FF:1354-25G3: Difference between revisions

Revision as of 20:34, 29 June 2012

Name:	spleen, neonate N25
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	C57BL/6J
tissue	spleen
dev stage	25 days neonate
sex	mixture
age	NA
cell type	CELL MIXTURE - tissue sample
cell line	NA
company	NA
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
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

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

CNhs11099

0	0
1	0
10	0
100	0
1000	0
1001	0.00373
1002	-0.00929
1003	-0.0952
1004	0
1005	0.0895
1006	-0.143
1007	0.0757
1008	0
1009	-0.11
101	0.109
1010	0
1011	-0.018
1012	0.281
1013	-0.0543
1014	-0.0874
1015	-0.0823
1016	-0.333
1017	0
1018	0
1019	0
102	0
1020	0
1021	0.0895
1022	-0.171
1023	0
1024	-0.117
1025	0
1026	0
1027	0
1028	0
1029	0.105
103	-0.061
1030	0.842
1031	-0.345
1032	-0.324
1033	0.0971
1034	0
1035	0
1036	0.17
1037	0
1038	-0.277
1039	-0.185
104	0
1040	-0.121
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 no result for this sample

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: CNhs11099

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00606
MA0003.1	MA0003.1	0.645
MA0004.1	MA0004.1	0.723
MA0006.1	MA0006.1	0.392
MA0007.1	MA0007.1	0.812
MA0009.1	MA0009.1	0.379
MA0014.1	MA0014.1	0.624
MA0017.1	MA0017.1	0.253
MA0018.2	MA0018.2	0.0161
MA0019.1	MA0019.1	0.258
MA0024.1	MA0024.1	1.26292e-4
MA0025.1	MA0025.1	0.126
MA0027.1	MA0027.1	0.591
MA0028.1	MA0028.1	0.0275
MA0029.1	MA0029.1	0.741
MA0030.1	MA0030.1	0.325
MA0031.1	MA0031.1	0.929
MA0035.2	MA0035.2	8.85354e-8
MA0038.1	MA0038.1	0.094
MA0039.2	MA0039.2	0.442
MA0040.1	MA0040.1	0.687
MA0041.1	MA0041.1	0.249
MA0042.1	MA0042.1	0.825
MA0043.1	MA0043.1	0.0049
MA0046.1	MA0046.1	1.33357e-10
MA0047.2	MA0047.2	0.945
MA0048.1	MA0048.1	0.249
MA0050.1	MA0050.1	2.32659e-13
MA0051.1	MA0051.1	3.16512e-8
MA0052.1	MA0052.1	4.80659e-5
MA0055.1	MA0055.1	0.256
MA0057.1	MA0057.1	0.671
MA0058.1	MA0058.1	0.772
MA0059.1	MA0059.1	0.175
MA0060.1	MA0060.1	0.485
MA0061.1	MA0061.1	2.44249e-4
MA0062.2	MA0062.2	4.41613e-6
MA0065.2	MA0065.2	0.222
MA0066.1	MA0066.1	0.117
MA0067.1	MA0067.1	0.917
MA0068.1	MA0068.1	0.878
MA0069.1	MA0069.1	0.754
MA0070.1	MA0070.1	0.246
MA0071.1	MA0071.1	0.727
MA0072.1	MA0072.1	0.465
MA0073.1	MA0073.1	0.804
MA0074.1	MA0074.1	0.791
MA0076.1	MA0076.1	0.0649
MA0077.1	MA0077.1	0.103
MA0078.1	MA0078.1	0.463
MA0079.2	MA0079.2	0.0487
MA0080.2	MA0080.2	7.98158e-12
MA0081.1	MA0081.1	0.0235
MA0083.1	MA0083.1	0.213
MA0084.1	MA0084.1	0.406
MA0087.1	MA0087.1	0.263
MA0088.1	MA0088.1	0.169
MA0090.1	MA0090.1	0.0474
MA0091.1	MA0091.1	0.135
MA0092.1	MA0092.1	0.79
MA0093.1	MA0093.1	0.75
MA0099.2	MA0099.2	0.636
MA0100.1	MA0100.1	0.101
MA0101.1	MA0101.1	5.6364e-4
MA0102.2	MA0102.2	0.933
MA0103.1	MA0103.1	0.999
MA0104.2	MA0104.2	0.627
MA0105.1	MA0105.1	6.56374e-7
MA0106.1	MA0106.1	0.338
MA0107.1	MA0107.1	6.24086e-4
MA0108.2	MA0108.2	6.75158e-4
MA0111.1	MA0111.1	0.581
MA0112.2	MA0112.2	0.00191
MA0113.1	MA0113.1	0.477
MA0114.1	MA0114.1	0.81
MA0115.1	MA0115.1	0.947
MA0116.1	MA0116.1	0.00247
MA0117.1	MA0117.1	0.772
MA0119.1	MA0119.1	0.252
MA0122.1	MA0122.1	0.708
MA0124.1	MA0124.1	0.807
MA0125.1	MA0125.1	0.0882
MA0131.1	MA0131.1	0.913
MA0135.1	MA0135.1	0.105
MA0136.1	MA0136.1	2.72686e-14
MA0137.2	MA0137.2	0.528
MA0138.2	MA0138.2	0.0141
MA0139.1	MA0139.1	0.175
MA0140.1	MA0140.1	3.12822e-36
MA0141.1	MA0141.1	0.517
MA0142.1	MA0142.1	0.0302
MA0143.1	MA0143.1	0.171
MA0144.1	MA0144.1	0.73
MA0145.1	MA0145.1	0.85
MA0146.1	MA0146.1	0.226
MA0147.1	MA0147.1	0.575
MA0148.1	MA0148.1	0.728
MA0149.1	MA0149.1	0.0287
MA0150.1	MA0150.1	0.0491
MA0152.1	MA0152.1	0.896
MA0153.1	MA0153.1	1.82653e-6
MA0154.1	MA0154.1	0.00235
MA0155.1	MA0155.1	0.657
MA0156.1	MA0156.1	3.68485e-12
MA0157.1	MA0157.1	0.921
MA0159.1	MA0159.1	0.0773
MA0160.1	MA0160.1	0.944
MA0162.1	MA0162.1	0.232
MA0163.1	MA0163.1	1.00564e-4
MA0164.1	MA0164.1	0.396
MA0258.1	MA0258.1	0.0554
MA0259.1	MA0259.1	0.971

