FF:1394-42H2: Difference between revisions

Latest revision as of 19:05, 4 June 2020

Name:	lung, neonate N30
Species:	Mouse (Mus musculus)
Library ID:	CNhs11133
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	lung
dev stage	30 days neonate
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		SAMD00004674

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11133		CAGE		DRX009043		DRR009917

Accession ID Mm9

Library id		BAM		CTSS
CNhs11133		DRZ001342		DRZ002725

Accession ID Mm10

Library id		BAM		CTSS
CNhs11133		DRZ012692		DRZ014075

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

CNhs11133

0	0
1	0
10	0
100	0
1000	0.0569
1001	0.244
1002	0.0331
1003	0.112
1004	0
1005	0.166
1006	0.0139
1007	0.0371
1008	0
1009	0.399
101	-0.132
1010	0
1011	-0.0958
1012	0.0598
1013	0.0242
1014	0.0174
1015	-0.155
1016	0.0634
1017	0
1018	0.0461
1019	0
102	0
1020	0
1021	0.0444
1022	0.157
1023	0
1024	0.608
1025	1.238
1026	0
1027	0
1028	0
1029	0.247
103	0.0913
1030	0.236
1031	0.29
1032	0.106
1033	0
1034	0.437
1035	0.0375
1036	-0.153
1037	0.00849
1038	0.481
1039	0.101
104	0
1040	0.527
1041	0.271

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: CNhs11133

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.429
MA0003.1	MA0003.1	0.122
MA0004.1	MA0004.1	0.0425
MA0006.1	MA0006.1	0.0251
MA0007.1	MA0007.1	0.92
MA0009.1	MA0009.1	0.637
MA0014.1	MA0014.1	0.684
MA0017.1	MA0017.1	0.131
MA0018.2	MA0018.2	2.40091e-4
MA0019.1	MA0019.1	0.816
MA0024.1	MA0024.1	2.83067e-5
MA0025.1	MA0025.1	0.232
MA0027.1	MA0027.1	0.336
MA0028.1	MA0028.1	0.00816
MA0029.1	MA0029.1	0.422
MA0030.1	MA0030.1	0.0538
MA0031.1	MA0031.1	2.3186e-4
MA0035.2	MA0035.2	0.197
MA0038.1	MA0038.1	0.82
MA0039.2	MA0039.2	0.00134
MA0040.1	MA0040.1	0.436
MA0041.1	MA0041.1	0.333
MA0042.1	MA0042.1	0.577
MA0043.1	MA0043.1	0.0873
MA0046.1	MA0046.1	8.42748e-8
MA0047.2	MA0047.2	4.6797e-7
MA0048.1	MA0048.1	0.887
MA0050.1	MA0050.1	5.32429e-8
MA0051.1	MA0051.1	3.98371e-5
MA0052.1	MA0052.1	0.985
MA0055.1	MA0055.1	0.829
MA0057.1	MA0057.1	0.311
MA0058.1	MA0058.1	0.0307
MA0059.1	MA0059.1	0.0112
MA0060.1	MA0060.1	4.38761e-7
MA0061.1	MA0061.1	0.127
MA0062.2	MA0062.2	0.0247
MA0065.2	MA0065.2	0.559
MA0066.1	MA0066.1	0.495
MA0067.1	MA0067.1	0.903
MA0068.1	MA0068.1	0.0996
MA0069.1	MA0069.1	0.65
MA0070.1	MA0070.1	0.804
MA0071.1	MA0071.1	0.505
MA0072.1	MA0072.1	0.423
MA0073.1	MA0073.1	0.826
MA0074.1	MA0074.1	0.558
MA0076.1	MA0076.1	0.0038
MA0077.1	MA0077.1	0.0413
MA0078.1	MA0078.1	4.82441e-4
MA0079.2	MA0079.2	0.0067
MA0080.2	MA0080.2	6.1009e-8
MA0081.1	MA0081.1	0.247
MA0083.1	MA0083.1	0.159
MA0084.1	MA0084.1	0.7
MA0087.1	MA0087.1	0.959
MA0088.1	MA0088.1	0.861
MA0090.1	MA0090.1	0.0232
MA0091.1	MA0091.1	0.773
MA0092.1	MA0092.1	0.646
MA0093.1	MA0093.1	0.0366
MA0099.2	MA0099.2	0.841
MA0100.1	MA0100.1	0.228
MA0101.1	MA0101.1	0.178
MA0102.2	MA0102.2	0.216
MA0103.1	MA0103.1	0.821
MA0104.2	MA0104.2	4.91083e-4
MA0105.1	MA0105.1	0.876
MA0106.1	MA0106.1	0.0288
MA0107.1	MA0107.1	0.00519
MA0108.2	MA0108.2	0.149
MA0111.1	MA0111.1	0.523
MA0112.2	MA0112.2	0.126
MA0113.1	MA0113.1	0.133
MA0114.1	MA0114.1	0.00868
MA0115.1	MA0115.1	0.253
MA0116.1	MA0116.1	0.705
MA0117.1	MA0117.1	0.651
MA0119.1	MA0119.1	0.0473
MA0122.1	MA0122.1	0.27
MA0124.1	MA0124.1	0.79
MA0125.1	MA0125.1	0.103
MA0131.1	MA0131.1	0.212
MA0135.1	MA0135.1	0.831
MA0136.1	MA0136.1	0.00591
MA0137.2	MA0137.2	0.395
MA0138.2	MA0138.2	0.507
MA0139.1	MA0139.1	0.122
MA0140.1	MA0140.1	0.644
MA0141.1	MA0141.1	0.0146
MA0142.1	MA0142.1	0.83
MA0143.1	MA0143.1	0.239
MA0144.1	MA0144.1	0.0989
MA0145.1	MA0145.1	5.45955e-4
MA0146.1	MA0146.1	0.22
MA0147.1	MA0147.1	1.07828e-4
MA0148.1	MA0148.1	9.93415e-6
MA0149.1	MA0149.1	0.554
MA0150.1	MA0150.1	0.264
MA0152.1	MA0152.1	0.356
MA0153.1	MA0153.1	1.04493e-5
MA0154.1	MA0154.1	0.0207
MA0155.1	MA0155.1	0.288
MA0156.1	MA0156.1	3.23465e-4
MA0157.1	MA0157.1	0.00121
MA0159.1	MA0159.1	0.293
MA0160.1	MA0160.1	0.054
MA0162.1	MA0162.1	0.342
MA0163.1	MA0163.1	0.461
MA0164.1	MA0164.1	0.492
MA0258.1	MA0258.1	0.606
MA0259.1	MA0259.1	0.00327

