FF:28-22B1: Difference between revisions

Latest revision as of 19:09, 4 June 2020

Name:	lung, adult
Species:	Mouse (Mus musculus)
Library ID:	CNhs10474
Sample type:	developmental
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	C57BL/6J
tissue	lung
dev stage	adult
sex	male
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		SAMD00005743

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs10474		CAGE		DRX009030		DRR009904

Accession ID Mm9

Library id		BAM		CTSS
CNhs10474		DRZ001329		DRZ002712

Accession ID Mm10

Library id		BAM		CTSS
CNhs10474		DRZ012679		DRZ014062

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

CNhs10474

0	0
1	0
10	0
100	0
1000	0.0382
1001	0.171
1002	0.00476
1003	0.192
1004	0
1005	0.245
1006	0.0829
1007	-0.0748
1008	0.0736
1009	0.204
101	-0.0767
1010	0
1011	0
1012	0.0736
1013	0.0666
1014	-0.0115
1015	-0.191
1016	-0.0866
1017	0
1018	0.0324
1019	0
102	0
1020	0
1021	0
1022	0.2
1023	0
1024	0.47
1025	1.04
1026	0
1027	0
1028	0.137
1029	0.206
103	-0.0384
1030	0.24
1031	0.136
1032	0.015
1033	0.0591
1034	0.284
1035	0
1036	-0.0535
1037	0.0736
1038	0.414
1039	0.0266
104	0
1040	0.519
1041	0.24

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: CNhs10474

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	7.6146e-4
MA0003.1	MA0003.1	0.055
MA0004.1	MA0004.1	0.232
MA0006.1	MA0006.1	0.0677
MA0007.1	MA0007.1	0.994
MA0009.1	MA0009.1	0.553
MA0014.1	MA0014.1	0.452
MA0017.1	MA0017.1	0.0815
MA0018.2	MA0018.2	0.0194
MA0019.1	MA0019.1	0.663
MA0024.1	MA0024.1	8.76242e-5
MA0025.1	MA0025.1	0.00146
MA0027.1	MA0027.1	0.81
MA0028.1	MA0028.1	0.04
MA0029.1	MA0029.1	0.747
MA0030.1	MA0030.1	2.14136e-4
MA0031.1	MA0031.1	3.3352e-6
MA0035.2	MA0035.2	0.235
MA0038.1	MA0038.1	0.748
MA0039.2	MA0039.2	5.93835e-4
MA0040.1	MA0040.1	0.0578
MA0041.1	MA0041.1	0.856
MA0042.1	MA0042.1	0.772
MA0043.1	MA0043.1	0.629
MA0046.1	MA0046.1	1.31541e-5
MA0047.2	MA0047.2	5.89002e-10
MA0048.1	MA0048.1	0.367
MA0050.1	MA0050.1	4.70277e-19
MA0051.1	MA0051.1	1.98694e-10
MA0052.1	MA0052.1	0.439
MA0055.1	MA0055.1	0.574
MA0057.1	MA0057.1	0.351
MA0058.1	MA0058.1	0.141
MA0059.1	MA0059.1	0.00811
MA0060.1	MA0060.1	1.48107e-6
MA0061.1	MA0061.1	0.0334
MA0062.2	MA0062.2	0.685
MA0065.2	MA0065.2	0.531
MA0066.1	MA0066.1	0.335
MA0067.1	MA0067.1	0.829
MA0068.1	MA0068.1	0.416
MA0069.1	MA0069.1	0.675
MA0070.1	MA0070.1	0.985
MA0071.1	MA0071.1	0.198
MA0072.1	MA0072.1	0.179
MA0073.1	MA0073.1	0.843
MA0074.1	MA0074.1	0.35
MA0076.1	MA0076.1	0.0379
MA0077.1	MA0077.1	0.059
MA0078.1	MA0078.1	0.0219
MA0079.2	MA0079.2	0.00811
MA0080.2	MA0080.2	5.2448e-13
MA0081.1	MA0081.1	0.0324
MA0083.1	MA0083.1	0.159
MA0084.1	MA0084.1	0.869
MA0087.1	MA0087.1	0.569
MA0088.1	MA0088.1	0.902
MA0090.1	MA0090.1	0.0749
MA0091.1	MA0091.1	0.289
MA0092.1	MA0092.1	0.908
MA0093.1	MA0093.1	0.229
MA0099.2	MA0099.2	0.472
MA0100.1	MA0100.1	0.408
MA0101.1	MA0101.1	0.0743
MA0102.2	MA0102.2	0.0287
MA0103.1	MA0103.1	0.369
MA0104.2	MA0104.2	0.0132
MA0105.1	MA0105.1	0.821
MA0106.1	MA0106.1	0.0945
MA0107.1	MA0107.1	0.00129
MA0108.2	MA0108.2	0.375
MA0111.1	MA0111.1	0.712
MA0112.2	MA0112.2	0.386
MA0113.1	MA0113.1	0.222
MA0114.1	MA0114.1	0.0228
MA0115.1	MA0115.1	0.193
MA0116.1	MA0116.1	0.537
MA0117.1	MA0117.1	0.685
MA0119.1	MA0119.1	0.0622
MA0122.1	MA0122.1	0.108
MA0124.1	MA0124.1	0.995
MA0125.1	MA0125.1	0.148
MA0131.1	MA0131.1	0.219
MA0135.1	MA0135.1	0.134
MA0136.1	MA0136.1	9.14572e-9
MA0137.2	MA0137.2	0.0902
MA0138.2	MA0138.2	0.855
MA0139.1	MA0139.1	0.0908
MA0140.1	MA0140.1	0.408
MA0141.1	MA0141.1	0.00511
MA0142.1	MA0142.1	0.116
MA0143.1	MA0143.1	0.333
MA0144.1	MA0144.1	0.0137
MA0145.1	MA0145.1	2.07387e-4
MA0146.1	MA0146.1	0.223
MA0147.1	MA0147.1	0.00367
MA0148.1	MA0148.1	1.60559e-8
MA0149.1	MA0149.1	0.956
MA0150.1	MA0150.1	0.986
MA0152.1	MA0152.1	0.681
MA0153.1	MA0153.1	1.6839e-5
MA0154.1	MA0154.1	0.00892
MA0155.1	MA0155.1	0.44
MA0156.1	MA0156.1	5.06007e-11
MA0157.1	MA0157.1	7.11136e-5
MA0159.1	MA0159.1	0.534
MA0160.1	MA0160.1	0.115
MA0162.1	MA0162.1	0.327
MA0163.1	MA0163.1	0.333
MA0164.1	MA0164.1	0.217
MA0258.1	MA0258.1	0.644
MA0259.1	MA0259.1	0.0138

