FF:11552-120C4: Difference between revisions

Revision as of 09:41, 28 November 2014

Name:	Mouse Astrocytes, donor2
Species:	Mouse (Mus musculus)
Library ID:	CNhs12078
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	brain
dev stage	NA
sex	NA
age	NA
cell type	astrocyte
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	lot:3931
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		SAMD00004832

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12078		CAGE		DRX008811		DRR009683

Accession ID Mm9

Library id		BAM		CTSS
CNhs12078		DRZ001108		DRZ002493

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

CNhs12078

0	0
1	0
10	0
100	0
1000	0.354
1001	-0.0465
1002	0.0991
1003	0.233
1004	0.13
1005	-0.0389
1006	-0.0355
1007	-0.259
1008	0
1009	0.19
101	-0.316
1010	0
1011	-0.115
1012	0
1013	0.163
1014	0.0569
1015	0.102
1016	0.207
1017	0
1018	0
1019	0
102	0
1020	0.563
1021	0.193
1022	-0.0487
1023	0
1024	0
1025	0
1026	0
1027	0.152
1028	0
1029	-0.176
103	0.322
1030	0
1031	0.923
1032	0.392
1033	-0.0183
1034	0
1035	0
1036	-0.125
1037	0
1038	0.0445
1039	-0.0332
104	0
1040	0.464
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: CNhs12078

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.821
MA0003.1	MA0003.1	0.295
MA0004.1	MA0004.1	0.744
MA0006.1	MA0006.1	0.337
MA0007.1	MA0007.1	0.0272
MA0009.1	MA0009.1	0.359
MA0014.1	MA0014.1	0.577
MA0017.1	MA0017.1	0.00361
MA0018.2	MA0018.2	0.0138
MA0019.1	MA0019.1	0.787
MA0024.1	MA0024.1	0.00658
MA0025.1	MA0025.1	0.454
MA0027.1	MA0027.1	0.77
MA0028.1	MA0028.1	0.0205
MA0029.1	MA0029.1	0.994
MA0030.1	MA0030.1	0.593
MA0031.1	MA0031.1	0.726
MA0035.2	MA0035.2	0.00238
MA0038.1	MA0038.1	0.315
MA0039.2	MA0039.2	0.0449
MA0040.1	MA0040.1	0.261
MA0041.1	MA0041.1	0.213
MA0042.1	MA0042.1	0.544
MA0043.1	MA0043.1	0.425
MA0046.1	MA0046.1	5.59394e-7
MA0047.2	MA0047.2	0.325
MA0048.1	MA0048.1	0.367
MA0050.1	MA0050.1	0.852
MA0051.1	MA0051.1	0.883
MA0052.1	MA0052.1	0.0234
MA0055.1	MA0055.1	0.056
MA0057.1	MA0057.1	0.362