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: CNhs11133

Novel motif	Logo	P-value
1	1	0.925
10	10	0.529
100	100	0.459
101	101	0.56
102	102	0.422
103	103	0.368
104	104	0.639
105	105	0.413
106	106	4.94388e-4
107	107	0.0038
108	108	0.638
109	109	0.284
11	11	0.977
110	110	0.949
111	111	0.416
112	112	0.46
113	113	0.758
114	114	0.783
115	115	0.476
116	116	0.632
117	117	0.172
118	118	0.82
119	119	0.131
12	12	0.612
120	120	0.158
121	121	0.24
122	122	0.838
123	123	0.921
124	124	0.585
125	125	0.492
126	126	0.332
127	127	0.66
128	128	0.00271
129	129	0.187
13	13	0.00295
130	130	0.00362
131	131	0.0305
132	132	0.367
133	133	0.757
134	134	0.678
135	135	0.745
136	136	0.901
137	137	0.455
138	138	0.0462
139	139	0.987
14	14	0.283
140	140	0.951
141	141	0.391
142	142	0.194
143	143	0.364
144	144	0.984
145	145	0.187
146	146	0.626
147	147	0.738
148	148	0.189
149	149	0.0733
15	15	0.348
150	150	0.136
151	151	0.282
152	152	0.0161
153	153	0.455
154	154	0.245
155	155	0.773
156	156	0.00683
157	157	0.737
158	158	0.974
159	159	0.108
160	160	0.16
161	161	0.67
162	162	0.459
163	163	0.748
164	164	0.649
165	165	0.935
166	166	0.115
167	167	0.367
168	168	0.26
169	169	0.0187
17	17	0.467
18	18	0.0507
19	19	0.0628
2	2	0.104
20	20	0.503
21	21	0.578
22	22	0.0965
23	23	0.0358
24	24	0.241
25	25	0.124
26	26	0.0714
27	27	0.913
28	28	0.518
29	29	0.408
3	3	0.602
30	30	0.73
31	31	0.865
32	32	0.62
33	33	0.974
34	34	0.502
35	35	0.0661
36	36	0.813
37	37	0.0529
38	38	0.163
39	39	0.0757
4	4	0.818
40	40	0.623
41	41	0.291
42	42	0.647
43	43	0.162
44	44	0.301
45	45	0.118
46	46	0.911
47	47	0.941
48	48	0.898
49	49	0.263
5	5	0.806
50	50	0.338
51	51	0.665
52	52	0.031
53	53	0.483
54	54	0.743
55	55	0.941
56	56	0.508
57	57	0.838
58	58	0.838
59	59	0.143
6	6	0.996
60	60	0.0289
61	61	0.855
62	62	0.844
63	63	0.217
64	64	0.436
65	65	0.127
66	66	0.114
67	67	0.878
68	68	0.818
69	69	0.982
7	7	0.503
70	70	0.45
71	71	0.74
72	72	0.922
73	73	0.107
74	74	0.813
75	75	0.46
76	76	0.768
77	77	0.203
78	78	0.792
79	79	0.871
8	8	0.49
80	80	0.897
81	81	0.48
82	82	0.563
83	83	0.476
84	84	0.141
85	85	0.0754
86	86	0.922
87	87	0.114
88	88	0.46
89	89	0.996
9	9	0.174
90	90	0.617
91	91	0.365
92	92	0.255
93	93	0.44
94	94	0.34
95	95	0.641
96	96	0.828
97	97	0.428
98	98	0.745
99	99	0.211