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: CNhs10474

Novel motif	Logo	P-value
1	1	0.903
10	10	0.365
100	100	0.215
101	101	0.354
102	102	0.522
103	103	0.337
104	104	0.865
105	105	0.389
106	106	0.00252
107	107	0.0252
108	108	0.896
109	109	0.185
11	11	0.9
110	110	0.991
111	111	0.672
112	112	0.484
113	113	0.395
114	114	0.431
115	115	0.732
116	116	0.666
117	117	0.111
118	118	0.683
119	119	0.183
12	12	0.75
120	120	0.138
121	121	0.116
122	122	0.631
123	123	0.673
124	124	0.348
125	125	0.478
126	126	0.417
127	127	0.284
128	128	0.00529
129	129	0.139
13	13	0.0421
130	130	0.0293
131	131	0.0431
132	132	0.417
133	133	0.662
134	134	0.548
135	135	0.239
136	136	0.498
137	137	0.222
138	138	0.213
139	139	0.987
14	14	0.237
140	140	0.5
141	141	0.21
142	142	0.474
143	143	0.603
144	144	0.611
145	145	0.353
146	146	0.492
147	147	0.726
148	148	0.412
149	149	0.0484
15	15	0.13
150	150	0.206
151	151	0.0886
152	152	0.0187
153	153	0.721
154	154	0.842
155	155	0.409
156	156	0.0184
157	157	0.656
158	158	0.922
159	159	0.0997
160	160	0.321
161	161	0.712
162	162	0.983
163	163	0.78
164	164	0.953
165	165	0.71
166	166	0.461
167	167	0.143
168	168	0.411
169	169	0.0367
17	17	0.51
18	18	0.0531
19	19	0.105
2	2	0.0485
20	20	0.247
21	21	0.866
22	22	0.126
23	23	0.0558
24	24	0.146
25	25	0.358
26	26	0.383
27	27	0.406
28	28	0.47
29	29	0.316
3	3	0.902
30	30	0.483
31	31	0.997
32	32	0.522
33	33	0.714
34	34	0.524
35	35	0.0934
36	36	0.887
37	37	0.0784
38	38	0.216
39	39	0.231
4	4	0.978
40	40	0.369
41	41	0.797
42	42	0.799
43	43	0.312
44	44	0.619
45	45	0.0516
46	46	0.891
47	47	0.577
48	48	0.854
49	49	0.553
5	5	0.747
50	50	0.513
51	51	0.62
52	52	0.0534
53	53	0.216
54	54	0.71
55	55	0.599
56	56	0.334
57	57	0.365
58	58	0.584
59	59	0.0661
6	6	0.996
60	60	0.0352
61	61	0.738
62	62	0.784
63	63	0.291
64	64	0.478
65	65	0.11
66	66	0.309
67	67	0.836
68	68	0.398
69	69	0.783
7	7	0.463
70	70	0.367
71	71	0.803
72	72	0.899
73	73	0.094
74	74	0.804
75	75	0.367
76	76	0.437
77	77	0.285
78	78	0.729
79	79	0.972
8	8	0.706
80	80	0.201
81	81	0.639
82	82	0.591
83	83	0.095
84	84	0.472
85	85	0.189
86	86	0.856
87	87	0.93
88	88	0.832
89	89	0.435
9	9	0.199
90	90	0.509
91	91	0.598
92	92	0.362
93	93	0.0724
94	94	0.306
95	95	0.654
96	96	0.439
97	97	0.626
98	98	0.401
99	99	0.408

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: CNhs10474

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011307 mouse lung- adult 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)
0007023 (adult organism)
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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011307 (mouse lung- adult 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)

