FF:11640-122D2: Difference between revisions

Latest revision as of 18:13, 4 June 2020

Name:	Mouse Mesenchymal stem cells - bone marrow derived, donor3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12616
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	RNAMCS3
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		SAMD00004986

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12616		CAGE		DRX008827		DRR009699

Accession ID Mm9

Library id		BAM		CTSS
CNhs12616		DRZ001124		DRZ002509

Accession ID Mm10

Library id		BAM		CTSS
CNhs12616		DRZ012474		DRZ013859

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

CNhs12616

0	0
1	0
10	0
100	0
1000	0
1001	-0.0668
1002	-0.0156
1003	-0.0349
1004	0
1005	0
1006	0.212
1007	-0.426
1008	0
1009	-0.19
101	-0.54
1010	0
1011	0
1012	0
1013	0.0678
1014	-0.0874
1015	0.00844
1016	-0.232
1017	0
1018	0
1019	0
102	0
1020	0.658
1021	0.23
1022	-0.0446
1023	0
1024	-0.14
1025	-0.0611
1026	0
1027	0
1028	0
1029	-0.176
103	0
1030	0
1031	-0.243
1032	-0.184
1033	-0.0752
1034	0
1035	0
1036	-0.185
1037	0
1038	-0.14
1039	-0.11
104	0
1040	-0.0211
1041	0.233

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: CNhs12616

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	5.06249e-6
MA0003.1	MA0003.1	0.133
MA0004.1	MA0004.1	0.414
MA0006.1	MA0006.1	0.504
MA0007.1	MA0007.1	0.628
MA0009.1	MA0009.1	0.76
MA0014.1	MA0014.1	0.698
MA0017.1	MA0017.1	0.105
MA0018.2	MA0018.2	0.12
MA0019.1	MA0019.1	0.743
MA0024.1	MA0024.1	0.00543
MA0025.1	MA0025.1	0.483
MA0027.1	MA0027.1	0.512
MA0028.1	MA0028.1	0.573
MA0029.1	MA0029.1	0.951
MA0030.1	MA0030.1	0.211
MA0031.1	MA0031.1	0.698
MA0035.2	MA0035.2	0.382
MA0038.1	MA0038.1	1.77467e-4
MA0039.2	MA0039.2	0.782
MA0040.1	MA0040.1	0.769
MA0041.1	MA0041.1	0.479
MA0042.1	MA0042.1	0.799
MA0043.1	MA0043.1	0.146
MA0046.1	MA0046.1	1.01955e-4
MA0047.2	MA0047.2	0.723
MA0048.1	MA0048.1	0.677
MA0050.1	MA0050.1	3.89121e-6
MA0051.1	MA0051.1	5.8423e-4
MA0052.1	MA0052.1	0.0399
MA0055.1	MA0055.1	0.987
MA0057.1	MA0057.1	0.28
MA0058.1	MA0058.1	0.26
MA0059.1	MA0059.1	0.244
MA0060.1	MA0060.1	7.57707e-13
MA0061.1	MA0061.1	0.0303
MA0062.2	MA0062.2	0.28
MA0065.2	MA0065.2	0.00357
MA0066.1	MA0066.1	0.0315
MA0067.1	MA0067.1	0.698
MA0068.1	MA0068.1	0.636
MA0069.1	MA0069.1	0.741
MA0070.1	MA0070.1	0.198
MA0071.1	MA0071.1	0.138
MA0072.1	MA0072.1	0.407
MA0073.1	MA0073.1	0.592
MA0074.1	MA0074.1	0.0174
MA0076.1	MA0076.1	0.255
MA0077.1	MA0077.1	0.516
MA0078.1	MA0078.1	0.539
MA0079.2	MA0079.2	0.566
MA0080.2	MA0080.2	3.02804e-13
MA0081.1	MA0081.1	0.00289
MA0083.1	MA0083.1	0.405
MA0084.1	MA0084.1	0.98
MA0087.1	MA0087.1	0.527
MA0088.1	MA0088.1	0.379
MA0090.1	MA0090.1	0.8
MA0091.1	MA0091.1	0.253
MA0092.1	MA0092.1	0.394
MA0093.1	MA0093.1	0.435
MA0099.2	MA0099.2	4.10203e-4
MA0100.1	MA0100.1	0.859
MA0101.1	MA0101.1	0.141
MA0102.2	MA0102.2	0.754
MA0103.1	MA0103.1	0.706
MA0104.2	MA0104.2	0.833
MA0105.1	MA0105.1	0.00555
MA0106.1	MA0106.1	0.22
MA0107.1	MA0107.1	0.144
MA0108.2	MA0108.2	0.181
MA0111.1	MA0111.1	0.313
MA0112.2	MA0112.2	9.40663e-5
MA0113.1	MA0113.1	0.267
MA0114.1	MA0114.1	0.251
MA0115.1	MA0115.1	0.814
MA0116.1	MA0116.1	0.00187
MA0117.1	MA0117.1	0.875
MA0119.1	MA0119.1	0.217
MA0122.1	MA0122.1	0.502
MA0124.1	MA0124.1	0.764
MA0125.1	MA0125.1	0.074
MA0131.1	MA0131.1	0.155
MA0135.1	MA0135.1	0.681
MA0136.1	MA0136.1	2.23736e-10
MA0137.2	MA0137.2	0.738
MA0138.2	MA0138.2	0.458
MA0139.1	MA0139.1	0.108
MA0140.1	MA0140.1	0.274
MA0141.1	MA0141.1	0.0126
MA0142.1	MA0142.1	0.816
MA0143.1	MA0143.1	0.214
MA0144.1	MA0144.1	0.415
MA0145.1	MA0145.1	0.0506
MA0146.1	MA0146.1	0.00606
MA0147.1	MA0147.1	0.777
MA0148.1	MA0148.1	0.641
MA0149.1	MA0149.1	0.213
MA0150.1	MA0150.1	0.0114
MA0152.1	MA0152.1	0.245
MA0153.1	MA0153.1	0.00269
MA0154.1	MA0154.1	0.00452
MA0155.1	MA0155.1	0.395
MA0156.1	MA0156.1	0.00297
MA0157.1	MA0157.1	0.667
MA0159.1	MA0159.1	0.00298
MA0160.1	MA0160.1	0.142
MA0162.1	MA0162.1	0.202
MA0163.1	MA0163.1	3.81235e-5
MA0164.1	MA0164.1	0.959
MA0258.1	MA0258.1	0.00667
MA0259.1	MA0259.1	0.584

