FF:12128-128D4: Difference between revisions

Revision as of 09:57, 28 November 2014

Name:	common myeloid progenitor CMP, biol_rep3
Species:	Mouse (Mus musculus)
Library ID:	CNhs12551
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/8J
tissue	bone marrow
dev stage	NA
sex	male
age	9-10weeks
cell type	common myeloid progenitor
cell line	NA
company	NA
collaboration	Kitamura/Nakahara
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	rep3
catalog number	NA
sample type	total RNA
extraction protocol (Details)	NA

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00004862

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs12551		CAGE		DRX008781		DRR009653

Accession ID Mm9

Library id		BAM		CTSS
CNhs12551		DRZ001078		DRZ002463

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

CNhs12551

0	0
1	0
10	0
100	0
1000	0
1001	-0.0749
1002	-0.116
1003	-0.0786
1004	0
1005	0.0413
1006	-0.2
1007	-0.288
1008	0
1009	-0.161
101	0.259
1010	0
1011	0
1012	0
1013	-0.16
1014	-0.0874
1015	-0.0554
1016	-0.496
1017	0
1018	0
1019	0
102	0.052
1020	0.0983
1021	0
1022	-0.221
1023	0.634
1024	0.457
1025	-0.0611
1026	0
1027	-0.048
1028	0
1029	-0.131
103	-0.0887
1030	0
1031	-0.911
1032	-0.436
1033	0.103
1034	0
1035	0
1036	0.544
1037	0
1038	-0.283
1039	0.0315
104	0
1040	-0.23
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: CNhs12551