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: CNhs11133

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011489 mouse lung- neonate N30 sample

part_of relathionship
UBERON:0000170 pair of lungs

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)
0002048 (lung)
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)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011489 (mouse lung- neonate N30 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: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: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@SAMD00004674
+|accession_numbers=CAGE;DRX009043;DRR009917;DRZ001342;DRZ002725;DRZ012692;DRZ014075
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,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: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:0000004,FF:0000303,FF:0000310,FF:0011489
 |comment=
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr5:77543897..77543911,-!p2@Hopx!2.36!424.98!Hopx;;chr11:85699862..85699920,+!p1@Tbx4!1.86!71.75!Tbx4;;chr8:123608252..123608268,+!p1@Foxf1a!1.84!98.65!Foxf1a;;chr12:57636034..57636087,-!p1@Nkx2-1!1.79!60.32!Nkx2-1;;chr17:87153240..87153254,+!p1@Epas1!1.65!794.12!Epas1;;chr10:22539932..22539956,-!p1@Tcf21!1.58!96.05!Tcf21;;chr17:87153462..87153473,+!p3@Epas1!1.53!120.49!Epas1;;chr13:72101161..72101177,-!p2@Irx1!1.48!39.78!Irx1;;chr12:57636178..57636194,-!p2@Nkx2-1!1.47!28.50!Nkx2-1;;chr11:116196664..116196679,-!p1@Foxj1!1.42!38.91!Foxj1;;chr5:77543935..77543947,-!p4@Hopx!1.42!25.17!Hopx;;chr17:87153028..87153049,+!p2@Epas1!1.39!468.81!Epas1;;chr2:103264213..103264233,+!p1@Elf5!1.35!21.26!Elf5;;chr2:147871627..147871641,-!p1@Foxa2!1.32!20.11!Foxa2;;chr17:87153519..87153533,+!p5@Epas1!1.29!26.90!Epas1;;chr11:85646303..85646329,+!p1@Tbx2!1.28!116.73!Tbx2;;chr2:103143336..103143367,-!p1@Ehf!1.27!28.50!Ehf;;chr6:88148650..88148669,+!p1@Gata2!1.26!139.15!Gata2;;chr9:48644037..48644067,-!p2@Zbtb16!1.26!42.09!Zbtb16;;chr13:31717548..31717596,+!p1@Foxf2!1.22!30.52!Foxf2;;chr11:85646341..85646352,+!p3@Tbx2!1.21!29.65!Tbx2;;chr5:77544170..77544181,-!p6@Hopx!1.21!15.33!Hopx;;chr17:87153440..87153451,+!p4@Epas1!1.20!30.23!Epas1;;chr6:88143711..88143717,+!p2@Gata2!1.16!21.41!Gata2;;chr6:52154386..52154407,-!p2@Hoxa5!1.14!16.20!Hoxa5;;chr13:72101178..72101203,-!p1@Irx1!1.12!19.09!Irx1;;chr14:64562503..64562524,+!p1@Sox7!1.11!70.44!Sox7;;chr1:4486481..4486501,-!p2@Sox17!1.11!17.65!Sox17;;chr5:98609885..98609900,+!p1@Prdm8!1.11!12.01!Prdm8;;chr13:72766279..72766296,+!p2@Irx2!1.10!17.36!Irx2;;chr12:57636220..57636236,-!p3@Nkx2-1!1.10!11.57!Nkx2-1;;chr17:87153505..87153516,+!p6@Epas1!1.08!15.48!Epas1;;chr3:30408674..30408716,-!p2@Mecom!1.06!17.21!Mecom;;chr11:85646469..85646488,+!p5@Tbx2!1.06!15.77!Tbx2;;chr6:52154414..52154462,-!p1@Hoxa5!1.06!14.46!Hoxa5;;chr13:72101141..72101158,-!p3@Irx1!1.06!13.31!Irx1;;chr16:95680889..95680991,-!p1@Erg!1.05!84.33!Erg;;chr11:85646427..85646451,+!p4@Tbx2!1.03!17.21!Tbx2;;chr12:57636240..57636256,-!p4@Nkx2-1!1.03!9.84!Nkx2-1;;chr18:52775