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: CNhs12616

Novel motif	Logo	P-value
1	1	0.126
10	10	0.0691
100	100	0.808
101	101	0.968
102	102	0.429
103	103	0.118
104	104	0.799
105	105	0.552
106	106	0.0215
107	107	0.285
108	108	0.393
109	109	0.0227
11	11	0.0569
110	110	0.085
111	111	0.0483
112	112	0.0938
113	113	0.751
114	114	0.0259
115	115	0.435
116	116	0.104
117	117	0.0546
118	118	0.421
119	119	0.234
12	12	0.814
120	120	0.0635
121	121	0.453
122	122	0.833
123	123	0.607
124	124	0.931
125	125	0.277
126	126	0.378
127	127	0.241
128	128	0.0377
129	129	0.0984
13	13	0.11
130	130	0.615
131	131	0.108
132	132	0.402
133	133	0.131
134	134	0.684
135	135	0.855
136	136	0.696
137	137	0.49
138	138	0.462
139	139	0.284
14	14	0.48
140	140	0.233
141	141	0.254
142	142	0.217
143	143	0.0216
144	144	0.93
145	145	0.173
146	146	0.624
147	147	0.85
148	148	0.0789
149	149	0.0144
15	15	0.103
150	150	0.147
151	151	0.206
152	152	0.0899
153	153	0.79
154	154	0.603
155	155	0.408
156	156	0.46
157	157	0.567
158	158	0.552
159	159	0.846
160	160	0.468
161	161	0.0728
162	162	0.783
163	163	0.831
164	164	0.182
165	165	0.177
166	166	0.673
167	167	0.409
168	168	0.517
169	169	0.00641
17	17	0.0221
18	18	0.0909
19	19	0.159
2	2	0.522
20	20	0.36
21	21	0.336
22	22	0.11
23	23	0.116
24	24	0.106
25	25	0.762
26	26	0.0117
27	27	0.49
28	28	0.756
29	29	0.0694
3	3	0.0267
30	30	0.744
31	31	0.244
32	32	0.166
33	33	0.331
34	34	0.362
35	35	0.573
36	36	0.013
37	37	0.0397
38	38	0.192
39	39	0.689
4	4	0.31
40	40	0.0653
41	41	0.36
42	42	0.225
43	43	0.0486
44	44	0.0411
45	45	0.516
46	46	0.066
47	47	0.234
48	48	0.188
49	49	0.0743
5	5	0.253
50	50	0.483
51	51	0.805
52	52	0.467
53	53	0.978
54	54	0.737
55	55	0.581
56	56	0.196
57	57	0.418
58	58	0.387
59	59	0.0071
6	6	0.885
60	60	0.123
61	61	0.444
62	62	0.136
63	63	0.11
64	64	0.243
65	65	0.0355
66	66	0.728
67	67	0.158
68	68	0.00837
69	69	0.119
7	7	0.427
70	70	6.16872e-4
71	71	0.035
72	72	0.151
73	73	0.0357
74	74	0.725
75	75	0.0551
76	76	0.462
77	77	0.118
78	78	0.0475
79	79	0.651
8	8	0.0486
80	80	0.991
81	81	0.15
82	82	0.244
83	83	0.714
84	84	0.391
85	85	0.0771
86	86	0.449
87	87	0.209
88	88	0.9
89	89	0.0915
9	9	0.547
90	90	0.306
91	91	0.235
92	92	0.0871
93	93	0.418
94	94	0.496
95	95	0.048
96	96	0.567
97	97	0.839
98	98	0.0499
99	99	0.93