@@ Line 1: / Line 1: @@
 {{f5samples
+|DRA_sample_Accession=CAGE@SAMD00005743
+|accession_numbers=CAGE;DRX009030;DRR009904;DRZ001329;DRZ002712;DRZ012679;DRZ014062
 |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,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=
@@ Line 7: / Line 9: @@
 |created_by=
 |creation_date=
-|datafreeze_phase=1
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr5:77543897..77543911,-!p2@Hopx!2.53!624.84!Hopx;;chr12:57636034..57636087,-!p1@Nkx2-1!1.91!80.00!Nkx2-1;;chr8:123608252..123608268,+!p1@Foxf1a!1.88!109.00!Foxf1a;;chr10:22539932..22539956,-!p1@Tcf21!1.76!146.51!Tcf21;;chr11:116196664..116196679,-!p1@Foxj1!1.70!74.09!Foxj1;;chr11:85699862..85699920,+!p1@Tbx4!1.69!47.48!Tbx4;;chr11:98636531..98636559,-!p1@Nr1d1!1.65!236.85!Nr1d1;;chr17:87153240..87153254,+!p1@Epas1!1.61!727.93!Epas1;;chr12:57636178..57636194,-!p2@Nkx2-1!1.58!36.95!Nkx2-1;;chr17:87153028..87153049,+!p2@Epas1!1.57!706.87!Epas1;;chr17:87153462..87153473,+!p3@Epas1!1.56!130.07!Epas1;;chr5:77543935..77543947,-!p4@Hopx!1.53!32.89!Hopx;;chr13:72101161..72101177,-!p2@Irx1!1.51!43.05!Irx1;;chr11:98636508..98636524,-!p3@Nr1d1!1.44!32.70!Nr1d1;;chr5:77544170..77544181,-!p6@Hopx!1.36!21.80!Hopx;;chr17:87153519..87153533,+!p5@Epas1!1.35!31.41!Epas1;;chr2:147871627..147871641,-!p1@Foxa2!1.34!20.69!Foxa2;;chr2:103143336..103143367,-!p1@Ehf!1.33!32.89!Ehf;;chr12:58646974..58647003,-!p1@Foxa1!1.32!26.79!Foxa1;;chr7:52960555..52960662,+!p1@Dbp!1.29!153.16!Dbp;;chr13:72766279..72766296,+!p2@Irx2!1.28!26.60!Irx2;;chr13:72766250..72766273,+!p1@Irx2!1.26!26.42!Irx2;;chr2:180069370..180069409,-!p1@Gata5!1.26!20.32!Gata5;;chr18:52775562..52775650,+!p1@Zfp474!1.26!17.37!Zfp474;;chr2:103264213..103264233,+!p1@Elf5!1.26!17.18!Elf5;;chr17:87153440..87153451,+!p4@Epas1!1.25!34.36!Epas1;;chr6:99216488..99216534,-!p2@Foxp1!1.21!43.23!Foxp1;;chr15:81633165..81633188,+!p2@Tef!1.20!118.80!Tef;;chr6:88148650..88148669,+!p1@Gata2!1.19!119.90!Gata2;;chr2:173044380..173044432,-!p1@Zbp1!1.18!33.81!Zbp1;;chr11:98636400..98636418,-!p4@Nr1d1!1.18!18.66!Nr1d1;;chr4:44723559..44723593,-!p1@Pax5!1.18!14.23!Pax5;;chr9:51021788..51021802,+!p1@Pou2af1!1.17!16.26!Pou2af1;;chr13:72101178..72101203,-!p1@Irx1!1.16!21.06!Irx1;;chr17:87153505..87153516,+!p6@Epas1!1.15!18.29!Epas1;;chr7:52960700..52960719,+!p2@Dbp!1.15!16.26!Dbp;;chr12:57636220..57636236,-!p3@Nkx2-1!1.15!13.12!Nkx2-1;;chr9:48644037..48644067,-!p2@Zbtb16!1.14!32.33!Zbtb16;;chr11:16908650..16908690,-!p1@Plek!1.13!75.38!Plek;;chr14:64562503..64562524,+!p1@Sox7!1.13!72.79!Sox7;;chr1:38721792..38721845,-!p1@Aff3!1.13!15.70!Aff3;;chr8:94325321..94325366,-!p1@Irx3!1.12!29.75!Irx3;;chr13:31717548..31717596,+!p1@Foxf2!1.11!23.83!Foxf2;;chr8:74842952..74842970,+!p1@Klf2!1.10!777.07!Klf2;;chr7:51787434..51787448,-!p1@Spib!1.09!16.26!Spib;;chr15:81633203..81633215,+!p3@Tef!1.08!17.37!Tef;;chr11:85646469..85646488,+!p5@Tbx2!1.07!16.26!Tbx2;;chr16:95680889..95680991,-!p1@Erg!1.06!85.91!Erg;;chr11:85646303..85646329,+!p1@Tbx2!1.05!68.36!Tbx2;;chr6:52154386..52154407,-!p2@Hoxa5!1.05!13.12!Hoxa5;;chr12:57636240..57636256,-!p4@Nkx2-1!1.05!10.16!Nkx2-1;;chr3:30408674..30408716,-!p2@Mecom!1.03!16.26!Mecom;;chr2:173044357..173044377,-!p2@Zbp1!1.03!14.04!Zbp1;;chr9:63869890..63869908,-!p6@Smad6!1.03!12.75!Smad6;;chr5:120120667..120120685,+!p3@Tbx3!1.02!18.48!