562..52775650,+!p1@Zfp474!1.03!9.84!Zfp474;;chr9:96159147..96159204,+!p2@Tfdp2!1.02!18.08!Tfdp2;;chr3:8666963..8666978,-!p1@Hey1!1.01!60.61!Hey1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.99!63.93!Tsc22d3;;chr13:72766250..72766273,+!p1@Irx2!0.99!13.89!Irx2;;chr12:58646974..58647003,-!p1@Foxa1!0.99!12.01!Foxa1;;chr2:103264245..103264268,+!p2@Elf5!0.97!8.24!Elf5;;chr2:181406327..181406350,-!p1@Sox18!0.96!257.04!Sox18;;chr11:16908650..16908690,-!p1@Plek!0.96!50.63!Plek;;chr9:48644306..48644364,-!p1@Zbtb16!0.96!33.56!Zbtb16;;chr13:99954640..99954681,+!p1@Zfp366!0.96!30.52!Zfp366;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.96!24.16!Tfcp2l1;;chr8:94325321..94325366,-!p1@Irx3!0.95!19.82!Irx3;;chr3:30408603..30408668,-!p1@Mecom!0.94!18.37!Mecom;;chr11:85646263..85646278,+!p2@Tbx2!0.93!19.82!Tbx2;;chr2:180069370..180069409,-!p1@Gata5!0.93!8.82!Gata5;;chr4:122911086..122911112,+!p1@Heyl!0.92!90.26!Heyl;;chr8:94881733..94881790,+!p1@Irx5!0.92!14.75!Irx5;;chr6:99216488..99216534,-!p2@Foxp1!0.91!21.12!Foxp1;;chr4:119486912..119486954,+!p3@Hivep3!0.91!12.73!Hivep3;;chr1:38721792..38721845,-!p1@Aff3!0.91!8.97!Aff3;;chr1:4483679..4483695,-!p1@Sox17!0.90!33.70!Sox17;;chr4:148275237..148275311,+!p2@Casz1!0.90!30.23!Casz1;;chr5:120285144..120285160,+!p1@Tbx5!0.89!6.80!Tbx5;;chr11:85703483..85703508,+!p2@Tbx4!0.89!6.80!Tbx4;;chr12:37835141..37835194,+!p1@Meox2!0.88!21.12!Meox2;;chr9:63869802..63869815,-!p3@Smad6!0.88!13.60!Smad6;;chr6:128250380..128250442,-!p2@Tead4!0.88!8.53!Tead4;;chr12:57637732..57637777,-!p5@Nkx2-1!0.88!6.65!Nkx2-1;;chr5:120120667..120120685,+!p3@Tbx3!0.86!12.30!Tbx3;;chr15:81633165..81633188,+!p2@Tef!0.84!52.07!Tef;;chr11:83664365..83664383,+!p1@Hnf1b!0.83!5.79!Hnf1b;;chr16:42907676..42907797,+!p1@Zbtb20!0.82!77.68!Zbtb20;;chr9:63869751..63869767,-!p1@Smad6!0.82!15.77!Smad6;;chr1:137155026..137155042,-!p1@Elf3!0.81!34.43!Elf3;;chr11:100683839..100683890,-!p2@Stat5b!0.81!13.60!Stat5b;;chr8:94325814..94325839,-!p2@Irx3!0.81!12.15!Irx3;;chr15:81633203..81633215,+!p3@Tef!0.81!8.97!Tef;;chr7:51787434..51787448,-!p1@Spib!0.81!8.10!Spib;;chr12:36219645..36219730,-!p1@Ahr!0.80!55.98!Ahr;;chr18:55147667..55147746,-!p2@Zfp608!0.80!26.47!Zfp608;;chr9:63869890..63869908,-!p6@Smad6!0.80!7.23!Smad6;;chr4:44723559..44723593,-!p1@Pax5!0.80!5.35!Pax5;;chr8:74842952..74842970,+!p1@Klf2!0.79!378.55!Klf2;;chr16:22439681..22439698,-!p1@Etv5!0.79!97.78!Etv5;;chr19:23215673..23215753,+!p1@Klf9!0.79!81.87!Klf9;;chr10:67599319..67599360,-!p2@Arid5b!0.78!60.75!Arid5b;;chr1:39250584..39250643,+!p1@Npas2!0.78!27.77!Npas2;;chr5:120121446..120121461,+!p2@Tbx3!0.78!17.94!Tbx3;;chr5:77544108..77544119,-!p7@Hopx!0.78!5.06!Hopx;;chr19:26679654..26679675,+!p1@Smarca2!0.77!49.90!Smarca2;;chr2:91035197..91035237,-!p1@Nr1h3!0.77!10.70!Nr1h3;;chr1:4486505..4486527,-!p5@Sox17!0.77!6.65!Sox17;;chr9:48644013..48644027,-!p5@Zbtb16!0.77!6.08!Zbtb16;;chr12:57637595..57637608,-!p7@Nkx2-1!0.77!4.92!Nkx2-1;;chr2:147871948..147871977,-!p3@Foxa2!0.77!4.92!Foxa2;;chr16:22439654..22439676,-!p2@Etv5!0.76!30.81