxb6;;chr15:76287876..76287894,+!p1@Scx!0.58!18.50!Scx;;chr1:170361730..170361769,-!p7@Pbx1!0.58!7.30!Pbx1;;chr3:30408384..30408431,-!p4@Mecom!0.58!3.73!Mecom;;chr12:12948633..12948651,-!p1@Mycn!0.57!32.25!Mycn;;chr14:98568971..98569025,-!p1@Dach1!0.57!25.80!Dach1;;chr4:126703093..126703158,+!p3@Sfpq!0.57!9.00!Sfpq;;chr2:35960919..35960954,-!p1@Lhx6!0.57!5.77!Lhx6;;chr6:52163319..52163342,-!p1@Hoxa3!0.57!4.24!Hoxa3;;chr15:37162834..37162849,+!p2@Grhl2!0.57!3.39!Grhl2;;chr12:57637649..57637665,-!p8@Nkx2-1!0.57!2.72!Nkx2-1;;chr14:56443806..56443848,+!p1@Nfatc4!0.56!6.11!Nfatc4;;chr14:98568761..98568814,-!p2@Dach1!0.55!21.56!Dach1;;chr14:64562503..64562524,+!p1@Sox7!0.55!18.33!Sox7;;chr17:35031460..35031518,+!p1@Zbtb12!0.55!15.62!Zbtb12;;chr18:11052606..11052633,+!p4@Gata6!0.55!7.64!Gata6;;chr11:3189683..3189744,+!p2@Patz1!0.55!5.94!Patz1;;chr4:82151126..82151133,-!p8@Nfib!0.55!3.56!Nfib;;chr12:58647114..58647128,-!p2@Foxa1!0.55!2.55!Foxa1;;chr2:44968512..44968530,-!p1@Zeb2!0.54!68.75!Zeb2;;chr10:110182489..110182589,+!p1@E2f7!0.54!37.85!E2f7;;chr17:48061584..48061601,-!p2@Foxp4!0.54!20.20!Foxp4;;chr15:37162796..37162828,+!p1@Grhl2!0.54!4.58!Grhl2;;chr11:116196664..116196679,-!p1@Foxj1!0.54!4.24!Foxj1;;chr10:86956396..86956411,-!p1@Ascl1!0.54!4.24!Ascl1;;chr13:15555496..15555544,+!p1@Gli3!0.53!10.18!Gli3;;chr2:104966766..104966786,+!p1@Wt1!0.53!4.24!Wt1;;chr13:15555555..15555574,+!p5@Gli3!0.53!3.39!Gli3;;chr13:31717614..31717628,+!p3@Foxf2!0.53!2.38!Foxf2;;chr2:147871948..147871977,-!p3@Foxa2!0.53!2.38!Foxa2;;chr6:52158644..52158677,-!p2@Hoxa6!0.53!2.38!Hoxa6;;chr17:26978409..26978442,-!p1@Nkx2-5!0.53!2.38!Nkx2-5;;chr8:123651727..123651748,+!p1@ENSMUST00000062634!0.53!2.38!Foxl1;;chr10:92773591..92773623,-!p1@Elk3!0.52!67.39!Elk3;;chr11:18918959..18918976,-!p2@Meis1!0.52!39.89!Meis1;;chr4:122911086..122911112,+!p1@Heyl!0.52!35.14!Heyl;;chr17:37139472..37139514,+!p1@Zfp57!0.52!19.86!Zfp57;;chr7:6649134..6649167,-!p1@Zim1!0.52!15.79!Zim1;;chr8:111227493..111227517,+!p@chr8:111227493..111227517,+!0.52!4.58!Zfhx3;;chr8:90483433..90483457,-!p2@Zfp423!0.52!3.39!Zfp423;;chr7:77505617..77505632,-!p1@Nr2f2!0.51!137.49!Nr2f2;;chr1:170362040..170362113,-!p2@Pbx1!0.51!22.58!Pbx1;;chrX:48558950..48559016,-!p1@Mbnl3!0.51!8.83!Mbnl3;;chr15:75447162..75447217,+!p2@Zfp41!0.51!8.15!Zfp41;;chr6:99216488..99216534,-!p2@Foxp1!0.51!7.81!Foxp1;;chr5:98609885..98609900,+!p1@Prdm8!0.51!2.21!Prdm8;;chr12:37835219..37835230,+!p5@Meox2!0.51!2.21!Meox2;;chr1:137155026..137155042,-!p1@Elf3!0.50!16.30!Elf3;;chr2:152223441..152223465,-!p2@Sox12!0.50!11.20!Sox12;;chr14:65568469..65568511,-!p2@Hmbox1!0.50!8.83!Hmbox1;;chr7:135019147..135019187,-!p3@Zfp668!0.50!5.60!Zfp668