FF:11735-123E7: Difference between revisions

Latest revision as of 18:16, 4 June 2020

Name:	Mouse Mesenchymal stem cells - bone marrow derived, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12633
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	link

Additional information

Sample information

strain	NA
tissue	bone marrow
dev stage	NA
sex	NA
age	NA
cell type	mesenchymal stem cell
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	RNAMCS2
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005570

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12633		CAGE		DRX008826		DRR009698

Accession ID Mm9

Library id		BAM		CTSS
CNhs12633		DRZ001123		DRZ002508

Accession ID Mm10

Library id		BAM		CTSS
CNhs12633		DRZ012473		DRZ013858

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

CNhs12633

0	0
1	0
10	0
100	0
1000	0.0777
1001	-0.0631
1002	0.00981
1003	-0.102
1004	0
1005	0
1006	0.145
1007	-0.406
1008	0
1009	-0.19
101	-0.472
1010	0
1011	0.119
1012	0
1013	0.187
1014	-0.0874
1015	-0.0653
1016	-0.321
1017	0
1018	0
1019	0
102	0
1020	0.695
1021	0
1022	-0.124
1023	0
1024	-0.14
1025	-0.0611
1026	0
1027	0
1028	0
1029	-0.176
103	0
1030	0
1031	-0.111
1032	-0.177
1033	0
1034	0
1035	0
1036	-0.0393
1037	0
1038	-0.298
1039	-0.0323
104	0
1040	-0.121
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: CNhs12633

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	4.88808e-6
MA0003.1	MA0003.1	0.125
MA0004.1	MA0004.1	0.426
MA0006.1	MA0006.1	0.493
MA0007.1	MA0007.1	0.639
MA0009.1	MA0009.1	0.669
MA0014.1	MA0014.1	0.816
MA0017.1	MA0017.1	0.234
MA0018.2	MA0018.2	0.0802
MA0019.1	MA0019.1	0.965
MA0024.1	MA0024.1	0.0051
MA0025.1	MA0025.1	0.765
MA0027.1	MA0027.1	0.539
MA0028.1	MA0028.1	0.485
MA0029.1	MA0029.1	0.728
MA0030.1	MA0030.1	0.204
MA0031.1	MA0031.1	0.771
MA0035.2	MA0035.2	0.244
MA0038.1	MA0038.1	4.23469e-5
MA0039.2	MA0039.2	0.995
MA0040.1	MA0040.1	0.589
MA0041.1	MA0041.1	0.541
MA0042.1	MA0042.1	0.712
MA0043.1	MA0043.1	0.0782
MA0046.1	MA0046.1	6.88112e-6
MA0047.2	MA0047.2	0.715
MA0048.1	MA0048.1	0.723
MA0050.1	MA0050.1	2.07149e-5
MA0051.1	MA0051.1	4.77704e-4
MA0052.1	MA0052.1	0.0562
MA0055.1	MA0055.1	0.912
MA0057.1	MA0057.1	0.314
MA0058.1	MA0058.1	0.255
MA0059.1	MA0059.1	0.156
MA0060.1	MA0060.1	1.20161e-12
MA0061.1	MA0061.1	0.0274
MA0062.2	MA0062.2	0.537
MA0065.2	MA0065.2	0.00696
MA0066.1	MA0066.1	0.0124
MA0067.1	MA0067.1	0.658
MA0068.1	MA0068.1	0.285
MA0069.1	MA0069.1	0.912
MA0070.1	MA0070.1	0.172
MA0071.1	MA0071.1	0.149
MA0072.1	MA0072.1	0.43
MA0073.1	MA0073.1	0.643
MA0074.1	MA0074.1	0.029
MA0076.1	MA0076.1	0.23
MA0077.1	MA0077.1	0.728
MA0078.1	MA0078.1	0.66
MA0079.2	MA0079.2	0.461
MA0080.2	MA0080.2	9.69998e-14
MA0081.1	MA0081.1	0.00374
MA0083.1	MA0083.1	0.384
MA0084.1	MA0084.1	0.76
MA0087.1	MA0087.1	0.942
MA0088.1	MA0088.1	0.294
MA0090.1	MA0090.1	0.665
MA0091.1	MA0091.1	0.226
MA0092.1	MA0092.1	0.392
MA0093.1	MA0093.1	0.457
MA0099.2	MA0099.2	0.00109
MA0100.1	MA0100.1	0.928
MA0101.1	MA0101.1	0.172
MA0102.2	MA0102.2	0.513
MA0103.1	MA0103.1	0.6
MA0104.2	MA0104.2	0.841
MA0105.1	MA0105.1	0.00166
MA0106.1	MA0106.1	0.23
MA0107.1	MA0107.1	0.164
MA0108.2	MA0108.2	0.0922
MA0111.1	MA0111.1	0.324
MA0112.2	MA0112.2	7.3374e-5
MA0113.1	MA0113.1	0.313
MA0114.1	MA0114.1	0.321
MA0115.1	MA0115.1	0.519
MA0116.1	MA0116.1	0.00101
MA0117.1	MA0117.1	0.777
MA0119.1	MA0119.1	0.206
MA0122.1	MA0122.1	0.718
MA0124.1	MA0124.1	0.222
MA0125.1	MA0125.1	0.0659
MA0131.1	MA0131.1	0.12
MA0135.1	MA0135.1	0.232
MA0136.1	MA0136.1	5.07696e-10
MA0137.2	MA0137.2	0.879
MA0138.2	MA0138.2	0.526
MA0139.1	MA0139.1	0.0593
MA0140.1	MA0140.1	0.32
MA0141.1	MA0141.1	0.0299
MA0142.1	MA0142.1	0.318
MA0143.1	MA0143.1	0.39
MA0144.1	MA0144.1	0.405
MA0145.1	MA0145.1	0.0392
MA0146.1	MA0146.1	0.0121
MA0147.1	MA0147.1	0.83
MA0148.1	MA0148.1	0.777
MA0149.1	MA0149.1	0.159
MA0150.1	MA0150.1	0.01
MA0152.1	MA0152.1	0.305
MA0153.1	MA0153.1	5.91161e-4
MA0154.1	MA0154.1	0.00461
MA0155.1	MA0155.1	0.378
MA0156.1	MA0156.1	0.00275
MA0157.1	MA0157.1	0.538
MA0159.1	MA0159.1	0.00245
MA0160.1	MA0160.1	0.148
MA0162.1	MA0162.1	0.184
MA0163.1	MA0163.1	6.16997e-5
MA0164.1	MA0164.1	0.943
MA0258.1	MA0258.1	0.00576
MA0259.1	MA0259.1	0.541