MA0058.1	MA0058.1	0.724
MA0059.1	MA0059.1	0.623
MA0060.1	MA0060.1	0.295
MA0061.1	MA0061.1	0.814
MA0062.2	MA0062.2	5.5672e-6
MA0065.2	MA0065.2	0.683
MA0066.1	MA0066.1	0.945
MA0067.1	MA0067.1	0.383
MA0068.1	MA0068.1	0.495
MA0069.1	MA0069.1	0.329
MA0070.1	MA0070.1	0.722
MA0071.1	MA0071.1	0.322
MA0072.1	MA0072.1	0.522
MA0073.1	MA0073.1	0.769
MA0074.1	MA0074.1	0.319
MA0076.1	MA0076.1	0.00365
MA0077.1	MA0077.1	0.0785
MA0078.1	MA0078.1	0.813
MA0079.2	MA0079.2	0.0231
MA0080.2	MA0080.2	3.95316e-5
MA0081.1	MA0081.1	0.0547
MA0083.1	MA0083.1	0.341
MA0084.1	MA0084.1	0.58
MA0087.1	MA0087.1	0.741
MA0088.1	MA0088.1	0.667
MA0090.1	MA0090.1	0.00108
MA0091.1	MA0091.1	0.312
MA0092.1	MA0092.1	0.631
MA0093.1	MA0093.1	0.866
MA0099.2	MA0099.2	2.24565e-5
MA0100.1	MA0100.1	0.771
MA0101.1	MA0101.1	0.472
MA0102.2	MA0102.2	0.0331
MA0103.1	MA0103.1	0.00296
MA0104.2	MA0104.2	0.749
MA0105.1	MA0105.1	0.997
MA0106.1	MA0106.1	0.0322
MA0107.1	MA0107.1	0.207
MA0108.2	MA0108.2	0.767
MA0111.1	MA0111.1	0.679
MA0112.2	MA0112.2	0.257
MA0113.1	MA0113.1	0.177
MA0114.1	MA0114.1	0.0332
MA0115.1	MA0115.1	0.122
MA0116.1	MA0116.1	0.587
MA0117.1	MA0117.1	0.395
MA0119.1	MA0119.1	0.335
MA0122.1	MA0122.1	0.87
MA0124.1	MA0124.1	0.608
MA0125.1	MA0125.1	0.772
MA0131.1	MA0131.1	0.108
MA0135.1	MA0135.1	0.313
MA0136.1	MA0136.1	1.03871e-6
MA0137.2	MA0137.2	0.971
MA0138.2	MA0138.2	0.199
MA0139.1	MA0139.1	0.637
MA0140.1	MA0140.1	1.81004e-6
MA0141.1	MA0141.1	0.907
MA0142.1	MA0142.1	0.913
MA0143.1	MA0143.1	0.393
MA0144.1	MA0144.1	0.784
MA0145.1	MA0145.1	0.05
MA0146.1	MA0146.1	0.029
MA0147.1	MA0147.1	0.73
MA0148.1	MA0148.1	0.15
MA0149.1	MA0149.1	0.795
MA0150.1	MA0150.1	0.676
MA0152.1	MA0152.1	0.427
MA0153.1	MA0153.1	5.13161e-5
MA0154.1	MA0154.1	0.34
MA0155.1	MA0155.1	0.316
MA0156.1	MA0156.1	1.25835e-9
MA0157.1	MA0157.1	0.592
MA0159.1	MA0159.1	0.645
MA0160.1	MA0160.1	0.588
MA0162.1	MA0162.1	0.111
MA0163.1	MA0163.1	0.324
MA0164.1	MA0164.1	0.889
MA0258.1	MA0258.1	0.905
MA0259.1	MA0259.1	0.472