!Etv5;;chr11:69579472..69579529,+!p1@Zbtb4!0.76!26.47!Zbtb4;;chr18:11052642..11052659,+!p1@Gata6!0.76!26.04!Gata6;;chr7:119822957..119822980,+!p2@Tead1!0.76!25.31!Tead1;;chr2:77357622..77357704,-!p1@Zfp385b!0.76!13.89!Zfp385b;;chr1:4486453..4486470,-!p3@Sox17!0.75!6.22!Sox17;;chr4:55545337..55545357,-!p1@Klf4!0.74!74.49!Klf4;;chr16:92697560..92697592,-!p2@Runx1!0.74!31.53!Runx1;;chr5:77524231..77524245,-!p3@Hopx!0.74!12.01!Hopx;;chr13:30841099..30841116,+!p1@Irf4!0.74!7.38!Irf4;;chr13:31717597..31717613,+!p2@Foxf2!0.74!4.48!Foxf2;;chr12:77278238..77278252,-!p1@Esr2!0.74!4.48!Esr2;;chr14:22807107..22807119,-!p2@Zfp503!0.73!20.97!Zfp503;;chr1:87546583..87546595,+!p1@Sp100!0.73!6.51!Sp100;;chr4:148178559..148178603,+!p1@Casz1!0.72!13.45!Casz1;;chr9:48644429..48644462,-!p3@Zbtb16!0.72!8.82!Zbtb16;;chr9:32503590..32503680,+!p1@Ets1!0.71!171.84!Ets1;;chr16:15887371..15887385,+!p1@Cebpd!0.71!158.97!Cebpd;;chr2:90936901..90936945,+!p1@Sfpi1!0.71!24.30!Sfpi1;;chr9:96653072..96653154,-!p1@Zbtb38!0.71!12.01!Zbtb38;;chr10:92773708..92773734,-!p3@Elk3!0.71!8.82!Elk3;;chr2:90936947..90936977,+!p2@Sfpi1!0.71!8.82!Sfpi1;;chr8:94325486..94325510,-!p4@Irx3!0.71!5.64!Irx3;;chr1:4486530..4486557,-!p4@Sox17!0.71!5.50!Sox17;;chr3:8666997..8667012,-!p2@Hey1!0.70!9.98!Hey1;;chr7:119822915..119822936,+!p5@Tead1!0.70!7.09!Tead1;;chr11:53583544..53583559,+!p1@Irf1!0.69!74.78!Irf1;;chr1:135320989..135321043,-!p1@Sox13!0.69!49.18!Sox13;;chr19:26681672..26681716,+!p5@Smarca2!0.69!18.23!Smarca2;;chr1:186556410..186556424,-!p1@Hlx!0.69!13.60!Hlx;;chr2:91034924..91034946,-!p2@Nr1h3!0.69!4.92!Nr1h3;;chr9:51021788..51021802,+!p1@Pou2af1!0.69!4.77!Pou2af1;;chr18:53623836..53623839,+!p1@Prdm6!0.69!4.63!Prdm6;;chr13:31717775..31717788,+!p4@Foxf2!0.69!3.91!Foxf2;;chr7:35904304..35904320,+!p1@Cebpa!0.68!89.39!Cebpa;;chr9:63869850..63869873,-!p2@Smad6!0.68!12.44!Smad6;;chr4:148178529..148178548,+!p3@Casz1!0.68!9.84!Casz1;;chr6:128250471..128250519,-!p1@Tead4!0.68!8.24!Tead4;;chr6:88148324..88148328,+!p3@Gata2!0.68!3.76!Gata2;;chr11:98407264..98407295,-!p1@Ikzf3!0.68!3.76!Ikzf3;;chr9:63869918..63869936,-!p9@Smad6!0.68!3.76!Smad6;;chr10:92773591..92773623,-!p1@Elk3!0.67!96.34!Elk3;;chr5:77524250..77524300,-!p1@Hopx!0.67!86.50!Hopx;;chr6:98978245..98978289,-!p1@Foxp1!0.67!62.34!Foxp1;;chr18:11052606..11052633,+!p4@Gata6!0.67!10.27!Gata6;;chr3:135271185..135271254,-!p4@Nfkb1!0.67!7.23!Nfkb1;;chr4:154010940..154010962,-!p3@Prdm16!0.66!8.53!Prdm16;;chr9:96653241..96653288,-!p1@E030011O05Rik,p5@Zbtb38!0.66!7.23!Zbtb38;;chr16:43363968..43364001,+!p7@Zbtb20!0.66!7.09!Zbtb20;;chr6:52114821..52114828,-!p1@Hoxa2!0.66!5.64!Hoxa2;;chr8:107793688..107793736,+!p1@Hsf4!0.66!4.92!Hsf4;;chr12:37835203..37835218,+!p3@Meox2!0.66!4.34!Meox2;;chr8:107793737..107793757,+!p2@Hsf4!0.66!4.19!Hsf4;;chr11:85699562..85699575,+!p6@Tbx4!0.66!3.62!Tbx4;;chr6:90412582..90412601,+!p1@Klf15!0.65!19.09!Klf15;;chr11:96213288..96213332,+!p@chr11:96213288..96213332,+!0.65!6.36!Hoxb2;;chr10:92773736..92773761,-!p4@Elk3!0.65!6.08!Elk3;;chr2:167363692..167363710