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: CNhs12616

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@SAMD00004986
-|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;DRX008827;DRR009699;DRZ001124;DRZ002509;DRZ012474;DRZ013859
+|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!704.80!Sfpi1;;chr2:90936947..90936977,+!p2@Sfpi1!1.89!146.36!Sfpi1;;chr6:29476690..29476724,+!p1@Irf5!1.72!226.64!Irf5;;chr19:5447886..5447905,+!p1@Fosl1!1.67!45.47!Fosl1;;chr2:173044380..173044432,-!p1@Zbp1!1.61!92.36!Zbp1;;chr2:90936978..90937023,+!p3@Sfpi1!1.61!73.89!Sfpi1;;chr1:193007123..193007139,-!p1@Atf3!1.60!206.04!Atf3;;chr7:35904304..35904320,+!p1@Cebpa!1.56!681.35!Cebpa;;chr7:148452314..148452329,-!p1@Irf7!1.55!226.64!Irf7;;chr2:90922554..90922575,+!p4@Sfpi1!1.53!58.26!Sfpi1;;chr2:160192793..160192809,-!p1@Mafb!1.50!435.52!Mafb;;chr7:87170879..87170914,+!p2@Zfp710!1.43!59.68!Zfp710;;chr2:91034924..91034946,-!p2@Nr1h3!1.42!31.26!Nr1h3;;chr8:87225329..87225396,+!p1@Lyl1!1.41!90.94!Lyl1;;chrX:7341077..7341091,+!p5@Tfe3!1.37!37.66!Tfe3;;chr8:123260252..123260264,+!p1@Irf8!1.36!148.49!Irf8;;chr2:90936886..90936898,+!p5@Sfpi1!1.34!24.87!Sfpi1;;chr17:27693887..27693908,+!p2@Hmga1-rs1,p2@Hmga1!1.33!142.10!Hmga1;;chrX:7339938..7339963,+!p1@Tfe3!1.32!97.34!Tfe3;;chr6:145814003..145814056,-!p1@Bhlhe41!1.32!56.84!Bhlhe41;;chr2:173044357..173044377,-!p2@Zbp1!1.28!25.58!Zbp1;;chr16:92826249..92826325,-!p1@Runx1!1.25!41.21!Runx1;;chr2:90922519..90922544,+!p6@Sfpi1!1.25!18.47!Sfpi1;;chr12:87027598..87027652,+!p1@Batf!1.23!36.23!Batf;;chr19:5447692..5447711,+!p2@Fosl1!1.22!15.63!Fosl1;;chr7:25917492..25917512,-!p1@Pou2f2!1.21!25.58!Pou2f2;;chr8:87502608..87502623,-!p1@Junb!1.18!227.35!Junb;;chr11:5761979..5761992,+!p2@Aebp1!1.18!28.42!Aebp1;;chr12:86814833..86814846,+!p1@Fos!1.17!316.16!Fos;;chr2:30700881..30700916,+!p1@Prrx2!1.15!24.87!Prrx2;;chr2:167514456..167514473,+!p1@Cebpb!1.14!566.25!Cebpb;;chr16:15887371..15887385,+!p1@Cebpd!1.14!428.42!Cebpd;;chr11:11586218..11586285,+!p1@Ikzf1!1.12!39.08!Ikzf1;;chr2:27532479..27532509,+!p3@Rxra!1.12!24.87!Rxra;;chr7:52960555..52960662,+!p1@Dbp!1.11!101.60!Dbp;;chr19:37509324..37509337,+!p1@Hhex!1.11!83.84!Hhex;;chr1:186556410..186556424,-!p1@Hlx!1.11!36.94!Hlx;;chr1:186556375..186556404,-!p3@Hlx!1.11!21.31!Hlx;;chr19:46379199..46379301,+!p1@Nfkb2!1.10!66.07!Nfkb2;;chr17:45692676..45692695,+!p2@Nfkbie!1.07!22.02!Nfkbie;;chr10:67000609..67000625,+!p1@Egr2!1.06!24.16!Egr2;;chr1:186556323..186556370,-!p2@Hlx!1.04!27.71!Hlx;;chr6:145813905..145813932,-!p2@Bhlhe41!1.02!18.47!Bhlhe41;;chr17:27693922..27693934,+!p10@Hmga1-rs1,p11@Hmga1!1.01!12.08!Hmga1;;chr15:79178060..79178074,+!p2@Maff!1.01!12.08!Maff;;chr11:5761889..5761969,+!p1@Aebp1