FF:12338-130I7: Difference between revisions

Revision as of 14:45, 4 February 2015

Name:	ST2 (Mesenchymal stem cells) cells, medium change (without induction)
Species:	Mouse (Mus musculus)
Library ID:	CNhs11939
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	bone marrow
dev stage	NA
sex	NA
age	NA
cell type	mesenchymal stem cell
cell line	ST2
company	NA
collaboration	Yasushi Okazaki (Saitama medical college)
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		SAMD00005927

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11939		CAGE		DRX008905		DRR009779

Accession ID Mm9

Library id		BAM		CTSS
CNhs11939		DRZ001204		DRZ002587

Download raw sequence, BAM & CTSS

Mm9

BAM	CTSS
[{{{mm9bam}}} download]	[{{{mm9ctss}}} donwload]

Mm10

BAM	CTSS
[{{{mm10bam}}} download]	[{{{mm10ctss}}} 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

CNhs11939

0	0
1	0
10	0
100	0
1000	0.247
1001	0.0155
1002	-0.116
1003	0.228
1004	0
1005	0
1006	-0.0916
1007	0.00293
1008	0
1009	0.746
101	0.0347
1010	0
1011	-0.229
1012	0
1013	0.0165
1014	-0.0874
1015	0.0378
1016	0.141
1017	0
1018	0
1019	0
102	0
1020	0
1021	-0.0487
1022	-0.124
1023	0
1024	-0.307
1025	-0.0611
1026	0
1027	-0.00273
1028	0.127
1029	-0.151
103	0.404
1030	0
1031	-0.195
1032	-0.115
1033	0.0157
1034	0
1035	0
1036	0.106
1037	0
1038	0.112
1039	-0.0843
104	0
1040	0.396
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: CNhs11939