,+!p1@Snai1!0.64!48.46!Snai1;;chr4:44723633..44723646,-!p3@Pax5!0.64!3.33!Pax5;;chr9:63869834..63869849,-!p5@Smad6!0.63!6.08!Smad6;;chr6:128250521..128250543,-!p3@Tead4!0.63!5.50!Tead4;;chr16:43363190..43363242,+!p2@Zbtb20!0.62!11.14!Zbtb20;;chr10:67599361..67599372,-!p5@Arid5b!0.62!5.35!Arid5b;;chr6:52141694..52141715,-!p1@Hoxa4!0.62!4.19!Hoxa4;;chr11:96164821..96164865,+!p1@Hoxb5!0.62!3.18!Hoxb5;;chr9:36954842..36954908,-!p1@Pknox2!0.61!42.82!Pknox2;;chr6:144730427..144730508,-!p1@Sox5!0.61!22.57!Sox5;;chr14:65568469..65568511,-!p2@Hmbox1!0.61!11.57!Hmbox1;;chr15:98126545..98126588,-!p1@Zfp641!0.61!7.52!Zfp641;;chr13:99954688..99954710,+!p2@Zfp366!0.61!6.65!Zfp366;;chr8:94325779..94325791,-!p7@Irx3!0.61!3.04!Irx3;;chr2:103143315..103143328,-!p2@Ehf!0.61!3.04!Ehf;;chr1:64167972..64168026,-!p1@Klf7!0.60!85.49!Klf7;;chr15:102076870..102076941,-!p1@Rarg!0.60!39.49!Rarg;;chr14:98568761..98568814,-!p2@Dach1!0.60!24.59!Dach1;;chr5:120121020..120121049,+!p1@Tbx3!0.60!21.84!Tbx3;;chr6:29476690..29476724,+!p1@Irf5!0.60!16.49!Irf5;;chr3:34548909..34548927,+!p1@Sox2!0.60!5.50!Sox2;;chr8:47825166..47825178,+!p2@Irf2!0.60!5.06!Irf2;;chr7:86956107..86956152,+!p@chr7:86956107..86956152,+!0.60!5.06!Mesp2;;chr14:98568971..98569025,-!p1@Dach1!0.59!26.90!Dach1;;chr9:69137672..69137702,+!p2@Rora!0.59!14.46!Rora;;chr2:160698288..160698358,-!p3@Zhx3!0.59!10.41!Zhx3;;chr4:63064364..63064384,-!p1@Akna!0.59!9.84!Akna;;chr19:26681226..26681299,+!p7@Smarca2!0.59!7.67!Smarca2;;chr4:122911056..122911065,+!p2@Heyl!0.59!4.77!Heyl;;chr4:119486980..119486993,+!p6@Hivep3!0.59!2.89!Hivep3;;chr7:71083428..71083518,-!p3@Klf13!0.58!26.18!Klf13;;chr1:38684260..38684312,-!p2@Aff3!0.58!23.72!Aff3;;chr14:79881330..79881415,+!p3@Elf1!0.58!10.99!Elf1;;chr9:63869729..63869749,-!p4@Smad6!0.58!6.22!Smad6;;chr11:70043257..70043263,-!p1@Bcl6b!0.58!5.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chr16:55822241..55822258,-!p1@Nfkbiz!0.48!84.62!Nfkbiz;;chr1:92949999..92950097,+!p1@Lrrfip1!0.48!73.19!Lrrfip1;;chr14:22807083..22807104,-!p1@Zfp503!0.48!47.73!Zfp503;;chr18:69753015..69753104,+!p1@Tcf4!0.48!36.31!Tcf4;;chr11:18918917..18918944,-!p1@Meis1!0.48!35.15!Meis1;;chr6:134780234..134780288,+!p1@Crebl2!0.48!8.24!Crebl2;;chr1:64167550..64167618,-!p4@Klf7!0.48!6.94!Klf7;;chr1:186556323..186556370,-!p2@Hlx!0.48!6.80!Hlx;;chr18:75528166..75528170,+!p3@Smad7!0.48!6.36!Smad7;;chr17:13897299..13897342,+!p3@Mllt4!0.48!5.79!Mllt4;;chr16:43363837..43363842,+!p11@Zbtb20!0.48!4.48!Zbtb20;;chr6:52167513..52167549,-!p2@Hoxa7!0.48!3.18!Hoxa7;;chr11:96160360..96160397,+!p3@Hoxb6!0.48!2.03!Hoxb6;;chr2:167514456..167514473,+!p1@Cebpb!0.47!119.77!Cebpb;;chr1:52176315..52176343,+!p1@Stat1!0.47!38.48!Stat1;;chr12:86940338..86940357,+!p1@Jdp2!0.47!25.89!Jdp2;;chr5:34530293..34530318,-!p2@Mxd4!0.47!14.75!Mxd4;;chr18:55152179..55152194,-!p5@Zfp608!0.47!6.94!Zfp608;;chr16:23988686..23988693,-!p2@Bcl6!0.47!4.77!Bcl6;;chr6:72185553..72185612,-!p2@Atoh8!0.47!4.48!Atoh8;;chr11:121380594..121380609,-!p2@Zfp750!0.47!3.91!Zfp750;;chr8:94325847..94325869