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: CNhs12633

Novel motif	Logo	P-value
1	1	0.126
10	10	0.0714
100	100	0.78
101	101	0.936
102	102	0.63
103	103	0.0842
104	104	0.949
105	105	0.756
106	106	0.0244
107	107	0.201
108	108	0.5
109	109	0.0281
11	11	0.059
110	110	0.0881
111	111	0.0105
112	112	0.061
113	113	0.891
114	114	0.0248
115	115	0.267
116	116	0.141
117	117	0.0914
118	118	0.297
119	119	0.192
12	12	0.779
120	120	0.0301
121	121	0.503
122	122	0.868
123	123	0.848
124	124	0.663
125	125	0.115
126	126	0.417
127	127	0.379
128	128	0.0332
129	129	0.118
13	13	0.109
130	130	0.994
131	131	0.0348
132	132	0.563
133	133	0.068
134	134	0.655
135	135	0.928
136	136	0.846
137	137	0.275
138	138	0.393
139	139	0.0821
14	14	0.599
140	140	0.313
141	141	0.187
142	142	0.672
143	143	0.00713
144	144	0.971
145	145	0.248
146	146	0.7
147	147	0.827
148	148	0.0845
149	149	0.0129
15	15	0.0913
150	150	0.179
151	151	0.223
152	152	0.182
153	153	0.809
154	154	0.72
155	155	0.411
156	156	0.422
157	157	0.505
158	158	0.599
159	159	0.923
160	160	0.478
161	161	0.0706
162	162	0.842
163	163	0.892
164	164	0.159
165	165	0.0588
166	166	0.835
167	167	0.42
168	168	0.711
169	169	0.00484
17	17	0.0371
18	18	0.0877
19	19	0.135
2	2	0.521
20	20	0.526
21	21	0.442
22	22	0.141
23	23	0.0929
24	24	0.142
25	25	0.752
26	26	0.0134
27	27	0.357
28	28	0.674
29	29	0.0968
3	3	0.0361
30	30	0.78
31	31	0.297
32	32	0.117
33	33	0.409
34	34	0.388
35	35	0.516
36	36	0.00894
37	37	0.0533
38	38	0.193
39	39	0.549
4	4	0.281
40	40	0.0735
41	41	0.292
42	42	0.295
43	43	0.0508
44	44	0.0521
45	45	0.486
46	46	0.0725
47	47	0.178
48	48	0.2
49	49	0.07
5	5	0.185
50	50	0.491
51	51	0.702
52	52	0.38
53	53	0.888
54	54	0.671
55	55	0.397
56	56	0.18
57	57	0.54
58	58	0.346
59	59	0.00906
6	6	0.667
60	60	0.134
61	61	0.484
62	62	0.117
63	63	0.117
64	64	0.251
65	65	0.0494
66	66	0.734
67	67	0.271
68	68	0.105
69	69	0.273
7	7	0.462
70	70	3.23278e-4
71	71	0.0341
72	72	0.186
73	73	0.0726
74	74	0.827
75	75	0.0681
76	76	0.401
77	77	0.139
78	78	0.0862
79	79	0.593
8	8	0.0691
80	80	0.678
81	81	0.168
82	82	0.093
83	83	0.802
84	84	0.608
85	85	0.0856
86	86	0.471
87	87	0.325
88	88	0.836
89	89	0.0523
9	9	0.448
90	90	0.286
91	91	0.174
92	92	0.0958
93	93	0.118
94	94	0.664
95	95	0.0721
96	96	0.669
97	97	0.832
98	98	0.0962
99	99	0.59