;;chr4:126700650..126700678,+!p5@Sfpq!0.50!5.09!Sfpq;;chr14:22807216..22807231,-!p3@Zfp503!0.50!4.24!Zfp503;;chr3:130813736..130813752,+!p3@Lef1!0.50!3.39!Lef1;;chr8:111227641..111227672,+!p@chr8:111227641..111227672,+!0.49!6.79!Zfhx3;;chr10:119913546..119913583,-!p3@Hmga2!0.49!5.26!Hmga2;;chr19:26681672..26681716,+!p5@Smarca2!0.48!10.86!Smarca2;;chr18:55150248..55150308,-!p6@Zfp608!0.48!5.94!Zfp608;;chr5:120121169..120121171,+!p4@Tbx3!0.48!4.24!Tbx3;;chr7:30088977..30089002,+!p2@Dpf1!0.48!3.06!Dpf1;;chr2:91034924..91034946,-!p2@Nr1h3!0.48!2.72!Nr1h3;;chr10:126778639..126778670,-!p3@Gli1!0.48!2.04!Gli1;;chr14:47896467..47896523,-!p1@Wdhd1!0.47!31.91!Wdhd1;;chr11:101413151..101413207,-!p1@Brca1!0.47!25.63!Brca1;;chrX:109714331..109714347,+!p1@Zfp711!0.47!10.52!Zfp711;;chrX:45245644..45245666,-!p2@Smarca1!0.47!7.98!Smarca1;;chr11:18918820..18918831,-!p4@Meis1!0.47!4.41!Meis1;;chr10:119913792..119913820,-!p5@Hmga2!0.47!3.90!Hmga2;;chr4:82151653..82151706,-!p2@Nfib!0.46!72.48!Nfib;;chr4:87678709..87678726,-!p4@Mllt3!0.46!7.47!Mllt3;;chr18:11052456..11052477,+!p3@Gata6!0.46!7.47!Gata6;;chr2:44966659..44966675,-!p7@Zeb2!0.46!6.96!Zeb2;;chr16:18587076..18587106,-!p1@Tbx1!0.46!3.06!Tbx1;;chr2:17976799..17976829,+!p5@Mllt10!0.46!2.55!Mllt10;;chr11:96160360..96160397,+!p3@Hoxb6!0.46!1.87!Hoxb6;;chr5:12028516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+|ffid_belonging_in_development=UBERON:0001041,UBERON:0008947,UBERON:0002532,UBERON:0006595,UBERON:0010316,FF:0000294
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:432-17C5
-|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011348
+|is_a=EFO:0002091;;FF:0011348
+|is_obsolete=
+|library_id=CNhs11020
+|library_id_phase_based=2:CNhs11020
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;432
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;432
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E15.CNhs11020.432-17C5.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E15.CNhs11020.432-17C5.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E15.CNhs11020.432-17C5.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E15.CNhs11020.432-17C5.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E15.CNhs11020.432-17C5.mm9.nobarcode.rdna.fa.gz
 |name=lung, embryo E15
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11020,LSID731,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.131942449287321,0,0,0.0680912293502604,0.0680912293502604,0.0618697529213159,0.471019565488187,0,0.030362922815961,0,0,0.723996177200526,0,0,0,0,0,0,0.180643209033375,0,0,0,0,0,0,0,0,0,0,0,0,0,0.067420020882618,0,0,0,0.0680912293502604,0.00196453970100401,-0.0858986397086539,0,-0.0665569670279