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: CNhs11099

Novel motif	Logo	P-value
1	1	0.0873
10	10	0.0265
100	100	0.858
101	101	0.947
102	102	0.583
103	103	0.0226
104	104	0.973
105	105	0.932
106	106	0.204
107	107	0.674
108	108	0.333
109	109	0.105
11	11	0.186
110	110	0.0717
111	111	0.0474
112	112	0.0297
113	113	0.727
114	114	0.449
115	115	0.522
116	116	0.839
117	117	7.74448e-4
118	118	0.0875
119	119	0.229
12	12	0.977
120	120	0.621
121	121	0.15
122	122	0.911
123	123	0.198
124	124	0.888
125	125	0.036
126	126	0.188
127	127	0.624
128	128	0.258
129	129	0.126
13	13	0.0109
130	130	0.34
131	131	0.815
132	132	0.137
133	133	0.391
134	134	0.0972
135	135	0.939
136	136	0.954
137	137	0.0308
138	138	0.891
139	139	0.563
14	14	0.64
140	140	0.382
141	141	0.487
142	142	0.0501
143	143	0.233
144	144	0.905
145	145	0.0344
146	146	0.971
147	147	0.783
148	148	0.0932
149	149	0.651
15	15	0.0407
150	150	0.199
151	151	0.25
152	152	0.829
153	153	0.357
154	154	0.384
155	155	0.101
156	156	0.76
157	157	0.989
158	158	0.0449
159	159	0.075
160	160	0.598
161	161	0.0604
162	162	0.95
163	163	0.299
164	164	0.023
165	165	0.202
166	166	0.552
167	167	0.0913
168	168	0.641
169	169	0.0277
17	17	0.349
18	18	0.193
19	19	0.355
2	2	0.262
20	20	0.052
21	21	0.338
22	22	0.539
23	23	0.954
24	24	0.267
25	25	0.268
26	26	0.00316
27	27	0.879
28	28	0.179
29	29	0.0333
3	3	0.0348
30	30	0.291
31	31	0.921
32	32	0.495
33	33	0.201
34	34	0.801
35	35	0.476
36	36	0.0419
37	37	0.138
38	38	0.49
39	39	0.894
4	4	0.936
40	40	0.204
41	41	0.757
42	42	0.0663
43	43	0.0766
44	44	0.609
45	45	0.738
46	46	0.148
47	47	0.181
48	48	0.21
49	49	0.0529
5	5	0.0932
50	50	0.997
51	51	0.828
52	52	0.905
53	53	0.892
54	54	0.886
55	55	0.307
56	56	0.506
57	57	0.128
58	58	0.332
59	59	0.352
6	6	0.547
60	60	0.368
61	61	0.277
62	62	0.134
63	63	0.403
64	64	0.623
65	65	0.417
66	66	0.708
67	67	0.535
68	68	0.21
69	69	0.357
7	7	0.0636
70	70	0.181
71	71	0.0255
72	72	0.211
73	73	0.29
74	74	0.759
75	75	0.0252
76	76	0.19
77	77	0.705
78	78	0.0247
79	79	0.797
8	8	0.0502
80	80	0.0458
81	81	0.391
82	82	0.669
83	83	0.336
84	84	0.0829
85	85	0.25
86	86	0.615
87	87	0.49
88	88	0.706
89	89	0.83
9	9	0.583
90	90	0.0256
91	91	0.18
92	92	0.676
93	93	0.478
94	94	0.0476
95	95	0.234
96	96	0.0146
97	97	0.885
98	98	0.154
99	99	0.676