Tbx3;;chr1:52065508..52065522,+!p2@Stat4!1.02!11.09!Stat4;;chr11:96976641..96976646,-!p1@Tbx21!1.02!9.42!Tbx21;;chr6:88143711..88143717,+!p2@Gata2!1.00!14.60!Gata2;;chr1:4486481..4486501,-!p2@Sox17!1.00!13.49!Sox17;;chr3:8666963..8666978,-!p1@Hey1!0.99!58.57!Hey1;;chr4:148275237..148275311,+!p2@Casz1!0.99!36.77!Casz1;;chr11:85646341..85646352,+!p3@Tbx2!0.99!17.55!Tbx2;;chr1:137155026..137155042,-!p1@Elf3!0.98!51.36!Elf3;;chr2:181406327..181406350,-!p1@Sox18!0.97!263.83!Sox18;;chr12:37835141..37835194,+!p1@Meox2!0.97!26.79!Meox2;;chr4:44723520..44723544,-!p2@Pax5!0.97!8.31!Pax5;;chr13:72101141..72101158,-!p3@Irx1!0.96!10.35!Irx1;;chr14:19071466..19071550,-!p1@Nr1d2!0.95!56.16!Nr1d2;;chr4:63064364..63064384,-!p1@Akna!0.95!23.83!Akna;;chr8:94881733..94881790,+!p1@Irx5!0.95!15.89!Irx5;;chr2:147871948..147871977,-!p3@Foxa2!0.95!7.94!Foxa2;;chr11:85646263..85646278,+!p2@Tbx2!0.94!20.32!Tbx2;;chr11:98636575..98636607,-!p2@Nr1d1!0.93!28.27!Nr1d1;;chr5:77544108..77544119,-!p7@Hopx!0.93!7.57!Hopx;;chr13:30841099..30841116,+!p1@Irf4!0.92!11.64!Irf4;;chr1:87546583..87546595,+!p1@Sp100!0.92!10.53!Sp100;;chr12:37835203..37835218,+!p3@Meox2!0.92!8.87!Meox2;;chr3:130815703..130815721,+!p2@Lef1!0.92!8.87!Lef1;;chr11:98407264..98407295,-!p1@Ikzf3!0.91!7.21!Ikzf3;;chr16:15887371..15887385,+!p1@Cebpd!0.90!247.38!Cebpd;;chr8:47825203..47825225,+!p3@Irf2!0.90!9.42!Irf2;;chr11:52096066..52096081,-!p2@Tcf7!0.90!8.50!Tcf7;;chr7:52960663..52960677,+!p6@Dbp!0.90!7.02!Dbp;;chr8:94325814..94325839,-!p2@Irx3!0.89!14.60!Irx3;;chr2:103264245..103264268,+!p2@Elf5!0.89!6.84!Elf5;;chr4:55545337..55545357,-!p1@Klf4!0.88!102.35!Klf4;;chr16:92697560..92697592,-!p2@Runx1!0.88!43.05!Runx1;;chr13:99954640..99954681,+!p1@Zfp366!0.88!24.94!Zfp366;;chr6:52154414..52154462,-!p1@Hoxa5!0.88!9.24!Hoxa5;;chr11:98407234..98407259,-!p2@Ikzf3!0.88!6.65!Ikzf3;;chr10:67599319..67599360,-!p2@Arid5b!0.87!74.64!Arid5b;;chr5:77524231..77524245,-!p3@Hopx!0.87!16.81!Hopx;;chr11:100683839..100683890,-!p2@Stat5b!0.87!15.52!Stat5b;;chr8:47825166..47825178,+!p2@Irf2!0.87!10.16!Irf2;;chr5:77524250..77524300,-!p1@Hopx!0.86!135.42!Hopx;;chr16:22439654..22439676,-!p2@Etv5!0.86!38.98!Etv5;;chr11:69579472..69579529,+!p1@Zbtb4!0.86!33.63!Zbtb4;;chr9:63869802..63869815,-!p3@Smad6!0.86!12.75!Smad6;;chr8:94325486..94325510,-!p4@Irx3!0.86!8.31!Irx3;;chr11:83664365..83664383,+!p1@Hnf1b!0.86!6.28!Hnf1b;;chr11:53583544..53583559,+!p1@Irf1!0.85!107.53!Irf1;;chr6:128250471..128250519,-!p1@Tead4!0.85!12.56!Tead4;;chr7:25917492..25917512,-!p1@Pou2f2!0.85!10.72!Pou2f2;;chr9:63869751..63869767,-!p1@Smad6!0.84!16.26!Smad6;;chr18:11052606..11052633,+!p4@Gata6!0.84!15.70!Gata6;;chr5:134720044..134720103,-!p6@Gtf2i!0.84!5.91!Gtf2i;;chr11:85703483..85703508,+!p2@Tbx4!0.84!5.91!Tbx4;;chr1:52176315..52176343,+!p1@Stat1!0.83!87.94!Stat1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.82!43.05!Tsc22d3;;chr11:85646427..85646451,+!p4@Tbx2!0.82!10.16!Tbx2;;chr11:98636373..98636387,-!p5@Nr1d1!0.82!6.47!Nr1d1;;chr2:147872790..147872821,-!p2@Foxa2!0.82!5.54!Foxa2;;chr12:37835248..37835260,+!p4@Meox2!0.82!5.54!Meox2;;chr19:23215673..23215753,+!p1@Klf9!0.81!86.28!Klf9;;chr16:42907676..42907797,+!p1@Zbtb20!0.81!76.30!Zbtb20;;chr18:11052642..11052659,+!p1@Gata6!0.81!29.75!Gata6;;chr9:96653072..96653154,-!p1@Zbtb38!0.81!15.52!Zbtb38;;chr6:128250380..128250442