FF:11856-125A2: Difference between revisions

Revision as of 09:54, 28 November 2014

Name:	Mouse CD19+ B Cells, donor1
Species:	Mouse (Mus musculus)
Library ID:	CNhs13531
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	spleen
dev stage	NA
sex	NA
age	NA
cell type	b cell, CD19+
cell line	NA
company	NA
collaboration	Kawamoto (RCAI)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	NA
catalog number	NA
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005132

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs13531		CAGE		DRX008813		DRR009685

Accession ID Mm9

Library id		BAM		CTSS
CNhs13531		DRZ001110		DRZ002495

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

CNhs13531

0	0
1	0
10	0
100	0
1000	-0.0355
1001	-0.0749
1002	-0.116
1003	-0.175
1004	0
1005	0.0674
1006	-0.272
1007	0.0648
1008	0
1009	-0.19
101	0.205
1010	0
1011	0.0626
1012	0
1013	-0.129
1014	-0.0874
1015	-0.119
1016	-0.594
1017	0
1018	0
1019	0
102	0.337
1020	0
1021	0.177
1022	-0.208
1023	0.177
1024	-0.14
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.0935
103	-0.0887
1030	0.566
1031	-0.911
1032	-0.728
1033	0.236
1034	0
1035	0
1036	0.366
1037	0
1038	-0.265
1039	-0.0984
104	0
1040	-0.216
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: CNhs13531

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00118
MA0003.1	MA0003.1	0.157
MA0004.1	MA0004.1	0.0329
MA0006.1	MA0006.1	0.705
MA0007.1	MA0007.1	0.816
MA0009.1	MA0009.1	0.592
MA0014.1	MA0014.1	0.741
MA0017.1	MA0017.1	0.986
MA0018.2	MA0018.2	1.80196e-7
MA0019.1	MA0019.1	0.173
MA0024.1	MA0024.1	0.566
MA0025.1	MA0025.1	0.845
MA0027.1	MA0027.1	0.728
MA0028.1	MA0028.1	3.42404e-6
MA0029.1	MA0029.1	0.132
MA0030.1	MA0030.1	0.675
MA0031.1	MA0031.1	0.351
MA0035.2	MA0035.2	0.552
MA0038.1	MA0038.1	0.0618
MA0039.2	MA0039.2	0.734
MA0040.1	MA0040.1	0.529
MA0041.1	MA0041.1	0.0847
MA0042.1	MA0042.1	0.505
MA0043.1	MA0043.1	0.0187
MA0046.1	MA0046.1	1.83514e-12
MA0047.2	MA0047.2	0.979
MA0048.1	MA0048.1	0.377
MA0050.1	MA0050.1	1.80868e-14
MA0051.1	MA0051.1	9.7858e-8
MA0052.1	MA0052.1	0.574
MA0055.1	MA0055.1	0.201
MA0057.1	MA0057.1	0.868
MA0058.1	MA0058.1	0.00467
MA0059.1	MA0059.1	0.00826
MA0060.1	MA0060.1	0.108
MA0061.1	MA0061.1	2.79301e-8
MA0062.2	MA0062.2	1.92873e-17
MA0065.2	MA0065.2	0.573
MA0066.1	MA0066.1	0.128
MA0067.1	MA0067.1	0.00277
MA0068.1	MA0068.1	0.0114
MA0069.1	MA0069.1	0.636
MA0070.1	MA0070.1	0.482
MA0071.1	MA0071.1	0.413
MA0072.1	MA0072.1	0.192
MA0073.1	MA0073.1	0.616
MA0074.1	MA0074.1	0.7
MA0076.1	MA0076.1	6.67479e-7
MA0077.1	MA0077.1	0.339
MA0078.1	MA0078.1	0.674
MA0079.2	MA0079.2	0.0906
MA0080.2	MA0080.2	1.40898e-12
MA0081.1	MA0081.1	3.21903e-4
MA0083.1	MA0083.1	0.0503
MA0084.1	MA0084.1	0.939
MA0087.1	MA0087.1	0.857
MA0088.1	MA0088.1	0.999
MA0090.1	MA0090.1	0.00759
MA0091.1	MA0091.1	0.537
MA0092.1	MA0092.1	0.567
MA0093.1	MA0093.1	0.0256
MA0099.2	MA0099.2	0.707
MA0100.1	MA0100.1	0.193
MA0101.1	MA0101.1	9.86383e-10
MA0102.2	MA0102.2	0.834
MA0103.1	MA0103.1	0.203
MA0104.2	MA0104.2	0.0461
MA0105.1	MA0105.1	3.85152e-8
MA0106.1	MA0106.1	0.906
MA0107.1	MA0107.1	1.34653e-9
MA0108.2	MA0108.2	7.60855e-4
MA0111.1	MA0111.1	0.755
MA0112.2	MA0112.2	0.226
MA0113.1	MA0113.1	0.441
MA0114.1	MA0114.1	0.173
MA0115.1	MA0115.1	0.51
MA0116.1	MA0116.1	0.0185
MA0117.1	MA0117.1	0.102
MA0119.1	MA0119.1	0.171
MA0122.1	MA0122.1	0.913
MA0124.1	MA0124.1	0.816
MA0125.1	MA0125.1	0.0357
MA0131.1	MA0131.1	0.239
MA0135.1	MA0135.1	0.72
MA0136.1	MA0136.1	3.19318e-22
MA0137.2	MA0137.2	0.474
MA0138.2	MA0138.2	0.0203
MA0139.1	MA0139.1	0.853
MA0140.1	MA0140.1	0.803
MA0141.1	MA0141.1	0.847
MA0142.1	MA0142.1	2.82262e-4
MA0143.1	MA0143.1	0.136
MA0144.1	MA0144.1	0.818
MA0145.1	MA0145.1	0.19
MA0146.1	MA0146.1	0.318
MA0147.1	MA0147.1	0.0372
MA0148.1	MA0148.1	0.928
MA0149.1	MA0149.1	0.115
MA0150.1	MA0150.1	0.408
MA0152.1	MA0152.1	0.908
MA0153.1	MA0153.1	9.51782e-9
MA0154.1	MA0154.1	0.0258
MA0155.1	MA0155.1	0.466
MA0156.1	MA0156.1	1.64819e-21
MA0157.1	MA0157.1	0.153
MA0159.1	MA0159.1	0.0388
MA0160.1	MA0160.1	0.808
MA0162.1	MA0162.1	0.976
MA0163.1	MA0163.1	0.00336
MA0164.1	MA0164.1	0.472
MA0258.1	MA0258.1	0.144
MA0259.1	MA0259.1	0.28