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: CNhs12078

Novel motif	Logo	P-value
1	1	0.424
10	10	0.646
100	100	0.666
101	101	0.845
102	102	0.367
103	103	0.272
104	104	0.783
105	105	0.457
106	106	0.0804
107	107	0.46
108	108	0.628
109	109	0.00725
11	11	0.209
110	110	0.433
111	111	0.36
112	112	0.42
113	113	0.305
114	114	0.895
115	115	0.936
116	116	0.0517
117	117	0.691
118	118	0.452
119	119	0.885
12	12	0.636
120	120	0.663
121	121	0.232
122	122	0.184
123	123	0.83
124	124	0.702
125	125	0.918
126	126	0.213
127	127	0.635
128	128	0.363
129	129	0.423
13	13	0.89
130	130	0.508
131	131	0.91
132	132	0.225
133	133	0.422
134	134	0.39
135	135	0.546
136	136	0.0109
137	137	0.305
138	138	0.835
139	139	0.146
14	14	0.722
140	140	0.073
141	141	0.638
142	142	0.159
143	143	0.117
144	144	0.978
145	145	0.989
146	146	0.863
147	147	0.357
148	148	0.622
149	149	0.146
15	15	0.759
150	150	0.231
151	151	0.845
152	152	0.0263
153	153	0.132
154	154	0.203
155	155	0.247
156	156	0.00168
157	157	0.547
158	158	0.0256
159	159	0.0359
160	160	0.884
161	161	0.512
162	162	0.616
163	163	0.211
164	164	0.0154
165	165	0.915
166	166	0.337
167	167	0.0293
168	168	0.738
169	169	0.148
17	17	0.34
18	18	0.527
19	19	0.195
2	2	0.0133
20	20	0.831
21	21	0.271
22	22	0.086
23	23	0.0563
24	24	0.105
25	25	0.122
26	26	0.91
27	27	0.487
28	28	0.403
29	29	0.716
3	3	0.875
30	30	0.0987
31	31	0.773
32	32	0.0558
33	33	0.762
34	34	0.0839
35	35	0.164
36	36	0.0581
37	37	0.149
38	38	0.467
39	39	0.175
4	4	0.737
40	40	0.909
41	41	0.909
42	42	0.966
43	43	0.556
44	44	0.308
45	45	0.238
46	46	0.532
47	47	0.593
48	48	0.986
49	49	0.107
5	5	0.0909
50	50	0.0946
51	51	0.559
52	52	0.0985
53	53	0.741
54	54	0.287
55	55	0.337
56	56	0.669
57	57	0.451
58	58	0.0695
59	59	0.0211
6	6	0.676
60	60	0.17
61	61	0.911
62	62	0.344
63	63	0.13
64	64	0.467
65	65	0.0336
66	66	0.461
67	67	0.972
68	68	0.424
69	69	0.175
7	7	0.364
70	70	0.88
71	71	0.733
72	72	0.67
73	73	0.00548
74	74	0.625
75	75	0.965
76	76	0.226
77	77	0.0081
78	78	0.0398
79	79	0.822
8	8	0.59
80	80	0.0955
81	81	0.33
82	82	0.966
83	83	0.932
84	84	0.288
85	85	0.0445
86	86	0.958
87	87	0.00104
88	88	0.541
89	89	0.879
9	9	0.999
90	90	0.648
91	91	0.989
92	92	0.583
93	93	0.104
94	94	0.197
95	95	0.00122
96	96	0.155
97	97	0.584
98	98	0.119
99	99	0.159