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	1.01348e-5
MA0003.1	MA0003.1	0.606
MA0004.1	MA0004.1	0.0749
MA0006.1	MA0006.1	0.93
MA0007.1	MA0007.1	0.54
MA0009.1	MA0009.1	0.519
MA0014.1	MA0014.1	0.845
MA0017.1	MA0017.1	0.411
MA0018.2	MA0018.2	5.50289e-6
MA0019.1	MA0019.1	0.842
MA0024.1	MA0024.1	7.82816e-5
MA0025.1	MA0025.1	0.109
MA0027.1	MA0027.1	0.329
MA0028.1	MA0028.1	3.98595e-8
MA0029.1	MA0029.1	0.188
MA0030.1	MA0030.1	0.187
MA0031.1	MA0031.1	0.62
MA0035.2	MA0035.2	0.821
MA0038.1	MA0038.1	0.059
MA0039.2	MA0039.2	0.884
MA0040.1	MA0040.1	0.071
MA0041.1	MA0041.1	0.143
MA0042.1	MA0042.1	0.373
MA0043.1	MA0043.1	2.77667e-6
MA0046.1	MA0046.1	1.43527e-15
MA0047.2	MA0047.2	0.832
MA0048.1	MA0048.1	0.00771
MA0050.1	MA0050.1	5.0758e-8
MA0051.1	MA0051.1	7.93014e-5
MA0052.1	MA0052.1	0.453
MA0055.1	MA0055.1	0.00272
MA0057.1	MA0057.1	0.722
MA0058.1	MA0058.1	0.0271
MA0059.1	MA0059.1	0.00155
MA0060.1	MA0060.1	0.519
MA0061.1	MA0061.1	4.96743e-6
MA0062.2	MA0062.2	1.23665e-17
MA0065.2	MA0065.2	0.27
MA0066.1	MA0066.1	0.176
MA0067.1	MA0067.1	0.00454
MA0068.1	MA0068.1	0.00676
MA0069.1	MA0069.1	0.424
MA0070.1	MA0070.1	0.141
MA0071.1	MA0071.1	0.323
MA0072.1	MA0072.1	0.892
MA0073.1	MA0073.1	0.713
MA0074.1	MA0074.1	0.344
MA0076.1	MA0076.1	2.69709e-9
MA0077.1	MA0077.1	0.275
MA0078.1	MA0078.1	0.734
MA0079.2	MA0079.2	0.0814
MA0080.2	MA0080.2	1.5801e-12
MA0081.1	MA0081.1	5.36974e-5
MA0083.1	MA0083.1	0.00622
MA0084.1	MA0084.1	0.625
MA0087.1	MA0087.1	0.923
MA0088.1	MA0088.1	0.209
MA0090.1	MA0090.1	0.00592
MA0091.1	MA0091.1	0.961
MA0092.1	MA0092.1	0.585
MA0093.1	MA0093.1	0.0636
MA0099.2	MA0099.2	5.22816e-14
MA0100.1	MA0100.1	3.48636e-4
MA0101.1	MA0101.1	1.80075e-9
MA0102.2	MA0102.2	9.73841e-5
MA0103.1	MA0103.1	0.177
MA0104.2	MA0104.2	0.0283
MA0105.1	MA0105.1	1.61349e-6
MA0106.1	MA0106.1	0.156
MA0107.1	MA0107.1	1.76886e-8
MA0108.2	MA0108.2	0.207
MA0111.1	MA0111.1	0.838
MA0112.2	MA0112.2	0.0669
MA0113.1	MA0113.1	0.57
MA0114.1	MA0114.1	0.56
MA0115.1	MA0115.1	0.914
MA0116.1	MA0116.1	0.00121
MA0117.1	MA0117.1	0.267
MA0119.1	MA0119.1	0.373
MA0122.1	MA0122.1	0.162
MA0124.1	MA0124.1	0.816
MA0125.1	MA0125.1	0.0343
MA0131.1	MA0131.1	0.114
MA0135.1	MA0135.1	0.0285
MA0136.1	MA0136.1	1.95447e-28
MA0137.2	MA0137.2	0.00159
MA0138.2	MA0138.2	4.2564e-4
MA0139.1	MA0139.1	0.388
MA0140.1	MA0140.1	0.541
MA0141.1	MA0141.1	0.594
MA0142.1	MA0142.1	0.791
MA0143.1	MA0143.1	0.202
MA0144.1	MA0144.1	0.103
MA0145.1	MA0145.1	0.655
MA0146.1	MA0146.1	0.191
MA0147.1	MA0147.1	0.0165
MA0148.1	MA0148.1	0.592
MA0149.1	MA0149.1	0.111
MA0150.1	MA0150.1	2.7925e-5
MA0152.1	MA0152.1	0.837
MA0153.1	MA0153.1	1.52204e-4
MA0154.1	MA0154.1	0.261
MA0155.1	MA0155.1	0.71
MA0156.1	MA0156.1	4.52944e-22
MA0157.1	MA0157.1	0.348
MA0159.1	MA0159.1	0.0473
MA0160.1	MA0160.1	0.264
MA0162.1	MA0162.1	0.431
MA0163.1	MA0163.1	2.561e-5
MA0164.1	MA0164.1	0.603
MA0258.1	MA0258.1	0.0828
MA0259.1	MA0259.1	0.187