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: CNhs13531

Novel motif	Logo	P-value
1	1	0.392
10	10	0.0387
100	100	0.607
101	101	0.625
102	102	0.554
103	103	0.278
104	104	0.77
105	105	0.565
106	106	0.563
107	107	0.103
108	108	0.595
109	109	0.351
11	11	0.437
110	110	0.176
111	111	0.18
112	112	0.0732
113	113	0.782
114	114	0.431
115	115	0.354
116	116	0.374
117	117	2.30193e-4
118	118	0.1
119	119	0.472
12	12	0.48
120	120	0.292
121	121	0.417
122	122	0.945
123	123	0.199
124	124	0.623
125	125	0.149
126	126	0.267
127	127	0.7
128	128	0.365
129	129	0.304
13	13	0.0448
130	130	0.986
131	131	0.274
132	132	0.454
133	133	0.802
134	134	0.779
135	135	0.524
136	136	0.858
137	137	0.0368
138	138	0.757
139	139	0.359
14	14	0.755
140	140	0.865
141	141	0.283
142	142	0.394
143	143	0.0371
144	144	0.476
145	145	0.259
146	146	0.727
147	147	0.823
148	148	0.106
149	149	0.364
15	15	0.184
150	150	0.455
151	151	0.32
152	152	0.506
153	153	0.287
154	154	0.22
155	155	0.301
156	156	0.678
157	157	0.705
158	158	0.0137
159	159	0.818
160	160	0.503
161	161	0.153
162	162	0.0718
163	163	0.083
164	164	0.12
165	165	0.34
166	166	0.56
167	167	0.0886
168	168	0.739
169	169	0.382
17	17	0.716
18	18	0.28
19	19	0.67
2	2	0.0307
20	20	0.00531
21	21	0.351
22	22	0.965
23	23	0.622
24	24	0.67
25	25	0.284
26	26	0.08
27	27	0.474
28	28	0.211
29	29	0.0431
3	3	0.184
30	30	0.126
31	31	0.541
32	32	0.351
33	33	0.105
34	34	0.403
35	35	0.159
36	36	0.0583
37	37	0.0698
38	38	0.776
39	39	0.383
4	4	0.984
40	40	0.187
41	41	0.175
42	42	0.311
43	43	0.35
44	44	0.304
45	45	0.386
46	46	0.469
47	47	0.76
48	48	0.418
49	49	0.169
5	5	0.249
50	50	0.582
51	51	0.778
52	52	0.27
53	53	0.387
54	54	0.626
55	55	0.738
56	56	0.908
57	57	0.81
58	58	0.193
59	59	0.681
6	6	0.633
60	60	0.818
61	61	0.107
62	62	0.0812
63	63	0.906
64	64	0.983
65	65	0.771
66	66	0.59
67	67	0.822
68	68	0.0155
69	69	0.646
7	7	0.422
70	70	0.0283
71	71	0.0606
72	72	0.354
73	73	0.087
74	74	0.747
75	75	0.00384
76	76	0.00325
77	77	0.078
78	78	0.0706
79	79	0.515
8	8	0.426
80	80	0.0766
81	81	0.761
82	82	0.43
83	83	0.0771
84	84	0.711
85	85	0.901
86	86	0.147
87	87	0.519
88	88	0.493
89	89	0.617
9	9	0.992
90	90	0.0142
91	91	0.958
92	92	0.358
93	93	0.0622
94	94	0.301
95	95	0.142
96	96	0.322
97	97	0.732
98	98	0.494
99	99	0.0539