!1.00!385.08!Aebp1;;chr16:92697560..92697592,-!p2@Runx1!1.00!58.26!Runx1;;chr15:103170516..103170531,-!p2@Zfp385a!1.00!22.02!Zfp385a;;chr13:37870307..37870337,+!p5@Rreb1!0.99!20.60!Rreb1;;chr7:20408047..20408125,-!p1@Bcl3!0.98!99.47!Bcl3;;chr7:26067619..26067702,+!p2@Cic!0.98!49.73!Cic;;chr4:135699731..135699747,+!p1@Id3!0.97!951.33!Id3;;chr15:103170533..103170556,-!p1@Zfp385a!0.97!31.97!Zfp385a;;chr2:168415815..168415872,-!p1@Nfatc2!0.95!44.76!Nfatc2;;chr19:6164433..6164446,+!p2@Batf2!0.95!7.82!Batf2;;chr11:96685444..96685473,-!p5@Nfe2l1!0.95!7.82!Nfe2l1;;chr7:20214704..20214800,-!p1@Relb!0.94!26.29!Relb;;chr2:91035197..91035237,-!p1@Nr1h3!0.94!16.34!Nr1h3;;chr6:29476741..29476752,+!p4@Irf5!0.94!8.53!Irf5;;chr8:118230866..118230891,-!p4@Maf!0.93!51.15!Maf;;chr8:118231350..118231385,-!p7@Maf!0.93!11.37!Maf;;chr11:16908650..16908690,-!p1@Plek!0.92!46.18!Plek;;chr17:34784132..34784161,+!p1@Atf6b!0.92!43.34!Atf6b;;chr17:71202822..71202877,-!p3@Tgif1!0.92!22.02!Tgif1;;chr19:5423800..5423821,-!p5@Drap1!0.91!10.66!Drap1;;chr7:31206743..31206761,+!p1@Nfkbid!0.91!9.95!Nfkbid;;chr17:71201096..71201114,-!p6@Tgif1!0.91!8.53!Tgif1;;chr9:32348943..32349001,-!p1@Fli1!0.90!58.97!Fli1;;chr4:124805092..124805135,-!p2@Zc3h12a!0.89!29.84!Zc3h12a;;chr10:119913278..119913298,-!p2@Hmga2!0.89!15.63!Hmga2;;chr2:27532513..27532525,+!p8@Rxra!0.89!7.82!Rxra;;chr2:152758901..152758925,-!p1@Foxs1!0.88!30.55!Foxs1;;chr7:133839456..133839523,+!p1@Bola2!0.85!319.01!Bola2;;chr6:97757008..97757061,+!p1@Mitf!0.85!27.71!Mitf;;chr17:71200529..71200556,-!p1@Tgif1!0.84!101.60!Tgif1;;chr11:100683839..100683890,-!p2@Stat5b!0.83!14.21!Stat5b;;chr5:53981592..53981616,+!p3@Rbpj!0.83!11.37!Rbpj;;chr15:102797288..102797302,+!p1@Hoxc10!0.83!5.68!Hoxc10;;chr7:52071956..52071978,-!p1@Atf5!0.81!192.54!Atf5;;chr12:78063057..78063070,-!p3@Max!0.81!12.08!Max;;chr18:83079981..83080037,+!p6@Zfp516!0.81!9.95!Zfp516;;chr6:145813964..145813994,-!p3@Bhlhe41!0.81!7.10!Bhlhe41;;chr16:22439681..22439698,-!p1@Etv5!0.79!98.76!Etv5;;chr11:70501419..70501483,-!p1@Camta2,p1@LOC100048818!0.79!58.26!Camta2;;chr12:56593574..56593592,-!p1@Nfkbia!0.78!281.35!Nfkbia;;chr7:31741846..31741930,-!p1@LOC100504922,p1@Usf2!0.78!141.39!Usf2;;chr7:52960663..52960677,+!p6@Dbp!0.78!4.97!Dbp;;chr4:149611832..149611846,+!p3@LOC100045967,p3@LOC100503183,p4@Eno1,p4@Gm5506!0.78!4.97!Eno1;;chr6:29479277..29479296,+!p2@Irf5!0.78!4.97!Irf5;;chr17:45692642..45692663,+!p1@Nfkbie!0.77!17.05!Nfkbie;;chr12:74147689..74147711,-!p1@Six1!0.77!11.37!Six1;;chr8:107793737..10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0!Stat5b;;chr17:46693107..46693137,-!p1@Srf!0.05!9.24!Srf;;chr17:88840082..88840127,+!p1@Foxn2!0.05!6.39!Foxn2;;chr10:127176572..127176648,+!p1@Zbtb39!0.05!5.68!Zbtb39;;chr6:47827619..47827639,+!p2@Zfp282!0.05!3.55!Zfp282;;chr11:98636575..98636607,-!p2@Nr1d1!0.05!2.84!Nr1d1;;chrX:20527723..20527739,-!p2@Elk1!0.05!2.13!Elk1;;chr10:13686815..13686846,+!p3@Hivep2!0.05!1.42!Hivep2;;chr17:47874123..47874156,+!p2@Tfeb!0.05!1.42!Tfeb;;chr14:55711114..55711159,-!p2@Zfhx2!0.05!1.42!Zfhx2;;chr7:134550321..134550345,-!p2@Zfp764!0.05!1.42!Zfp764;;chr8:74405860..74405905,+!p2@Zfp709!0.05!1.42!Zfp709;;chr19:23216132..23216157,+!p3@Klf9!0.05!0.71!Klf9;;chr17:15636925..15636940,+!p2@Tbp!0.05!0.71!Tbp;;chr15:80085678..80085693,+!p2@Atf4!0.05!0.71!Atf4;;chr19:55817590..55817625,+!p11@Tcf7l2!0.05!0.71!Tcf7l2;;chr2:34227659..34227674,-!p3@Pbx3!0.05!0.71!Pbx3;;chr11:96153767..96153822,+!p1@Hoxb6!0.05!0.71!Hoxb6;;chr11:99092280..99092302,-!p3@Smarce1!0.05!0.71!Smarce1;;chr7:148513548..148513560,-!p7@Deaf1!0.05!0.71!Deaf1;;chr5:34530519..34530545,-!p4@Mxd4!0.05!0.71!Mxd4;;chr5:147760370..147760377,+!p6@Gtf3a!0.05!0.71!Gtf3a;;chr15:50721640..50721654,-!p7@Trps1!0.05!0.71!Trps1;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.05!0.71!Ncoa4;;chr14:52634651..52634678,-!p7@Zfp219!0.05!0.71!Zfp219;;chr18:74375851..74375891,+!p1@Cxxc1!0.04!38.37!Cxxc1;;chr3:94819338..94819384,-!p1@Zfp687!0.04!8.53!Zfp687;;chr5:38611639..38611698,-!p1@Zbtb49!0.04!4.26!Zbtb49;;chr5:65194602..65194613,+!p3@Klf3!0.04!3.55!Klf3;;chr14:22807107..22807119,-!p2@Zfp503!0.04!3.55!Zfp503;;chr3:135354903..135354945,-!p7@Nfkb1!0.04!1.42!Nfkb1;;chr18:76401074..76401118,+!p3@Smad2!0.04!1.42!Smad2;;chr16:95923651..95923701,+!p3@Ets2!0.04!0.71!Ets2;;chr16:4594853..4594884,+!p3@Glis2!0.04!0.71!Glis2;;chr8:94325847..94325869,-!p3@Irx3!0.04!0.71!Irx3;;chrX:137077682..137077692,-!p5@Tsc22d3!0.04!0.71!Tsc22d3;;chr10:92773736..92773761,-!p4@Elk3!0.04!0.71!Elk3;;chr13:53076382..53076393,-!p2@Nfil3!0.04!0.71!Nfil3;;chr5:31262609..31262693,-!p1@Preb!0.03!49.02!Preb;;chr2:31428295..31428361,+!p1@Fubp3!0.03!25.58!Fubp3;;chr8:86590723..86590781,+!p1@Rfx1!0.03!17.05!Rfx1;;chr18:36440723..36440805,+!p1@Pura!0.03!14.92!Pura;;chr6:47870583..47870635,+!p1@Zfp212!0.03!11.37!Zfp212;;chr17:24592210..24592290,-!p1@E4f1!0.03!9.24!E4f1;;chr7:13551180..13551243,+!p1@Zfp324!0.03!7.10!Zfp324;;chr10:126726055..126726091,-!p2@Mbd6!0.03!7.10!Mbd6;;chr10:41996550..41996569,-!p2@Foxo3!0.03!3.55!Foxo3;;chr14:19071567..19071612,-!p2@Nr1d2!0.03!2.84!Nr1d2;;chr4:120498270..120498285,-!p3@Nfyc!0.03!2.84!Nfyc;;chr4:45025159..45025197,-!p1@Zbtb5!0.03!2.13!Zbtb5;;chr7:134489096..134489123,-!p2@Zfp768!0.03!2.13!Zfp768;;chr7:134550289..134550313,-!p1@Zfp764!0.03!1.42!Zfp764;;chr5:24107993..24108036,-!p2@Smarcd3!0.03!1.42!Smarcd3;;chr10:82226709..82226720,-!p6@Nfyb!0.03!0.71!Nfyb;;chr10:5734525..5734569,-!p3@