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: CNhs12078

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000105 mouse astrocyte 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)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000128 (oligodendrocyte)
0000126 (macroglial cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0000127 (astrocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte 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:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr13:99124189..99124205,+!p1@Foxd1!2.12!195.84!Foxd1;;chr14:122874619..122874634,+!p1@Zic2!2.06!114.79!Zic2;;chr16:91270004..91270023,+!p1@Olig1!2.00!112.13!Olig1;;chr11:116196664..116196679,-!p1@Foxj1!1.88!112.55!Foxj1;;chr5:138199361..138199441,+!p2@Tsc22d4!1.81!116.61!Tsc22d4;;chr8:123640063..123640077,+!p1@Foxc2!1.56!62.57!Foxc2;;chr1:42752574..42752621,+!p@chr1:42752574..42752621,+!1.54!42.14!Pou3f3;;chr13:31898767..31898785,+!p4@Foxc1!1.51!38.22!Foxc1;;chr9:91260594..91260612,-!p1@Zic1!1.43!25.62!Zic1;;chr2:30700881..30700916,+!p1@Prrx2!1.42!47.04!Prrx2;;chr3:34548909..34548927,+!p1@Sox2!1.42!42.42!Sox2;;chrX:90531838..90531861,+!p1@Arx!1.39!29.68!Arx;;chr10:86956396..86956411,-!p1@Ascl1!1.33!31.36!Ascl1;;chr12:74147689..74147711,-!p1@Six1!1.31!41.86!Six1;;chr3:99057269..99057306,+!p1@Tbx15!1.30!23.10!Tbx15;;chr9:91260616..91260653,-!p2@Zic1!1.30!19.04!Zic1;;chr13:31898729..31898761,+!p1@Foxc1!1.25!40.60!Foxc1;;chr8:123640090..123640101,+!p2@Foxc2!1.24!18.20!Foxc2;;chr2:38206744..38206766,+!p1@Lhx2!1.22!19.04!Lhx2;;chr16:91225808..91225824,+!p1@Olig2!1.22!15.54!Olig2;;chr5:38215819..38215823,-!p1@Msx1!1.21!39.34!Msx1;;chr13:31898637..31898653,+!p2@Foxc1!1.18!25.20!Foxc1;;chr10:84218800..84218829,+!p2@Rfx4!1.18!14.14!Rfx4;;chr10:84218895..84218909,+!p1@Rfx4!1.16!13.30!Rfx4;;chr16:91270091..91270143,+!p2@Olig1!1.12!12.04!Olig1;;chr17:86087592..86087615,-!p1@Six2!1.12!12.04!Six2;;chr12:34642510..34642530,+!p1@Twist1!1.11!37.66!Twist1;;chr16:15887371..15887385,+!p1@Cebpd!1.09!379.36!Cebpd;;chr12:34642682..34642753,+!p2@Twist1!1.09!29.82!Twist1;;chr8:87297280..87297326,-!p2@Nfix!1.08!26.32!Nfix;;chr2:30700857..30700873,+!p3@Prrx2!1.07!14.84!Prrx2;;chrX:108009761..108009788,+!p1@Pou3f4!1.07!10.78!Pou3f4;;chr4:135699731..135699747,+!p1@Id3!1.06!1170.85!Id3;;chr12:9581262..9581282,+!p1@Osr1!1.06!127.53!Osr1;;chr2:173044380..173044432,-!p1@Zbp1!1.05!24.64!Zbp1;;chr11:5761889..5761969,+!p1@Aebp1!1.04!423.32!Aebp1;;chr12:54349410..54349461,+!p1@Npas3!1.03!11.62!Npas3;;chr3:34548946..34548972,+!p2@Sox2!1.03!10.78!Sox2;;chr14:118636214..118636235,-!p1@Sox21!1.02!11.34!Sox21;;chr7:17647736..17647772,-!p1@Hif3a!1.00!32.48!Hif3a;;chr7:25292141..25292158,+!p2@Zfp428!1.00!31.92!Zfp428;;chr14:122874593..122874610,+!p2@Zic2!1.00!9.10!Zic2;;chrX:55284180..55284195,+!p2@Zic3!1.00!9.10!Zic3;;chr10:119913278..119913298,-!p2@Hmga2!0.99!20.16!Hmga2;;chr8:12395603..12395621,+!p1@Sox1!0.99!8.82!Sox1;;chr9:87626083..87626108,-!p1@Tbx18!0.98!19.04!Tbx18;;chr11:5761979..5761992,+!p2@Aebp1!0.98!17.50!Aebp1;;chr4:154010409..154010466,-!p2@Prdm16!0.94!18.62!Prdm16;;chr1:165243379..165243402,-!p3@Prrx1!0.92!11.20!Prrx1;;chr14:99698164..99698208,+!p2@Klf5!0.92!8.40!Klf5;;chr9:48644037..48644067,-!p2@Zbtb16!0.91!18.34!Zbtb16;;chr13:99124236..99124243,+!p2@Foxd1!0.90!7.00!Foxd1;;chr12:9581284..9581303,+!p2@Osr1!0.87!12.74!Osr1;;chr7:91558392..91558434,-!p1@Arnt2!0.85!17.78!Arnt2;;chr5:28492