,-!p3@Irx3!0.47!3.62!Irx3;;chrX:137077699..137077705,-!p8@Tsc22d3!0.47!2.75!Tsc22d3;;chr10:80893549..80893590,-!p2@Nfic!0.46!29.07!Nfic;;chrX:98449492..98449510,+!p1@Foxo4!0.46!26.76!Foxo4;;chr17:56970339..56970428,-!p1@Rfx2!0.46!7.52!Rfx2;;chr16:42907554..42907591,+!p5@Zbtb20!0.46!5.93!Zbtb20;;chr11:98821937..98821987,+!p4@Rara!0.46!5.21!Rara;;chr4:97439519..97439539,+!p11@Nfia!0.46!4.92!Nfia;;chr2:90922554..90922575,+!p4@Sfpi1!0.46!4.05!Sfpi1;;chr1:186556375..186556404,-!p3@Hlx!0.46!4.05!Hlx;;chr7:25917492..25917512,-!p1@Pou2f2!0.46!3.76!Pou2f2;;chr3:34548946..34548972,+!p2@Sox2!0.46!2.17!Sox2;;chr11:85703335..85703350,+!p4@Tbx4!0.46!1.88!Tbx4;;chr6:97879817..97879857,+!p2@Mitf!0.46!1.88!Mitf;;chr5:120130275..120130296,+!p11@Tbx3!0.46!1.88!Tbx3;;chr16:95924055..95924077,+!p1@Ets2!0.45!139.15!Ets2;;chr4:82151653..82151706,-!p2@Nfib!0.45!71.75!Nfib;;chr12:86814833..86814846,+!p1@Fos!0.45!59.74!Fos;;chr11:18918959..18918976,-!p2@Meis1!0.45!34.28!Meis1;;chr4:128483347..128483411,-!p2@Zfp362!0.45!18.52!Zfp362;;chr18:3281034..3281104,-!p1@Crem!0.45!17.65!Crem;;chr18:75527030..75527055,+!p2@Smad7!0.45!15.48!Smad7;;chr9:96619968..96619983,-!p6@Zbtb38!0.45!3.62!Zbtb38;;chr8:24780125..24780143,+!p1@Zmat4!0.45!3.04!Zmat4;;chr11:96213264..96213282,+!p@chr11:96213264..96213282,+!0.45!2.46!Hoxb2;;chr1:52065508..52065522,+!p2@Stat4!0.45!2.31!Stat4;;chr16:4594740..4594759,+!p1@Glis2!0.44!27.77!Glis2;;chr1:133904183..133904211,+!p1@Elk4!0.44!20.97!Elk4;;chr5:140267476..140267493,+!p1@Mafk!0.44!13.60!Mafk;;chr1:172797934..172797945,-!p4@Atf6!0.44!6.65!Atf6;;chr6:145814003..145814056,-!p1@Bhlhe41!0.44!6.51!Bhlhe41;;chr2:91077034..91077078,-!p2@Ddb2!0.44!4.92!Ddb2;;chr2:90936978..90937023,+!p3@Sfpi1!0.44!4.05!Sfpi1;;chr6:39068163..39068176,-!p2@Parp12!0.44!4.05!Parp12;;chr7:74517982..74518012,-!p2@Mef2a!0.44!3.91!Mef2a;;chr12:113916993..113917009,+!p2@Zbtb42!0.44!3.62!Zbtb42;;chr11:98407234..98407259,-!p2@Ikzf3!0.44!1.74!Ikzf3;;chr2:103264952..103264963,+!p7@Elf5!0.44!1.74!Elf5;;chrX:48499591..48499593,-!p3@Mbnl3!0.44!1.74!Mbnl3;;chr12:37835219..37835230,+!p5@Meox2!0.44!1.74!Meox2;;chr5:77524175..77524186,-!p8@Hopx!0.44!1.74!Hopx;;chr2:160698721..160698745,-!p1@Zhx3!0.43!34.72!Zhx3;;chr12:25336211..25336274,+!p1@Klf11!0.43!25.17!Klf11;;chr17:23004085..23004108,-!p1@Zfp945!0.43!23.43!Zfp945;;chr3:94176733..94176794,+!p1@Rorc!0.43!18.52!Rorc;;chr13:37918486..37918575,+!p2@Rreb1!0.43!14.75!Rreb1;;chr1:133904901..133904934,+!p3@Elk4!0.43!6.51!Elk4;;chr13:64253718..64253763,-!p2@Zfp367!0.43!5.64!Zfp367;;chr16:43619101..43619151,+!p6@Zbtb20!0.43!5.21!Zbtb20;;chr6:72185210..72185228,-!p3@Atoh8!0.43!3.47!Atoh8;;chr4:135700687..135700719,+!p2@Id3!0.43!3.04!Id3;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!0.43!2.17!Ncoa4;;chr15:37162834..37162849,+!p2@Grhl2!0.43!2.17!Grhl2;;chr9:63869705..63869713,-!p8@Smad6!0.43!2.17!Smad6;;chr7:77505617..77505632,-!p1@Nr2f2!0.42!109.79!Nr2f2;;chr12:85559785..85559840,-!p1@C130039O16Rik!0.42!31.68!C130039O16Rik;;chr11:98821749..98821799,+!p2@Rara!0.42!14.32!Rara