Esr1!0.03!0.71!Esr1;;chr7:19945089..19945107,+!p2@Ppp1r13l!0.03!0.71!Ppp1r13l;;chr8:81923366..81923371,-!p5@Smad1!0.03!0.71!Smad1;;chr3:51144740..51144743,-!p7@Elf2!0.03!0.71!Elf2;;chr15:25914138..25914146,+!p4@Zfp622!0.03!0.71!Zfp622;;chr15:100382267..100382287,-!p3@Tfcp2!0.03!0.71!Tfcp2;;chr12:85559762..85559778,-!p5@C130039O16Rik!0.03!0.71!C130039O16Rik;;chr8:81923316..81923334,-!p1@Smad1!0.02!14.21!Smad1;;chr12:110031156..110031198,+!p2@Yy1!0.02!12.79!Yy1;;chr6:47827642..47827707,+!p1@Zfp282!0.02!9.24!Zfp282;;chr4:133276801..133276891,-!p3@Arid1a!0.02!9.24!Arid1a;;chr7:5003117..5003159,+!p1@Zfp580!0.02!6.39!Zfp580;;chr2:181022721..181022746,-!p2@Gmeb2!0.02!4.26!Gmeb2;;chr16:4559777..4559825,-!p2@Tfap4!0.02!3.55!Tfap4;;chr16:14705961..14705978,+!p2@Snai2!0.02!3.55!Snai2;;chr8:125778131..125778178,+!p1@Zfp276!0.02!3.55!Zfp276;;chr7:134170541..134170569,-!p9@Maz!0.02!2.84!Maz;;chrX:45807489..45807502,-!p2@Elf4!0.02!2.13!Elf4;;chrX:71330995..71331011,-!p2@Mecp2!0.02!2.13!Mecp2;;chr16:84835570..84835584,+!p4@Gabpa!0.02!2.13!Gabpa;;chr17:15701263..15701277,-!p2@Prdm9!0.02!1.42!Prdm9;;chr1:138521574..138521597,+!p3@Zfp281!0.02!1.42!Zfp281;;chr3:90097217..90097233,+!p3@Gatad2b!0.02!1.42!Gatad2b;;chr14:65977427..65977452,+!p4@Zfp395!0.02!1.42!Zfp395;;
+|ffid_belonging_in_development=CL:0000134
 |fonse_cell_line=
 |fonse_cell_line_closure=
@@ Line 36: / Line 42: @@
 |has_quality=
 |id=FF:11640-122D2
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000112
+|is_a=EFO:0002091;;FF:0000112
+|is_obsolete=
+|library_id=CNhs12616
+|library_id_phase_based=2:CNhs12616
+|microRNAs=
+|microRNAs_nn=
+|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11640
+|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11640
+|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%2520donor3.CNhs12616.11640-122D2.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%2520donor3.CNhs12616.11640-122D2.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%2520donor3.CNhs12616.11640-122D2.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%2520donor3.CNhs12616.11640-122D2.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%2520donor3.CNhs12616.11640-122D2.mm9.nobarcode.rdna.fa.gz
 |name=Mouse Mesenchymal stem cells - bone marrow derived, donor3
 |namespace=FANTOM5
@@ Line 42: / Line 60: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12616,LSID952,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