,-!p2@Tead4!0.81!7.02!Tead4;;chr2:90936901..90936945,+!p1@Sfpi1!0.80!29.75!Sfpi1;;chr11:11586218..11586285,+!p1@Ikzf1!0.80!18.11!Ikzf1;;chr11:11590140..11590187,+!p3@Ikzf1!0.80!6.47!Ikzf1;;chr19:26679654..26679675,+!p1@Smarca2!0.79!52.29!Smarca2;;chr18:36441119..36441158,+!p2@Pura!0.79!13.30!Pura;;chr8:94325779..94325791,-!p7@Irx3!0.79!5.17!Irx3;;chr3:34548909..34548927,+!p1@Sox2!0.78!8.87!Sox2;;chr9:24578720..24578735,-!p1@Tbx20!0.78!4.99!Tbx20;;chr5:120285144..120285160,+!p1@Tbx5!0.78!4.99!Tbx5;;chr7:119822957..119822980,+!p2@Tead1!0.77!25.68!Tead1;;chr4:148178559..148178603,+!p1@Casz1!0.77!14.97!Casz1;;chr4:148178529..148178548,+!p3@Casz1!0.77!12.38!Casz1;;chr2:91035197..91035237,-!p1@Nr1h3!0.77!10.72!Nr1h3;;chr2:90922554..90922575,+!p4@Sfpi1!0.77!9.42!Sfpi1;;chr7:119822915..119822936,+!p5@Tead1!0.77!8.50!Tead1;;chr10:67599361..67599372,-!p5@Arid5b!0.77!7.94!Arid5b;;chr11:98636321..98636332,-!p8@Nr1d1!0.77!5.91!Nr1d1;;chr16:22439681..22439698,-!p1@Etv5!0.76!90.71!Etv5;;chr7:148452314..148452329,-!p1@Irf7!0.76!36.40!Irf7;;chr2:9800207..9800234,-!p1@Gata3!0.76!15.70!Gata3;;chr6:145814003..145814056,-!p1@Bhlhe41!0.76!14.97!Bhlhe41;;chr15:81633139..81633152,+!p4@Tef!0.76!8.31!Tef;;chr15:81633224..81633235,+!p5@Tef!0.76!6.10!Tef;;chr1:4483679..4483695,-!p1@Sox17!0.75!24.02!Sox17;;chr9:63869918..63869936,-!p9@Smad6!0.75!4.62!Smad6;;chr4:44723633..44723646,-!p3@Pax5!0.75!4.62!Pax5;;chr14:22807107..22807119,-!p2@Zfp503!0.74!21.80!Zfp503;;chr10:92773708..92773734,-!p3@Elk3!0.74!9.61!Elk3;;chr9:63869834..63869849,-!p5@Smad6!0.74!8.13!Smad6;;chr1:4486453..4486470,-!p3@Sox17!0.74!6.10!Sox17;;chr9:48644013..48644027,-!p5@Zbtb16!0.74!5.54!Zbtb16;;chr5:120130377..120130432,+!p10@Tbx3!0.74!4.43!Tbx3;;chr6:90412582..90412601,+!p1@Klf15!0.73!22.72!Klf15;;chr1:120524520..120524528,+!p1@Tfcp2l1!0.73!13.67!Tfcp2l1;;chr6:145813905..145813932,-!p2@Bhlhe41!0.73!8.87!Bhlhe41;;chr18:80904854..80904919,-!p2@Nfatc1!0.72!56.90!Nfatc1;;chr5:104121391..104121450,+!p3@Aff1!0.72!24.76!Aff1;;chr3:30408603..30408668,-!p1@Mecom!0.72!10.53!Mecom;;chr1:52065454..52065495,+!p1@Stat4!0.72!7.39!Stat4;;chr8:107793737..107793757,+!p2@Hsf4!0.72!4.99!Hsf4;;chr12:77278238..77278252,-!p1@Esr2!0.72!4.25!Esr2;;chr12:57637595..57637608,-!p7@Nkx2-1!0.72!4.25!Nkx2-1;;chr10:92773591..92773623,-!p1@Elk3!0.71!103.83!Elk3;;chr12:36219645..36219730,-!p1@Ahr!0.71!45.45!Ahr;;chr11:90252223..90252240,-!p1@Hlf!0.71!38.61!Hlf;;chr5:120121446..120121461,+!p2@Tbx3!0.71!15.15!Tbx3;;chr6:39068163..39068176,-!p2@Parp12!0.71!8.31!Parp12;;chr7:52960730..52960762,+!p3@Dbp!0.71!5.36!Dbp;;chr9:32503590..32503680,+!p1@Ets1!0.70!167.76!Ets1;;chr3:135271185..135271254,-!p4@Nfkb1!0.70!7.76!Nfkb1;;chr12:37835120..37835133,+!p2@Meox2!0.70!6.10!Meox2;;chr11:11584970..11585030,+!p2@Ikzf1!0.70!6.10!Ikzf1;;chr13:31717597..31717613,+!p2@Foxf2!0.70!4.06!Foxf2;;chr7:52963269..52963305,+!p4@Dbp!0.69!5.73!Dbp;;chr1:135320989..135321043,-!p1@Sox13!0.68!47.67!Sox13;;chr14:79915425..79915501,+!p1@Elf1!0.68!38.06!Elf1;;chr6:29476690..29476724,+!p1@Irf5!0.68!19.77!Irf5;;chr16:18587076..18587106,-!p1@Tbx1!0.68!5.73!Tbx1;;chr6:98978245..98978289,-!p1@Foxp1!0.67!63.37!Foxp1;;chr6:86619104..86619119,-!p1@Mxd1!0.67!34.55!Mxd1;;chr19:26681672..26681716,+!p5@Smarca2!0.67!17.55!Smarca2;;chr3:8666997..8667012,-!p2@Hey1!0.67!9.42!Hey1;;chr12:74147689..74147