529,0.544201382690606,0.187588735537718,0,0,0,0,0,0,0,0,0,0,0.178756942224084,0,0.274084562356869,0,0,0,0,-0.0147651692557635,0,0,0.0680912293502604,0.0680912293502604,0.0167480986560176,0.0955537066235346,0.120302884096529,-0.0899998134208221,0.163164610028582,0,0,0,0,0,0,0.0497827618254933,-0.0469134226909459,0.10942548717223,0.0481079364995445,0,0,0,0,0,0,0.129674089103534,0.208664744827462,-0.027913326259527,0.00578490733352337,0,0.0680912293502604,0,0
 |rna_box=17
 |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=lung
 |top_motifs=IKZF2:1.99239853601;NKX3-1:1.95246091064;ZNF384:1.78696186364;GFI1:1.53203031987;HBP1_HMGB_SSRP1_UBTF:1.38935697567;E2F1..5:1.37494153111;STAT1,3:1.35456517513;GATA4:1.2997402143;POU1F1:1.16725471655;TOPORS:1.13878088195;FOXP1:1.12195806797;TFDP1:1.05260474632;PAX4:1.02983313789;NKX6-1,2:1.01724174466;T:1.00189421004;GZF1:0.984108996683;HOX{A5,B5}:0.97635917503;ZBTB16:0.974957282781;TEF:0.973746676381;DBP:0.965275915415;EVI1:0.9189729487;EP300:0.883956351776;NFY{A,B,C}:0.830424210031;SOX2:0.819690301646;FOXD3:0.790060940236;CDX1,2,4:0.784166726075;PITX1..3:0.765254125966;HMX1:0.757444548224;SRF:0.754395005646;TEAD1:0.721349988769;ZNF238:0.709662030722;NKX2-1,4:0.706832018273;HMGA1,2:0.660014301992;MAZ:0.605211670087;BPTF:0.602450278879;IKZF1:0.594846124858;MYBL2:0.594731327274;ZNF143:0.594445173634;RREB1:0.593764718417;MZF1:0.584449678545;SOX{8,9,10}:0.574640392716;PAX6:0.565735591659;CDC5L:0.546993104944;TLX1..3_NFIC{dimer}:0.53764775722;XCPE1{core}:0.528479664837;ALX1:0.516899701813;PATZ1:0.494956210033;SOX5:0.479920052151;NANOG{mouse}:0.468281378759;FOXL1:0.452804546571;KLF4:0.428881707143;UFEwm:0.422043107611;HIF1A:0.416389529109;POU3F1..4:0.408689052446;NKX2-2,8:0.406483271648;ZNF423:0.389635675089;NRF1:0.378495783984;FOX{I1,J2}:0.341400042203;AIRE:0.337438318305;SOX17:0.328158116521;ELF1,2,4:0.327663712487;SPIB:0.317837601657;ONECUT1,2:0.295003548499;HAND1,2:0.294351781123;BREu{core}:0.27850489479;GTF2I:0.27349325248;PAX5:0.270513192739;GTF2A1,2:0.253022421211;NANOG:0.244418233671;PRDM1:0.239349180347;FOXP3:0.211713006034;RFX2..5_RFXANK_RFXAP:0.201958701082;CRX:0.196472084299;TFCP2:0.196198746521;SPZ1:0.176681823133;HIC1:0.175009441707;ZIC1..3:0.17469735926;NKX2-3_NKX2-5:0.159060900074;NKX3-2:0.153493571703;LEF1_TCF7_TCF7L1,2:0.151674412353;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.143856847268;ALX4:0.141481763913;RXR{A,B,G}:0.134750715281;FOXQ1:0.130392681875;ELK1,4_GABP{A,B1}:0.124697546354;ADNP_IRX_SIX_ZHX:0.0933195090168;RXRA_VDR{dimer}:0.0900190323307;GATA6:0.0683438706019;MYB:0.0656653316303;MEF2{A,B,C,D}:0.0513227405029;POU6F1:0.0326517788514;PRRX1,2:0.0264219970388;POU