+|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.7093520502438,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.908742363940707,-0.558422792324031,0,0,0,0,-0.000968260486078455,-0.0927637106490179,-0.0661618130246221,-0.115636429119861,-0.984211366477826,-0.269868638010351,0.383987655166546,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,-0.0601091194109999,-0.243225778194271,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0787037500278776,0,0,0,-0.142843231051677,-0.0967654665782265,0.851215918986814,0.154286434853709,0,0,0,0,0,0,0.640549623890702,0.678765224720638,0.334703877756715,0,0,0,0.434338897795685,0
 |rna_box=122
 |rna_catalog_number=custom
@@ Line 57: / Line 76: @@
 |rna_weight_ug=10
 |sample_age=
+|sample_category=primary cells
 |sample_cell_catalog=
 |sample_cell_line=
@@ Line 76: / Line 96: @@
 |sample_tissue=bone marrow
 |top_motifs=SREBF1,2:2.18399667172;SPIB:1.97263424731;PAX2:1.7825977179;ZNF423:1.68755952211;NFE2L1:1.56792208815;SPI1:1.56193919589;NFE2L2:1.48920554351;TP53:1.48426343853;RXRA_VDR{dimer}:1.46020118568;ESR1:1.44293680042;EBF1:1.37806016345;BACH2:1.23577232601;GLI1..3:1.21541604358;RUNX1..3:1.20322554544;IRF7:1.18733748195;HAND1,2:1.16071466238;FOS_FOS{B,L1}_JUN{B,D}:1.15222299132;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.11042676133;TFAP2{A,C}:1.06207920965;GTF2A1,2:0.999324102445;NFKB1_REL_RELA:0.978037792378;DMAP1_NCOR{1,2}_SMARC:0.97759242591;IRF1,2:0.973085604865;ETS1,2:0.936356618049;TFCP2:0.929854544555;POU2F1..3:0.846824367717;RXR{A,B,G}:0.833063831012;FOXM1:0.822001497404;SPZ1:0.814974071703;ALX4:0.801705944176;HLF:0.760457536257;CEBPA,B_DDIT3:0.74920743432;FOXL1:0.736036258665;NR1H4:0.666228052439;STAT2,4,6:0.644449298268;ATF6:0.588412863169;UFEwm:0.535808710733;HOXA9_MEIS1:0.518005277252;HES1:0.454856266963;NFIL3:0.45320905626;ZNF148:0.447657373275;FOXO1,3,4:0.440366903881;IKZF1:0.416784459477;POU6F1:0.411281332615;SRF:0.404019038795;ZBTB6:0.384404699227;bHLH_family:0.378879673432;HOX{A5,B5}:0.353030323593;ARID5B:0.321333028736;TFAP4:0.248837623367;ZNF238:0.244911912912;PAX4:0.241386390218;MTF1:0.21816368264;FOSL2:0.163447497388;ATF4:0.163255394432;NKX2-3_NKX2-5:0.144456505582;HIF1A:0.140045263882;NFE2:0.108688409995;NR6A1:0.0896337056361;GCM1,2:0.0836486794785;POU3F1..4:0.0835157838313;ESRRA:0.0722651386131;IKZF2:0.0280936836389;ZIC1..3:0.00910239220713;EN1,2:-0.00944812183937;ALX1:-0.0145632575583;TBP:-0.0437475140915;HOX{A4,D4}:-0.047035676158;MYB:-0.0777225671717;TLX1..3_NFIC{dimer}:-0.0795922526397;TEAD1:-0.103711774777;NKX3-2:-0.106277587399;JUN:-0.107798276033;CDC5L:-0.13915693205;HMX1:-0.14083570964;NR5A1,2:-0.15675967501;NKX2-2,8:-0.163347568097;VSX1,2:-0.179042185273;FOX{F1,F2,J1}:-0.18273807509;ZBTB16:-0.18391975241;ELF1,2,4:-0.189126345102;NFATC1..3:-0.190504511503;GATA4:-0.194511959838;FOXQ1:-0.197539185789;REST:-0.203052286042;NKX3-1:-0.213419170189;RREB1:-0.231171719648;TEF:-0.234934458089;POU5F1:-0.256528851482;PRDM1:-0.273113516313;KLF4:-0.308287928868;HNF4A_NR