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: CNhs13531

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000025 CD19-positive B cell sample
FF:0000103 mouse 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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000945 (lymphocyte of B lineage)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000236 (B cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000025 (CD19-positive B cell 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)
CL:0000051 (common lymphoid progenitor)

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
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8!2.18!Aebp2;;chr2:153475381..153475419,+!p3@Dnmt3b!0.18!2.01!Dnmt3b;;chr5:65194709..65194716,+!p10@Klf3!0.18!1.85!Klf3;;chr1:74634786..74634804,-!p5@Zfp142!0.18!1.01!Zfp142;;chr13:64254437..64254453,-!p4@Zfp367!0.18!1.01!Zfp367;;chr5:77695181..77695196,+!p6@Rest!0.18!0.84!Rest;;chr4:128483422..128483430,-!p6@Zfp362!0.18!0.84!Zfp362;;chr4:48064251..48064268,+!p12@Nr4a3!0.18!0.50!Nr4a3;;chr4:48061952..48061964,+!p10@Nr4a3!0.18!0.50!Nr4a3;;chr3:135271325..135271343,-!p15@Nfkb1!0.18!0.50!Nfkb1;;chr4:48058252..48058261,+!p6@Nr4a3!0.18!0.50!Nr4a3;;chr3:58219238..58219246,+!p3@Tsc22d2!0.18!0.50!Tsc22d2;;chr15:75578748..75578752,-!p1@Mafa!0.18!0.50!Mafa;;chr12:36219283..36219298,-!p2@Ahr!0.18!0.50!Ahr;;chr1:179372514..179372525,+!p7@Zfp238!0.18!0.50!Zfp238;;chr2:56967316..56967327,-!p3@Nr4a2!0.18!0.50!Nr4a2;;chr19:46380462..46380471,+!p11@Nfkb2!0.18!0.50!Nfkb2;;chr16:43508231..43508271,+!p21@Zbtb20!0.18!0.50!Zbtb20;;chr6:120314480..120314487,+!p6@Kdm5a!0.18!0.50!Kdm5a;;chr5:77524043..77524064,-!p9@Hopx!0.18!0.50!Hopx;;chr8:86590801..86590818,+!p2@Rfx1!0.18!0.50!Rfx1;;chr7:20213752..20213778,-!p2@Relb!0.18!0.50!Relb;;chr7:19895546..19895577,-!p3@Fosb!0.18!0.50!Fosb;;chr7:31210542..31210567,+!p14@Nfkbid!0.18!0.50!Nfkbid;;chr10:20881160..20881175,-!p4@Myb!0.18!0.50!Myb;;chr18:60720384..60720450,+!p1@Rbm22!0.17!68.79!Rbm22;;chr5:107125549..107125605,-!p1@Zfp644!0.17!22.82!Zfp644;;chr15:75672337..75672362,-!p1@Zc3h3!0.17!14.43!Zc3h3;;chr19:26679654..26679675,+!p1@Smarca2!0.17!11.74!Smarca2;;chr13:67601387..67601448,-!p2@Zfp58!0.17!10.40!Zfp58;;chr17:4994904..4994953,+!p3@Arid1b!0.17!9.73!Arid1b;;chr2:126501197..126501245,-!p1@Gabpb1!0.17!9.56!Gabpb1;;chr7:26052688..26052742,+!p1@Cic!0.17!8.72!Cic;;chr8:72519989..72520007,-!p5@Gatad2a!0.17!5.70!Gatad2a;;chr6:47785797..47785823,+!p2@Zfp398!0.17!5.20!Zfp398;;chr15:99532528..99532550,+!p3@Smarcd1!0.17!4.03!Smarcd1;;chr8:125778192..125778217,+!p2@Zfp276!0.17!3.02!Zfp276;;chr8:74405860..74405905,+!p2@Zfp709!0.17!2.18!Zfp709;;chr18:76401789..76401814,+!p4@Smad2!0.17!2.18!Smad2;;chr15:61818965..61819046,+!p3@Myc!0.17!1.51!Myc;;chr5:125342568..125342602,+!p2@Zfp664!0.17!1.34!Zfp664;;chr16:95923651..95923701,+!p3@Ets2!0.17!1.34!Ets2;;chr18:69505476..69505494,+!p15@Tcf4!0.17!1.34!Tcf4;;chr4:102786990..102786999,+!p11@Mier1!0.17!1.01!Mier1;;chr7:135020660..135020688,+!p3