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.136
MA0003.1	MA0003.1	0.644
MA0004.1	MA0004.1	0.282
MA0006.1	MA0006.1	0.394
MA0007.1	MA0007.1	0.853
MA0009.1	MA0009.1	0.588
MA0014.1	MA0014.1	0.32
MA0017.1	MA0017.1	0.0165
MA0018.2	MA0018.2	0.685
MA0019.1	MA0019.1	0.52
MA0024.1	MA0024.1	0.0412
MA0025.1	MA0025.1	0.253
MA0027.1	MA0027.1	0.454
MA0028.1	MA0028.1	4.99891e-5
MA0029.1	MA0029.1	0.61
MA0030.1	MA0030.1	0.783
MA0031.1	MA0031.1	0.636
MA0035.2	MA0035.2	0.00121
MA0038.1	MA0038.1	0.468
MA0039.2	MA0039.2	0.289
MA0040.1	MA0040.1	0.258
MA0041.1	MA0041.1	0.664
MA0042.1	MA0042.1	0.347
MA0043.1	MA0043.1	0.36
MA0046.1	MA0046.1	1.46058e-6
MA0047.2	MA0047.2	0.709
MA0048.1	MA0048.1	4.64156e-4
MA0050.1	MA0050.1	0.216
MA0051.1	MA0051.1	0.23
MA0052.1	MA0052.1	8.49384e-4
MA0055.1	MA0055.1	3.88065e-4
MA0057.1	MA0057.1	0.135
MA0058.1	MA0058.1	0.0621
MA0059.1	MA0059.1	0.829
MA0060.1	MA0060.1	0.834
MA0061.1	MA0061.1	0.309
MA0062.2	MA0062.2	3.48067e-6
MA0065.2	MA0065.2	0.669
MA0066.1	MA0066.1	0.44
MA0067.1	MA0067.1	0.608
MA0068.1	MA0068.1	0.362
MA0069.1	MA0069.1	0.659
MA0070.1	MA0070.1	0.152
MA0071.1	MA0071.1	0.907
MA0072.1	MA0072.1	0.899
MA0073.1	MA0073.1	0.547
MA0074.1	MA0074.1	0.745
MA0076.1	MA0076.1	1.18221e-4
MA0077.1	MA0077.1	0.401
MA0078.1	MA0078.1	0.262
MA0079.2	MA0079.2	0.641
MA0080.2	MA0080.2	0.32
MA0081.1	MA0081.1	0.983
MA0083.1	MA0083.1	3.11196e-4
MA0084.1	MA0084.1	0.552
MA0087.1	MA0087.1	0.902
MA0088.1	MA0088.1	1.1465e-4
MA0090.1	MA0090.1	0.0179
MA0091.1	MA0091.1	0.795
MA0092.1	MA0092.1	0.352
MA0093.1	MA0093.1	0.257
MA0099.2	MA0099.2	1.73472e-7
MA0100.1	MA0100.1	0.0798
MA0101.1	MA0101.1	0.232
MA0102.2	MA0102.2	0.471
MA0103.1	MA0103.1	2.43676e-7
MA0104.2	MA0104.2	0.629
MA0105.1	MA0105.1	0.259
MA0106.1	MA0106.1	1.71478e-4
MA0107.1	MA0107.1	0.701
MA0108.2	MA0108.2	0.00448
MA0111.1	MA0111.1	0.149
MA0112.2	MA0112.2	0.062
MA0113.1	MA0113.1	0.772
MA0114.1	MA0114.1	0.314
MA0115.1	MA0115.1	0.22
MA0116.1	MA0116.1	0.108
MA0117.1	MA0117.1	0.294
MA0119.1	MA0119.1	0.394
MA0122.1	MA0122.1	0.699
MA0124.1	MA0124.1	0.28
MA0125.1	MA0125.1	0.0191
MA0131.1	MA0131.1	0.603
MA0135.1	MA0135.1	0.0407
MA0136.1	MA0136.1	0.445
MA0137.2	MA0137.2	0.00396
MA0138.2	MA0138.2	1.00494e-4
MA0139.1	MA0139.1	0.848
MA0140.1	MA0140.1	9.79602e-5
MA0141.1	MA0141.1	0.975
MA0142.1	MA0142.1	0.0175
MA0143.1	MA0143.1	0.857
MA0144.1	MA0144.1	0.024
MA0145.1	MA0145.1	0.235
MA0146.1	MA0146.1	5.4912e-4
MA0147.1	MA0147.1	0.473
MA0148.1	MA0148.1	0.683
MA0149.1	MA0149.1	0.198
MA0150.1	MA0150.1	0.107
MA0152.1	MA0152.1	0.0397
MA0153.1	MA0153.1	4.8865e-6
MA0154.1	MA0154.1	0.372
MA0155.1	MA0155.1	0.761
MA0156.1	MA0156.1	0.179
MA0157.1	MA0157.1	0.738
MA0159.1	MA0159.1	0.931
MA0160.1	MA0160.1	0.781
MA0162.1	MA0162.1	0.118
MA0163.1	MA0163.1	0.666
MA0164.1	MA0164.1	0.556
MA0258.1	MA0258.1	0.751
MA0259.1	MA0259.1	0.413