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: CNhs12633

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000112 mouse mesenchymal stem cell of bone marrow sample

Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship Analyst: Hideya Kawaji link to source data data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002092 (bone marrow cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000112 (mouse mesenchymal stem cell of bone marrow 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
CL:0000134 (mesenchymal cell)

@@ Line 1: / Line 1: @@
 {{f5samples
-|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002371,UBERON:0001474,UBERON:0002384,UBERON:0000926,UBERON:0000479,UBERON:0000062,UBERON:0004765,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000467,UBERON:0001062,UBERON:0005291,UBERON:0006598,UBERON:0002532,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405,UBERON:0003081,UBERON:0006603,UBERON:0003061
+|DRA_sample_Accession=CAGE@SAMD00005570
-|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000219,CL:0000004,CL:0000134,CL:0000255,CL:0002092,CL:0002540
+|accession_numbers=CAGE;DRX008826;DRR009698;DRZ001123;DRZ002508;DRZ012473;DRZ013858
+|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002371,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405
+|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000255,CL:0000034,CL:0002092,CL:0002540
 |ancestors_in_disease_facet=
+|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000112
 |comment=
 |created_by=
 |creation_date=
+|data_phase=2
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:90936901..90936945,+!p1@Sfpi1!2.16!706.05!Sfpi1;;chr2:90936947..90936977,+!p2@Sfpi1!1.88!142.40!Sfpi1;;chr6:29476690..29476724,+!p1@Irf5!1.72!229.42!Irf5;;chr2:173044380..173044432,-!p1@Zbp1!1.72!119.65!Zbp1;;chr19:5447886..5447905,+!p1@Fosl1!1.70!49.44!Fosl1;;chr7:148452314..148452329,-!p1@Irf7!1.62!271.94!Irf7;;chr2:90936978..90937023,+!p3@Sfpi1!1.60!72.19!Sfpi1;;chr7:35904304..35904320,+!p1@Cebpa!1.58!712.97!Cebpa;;chr1:193007123..193007139,-!p1@Atf3!1.58!198.76!Atf3;;chr2:160192793..160192809,-!p1@Mafb!1.54!478.61!Mafb;;chr2:90922554..90922575,+!p4@Sfpi1!1.54!60.32!Sfpi1;;chrX:7341077..7341091,+!p5@Tfe3!1.48!48.45!Tfe3;;chr2:90936886..90936898,+!p5@Sfpi1!1.48!34.61!Sfpi1;;chr2:90922519..90922544,+!p6@Sfpi1!1.47!31.64!Sfpi1;;chr8:87225329..87225396,+!p1@Lyl1!1.44!96.91!Lyl1;;chr16:92826249..92826325,-!p1@Runx1!1.33!49.44!Runx1;;chr17:27693887..27693908,+!p2@Hmga1-rs1,p2@Hmga1!1.32!137.45!Hmga1;;chr2:173044357..173044377,-!p2@Zbp1!1.31!27.69!Zbp1;;chrX:7339938..7339963,+!p1@Tfe3!1.30!92.95!Tfe3;;chr8:123260252..123260264,+!p1@Irf8!1.29!127.56!Irf8;;chr2:91034924..91034946,-!p2@Nr1h3!1.29!22.74!Nr1h3;;chr7:25917492