2F1,2:-0.315925242721;NANOG{mouse}:-0.324384514098;EP300:-0.372121224884;TAL1_TCF{3,4,12}:-0.388511213604;NHLH1,2:-0.409757801605;SMAD1..7,9:-0.41145669167;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.415267607471;PAX1,9:-0.416787916403;NR3C1:-0.417028810292;RFX1:-0.418870876332;SOX17:-0.43626390669;TLX2:-0.446068603343;MYFfamily:-0.448591549906;FOXP3:-0.450451515456;SP1:-0.471799497409;OCT4_SOX2{dimer}:-0.474475831873;MTE{core}:-0.506758221175;PAX5:-0.516002406639;GFI1B:-0.527346765037;PPARG:-0.53395193787;HNF1A:-0.594976279374;FOXN1:-0.600133202318;ELK1,4_GABP{A,B1}:-0.603727963242;HIC1:-0.605629496742;MEF2{A,B,C,D}:-0.621193870819;XCPE1{core}:-0.655744825352;ADNP_IRX_SIX_ZHX:-0.658416461948;PDX1:-0.685890247963;TBX4,5:-0.689367047589;RORA:-0.693596449909;CRX:-0.699665040004;ONECUT1,2:-0.704062214762;GTF2I:-0.705214026857;PATZ1:-0.708173678034;ZNF384:-0.712184522294;ZEB1:-0.713090467128;RFX2..5_RFXANK_RFXAP:-0.762303079046;PRRX1,2:-0.785740922814;TFAP2B:-0.815622814661;PAX8:-0.830425450791;EGR1..3:-0.831468996004;MAFB:-0.870171379432;HBP1_HMGB_SSRP1_UBTF:-0.877597042382;YY1:-0.932768194069;LHX3,4:-0.934553625992;MED-1{core}:-0.979732847525;TFDP1:-0.983253115498;ATF5_CREB3:-0.989880040714;ATF2:-0.991018891386;TOPORS:-1.00824817317;E2F1..5:-1.02477961298;MAZ:-1.0265286166;NANOG:-1.04377216632;GZF1:-1.04872576941;GATA6:-1.05275866446;SOX2:-1.10402625845;FOX{D1,D2}:-1.12036173322;MYOD1:-1.12181606491;SNAI1..3:-1.17875798583;FOX{I1,J2}:-1.18616612905;BREu{core}:-1.20717234626;MZF1:-1.2222723726;LMO2:-1.22299172747;LEF1_TCF7_TCF7L1,2:-1.24492908012;ZFP161:-1.25005729986;HSF1,2:-1.26890499327;SOX5:-1.27339273308;EVI1:-1.27768304893;STAT5{A,B}:-1.35316026815;AR:-1.36422818172;HMGA1,2:-1.36468627793;AHR_ARNT_ARNT2:-1.39256830542;TGIF1:-1.40412529665;CREB1:-1.42821591691;DBP:-1.47146837208;STAT1,3:-1.47519994978;SOX{8,9,10}:-1.51505333449;POU1F1:-1.55738128714;NRF1:-1.56142881144;FOXA2:-1.56625669472;AIRE:-1.60639355659;CDX1,2,4:-1.65828539188;ZNF143:-1.65879483083;PBX1:-1.68625110307;GFI1:-1.69880516691;NKX6-1,2:-1.69953252382;FOXP1:-1.7070150006;CUX2:-1.79517732196;NFIX:-1.80203336871;FOXD3:-1.83832744216;RBPJ:-1.83894908044;PITX1..3:-1.84541899122;NKX2-1,4:-1.95068440038;MYBL2:-1.96126734971;BPTF:-1.96164849518;PAX6:-2.04947811877;T:-2.19361000721;NFY{A,B,C}:-2.45431286787
+|xref=
+|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11640-122D2;search_select_hide=table117:11640-122D2
 }}

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FF:11640-122D2: Difference between revisions

From FANTOM5_SSTAR

Latest revision as of 18:13, 4 June 2020

CNhs12616

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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