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: CNhs11939

Novel motif	Logo	P-value
1	1	0.301
10	10	0.0391
100	100	0.788
101	101	0.276
102	102	0.0974
103	103	0.569
104	104	0.962
105	105	0.802
106	106	0.904
107	107	0.373
108	108	0.523
109	109	0.0698
11	11	0.167
110	110	0.0373
111	111	0.791
112	112	0.947
113	113	0.139
114	114	0.911
115	115	0.89
116	116	0.344
117	117	4.42548e-4
118	118	0.907
119	119	0.2
12	12	0.652
120	120	0.232
121	121	0.41
122	122	0.32
123	123	0.19
124	124	0.213
125	125	0.578
126	126	0.549
127	127	0.0773
128	128	0.228
129	129	0.818
13	13	0.0129
130	130	0.612
131	131	0.598
132	132	0.227
133	133	0.152
134	134	0.901
135	135	0.298
136	136	0.293
137	137	0.97
138	138	0.595
139	139	0.0109
14	14	0.428
140	140	0.983
141	141	0.725
142	142	0.801
143	143	0.206
144	144	0.153
145	145	0.266
146	146	0.361
147	147	0.516
148	148	0.892
149	149	0.0859
15	15	0.537
150	150	0.0368
151	151	0.942
152	152	0.0821
153	153	0.91
154	154	0.403
155	155	0.186
156	156	1.19319e-28
157	157	0.771
158	158	0.543
159	159	0.148
160	160	0.931
161	161	0.793
162	162	0.814
163	163	0.723
164	164	0.00481
165	165	0.529
166	166	0.82
167	167	0.111
168	168	0.265
169	169	0.00175
17	17	0.55
18	18	0.497
19	19	0.393
2	2	0.539
20	20	0.0564
21	21	0.0503
22	22	0.204
23	23	0.288
24	24	0.712
25	25	0.978
26	26	0.232
27	27	0.376
28	28	0.909
29	29	0.0182
3	3	0.261
30	30	0.471
31	31	0.282
32	32	0.563
33	33	0.277
34	34	0.765
35	35	0.138
36	36	0.302
37	37	0.0132
38	38	0.917
39	39	0.724
4	4	0.552
40	40	0.917
41	41	0.312
42	42	0.505
43	43	0.835
44	44	0.222
45	45	0.855
46	46	0.545
47	47	0.231
48	48	0.356
49	49	0.412
5	5	0.433
50	50	0.575
51	51	0.844
52	52	0.735
53	53	0.608
54	54	0.313
55	55	0.779
56	56	0.57
57	57	0.409
58	58	0.826
59	59	0.445
6	6	0.844
60	60	0.445
61	61	0.922
62	62	0.555
63	63	0.742
64	64	0.666
65	65	0.844
66	66	0.477
67	67	0.278
68	68	0.251
69	69	0.863
7	7	0.247
70	70	0.0477
71	71	0.00954
72	72	0.785
73	73	0.0094
74	74	0.813
75	75	0.0975
76	76	0.485
77	77	0.344
78	78	0.0108
79	79	0.713
8	8	0.639
80	80	0.0124
81	81	0.887
82	82	0.512
83	83	0.767
84	84	0.794
85	85	0.996
86	86	0.791
87	87	0.0191
88	88	0.384
89	89	0.262
9	9	0.67
90	90	0.0552
91	91	0.943
92	92	0.544
93	93	0.245
94	94	0.751
95	95	0.0121
96	96	0.749
97	97	0.384
98	98	0.248
99	99	0.746