..25917512,-!p1@Pou2f2!1.27!29.67!Pou2f2;;chr6:145814003..145814056,-!p1@Bhlhe41!1.25!47.47!Bhlhe41;;chr7:87170879..87170914,+!p2@Zfp710!1.25!38.57!Zfp710;;chr10:67000609..67000625,+!p1@Egr2!1.23!36.59!Egr2;;chr19:5447692..5447711,+!p2@Fosl1!1.23!15.82!Fosl1;;chr2:27532479..27532509,+!p3@Rxra!1.19!29.67!Rxra;;chr15:103170516..103170531,-!p2@Zfp385a!1.17!32.63!Zfp385a;;chr1:186556410..186556424,-!p1@Hlx!1.15!40.54!Hlx;;chr6:145813905..145813932,-!p2@Bhlhe41!1.15!24.72!Bhlhe41;;chr2:167514456..167514473,+!p1@Cebpb!1.14!556.73!Cebpb;;chr7:52960555..52960662,+!p1@Dbp!1.14!108.78!Dbp;;chr8:118231705..118231722,-!p3@Maf!1.14!100.86!Maf;;chr11:11586218..11586285,+!p1@Ikzf1!1.14!40.54!Ikzf1;;chr8:87502608..87502623,-!p1@Junb!1.12!195.80!Junb;;chr16:92697560..92697592,-!p2@Runx1!1.12!76.14!Runx1;;chr12:86814833..86814846,+!p1@Fos!1.11!273.92!Fos;;chr16:15887371..15887385,+!p1@Cebpd!1.10!388.62!Cebpd;;chr11:5761979..5761992,+!p2@Aebp1!1.08!22.74!Aebp1;;chr7:20408047..20408125,-!p1@Bcl3!1.07!121.63!Bcl3;;chr19:37509324..37509337,+!p1@Hhex!1.07!76.14!Hhex;;chr2:168415815..168415872,-!p1@Nfatc2!1.05!56.37!Nfatc2;;chr2:30700881..30700916,+!p1@Prrx2!1.04!18.79!Prrx2;;chr6:29479308..29479325,+!p3@Irf5!1.04!9.89!Irf5;;chr12:87027598..87027652,+!p1@Batf!1.03!22.74!Batf;;chr1:186556375..186556404,-!p3@Hlx!1.03!17.80!Hlx;;chr11:5761889..5761969,+!p1@Aebp1!1.01!394.56!Aebp1;;chr6:145813964..145813994,-!p3@Bhlhe41!1.01!11.87!Bhlhe41;;chr17:71201096..71201114,-!p6@Tgif1!1.01!10.88!Tgif1;;chr9:32348943..32349001,-!p1@Fli1!1.00!74.16!Fli1;;chr2:90936867..90936874,+!p7@Sfpi1!1.00!8.90!Sfpi1;;chr1:186556323..186556370,-!p2@Hlx!0.98!23.73!Hlx;;chr13:37870307..37870337,+!p5@Rreb1!0.98!19.78!Rreb1;;chr7:26067619..26067702,+!p2@Cic!0.96!47.47!Cic;;chr17:45692676..45692695,+!p2@Nfkbie!0.96!16.81!Nfkbie;;chr11:16908650..16908690,-!p1@Plek!0.95!49.44!Plek;;chr19:46379199..46379301,+!p1@Nfkb2!0.95!46.48!Nfkb2;;chr7:20214704..20214800,-!p1@Relb!0.95!26.70!Relb;;chr2:91035197..91035237,-!p1@Nr1h3!0.95!16.81!Nr1h3;;chr5:140267510..140267555,+!p2@Mafk!0.94!18.79!Mafk;;chr17:45692642..45692663,+!p1@Nfkbie!0.93!24.72!Nfkbie;;chr7:52071956..52071978,-!p1@Atf5!0.92!248.21!Atf5;;chrX:7339915..7339935,+!p4@Tfe3!0.92!16.81!Tfe3;;chr2:152758901..152758925,-!p1@Foxs1!0.91!32.63!Foxs1;;chr15:103170533..103170556,-!p1@Zfp385a!0.91!27.69!Zfp385a;;chr11:96685444..96685473,-!p5@Nfe2l1!0.90!6.92!Nfe2l1;;chr6:52190467..52190500,-!p1@Hoxa10!0.90!6.92!Hoxa10;;chr15:79178060..79178074,+!p2@Maff!0.89!8.90!Maff;;chr12:74147689..74147711,-!p1@Six1!0.88!14.83!Six1;;chr5:138188113..138188145,+!p9@Tsc22d4!0.88!10.88!Tsc22d4;;chr8:118231350..118231385,-!p7@Maf!0.88!9.89!Maf;;chr19:5423800..5423821,-!p5@Drap1!0.88!9.89!Drap1;;chr17:27693922..27693934,+!p10@Hmga