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: CNhs12551

Novel motif	Logo	P-value
1	1	0.392
10	10	0.0457
100	100	0.637
101	101	0.905
102	102	0.674
103	103	0.27
104	104	0.81
105	105	0.544
106	106	0.17
107	107	0.912
108	108	0.499
109	109	0.0889
11	11	0.236
110	110	0.148
111	111	0.257
112	112	0.144
113	113	0.544
114	114	0.493
115	115	0.571
116	116	0.777
117	117	2.68768e-4
118	118	0.215
119	119	1
12	12	0.685
120	120	0.306
121	121	0.431
122	122	0.435
123	123	0.162
124	124	0.412
125	125	0.423
126	126	0.512
127	127	0.611
128	128	0.244
129	129	0.302
13	13	0.00129
130	130	0.529
131	131	0.338
132	132	0.405
133	133	0.353
134	134	0.683
135	135	0.713
136	136	0.233
137	137	0.00671
138	138	0.793
139	139	0.521
14	14	0.492
140	140	0.481
141	141	0.519
142	142	0.861
143	143	0.194
144	144	0.89
145	145	0.0553
146	146	0.684
147	147	0.576
148	148	0.24
149	149	0.151
15	15	0.034
150	150	0.573
151	151	0.811
152	152	0.802
153	153	0.411
154	154	0.663
155	155	0.947
156	156	0.372
157	157	0.937
158	158	0.0595
159	159	0.465
160	160	0.567
161	161	0.152
162	162	0.396
163	163	0.261
164	164	0.0109
165	165	0.158
166	166	0.382
167	167	0.224
168	168	0.673
169	169	0.0396
17	17	0.683
18	18	0.374
19	19	0.623
2	2	0.0711
20	20	0.0123
21	21	0.389
22	22	0.83
23	23	0.201
24	24	0.037
25	25	0.294
26	26	0.0043
27	27	0.354
28	28	0.694
29	29	0.0103
3	3	0.144
30	30	0.173
31	31	0.708
32	32	0.313
33	33	0.0919
34	34	0.613
35	35	0.525
36	36	0.0486
37	37	0.0477
38	38	0.518
39	39	0.641
4	4	0.594
40	40	0.156
41	41	0.0767
42	42	0.366
43	43	0.519
44	44	0.7
45	45	0.693
46	46	0.317
47	47	0.674
48	48	0.333
49	49	0.462
5	5	0.561
50	50	0.682
51	51	0.978
52	52	0.531
53	53	0.606
54	54	0.743
55	55	0.593
56	56	0.788
57	57	0.413
58	58	0.265
59	59	0.929
6	6	0.785
60	60	0.527
61	61	0.212
62	62	0.189
63	63	0.93
64	64	0.81
65	65	0.885
66	66	0.32
67	67	0.339
68	68	0.685
69	69	0.704
7	7	0.265
70	70	0.168
71	71	0.0155
72	72	0.117
73	73	0.0509
74	74	0.655
75	75	0.00647
76	76	0.049
77	77	0.132
78	78	0.143
79	79	0.691
8	8	0.0949
80	80	0.711
81	81	0.938
82	82	0.345
83	83	0.0703
84	84	0.38
85	85	0.52
86	86	0.213
87	87	0.0452
88	88	0.508
89	89	0.994
9	9	0.882
90	90	0.0306
91	91	0.843
92	92	0.991
93	93	0.167
94	94	0.458
95	95	0.003
96	96	0.998
97	97	0.938
98	98	0.523
99	99	0.231

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: CNhs12551

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000041 common myeloid progenitor 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)
0002032 (hematopoietic oligopotent progenitor cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000049 (common myeloid progenitor)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000041 (common myeloid progenitor 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