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: CNhs11939

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000488 mouse ST2 Mesenchymal stem cells, cells 0hr after medium change , without induction 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)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000404 (mouse mesenchymal stem cell line: ST2 sample)
0000333 (medium change sample)
0000357 (0 hr sample)
0000488 (mouse ST2 Mesenchymal stem cells, cells 0hr after medium change , without induction 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 12: / Line 12: @@
 |datafreeze_phase=2
 |def=
+|donor=biol_rep1
 |expression_enrichment_score=chr15:102828658..102828678,+!p1@Hoxc6!1.89!75.84!Hoxc6;;chr19:5447886..5447905,+!p1@Fosl1!1.84!67.83!Fosl1;;chr6:52190467..52190500,-!p1@Hoxa10!1.66!44.65!Hoxa10;;chr2:30700881..30700916,+!p1@Prrx2!1.63!76.86!Prrx2;;chr3:99057269..99057306,+!p1@Tbx15!1.62!48.57!Tbx15;;chr12:74147689..74147711,-!p1@Six1!1.59!81.64!Six1;;chr16:14705925..14705951,+!p1@Snai2!1.57!244.40!Snai2;;chr15:102797288..102797302,+!p1@Hoxc10!1.53!32.72!Hoxc10;;chr16:14705961..14705978,+!p2@Snai2!1.51!139.92!Snai2;;chr17:44951553..44951586,-!p2@Runx2!1.51!34.77!Runx2;;chr2:30700857..30700873,+!p3@Prrx2!1.48!39.71!Prrx2;;chr15:102751603..102751630,+!p1@Hoxc13!1.48!29.48!Hoxc13;;chr19:5447692..5447711,+!p2@Fosl1!1.44!26.76!Fosl1;;chr15:102797225..102797243,+!p2@Hoxc10!1.42!25.22!Hoxc10;;chr15:102751578..102751600,+!p2@Hoxc13!1.40!24.20!Hoxc13;;chr6:52176164..52176195,-!p1@Hoxa9!1.36!26.93!Hoxa9;;chr6:6831950..6831985,-!p2@Dlx5!1.36!24.03!Dlx5;;chr2:152758901..152758925,-!p1@Foxs1!1.31!85.04!Foxs1;;chr13:99124189..99124205,+!p1@Foxd1!1.31!29.65!Foxd1;;chr6:83661226..83661282,+!p1@Vax2!1.31!19.60!Vax2;;chr6:6831986..6832007,-!p4@Dlx5!1.29!18.41!Dlx5;;chr15:102797170..102797182,+!p3@Hoxc10!1.21!15.34!Hoxc10;;chr13:31898637..31898653,+!p2@Foxc1!1.20!26.42!Foxc1;;chr13:55932591..55932622,-!p1@Pitx1!1.20!17.72!Pitx1;;chr7:52071956..52071978,-!p1@Atf5!1.19!455.05!Atf5;;chr13:31898729..31898761,+!p1@Foxc1!1.19!35.45!Foxc1;;chr1:165243792..165243808,-!p1@Prrx1!1.18!48.74!Prrx1;;chr8:94881733..94881790,+!p1@Irx5!1.16!26.59!Irx5;;chr1:140739014..140739032,-!p1@Lhx9!1.11!15.00!Lhx9;;chr15:102751552..102751563,+!p3@Hoxc13!1.11!11.93!Hoxc13;;chr15:97738692..97738747,-!p1@Vdr!1.10!63.40!Vdr;;chr13:72766250..72766273,+!p1@Irx2!1.07!16.53!Irx2;;chr6:6832076..6832092,-!p1@Dlx5!1.06!12.27!Dlx5;;chr13:55932624..55932641,-!p2@Pitx1!1.06!10.40!Pitx1;;chr9:87626083..87626108,-!p1@Tbx18!1.05!22.84!Tbx18;;chr10:67000609..67000625,+!p1@Egr2!1.03!22.84!Egr2;;chr13:31898496..31898519,+!p3@Foxc1!1.02!15.51!Foxc1;;chr15:102839948..102839975,+!p3@Hoxc6!1.00!9.03!Hoxc6;;chr9:87625971..87625992,-!p2@Tbx18!0.99!8.86!Tbx18;;chr15:102828642..102828653,+!p2@Hoxc6!0.98!8.52!Hoxc6;;chr16:14705668..14705683,+!p3@Snai2!0.98!8.52!Snai2;;chr15:102087737..102087801,-!p3@Rarg!0.95!13.46!Rarg;;chr16:14705746..14705761,+!p4@Snai2!0.95!8.01!Snai2;;chr3:66785181..66785199,-!p2@Shox2!0.95!7.84!Shox2;;chr10:67375368..67375433,-!p1@Zfp365!0.93!13.63!Zfp365;;chr6:52163319..52163342,-!p1@Hoxa3!0.93!11.08!Hoxa3;;chr12:34642682..34642753,+!p2@Twist1!0.91!19.60!Twist1;;chr13:31717548..31717596,+!p1@Foxf2!0.91!14.49!Foxf2;;chr6:72185210..72185228,-!p3@Atoh8!0.90!12.10!Atoh8;;chr15:102797183..102797205,+!p4@Hoxc10!0.90!6.99!Hoxc10;;chr4:134676555..134676575,+!p2@Runx3!0.89!6.82!Runx3;;chr6:52190668..52190682,-!p3@Hoxa10!0.88!6.65!Hoxa10;;chr6:72185232..72185272,-!p1@Atoh8!0.87!19.26!Atoh8;;chr13:55932739..55932756,-!p5@Pitx1!0.87!6.48!Pitx1;;chr15:102076870..102076941,-!p1@Rarg!0.86!72.60!Rarg;;chr11:44430812..44430838,+!p1@Ebf1!0.86!65.10!Ebf1;;chr9:96653072..96653154,-!p1@Zbtb38!0.86!17.38!Zbtb38;;chr8:94325321..94325366,-!p1@Irx3!0.86!15.85!Irx3;;chr1:186556375..186556404,-!p3@Hlx!0.86!11.59!Hlx;;chr2:30700788..30700824,+!p2@Prrx2!0.86!9.88!Prrx2;;chr1:165243591..165243625,-!p2@Prrx1!0.84!9.20!Prrx1;;chr8:123640063..123640077,+!p1@Foxc2!0.83!10.91!Foxc2;;chr3:66785857..66785873,-!p1@Shox2!0.83!5.79!Shox2;;chr3:66785201..66785226,-!p3@Shox2!0.82!5.62!Shox2;;chr11:96153767..96153822,+!p1@Hoxb6!0.81!8.69!Hoxb6;;chr10:80889867..80889924,-!p1@Nfic!0.80!161.06!Nfic;;chr3:99057256..99057268,+!p3@Tbx15!0.80!5.28!Tbx15;;chr2:167363692..167363710,+!p1@Snai1!0.79!68.00!Snai1;;chr15:102820964..102821006,+!p1@Hoxc8!0.79!5.11!Hoxc8;;chr6:52184901..52184959,-!p2@Hoxa10!0.79!5.11!Hoxa10;;chr3:5218629..5218684,+!p1@Zfhx4!0.78!17.72!Zfhx4;;chr1:57029281..57029326,-!p1@Satb2!0.78!8.18!Satb2;;chr2:152758938..152758954,-!p2@Foxs1!0.77!6.99!Foxs1;;chr6:52176144..52176161,-!p2@Hoxa9!0.77!4.94!Hoxa9;;chr17:44951431..44951445,-!p3@Runx2!0.76!4.77!Runx2;;chr19:55816546..55816556,+!p3@Tcf7l2!0.75!19.26!Tcf7l2;;chr12:9581262..9581282,+!p1@Osr1!0.74!60.33!Osr1;;chr12:86940338..86940357,+!p1@Jdp2!0.73!47.72!Jdp2;;chr19:28754692..28754757,-!p1@Glis3!0.73!20.11!Glis3;;chr15:102087880..102087927,-!p2@Rarg!0.73!10.74!Rarg;;chr1:57028538..57028553,-!p6@Satb2!0.73!4.43!Satb2;;chr1:165243379..165243402,-!p3@Prrx1!0.72!6.65!Prrx1;;chr11:94981424..94981439,+!p1@Dlx3!0.72!4.94!Dlx3;;chr16:92697560..92697592,-!p2@Runx1!0.71!28.80!Runx1;;chr16:43363152..43363186,+!p3@Zbtb20!0.71!10.23!Zbtb20;;chr13:31898529..31898542,+!p5@Foxc1!0.71!5.11!Foxc1;;chr8:94325814..94325839,-!p2@Irx3!0.70!9.03!Irx3;;chr5:53981592..53981616,+!p3@Rbpj!0.70!8.18!Rbpj;;chr13:72101178..72101203,-!p1@Irx1!0.70!6.65!Irx1;;chr7:144506077..144506128,-!p1@Ebf3!0.69!9.88!Ebf3;;chr12:9581284..9581303,+!p2@Osr1!0.69!8.01!Osr1;;chr15:102839976..102839989,+!p4@Hoxc6!0.69!3.92!Hoxc6;;chr1:186556410..186556424,-!p1@Hlx!0.68!13.29!Hlx;;chr12:95813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 |ffid_belonging_in_development=CL:0000134
@@ Line 46: / Line 47: @@
 |library_id=CNhs11939
 |library_id_phase_based=2:CNhs11939
-|name=ST2 (Mesenchymal stem cells) cells, medium change (without induction), 00hr, biol_rep1 (000hC4)
+|name=ST2 (Mesenchymal stem cells) cells, medium change (without induction)
 |namespace=FANTOM5
 |part_of=
@@ Line 86: / Line 87: @@
 |sample_strain=
 |sample_tissue=bone marrow
-|timecourse=ST2_adipocytes,ST2_osteocytes
+|time=00hr
+|timecourse=mouse_MSC_adipocytes,mouse_MSC_osteocytes
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 |xref=
 }}

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FF:12338-130I7: Difference between revisions

From FANTOM5_SSTAR

Revision as of 14:45, 4 February 2015

CNhs11939

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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