230..28492257,+!p1@En2!0.85!6.02!En2;;chr1:165243591..165243625,-!p2@Prrx1!0.84!9.38!Prrx1;;chr3:34549096..34549111,+!p3@Sox2!0.84!5.88!Sox2;;chr2:167363692..167363710,+!p1@Snai1!0.83!74.61!Snai1;;chr8:87297330..87297365,-!p5@Nfix!0.83!5.74!Nfix;;chr11:74981654..74981658,-!p1@Hic1!0.82!24.08!Hic1;;chr10:67375368..67375433,-!p1@Zfp365!0.81!10.08!Zfp365;;chr11:21901608..21901634,-!p1@Otx1!0.80!5.32!Otx1;;chr4:114581497..114581519,-!p2@Foxd2!0.80!5.32!Foxd2;;chr19:28754692..28754757,-!p1@Glis3!0.79!23.24!Glis3;;chr2:30700788..30700824,+!p2@Prrx2!0.79!8.12!Prrx2;;chr17:86020510..86020589,+!p3@Six3!0.79!5.18!Six3;;chr11:96690797..96690813,-!p1@Nfe2l1!0.78!104.29!Nfe2l1;;chrX:137077716..137077734,-!p1@Tsc22d3!0.78!38.92!Tsc22d3;;chr8:87297878..87297935,-!p3@Nfix!0.78!11.90!Nfix;;chr17:25707623..25707639,-!p1@Sox8!0.77!22.82!Sox8;;chr14:118636238..118636257,-!p2@Sox21!0.77!4.90!Sox21;;chr2:146047829..146047847,+!p1@Insm1!0.76!8.96!Insm1;;chr13:53568104..53568156,-!p1@Msx2!0.76!7.42!Msx2;;chr14:99697871..99697934,+!p1@Klf5!0.75!102.61!Klf5;;chr7:119822957..119822980,+!p2@Tead1!0.75!24.92!Tead1;;chr7:25292160..25292213,+!p3@Zfp428!0.75!12.32!Zfp428;;chr3:107398056..107398082,+!p1@Alx3!0.75!4.62!Alx3;;chr3:99057256..99057268,+!p3@Tbx15!0.75!4.62!Tbx15;;chr14:49287186..49287225,-!p1@Otx2!0.75!4.62!Otx2;;chr7:134169741..134169760,-!p10@Maz!0.74!14.70!Maz;;chr14:122874718..122874729,+!p3@Zic2!0.74!4.48!Zic2;;chr13:48356475..48356492,+!p1@Id4!0.73!106.53!Id4;;chr6:72185232..72185272,-!p1@Atoh8!0.73!13.72!Atoh8;;chr11:5761871..5761882,+!p3@Aebp1!0.73!12.46!Aebp1;;chr19:19185671..19185693,-!p1@Rorb!0.73!11.34!Rorb;;chr6:128250471..128250519,-!p1@Tead4!0.73!9.24!Tead4;;chr1:78193687..78193692,-!p1@Pax3!0.73!4.34!Pax3;;chr11:80196900..80196917,+!p3@Zfp207!0.72!15.54!Zfp207;;chr6:72185210..72185228,-!p3@Atoh8!0.72!7.70!Atoh8;;chr13:31898529..31898542,+!p5@Foxc1!0.71!5.18!Foxc1;;chr9:106356278..106356292,+!p3@Pcbp4!0.70!7.28!Pcbp4;;chr4:154010228..154010244,-!p4@Prdm16!0.70!5.74!Prdm16;;chr3:99057677..99057730,+!p2@Tbx15!0.70!4.06!Tbx15;;chr2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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs12078
-|library_id_phase_based=1:CNhs12078
+|library_id_phase_based=2:CNhs12078
 |name=Mouse Astrocytes, donor2
 |namespace=FANTOM5
@@ Line 51: / Line 51: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12078,LSID838,release011,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.0893457570968351,0,0,0,0,0,-0.6239816537174,0,0,0,0,-0.0274395619094528,0,0,0,0,0.0284498392435444,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0.311478974606717,-0.451222036856999,0,0,0,0,0,-0.209322725495826,-0.00257065767513376,-0.22227340720995,-0.533989443821847,-0.11759275228454,0.296644341734729,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.0236221220205411,0,0,-0.0276268839918301,-0.214775938950726,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0780086007519514,-0.0398282379913335,0.00591131580555515,0,0,0,-0.0512319033244535,0.599945331254664,-0.0788315948399074,0,0,0,0,0,0,0.264591905432095,0.0214695456629341,0.213080815224162,0,0,0.0568996784870888,0.24036414809762,0

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FF:11552-120C4: Difference between revisions

From FANTOM5_SSTAR

Revision as of 09:41, 28 November 2014

CNhs12078

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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