1-rs1,p11@Hmga1!0.88!8.90!Hmga1;;chr4:135699731..135699747,+!p1@Id3!0.87!760.44!Id3;;chr11:100683839..100683890,-!p2@Stat5b!0.85!14.83!Stat5b;;chr18:83079981..83080037,+!p6@Zfp516!0.85!10.88!Zfp516;;chr7:133839456..133839523,+!p1@Bola2!0.84!312.48!Bola2;;chr2:27532513..27532525,+!p8@Rxra!0.84!6.92!Rxra;;chr19:6164433..6164446,+!p2@Batf2!0.84!5.93!Batf2;;chr3:135271185..135271254,-!p4@Nfkb1!0.83!10.88!Nfkb1;;chr16:23988711..23988727,-!p1@Bcl6!0.82!71.20!Bcl6;;chr4:124805092..124805135,-!p2@Zc3h12a!0.82!25.71!Zc3h12a;;chr17:84586544..84586592,-!p3@Zfp36l2!0.82!7.91!Zfp36l2;;chr7:51809271..51809325,-!p1@Nr1h2!0.81!330.28!Nr1h2;;chr6:39068181..39068206,-!p3@Parp12!0.81!11.87!Parp12;;chr16:22439681..22439698,-!p1@Etv5!0.80!99.88!Etv5;;chr6:29476741..29476752,+!p4@Irf5!0.80!5.93!Irf5;;chr16:22439654..22439676,-!p2@Etv5!0.78!32.63!Etv5;;chr17:71202822..71202877,-!p3@Tgif1!0.78!15.82!Tgif1;;chr10:119913278..119913298,-!p2@Hmga2!0.78!11.87!Hmga2;;chr17:27693706..27693724,+!p4@Hmga1,p5@Hmga1-rs1!0.77!12.86!Hmga1;;chr17:47906140..47906150,+!p6@Tfeb!0.77!4.94!Tfeb;;chr2:27532754..27532815,+!p1@Rxra!0.76!153.27!Rxra;;chr8:28087578..28087599,+!p2@Zfp703!0.76!50.43!Zfp703;;chr8:118230894..118230918,-!p5@Maf!0.76!14.83!Maf;;chr18:80904854..80904919,-!p2@Nfatc1!0.75!60.32!Nfatc1;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.75!53.40!Camta2;;chr8:118230866..118230891,-!p4@Maf!0.75!33.62!Maf;;chr8:28087609..28087634,+!p1@Zfp703!0.74!114.71!Zfp703;;chr6:39068210..39068251,-!p1@Parp12!0.74!22.74!Parp12;;chr11:120491440..120491474,-!p3@Mafg!0.74!6.92!Mafg;;chr12:56593574..56593592,-!p1@Nfkbia!0.73!253.15!Nfkbia;;chr7:31741846..31741930,-!p1@LOC100504922,p1@Usf2!0.73!124.60!Usf2;;chr11:53583544..53583559,+!p1@Irf1!0.73!82.08!Irf1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.73!34.61!Tsc22d3;;chr19:46380172..46380231,+!p2@Nfkb2!0.73!33.62!Nfkb2;;chr5:53981592..53981616,+!p3@Rbpj!0.73!8.90!Rbpj;;chr17:71200529..71200556,-!p1@Tgif1!0.72!76.14!Tgif1;;chr19:6996294..6996324,-!p2@Esrra!0.72!31.64!Esrra;;chr11:98636531..98636559,-!p1@Nr1d1!0.72!26.70!Nr1d1;;chr8:72662966..72662991,-!p3@LOC100048268,p3@Rfxank!0.72!16.81!Rfxank;;chr8:47825166..47825178,+!p2@Irf2!0.72!6.92!Irf2;;chr6:53523358..53523388,+!p1@Creb5!0.71!55.38!Creb5;;chr8:118231678..118231692,-!p2@Maf!0.71!42.52!Maf;;chr8:94325321..94325366,-!p1@Irx3!0.71!10.88!Irx3;;chr6:108610766..108610781,+!p2@Bhlhe40!0.71!7.91!Bhlhe40;;chr3:32264530..32264544,-!p2@Zmat3!0.71!6.92!Zmat3;;chr19:5637528..5637548,+!p2@Rela!0.70!26.70!Rela;;chr8:87225670..87225697,+!p2@Lyl1!0.70!12.86!Lyl1;;chr11:70501599..70501634,-!p2@Camta2,p2@LOC100048818!0.70!8.90!Camta2;;chr4:134676555..134676575,+!p2@Runx3!0.70!3.96!Runx3;;chr17:71201050..71201078,-!p9@Tgif1!0.70!3.96!Tgif1;;chr6:52195795..52195825,-!p1@Hoxa11!0.70!3.96!Hoxa11;;chr12:25780945..25780961,-!p1@Id2!0.69!745.61!Id2;;chr19:5637736..5637766,+!p1@Rela!0.69!120.64!Rela;;chr12:78063057..78063070,-!p3@Max!0.69!8.90!Max;;chr3:99057269..99057306,+!p1@Tbx15!0.69!4.94!Tbx15;;chr17:84587279..84587294,-!p1@Zfp36l2!0.68!460.81!Zfp36l2;;chr11:120494853..120494905,-!p1@Mafg!0.68!42.52!Mafg;;chr17:47873985..47874056,+!p1@Tfeb!0.67!34.61!Tfeb;;chr17:27693546..27693557,+!p6@Hmga1!0.67!14.83!Hmga1;;chr7:87171047..87171078,+!p1@Zfp710!0.67!13.84!Zfp710;;chr2:27532734..27532749,+!p2@Rxra!0.67!11.87!Rxra;;chr2:166888107..166888224,-!p1@Znfx1!0.66!60.32!Znfx1;;chr17:34784132..34784161,+!p1@Atf6b!0.66!23.73!Atf6b;;chr2:25562263..25562314,+!p2@Bmyc!0.66!15.82!Bmyc;;chr17:84587167..84587239,-!p2@Zfp36l2!0.66!13.84!Zfp36l2;;chr2:133377954..133377973,+!p1@Bmp2!0.66!12.86!Bmp2;;chr16:92697354..92697362,-!p3@Runx1!0.66!5.93!Runx1;;chr17:27693558..27693580,+!p1@Hmga1-rs1,p1@Hmga1!0.65!189.86!Hmga1;;chr8:72520162..72520197,-!p4@Gatad2a!0.65!20.77!Gatad2a;;chr7:6124098..6124133,+!p1@Zfp444!0.65!17.80!Zfp444;;chrX:137077653..137077669,-!p3@Tsc22d3!0.65!17.80!Tsc22d3;;chr17:33766353..33766393,+!p2@Zfp414!0.65!10.88!Zfp414;;chr7:31206743..31206761,+!p1@Nfkbid!0.65!4.94!Nfkbid;;chrX:137077608..137077619,-!p6@Tsc22d3!0.65!4.94!Tsc22d3;;chr19:5637501..5637517,+!p4@Rela!0.64!15.82!Rela;;chr3:89197057..89197114,-!p1@Zbtb7b!0.64!12.86!Zbtb7b;;chr6:39068163..39068176,-!p2@Parp12!0.64!6.92!Parp12;;chr4:114729646..114729665,+!p4@Tal1!0.64!4.94!Tal1;;chr8:118230847..118230856,-!p8@Maf!0.64!4.94!Maf;;chr16:91270004..91270023,+!p1@Olig1!0.64!3.96!Olig1;;chr8:118231723..118231740,-!p1@Maf!0.63!87.02!Maf;;chr7:133838869..133838945,+!p2@Bola2!0.63!15.82!Bola2;;chrX:7339829..7339855,+!p3@Tfe3!0.63!9.89!Tfe3;;chr10:80598209..80598236,+!p4@Zbtb7a!0.63!5.93!Zbtb7a;;chr11:96180045..96180059,+!p1@Hoxb4!0.63!4.94!Hoxb4;;chr13:37870253..37870272,+!p13@Rreb1!0.63!4.94!Rreb1;;chr7:4967068..4967111,+!p1@Zfp524!0.62!41.53!Zfp524;;chr3:135354384..135354443,-!p1@Nfkb1!0.62!22.74!Nfkb1;;chr4:63064395..63064410,-!p2@Akna!0.62!5.93!Akna;;chr15:61818593..61818614,+!p4@Myc!0.62!5.93!Myc;;chr15:103170561..103170572,-!p4@Zfp385a!0.62!4.94!Zfp385a;;chr10:44178474..44178487,-!p4@Prdm1!0.62!4.94!Prdm1;;chr11:11590140..11590187,+!p3@Ikzf1!0.62!3.96!Ikzf1;;chr14:32979290..32979309,+!p3@Gm6768,p3@Ncoa4!0.62!3.96!Ncoa4;;chr5:138187195..138187255,+!p1@Tsc22d4!0.61!157.23!Tsc22d4;;chr2:44965856..44965896,-!p5@Zeb2!0.61!13.84!Zeb2;;chr19:8876976..8877011,+!p1@Zbtb3!0.61!11.87!Zbtb3;;chr19:5637489..5637500,+!p5@Rela!0.61!8.90!Rela;;chr11:98636508..98636524,-!p3@Nr1d1!0.61!3.96!Nr1d1;;chr15:79178029..79178044,+!p4@Maff!0.61!3.96!Maff;;chr19:6996243..6996293,-!p1@Esrra!0.60!39.55!Esrra;;chr10