@Zfp646!0.17!1.01!Zfp646;;chr9:56266504..56266516,+!p5@Hmg20a!0.17!0.67!Hmg20a;;chr15:76307834..76307891,+!p1@Hsf1!0.16!51.51!Hsf1;;chr1:64579394..64579433,+!p1@Creb1!0.16!46.98!Creb1;;chr1:173341436..173341468,+!p1@Usf1!0.16!31.88!Usf1;;chr5:77694479..77694574,+!p1@Rest!0.16!27.68!Rest;;chr5:25004592..25004630,-!p2@Mll3!0.16!26.17!Mll3;;chr4:141000572..141000629,+!p1@Zbtb17!0.16!23.99!Zbtb17;;chr1:181476358..181476391,-!p1@Tfb2m!0.16!19.63!Tfb2m;;chr1:167932744..167932778,-!p1@Pou2f1!0.16!10.91!Pou2f1;;chr9:21420572..21420591,+!p2@Smarca4!0.16!6.54!Smarca4;;chr19:5610038..5610066,-!p1@Kat5!0.16!5.54!Kat5;;chr17:48061605..48061629,-!p6@Foxp4!0.16!4.53!Foxp4;;chr5:138186979..138187025,+!p4@Tsc22d4!0.16!4.03!Tsc22d4;;chr2:166888058..166888105,-!p2@Znfx1!0.16!3.36!Znfx1;;chr7:134519542..134519569,-!p1@Zfp747!0.16!3.19!Zfp747;;chrX:91368698..91368751,-!p2@Zfx!0.16!3.19!Zfx;;chr17:45570631..45570658,-!p4@Cdc5l!0.16!3.02!Cdc5l;;chr10:85379814..85379844,-!p2@Prdm4!0.16!2.35!Prdm4;;chr6:47827547..47827568,+!p4@Zfp282!0.16!2.18!Zfp282;;chr10:44178521..44178557,-!p1@Prdm1!0.16!1.51!Prdm1;;chr18:3337399..3337422,-!p11@Crem!0.16!1.34!Crem;;chr18:36953486..36953503,+!p2@Zmat2!0.16!1.34!Zmat2;;chr17:15636925..15636940,+!p2@Tbp!0.16!1.17!Tbp;;chr6:133985790..133985801,+!p8@Etv6!0.16!0.84!Etv6;;chr9:71958979..71959032,-!p4@Tcf12!0.16!0.84!Tcf12;;chrX:137077699..137077705,-!p8@Tsc22d3!0.16!0.84!Tsc22d3;;chr10:80598968..80599012,+!p5@Zbtb7a!0.16!0.84!Zbtb7a;;chr15:102301149..102301221,+!p2@Pcbp2!0.15!47.15!Pcbp2;;chr8:124900511..124900552,+!p1@Zc3h18!0.15!44.13!Zc3h18;;chr5:53981912..53981942,+!p1@Rbpj!0.15!24.33!Rbpj;;chr18:36440723..36440805,+!p1@Pura!0.15!19.97!Pura;;
@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs13531
-|library_id_phase_based=1:CNhs13531
+|library_id_phase_based=2:CNhs13531
 |name=Mouse CD19+ B Cells, donor1
 |namespace=
@@ Line 51: / Line 51: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs13531,LSID1029,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0.0673620022139481,0.302481506279645,0,0.0156257432051787,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0726678392805361,0,0.033681001106974,0,0,0,0,0,0,0,0,0,0,0,-0.188787533210522,0,0,0,0,0,-0.0871119885738747,-0.0963101821295853,0.075779446277259,-0.984211366477826,-0.269868638010351,0.22301034595168,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,-0.0160396022696727,0,-0.0970155643438125,0,0,0,-0.005884629932486,0.360634895934694,-0.158091042771083,0.00741019870540075,0,0.0453225344596994,-0.127378513298283,-0.187197104386206,0,0,-0.0624085794533537,-0.0570185897332497,-0.293433374460924,0.0468335034856353,0,0,0,0,0,0,-0.059548030401287,-0.0892067893905786,0.426218479484419,0,0,0,0,0

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FF:11856-125A2: Difference between revisions

From FANTOM5_SSTAR

Revision as of 09:54, 28 November 2014

CNhs13531

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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