711,-!p1@Six1!0.67!8.87!Six1;;chr2:90936947..90936977,+!p2@Sfpi1!0.67!7.94!Sfpi1;;chr10:67599375..67599386,-!p3@Arid5b!0.67!7.21!Arid5b;;chr12:113917014..113917034,+!p1@Zbtb42!0.67!7.02!Zbtb42;;chr5:120130275..120130296,+!p11@Tbx3!0.67!3.70!Tbx3;;chr1:64167972..64168026,-!p1@Klf7!0.66!98.10!Klf7;;chr8:79426176..79426275,+!p1@Nr3c2!0.66!20.32!Nr3c2;;chr19:26681226..26681299,+!p7@Smarca2!0.66!9.24!Smarca2;;chr1:448650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520,-!p3@Prdm1!0.22!1.29!Prdm1;;chr15:40486427..40486437,+!p5@Zfpm2!0.22!1.11!Zfpm2;;chr1:92950099..92950109,+!p3@Lrrfip1!0.22!0.92!Lrrfip1;;chr5:120121091..120121100,+!p7@Tbx3!0.22!0.92!Tbx3;;chr6:16848395..16848416,-!p2@Tfec!0.22!0.92!Tfec;;chr5:137042233..137042245,-!p4@Cux1!0.22!0.92!Cux1;;chr12:81213989..81214006,-!p1@Zfp36l1!0.21!75.56!Zfp36l1;;chr1:64579394..64579433,+!p1@Creb1!0.21!52.29!Creb1;;chr7:105851749..105851802,+!p1@Prkrir!0.21!49.88!Prkrir;;chr2:72817045..72817123,-!p1@Sp3!0.21!46.93!Sp3;;chr3:87329494..87329565,+!p1@Etv3!0.21!21.80!Etv3;;chr11:100711801..100711910,-!p1@Stat5b!0.21!19.77!Stat5b;;chr14:79880971..79880992,+!p2@Elf1!0.21!18.11!Elf1;;chr2:37286355..37286418,-!p1@Zbtb6!0.21!16.63!Zbtb6;;chr15:50721588..50721610,-!p1@Trps1!0.21!14.04!Trps1;;chr11:95574298..95574344,+!p1@Zfp652,p4@Phospho1!0.21!12.38!Zfp652;;chr17:47873985..47874056,+!p1@Tfeb!0.21!11.45!Tfeb;;chr6:47785649..47785724,+!p1@Zfp398!0.21!11.27!Zfp398;;chr2:91077082..91077122,-!p1@Ddb2!0.21!8.50!Ddb2;;chr10:80893711..80893784,-!p3@Nfic!0.21!7.02!Nfic;;chr2:92886297..92886329,-!p1@Prdm11!0.21!6.10!Prdm11;;chr13:37918773..37918818,+!p3@Rreb1!0.21!5.54!Rreb1;;chr5:9160908..9160912,-!p2@Dmtf1!0.21!5.36!Dmtf1;;chr1:165243792..165243808,-!p1@Prrx1!0.21!4.43!Prrx1;;chr3:95021663..95021687,-!p3@Gabpb2!0.21!4.25!Gabpb2;;chr1:172797920..172797931,-!p3@Atf6!0.21!3.70!Atf6;;chr2:38781916..38781974,-!p1@Nr6a1!0.21!3.70!Nr6a1;;chr2:44966659..44966675,-!p7@Zeb2!0.21!3.51!Zeb2;;chr11:53164533..53164548,+!p4@Aff4!0.21!3.51!Aff4;;chr10:127080141..127080160,+!p2@Stat6!0.21!3.14!Stat6;;chr8:92872242..92872285,-!p1@Tox3!0.21!2.96!Tox3;;chr18:55149735..55149776,-!p4@Zfp608!0.21!2.77!Zfp608;;chr6:90412556..90412581,+!p3@Klf15!0.21!2.40!Klf15;;chr12:9581284..9581303,+!p2@Osr1!0.21!2.03!Osr1;;chr11:100712053..100712077,-!p3@Stat5b!0.21!2.03!Stat5b;;chr3:30993616..30993634,+!p3@Skil!0.21!1.85!Skil;;chr15:50721239..50721260,-!p9@Trps1!0.21!1.66!Trps1;;chr7:46773162..46773172,+!p2@Zfp619!0.21!1.66!Zfp619;;chr8:87237732..87237745,-!p7@Nfix!0.21!1.48!Nfix;;chr19:23216132..23216157,+!p3@Klf9!0.21!1.48!Klf9;;chrX:7339674..7339688,+!p6@Tfe3!0.21!1.48!Tfe3;;chr2:104966766..104966786,+!p1@Wt1!0.21!1.48!Wt1;;chr5:144951153..144951203,+!p1@Bhlha15!0.21!1.29!Bhlha15;;chr16:3872255..3872283,-!p4@Zfp597!0.21!1.29!Zfp597;;chr17:46520492..46520515,+!p4@Zfp318!0.21!1.29!Zfp318;;chr3:9610233..9610247,-!p4@Zfp704!0.21!1.29!Zfp704;;chr4:63071779..63071791,-!p3@Akna!0.21!1.29!Akna;;chr15:79178013..79178028,+!p3@Maff!0.21!1.11!Maff;;chr17:27693922..27693934,+!p10@Hmga1-rs1,p11@Hmga1!0.21!1.11!Hmga1;;chr17:44873258..44873281,-!p5@Runx2!0.21!1.11!Runx2;;chr11:96213434..96213452,+!p@chr11:96213434..96213452,+!0.21!1.11!Hoxb2;;chr12:72149359..72149406,+!p4@Arid4a!0.21!1.11!Arid4a;;chr6:52167459..52167492,-!p1@Hoxa7!0.21!0.92!Hoxa7;;chr7:89137163..89137200,-!p1