;;chr2:44968737..44968758,-!p2@Zeb2!0.42!13.02!Zeb2;;chr4:124805061..124805087,-!p1@Zc3h12a!0.42!6.80!Zc3h12a;;chr5:140267510..140267555,+!p2@Mafk!0.42!4.92!Mafk;;chr16:43363152..43363186,+!p3@Zbtb20!0.42!4.77!Zbtb20;;chr1:133904862..133904893,+!p6@Elk4!0.42!4.19!Elk4;;chr12:113917014..113917034,+!p1@Zbtb42!0.42!3.47!Zbtb42;;chr14:79915502..79915514,+!p4@Elf1!0.42!2.89!Elf1;;chr6:52163319..52163342,-!p1@Hoxa3!0.42!2.75!Hoxa3;;chr11:96180045..96180059,+!p1@Hoxb4!0.42!2.60!Hoxb4;;chr7:19895384..19895399,-!p2@Fosb!0.42!2.60!Fosb;;chr10:127080031..127080090,+!p1@Stat6!0.41!50.63!Stat6;;chr4:32325688..32325777,+!p1@Bach2!0.41!20.11!Bach2;;chr11:52096804..52096896,-!p1@Tcf7!0.41!18.23!Tcf7;;chr11:11584970..11585030,+!p2@Ikzf1!0.41!2.60!Ikzf1;;chr8:87324203..87324206,-!p10@Nfix!0.41!2.46!Nfix;;chr9:96159210..96159221,+!p10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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 39: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011489
 |is_obsolete=
+|library_id=CNhs11133
+|library_id_phase_based=2:CNhs11133
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1394
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1394
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N30.CNhs11133.1394-42H2.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N30.CNhs11133.1394-42H2.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N30.CNhs11133.1394-42H2.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N30.CNhs11133.1394-42H2.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N30.CNhs11133.1394-42H2.mm9.nobarcode.rdna.fa.gz
 |name=lung, neonate N30
 |namespace=FANTOM5
@@ Line 44: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs11133,LSID735,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=0.05960651136546,0.0586723554240733,0,0,0.236347100880389,0.0139476656122441,0.480397264466182,0,0.143337523760677,0,0.110353348438991,-0.0843392403965415,0.00178599920768426,0,0,0,0,0,0.0794589579157515,0,0.0293361777120366,0,0,0,0,0,0,0,0,0,0,0,0.36467101050133,0,0,0,0.0586723554240733,0.0382357492932679,0.320356162966994,0.00382556360052355,-0.00524405998482735,-0.524752870738654,0.0640202573678038,0,0,0,0,0,0,0,0,0,0,0.388543548918188,0,0.472949282780789,0,0,0,0,0.0148284523368354,0,0.217309081680009,0,0,0.103420080835662,0.221845205036699,0.190372418382411,-0.158091042771083,0.108760765411297,0,0.259394740373986,0.0513196074823079,0.0799629875964696,0.0586723554240733,0,0.0620563805023728,-0.00747327108075251,0.068372225708355,0.0315217535990839,0,0,0,0,0.0293361777120366,0,0.0331019865304614,0.171687260214382,-0.0733628753251791,0.0420303024573271,0,0,0,0
 |rna_box=42
 |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=table111:1394-42H2;search_select_hide=table117:1394-42H2
 }}

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FF:1394-42H2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:05, 4 June 2020

CNhs11133

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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