@@ 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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0306,+!p8@Tal1!0.10!0.25!Tal1;;chr5:104182999..104183006,+!p18@Aff1!0.10!0.25!Aff1;;chr4:133109285..133109308,+!p1@Nr0b2!0.10!0.25!Nr0b2;;chr3:133207614..133207630,-!p4@Tet2!0.10!0.25!Tet2;;chr4:114729957..114730012,+!p3@Tal1!0.10!0.25!Tal1;;chr6:52190467..52190500,-!p1@Hoxa10!0.10!0.25!Hoxa10;;chr6:99385365..99385376,-!p21@Foxp1!0.10!0.25!Foxp1;;chr7:122989632..122989668,-!p2@Sox6!0.10!0.25!Sox6;;chr7:17200127..17200137,-!p11@Grlf1!0.10!0.25!Grlf1;;chr7:13563672..13563687,+!p5@Zfp446!0.10!0.25!Zfp446;;chr6:16848460..16848471,-!p5@Tfec!0.10!0.25!Tfec;;chr6:88143570..88143590,+!p4@Gata2!0.10!0.25!Gata2;;chr6:52161666..52161711,-!p1@Hoxa6!0.10!0.25!Hoxa6;;chr7:31065553..31065603,+!p@chr7:31065553..31065603,+!0.10!0.25!Thap8;;chr7:31210290..31210308,+!p10@Nfkbid!0.10!0.25!Nfkbid;;chr8:87425854..87425891,+!p1@Klf1!0.10!0.25!Klf1;;chr7:31207291..31207314,+!p15@Nfkbid!0.10!0.25!Nfkbid;;chr11:98799690..98799701,+!p17@Rara!0.10!0.25!Rara;;chr10:30375530..30375535,-!p12@Ncoa7!0.10!0.25!Ncoa7;;chr10:79957600..79957618,+!p1@Onecut3!0.10!0.25!Onecut3;;chr11:100683822..100683831,-!p8@Stat5b!0.10!0.25!Stat5b;;chr11:90252071..90252093,-!p7@Hlf!0.10!0.25!Hlf;;chr11:5420655..5420659,+!p3@Xbp1!0.10!0.25!Xbp1;;chr11:90249836..90249849,-!p15@Hlf!0.10!0.25!Hlf;;chr11:96180069..96180089,+!p3@Hoxb4!0.10!0.25!Hoxb4;;chr11:100721732..100721742,+!p3@Stat5a!0.10!0.25!Stat5a;;chr10:5734677..5734702,-!p4@Esr1!0.10!0.25!Esr1;;chr11:120491830..120491851,-!p10@Mafg!0.10!0.25!Mafg;;chr11:120624106..120624107,+!p13@Hmga1-rs1,p14@Hmga1!0.10!0.25!Hmga1;;chr12:86815252..86815257,+!p11@Fos!0.10!0.25!Fos;;chr14:70477113..70477173,+!p1@Egr3!0.10!0.25!Egr3;;chr14:55330957..55330971,-!p2@Cebpe!0.10!0.25!Cebpe;;chr13:83712735..83712761,+!p9@Mef2c!0.10!0.25!Mef2c;;chr13:58503837..58503885,-!p1@Hnrnpk!0.09!314.75!Hnrnpk;;chr4:149611320..149611348,+!p1@Eno1,p1@Gm5506,p1@LOC100045967,p1@LOC100503183!0.09!47.40!Eno1;;chr18:74375851..74375891,+!p1@Cxxc1!0.09!43.46!Cxxc1;;chr7:30954720..30954785,-!p1@LOC677248,p1@Zfp146!0.09!28.46!Zfp146;;chr11:98798983..98799049,+!p1@Rara!0.09!27.45!Rara;;chr13:14156043..14156089,+!p1@Arid4b!0.09!26.56!Arid4b;;chr18:76401546..76401613,+!p1@Smad2!0.09!23.13!Smad2;;chr8:109817400..109817417,+!p1@Nfat5!0.09!22.62!Nfat5;;chr10:80599279..80599353,+!p1@Zbtb7a!0.09!19.44!Zbtb7a;;chr15:81575569..81575599,+!p2@Zc3h7b!0.09!11.69!Zc3h7b;;chr4:102791976..102792008,+!p2@Mier1!0.09!11.56!Mier1;;chr19:38893646..38893732,-!p1@Noc3l!0.09!11.31!Noc3l;;chr2:181022663..181022712,-!p1@Gmeb2!0.09!10.93!Gmeb2;;chr5:20387850..20387869,-!p1@Phtf2!0.09!10.67!Phtf2;;chr14:98568971..98569025,-!p1@Dach1!0.09!7.75!Dach1;;chr3:32409487