@Bnc1!0.21!0.92!Bnc1;;chr2:27532912..27532923,+!p9@Rxra!0.21!0.74!Rxra;;chr9:44689360..44689406,-!p1@Mll1!0.20!53.39!Mll1;;chr5:139060930..139060975,-!p1@Zfp68!0.20!51.18!Zfp68;;chr11:96691218..96691265,-!p2@Nfe2l1!0.20!39.72!Nfe2l1;;chr7:4947646..4947696,-!p1@Zfp579!0.20!38.61!Zfp579;;chr19:5424906..5425026,-!p1@Drap1!0.20!38.06!Drap1;;chr7:52253030..52253070,+!p1@Irf3!0.20!31.41!Irf3;;chr4:119212257..119212303,+!p1@Foxj3!0.20!24.94!Foxj3;;chr2:17986191..17986271,+!p1@Mllt10!0.20!24.39!Mllt10;;
@@ Line 41: / Line 44: @@
 |is_a=EFO:0002091;;FF:0011307
 |is_obsolete=
+|library_id=CNhs10474
+|library_id_phase_based=2:CNhs10474
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;28
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;28
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm9.nobarcode.rdna.fa.gz
 |name=lung, adult
 |namespace=FANTOM5
@@ Line 46: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs10474,LSID646,release008,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=0.0391697314626784,0,0,0,0.136564059910207,0,0.123777661414995,0,0.132575718524345,0,0,-0.0843392403965415,0.0736278867910527,0,0,0,0,0,-0.000369800624937688,0,0,0,0,0,0.0736278867910527,0,0,0,0,0,0,0,0.325301928605915,0,0,0,0,0,0.0748295082949992,0,-0.0679882507704692,-0.847647306567619,0.0541089098554874,0,0,0,0,0,0,0,0,0,0,0.507456228934955,0,0.257972000302398,0,0,0,0,0,0,0,0,0.191523550257637,0.0231791970927544,0.0332367720915428,-0.0264984235485609,-0.158091042771083,0.0160564101370923,0.0736278867910527,0.0728301526975698,0.00869041596116804,0,0,0,0,0.0826838797633651,0.167781314981847,0.112691955417729,0,0,0,0,0.0368139433955263,0,0,-0.250191089245817,-0.00757550092845483,0.0153453566723565,0,0,0,0
@@ Line 62: / Line 76: @@
 |rna_weight_ug=
 |sample_age=
+|sample_category=developmental
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 82: / Line 97: @@
 |top_motifs=FOXO1,3,4:3.01034917163;FOX{D1,D2}:2.86433199852;FOX{I1,J2}:2.79800830549;FOXN1:2.62885401585;EBF1:2.33736098;TLX2:2.22001709873;IRF1,2:2.13243928931;HBP1_HMGB_SSRP1_UBTF:1.96655731406;ETS1,2:1.83949157054;STAT2,4,6:1.70831318039;EP300:1.69482030589;SPIB:1.65834895896;NFIL3:1.55103911027;BPTF:1.50320335024;NFATC1..3:1.47783745929;XCPE1{core}:1.43204409422;RFX2..5_RFXANK_RFXAP:1.347787049;SP1:1.30646945252;TEAD1:1.23126164988;T:1.22999651315;SPI1:1.17071685805;ELF1,2,4:1.13574740295;ZNF148:1.09743530907;DMAP1_NCOR{1,2}_SMARC:1.07597694188;TLX1..3_NFIC{dimer}:1.05496265159;IRF7:1.01977083977;TBX4,5:0.962352650919;POU2F1..3:0.94663552462;HAND1,2:0.928982845409;BACH2:0.927847490583;ZEB1:0.919061100332;CEBPA,B_DDIT3:0.901301696493;IKZF2:0.895871627603;IKZF1:0.870382525242;TFCP2:0.829771709891;NKX2-1,4:0.820390331124;TOPORS:0.78583606179;SNAI1..3:0.773480615504;SPZ1:0.772914686895;GZF1:0.760425200058;GTF2A1,2:0.735930906225;NFIX:0.726264569069;TFAP4:0.714595854844;MYBL2:0.705645885415;AR:0.674931264953;RUNX1..3:0.663042091602;SMAD1..7,9:0.634188013939;FOXA2:0.633375632411;HMX1:0.601200396825;MTF1:0.580706771617;PRDM1:0.537292889721;RFX1:0.533563268835;NFE2L1:0.498584769289;RXRA_VDR{dimer}:0.497925122138;STAT5{A,B}:0.496923951978;TFAP2B:0.477565319373;FOS_FOS{B,L1}_JUN{B,D}:0.461805651955;NFKB1_REL_RELA:0.444097211379;SRF:0.420437022741;TGIF1:0.415403595623;FOX{F1,F2,J1}:0.386862065486;FOXQ1:0.379824602217;MAZ:0.364694950241;TFAP2{A,C}:0.329184898367;NKX3-1:0.294898295018;ESR1:0.286117325579;GTF2I:0.243494953492;RBPJ:0.238133406495;NFE2L2:0.217639499811;MEF2{A,B,C,D}:0.211408038543;FOSL2:0.202577522405;ZNF384:0.201221869383;GCM1,2:0.186329651708;PAX5:0.174984992497;HIC1:0.168828122544;JUN:0.160203902611;ZNF423:0.156384511668;NR1H4:0.153097470371;SREBF1,2:0.0974005875516;FOXP1:0.0919388415126;POU5F1:0.0829282801425;FOXD3:0.0672692063648;GATA6:0.0590717149424;CRX:0.0551469359862;GLI1..3:0.0246734689712;ATF6:0.0213460544777;MYOD1:0.0107688292444;ZNF238:0.00804727699302;MYFfamily:-0.00763525423161;TP53:-0.0251820569897;PATZ1:-0.0303455370048;RREB1:-0.0490010217856;NKX3-2:-0.0591072028974;NKX2-2,8:-0.0629451890303;STAT1,3:-0.089458702809;HLF:-0.119867570764;EGR1..3:-0.143784726531;RXR{A,B,G}:-0.145977075557;SOX5:-0.146879891606;ALX1:-0.160254677317;GFI1B:-0.168567898149;MED-1{core}:-0.186518291926;ZFP161:-0.199894261148;SOX2:-0.223585981094;TBP:-0.265996718703;NKX2-3_NKX2-5:-0.275655051702;PPARG:-0.283271460844;NHLH1,2:-0.289277151709;HNF4A_NR2F1,2:-0.316029040077;ZBTB6:-0.325521584558;GATA4:-0.325610795531;TFDP1:-0.337965143299;HNF1A:-0.35629021915;ALX4:-0.368509736875;HMGA1,2:-0.374434594474;LMO2:-0.378982091617;ATF2:-0.390573494609;ATF4:-0.39972866542;REST:-0.425577591319;bHLH_family:-0.427800016498;SOX{8,9,10}:-0.475727363945;MYB:-0.484162220575;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.505068971803;ZIC1..3:-0.511770791859;NFE2:-0.520141454363;GFI1:-0.524036598592;MZF1:-0.532606843995;MTE{core}:-0.561592322299;MAFB:-0.572082968288;ZBTB16:-0.598292439119;PITX1..3:-0.604165134955;HOX{A5,B5}:-0.60978155733;PBX1:-0.61993355329;FOXP3:-0.623775484787;CREB1:-0.62884963766;PAX1,9:-0.64486170729;PAX2:-0.651644819225;ADNP_IRX_SIX_ZHX:-0.656776260698;POU6F1:-0.661330724581;ATF5_CREB3:-0.694752580518;KLF4:-0.706655139625;LEF1_TCF7_TCF7L1,2:-0.710600670569;AHR_ARNT_ARNT2:-0.727171042292;PAX6:-0.728679482385;NR3C1:-0.73163262844;BREu{core}:-0.734210884883;NKX6-1,2:-0.74014348901;PAX4:-0.766067850809;DBP:-0.798496583742;AIRE:-0.808541664216;PDX1:-0.820425086861;HSF1,2:-0.8211335047;ELK1,4_GABP{A,B1}:-0.850678462638;SOX17:-0.857592740691;FOXM1:-0.911579399226;E2F1..5:-0.921967803943;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.938293636651;LHX3,4:-0.944353367806;CUX2:-0.991000356925;NANOG:-0.99608628711;ARID5B:-0.996740590354;PRRX1,2:-1.00310116185;TEF:-1.0123867206;NR6A1:-1.03971097175;NRF1:-1.10175637472;ESRRA:-1.10340800501;HIF1A:-1.22149871385;FOXL1:-1.26978360793;VSX1,2:-1.2792486085;CDX1,2,4:-1.35424372138;OCT4_SOX2{dimer}:-1.39583988333;CDC5L:-1.41234812567;UFEwm:-1.45505173211;TAL1_TCF{3,4,12}:-1.47248570397;HOX{A4,D4}:-1.47780908375;NFY{A,B,C}:-1.48968129045;ONECUT1,2:-1.51596331362;NR5A1,2:-1.52500019402;RORA:-1.53529171198;HOXA9_MEIS1:-1.61420615454;EVI1:-1.62877534909;EN1,2:-1.65854085888;POU3F1..4:-1.66958854754;ZNF143:-1.79163831129;PAX8:-1.90292039046;YY1:-2.04062216802;POU1F1:-2.18573110424;HES1:-2.26305901727;NANOG{mouse}:-2.45772797336
 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:28-22B1;search_select_hide=table117:28-22B1
 }}

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FF:28-22B1: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 19:09, 4 June 2020

CNhs10474

	FAQ
	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0