5F1:0.0144477645932;EBF1:0.0113461696296;TBX4,5:0.0108777364031;CUX2:-0.00485791385906;MED-1{core}:-0.00574966317122;RFX1:-0.0148987372786;YY1:-0.0305173836421;NFATC1..3:-0.048692701884;GFI1B:-0.0567816003014;PAX8:-0.0578898459967;TFAP2B:-0.0627268082635;OCT4_SOX2{dimer}:-0.0648088410461;NFIX:-0.0695477431276;SP1:-0.0763389329324;FOX{D1,D2}:-0.0786199595155;ZFP161:-0.0873348990845;FOXO1,3,4:-0.105741816892;EGR1..3:-0.126081911022;ETS1,2:-0.12855239619;LHX3,4:-0.13568758186;GCM1,2:-0.135756826489;NR6A1:-0.139725206807;PBX1:-0.143888551153;HOXA9_MEIS1:-0.146059638719;GLI1..3:-0.14670631269;EN1,2:-0.15000199537;DMAP1_NCOR{1,2}_SMARC:-0.163835625696;RBPJ:-0.170506371015;AHR_ARNT_ARNT2:-0.186451798491;VSX1,2:-0.202876169805;HSF1,2:-0.217350067538;TFAP4:-0.223318968205;POU2F1..3:-0.235229905765;TBP:-0.238346602066;MTE{core}:-0.24135621891;SPI1:-0.247482330272;SNAI1..3:-0.250685587385;ATF2:-0.259528835353;RUNX1..3:-0.264075938783;ARID5B:-0.27314484462;FOXA2:-0.29652011019;HNF1A:-0.307967351891;NR3C1:-0.310733250393;bHLH_family:-0.37016570359;TFAP2{A,C}:-0.38873818163;CREB1:-0.399844378371;TLX2:-0.400446921647;HNF4A_NR2F1,2:-0.412240835013;FOXN1:-0.413739902439;PAX1,9:-0.415960730182;TP53:-0.447720290081;IRF7:-0.469569633593;JUN:-0.47922369498;NFKB1_REL_RELA:-0.48483059827;IRF1,2:-0.48799732961;MTF1:-0.498099599114;NFE2L1:-0.503706223963;TGIF1:-0.514324920581;AR:-0.5279600947;REST:-0.555659329877;ZNF148:-0.574137768376;STAT5{A,B}:-0.577446645632;ZEB1:-0.595640689803;HOX{A4,D4}:-0.618031071685;NR1H4:-0.625170336397;ESR1:-0.63651058816;MYFfamily:-0.64550415377;BACH2:-0.662008873569;NFIL3:-0.670422527875;FOS_FOS{B,L1}_JUN{B,D}:-0.683372123779;HLF:-0.688765990744;FOSL2:-0.725545313984;FOX{F1,F2,J1}:-0.754790653668;PPARG:-0.766028455268;FOXM1:-0.793272180963;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.809574997312;PDX1:-0.848167791632;NHLH1,2:-0.854594234059;ZBTB6:-0.8554550263;HES1:-0.85882085854;ESRRA:-0.860316417131;ATF4:-0.863271003783;ATF5_CREB3:-0.870677827539;CEBPA,B_DDIT3:-0.898998724601;SMAD1..7,9:-0.929002581599;LMO2:-0.935941412661;PAX2:-0.936760309744;NFE2L2:-0.986975073988;RORA:-1.00213118595;TAL1_TCF{3,4,12}:-1.0368720663;ATF6:-1.11423312518;NFE2:-1.13419378589;STAT2,4,6:-1.2537579439;NR5A1,2:-1.27368457064;SREBF1,2:-1.48759162555;MYOD1:-1.51109879756;MAFB:-1.66900620006
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:432-17C5;search_select_hide=table117:432-17C5
 }}

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FF:432-17C5: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:16, 4 June 2020

CNhs11020

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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