..32409563,+!p1@Zfp639!0.09!7.37!Zfp639;;chr18:3281034..3281104,-!p1@Crem!0.09!7.12!Crem;;chr2:169956656..169956684,-!p1@Zfp217!0.09!6.73!Zfp217;;chr16:17233653..17233683,+!p1@Hic2!0.09!6.35!Hic2;;chr7:138554009..138554034,-!p1@Ikzf5!0.09!6.23!Ikzf5;;chr11:99092233..99092273,-!p2@Smarce1!0.09!4.57!Smarce1;;chr9:69137672..69137702,+!p2@Rora!0.09!3.94!Rora;;chr9:96096665..96096699,+!p4@Tfdp2!0.09!2.92!Tfdp2;;chr15:100058660..100058711,+!p1@Gm1862,p2@Atf1!0.09!2.92!Atf1;;chr5:138187181..138187192,+!p5@Tsc22d4!0.09!2.03!Tsc22d4;;chr18:76401789..76401814,+!p4@Smad2!0.09!1.65!Smad2;;chrX:45947746..45947762,-!p2@Zfp280c!0.09!1.52!Zfp280c;;chr11:3189171..3189197,+!p4@Patz1!0.09!1.27!Patz1;;chr10:22451100..22451111,-!p5@Tbpl1!0.09!1.14!Tbpl1;;chrX:7341077..7341091,+!p5@Tfe3!0.09!1.02!Tfe3;;chr2:120996813..120996829,-!p2@Zscan29!0.09!1.02!Zscan29;;chr15:50721239..50721260,-!p9@Trps1!0.09!1.02!Trps1;;chr11:120494908..120494919,-!p4@Mafg!0.09!0.76!Mafg;;chr3:100773602..100773607,-!p2@Ttf2!0.09!0.51!Ttf2;;chr7:31741624..31741643,-!p7@LOC100504922,p7@Usf2!0.09!0.51!Usf2;;chr18:61336630..61336641,-!p3@Hmgxb3!0.09!0.51!Hmgxb3;;chr4:48058102..48058110,+!p5@Nr4a3!0.09!0.38!Nr4a3;;chr10:127080230..127080241,+!p6@Stat6!0.09!0.38!Stat6;;chr15:102300965..102300977,+!p1@Pcbp2!0.08!349.57!Pcbp2;;chr15:36937029..36937108,-!p1@Gm10193,p1@Zfp706!0.08!133.55!Zfp706;;chr17:57170891..57170961,-!p1@Khsrp!0.08!95.94!Khsrp;;
@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs12551
-|library_id_phase_based=1:CNhs12551
+|library_id_phase_based=2:CNhs12551
 |name=common myeloid progenitor CMP, biol_rep3
 |namespace=FANTOM5
@@ Line 51: / Line 51: @@
 |profile_cagescan=,,,
 |profile_hcage=CNhs12551,LSID921,release012,COMPLETED
-|profile_rnaseq=,,,
+|profile_rnaseq=
 |profile_srnaseq=,,,
 |repeat_enrich_byfamily=-0.11779559634038,0,0,0,0.0519509775191307,0,-0.24735381395849,0,0,0,0,-0.0843392403965415,0,0,0,0,0.316927347580919,0,-0.139942373363444,0,0.089241116907443,0,0,0,0,0,0,0,0,0,0,0,-0.0251167495389848,0,0,0,0,-0.0233343073597331,0.0322241612137505,-0.184929286974461,-0.159791356656061,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,0.112476686251446,0,0,0,0,-0.0428469550828748,0,0,0,0.0519509775191307,0,-0.0914143141487609,0.133235260693963,-0.158091042771083,-0.0655391060670712,0,0,-0.163649328246584,-0.284051586260151,0.516834595184949,0,-0.111471060110387,-0.24115538758951,-0.59591488074057,0.061428333349397,0,0,0,0,0,0,-0.264295134298998,-0.708543480381515,-0.217852024712268,0,0,0,0,0

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FF:12128-128D4: Difference between revisions

From FANTOM5_SSTAR

Revision as of 09:57, 28 November 2014

CNhs12551

	FAQ
	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0