:119913546..119913583,-!p3@Hmga2!0.60!6.92!Hmga2;;chr10:44178521..44178557,-!p1@Prdm1!0.60!5.93!Prdm1;;chr2:30700788..30700824,+!p2@Prrx2!0.60!4.94!Prrx2;;chr1:165243591..165243625,-!p2@Prrx1!0.60!4.94!Prrx1;;chr1:186556495..186556506,-!p8@Hlx!0.60!2.97!Hlx;;chr19:46380346..46380360,+!p6@Nfkb2!0.60!2.97!Nfkb2;;chr16:92826232..92826245,-!p4@Runx1!0.60!2.97!Runx1;;chr16:91225808..91225824,+!p1@Olig2!0.60!2.97!Olig2;;chr16:92826180..92826191,-!p5@Runx1!0.60!2.97!Runx1;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!0.60!2.97!Eno1;;chr4:149611803..149611814,+!p6@LOC100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+|ffid_belonging_in_development=CL:0000134
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 38: / Line 44: @@
 |is_a=EFO:0002091;;FF:0000112
 |is_obsolete=
+|library_id=CNhs12633
+|library_id_phase_based=2:CNhs12633
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11735
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11735
+|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm10.nobarcode.bam
+|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm10.nobarcode.ctss.bed.gz
+|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm9.nobarcode.bam
+|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm9.ctss.bed.gz
+|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Mesenchymal stem cells - bone marrow derived, donor2
 |namespace=FANTOM5
@@ Line 43: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12633,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.720281264647295,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.938954097886573,-0.558422792324031,0,0,0,0,-0.00360570357009682,-0.0600199241672839,-0.0661618130246221,-0.232307665022887,-0.984211366477826,-0.269868638010351,0.298605602657084,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,-0.0611083211276296,-0.117389802908326,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0760168881589905,0,0,0,-0.100514125913501,-0.0529946128728175,1.31835972401451,-0.0788315948399074,0,0,0,0,0,0,0.525377903383493,0.465881032051421,0.299966606123791,0,0,0,0.473885713829627,0
 |rna_box=123
 |rna_catalog_number=custom
@@ Line 55: / Line 73: @@
 |rna_rin=
 |rna_sample_type=total RNA
-|rna_tube_id=123E7
+|rna_tube_id=1.23E+09
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 78: / Line 97: @@
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 |xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11735-123E7;search_select_hide=table117:11735-123E7
 }}

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FF:11735-123E7: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:16, 4 June 2020

CNhs12633

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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