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: CNhs11099

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0011491 mouse spleen- neonate N25 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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002106 (spleen)
0000945 (stomach)
0002100 (trunk)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0010039 (food storage organ)
0002323 (body cavity)
0005177 (trunk region element)
0000042 (serous membrane)
0003104 (mesenchyme)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0001048 (primordium)
0000925 (endoderm)
0004854 (gastrointestinal system mesentery)
0009034 (stomach region)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0002095 (mesentery)
0004782 (gastrointestinal system serosa)
0004185 (endodermal part of digestive tract)
0005173 (abdominal segment element)
0003281 (mesentery of stomach)
0002532 (epiblast (generic))
0001555 (digestive tract)
0005409 (gastrointestinal system)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0007026 (primitive gut)
0001041 (foregut)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)
0003887 (intraembryonic coelom)
0009664 (gut mesentery)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0002296 (dorsal mesentery)
0005602 (dorsal mesogastrium)
0001179 (peritoneal cavity)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0004872 (splanchnic layer of lateral plate mesoderm)
0006293 (spleen primordium)
0003061 (blood island)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship Analyst: Hideya Kawaji link to source data data
NA

@@ Line 6: / Line 6: @@
 |created_by=
 |creation_date=
+|datafreeze_phase=1
 |def=
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0.77!8.01!Irf2;;chr7:31206743..31206761,+!p1@Nfkbid!0.77!6.86!Nfkbid;;chr11:23670953..23671028,-!p1@Rel!0.76!29.51!Rel;;chr2:90936947..90936977,+!p2@Sfpi1!0.76!10.07!Sfpi1;;chr2:90922554..90922575,+!p4@Sfpi1!0.76!9.15!Sfpi1;;chr4:134708909..134708939,+!p3@Runx3!0.76!4.80!Runx3;;chr6:83301243..83301258,+!p2@Bola3!0.76!4.80!Bola3;;chr4:114732159..114732166,+!p6@Tal1!0.75!4.58!Tal1;;chr11:23978111..23978134,+!p3@Bcl11a!0.74!10.07!Bcl11a;;chr4:32325688..32325777,+!p1@Bach2!0.73!43.01!Bach2;;chr10:30522690..30522752,-!p2@Ncoa7!0.73!29.74!Ncoa7;;chr12:85534957..85535017,-!p2@C130039O16Rik!0.73!24.25!C130039O16Rik;;chr1:52065454..52065495,+!p1@Stat4!0.73!7.55!Stat4;;chr1:38721767..38721778,-!p5@Aff3!0.73!4.35!Aff3;;chr11:23980664..23980706,+!p2@Bcl11a!0.72!20.59!Bcl11a;;chr10:20880629..20880683,-!p1@Myb!0.72!13.27!Myb;;chr12:87027598..87027652,+!p1@Batf!0.72!10.52!Batf;;chr11:11590140..11590187,+!p3@Ikzf1!0.72!5.26!Ikzf1;;chr9:32348943..32349001,-!p1@Fli1!0.71!37.75!Fli1;;chr7:20162663..20162678,+!p1@Zfp296!0.71!5.72!Zfp296;;chr11:98407340..98407359,-!p4@Ikzf3!0.71!4.12!Ikzf3;;chr14:32978970..32978984,+!p2@Gm6768,p2@Ncoa4!0.70!6.63!Ncoa4;;chr17:51971932..51971958,-!p2@Satb1!0.69!5.49!Satb1;;chr17:51971960..51971979,-!p1@Satb1!0.69!5.49!Satb1;;chr1:87546602..87546617,+!p2@Sp100!0.69!4.80!Sp100;;chr4:114730015..114730042,+!p7@Tal1!0.69!3.89!Tal1;;chr11:52095821..52095836,-!p3@Tcf7!0.69!3.89!Tcf7;;chr18:80909801..80909819,-!p1@Nfatc1!0.68!25.62!Nfatc1;;chr7:56136402..56136420,-!p3@E2f8!0.67!7.32!E2f8;;chr3:135271185..135271254,-!p4@Nfkb1!0.67!7.32!Nfkb1;;chr10:20880698..20880717,-!p3@Myb!0.67!6.18!Myb;;chr11:96976641..96976646,-!p1@Tbx21!0.67!3.66!Tbx21;;chr4:44717308..44717321,-!p6@Pax5!0.67!3.66!Pax5;;chr11:44430812..44430838,+!p1@Ebf1!0.66!40.72!Ebf1;;chr4:124805061..124805087,-!p1@Zc3h12a!0.66!12.35!Zc3h12a;;chr8:47825203..47825225,+!p3@Irf2!0.66!5.03!Irf2;;chr11:23978022..23978076,+!p1@Bcl11a!0.65!87.16!Bcl11a;;chr19:37509324..37509337,+!p1@Hhex!0.65!28.14!Hhex;;chr19:46379199..46379301,+!p1@Nfkb2!0.65!23.11!Nfkb2;;chr11:100683839..100683890,-!p2@Stat5b!0.65!8.92!Stat5b;;chr19:45225276..45225304,+!p2@Tlx1!0.65!3.43!Tlx1;;chr1:167865149..167865167,-!p3@Pou2f1!0.65!3.43!Pou2f1;;chr6:83301229..83301242,+!p3@Bola3!0.65!3.43!Bola3;;chr17:56970339..56970428,-!p1@Rfx2!0.64!11.90!Rfx2;;chr8:107821563..107821642,+!p1@E2f4!0.63!109.58!E2f4;;chr2:17977331..17977360,+!p11@Mllt10!0.63!3.66!Mllt10;;chr10:30522881..30522960,-!p1@Ncoa7!0.62!44.84!Ncoa7;;chr14:56223010..56223067,+!p1@Irf9!0.62!29.74!Irf9;;chr18:74375772..74375799,+!p2@Cxxc1!0.62!10.52!Cxxc1;;chr10:41995430..41995458,-!p3@Foxo3!0.62!9.38!Foxo3;;chr11:98407142..98407159,-!p5@Ikzf3!0.62!3.20!Ikzf3;;chr11:11590117..11590138,+!p4@Ikzf1!0.62!3.20!Ikzf1;;chr1:52065530..52065548,+!p3@Stat4!0.62!3.20!Stat4;;chrX:7156792..7156811,+!p1@Foxp3!0.62!3.20!Foxp3;;chr16:92826338..92826347,-!p6@Runx1!0.62!3.20!Runx1;;chr19:46380235..46380277,+!p3@Nfkb2!0.61!7.55!Nfkb2;;chr11:44431626..44431637,+!p10@Ebf1!0.61!3.66!Ebf1;;chr4:135736690..135736705,+!p6@E2f2!0.61!3.66!E2f2;;chr9:32503590..32503680,+!p1@Ets1!0.60!130.86!Ets1;;chr10:30523091..30523182,-!p4@Ncoa7!0.60!12.13!Ncoa7;;chr17:56970481..56970551,-!p2@Rfx2!0.60!10.75!Rfx2;;chr1:133904901..133904934,+!p3@Elk4!0.60!10.07!Elk4;;chr11:44430788..44430804,+!p3@Ebf1!0.60!8.46!Ebf1;;chr7:87170879..87170914,+!p2@Zfp710!0.60!7.78!Zfp710;;chr2:91035197..91035237,-!p1@Nr1h3!0.60!6.86!Nr1h3;;chr4:63064395..63064410,-!p2@Akna!0.60!5.72!Akna;;chr4:32325445..32325468,+!p4@Bach2!0.60!4.58!Bach2;;chr2:90936886..90936898,+!p5@Sfpi1!0.60!3.66!Sfpi1;;chr4:135728282..135728310,+!p4@E2f2!0.60!3.43!E2f2;;chr4:63064279..63064293,-!p7@Akna!0.60!2.97!Akna;;chr15:103083199..103083215,-!p8@Nfe2!0.60!2.97!Nfe2;;chr7:122989672..122989673,-!p20@Sox6!0.60!2.97!Sox6;;chr6:29479277..29479296,+!p2@Irf5!0.60!2.97!Irf5;;chr6:99216375..99216395,-!p5@Foxp1!0.60!2.97!Foxp1;;chr7:25917459..25917474,-!p2@Pou2f2!0.60!2.97!Pou2f2;;chr18:70727922..70728052,+!p1@Mbd2!0.59!128.34!Mbd2;;chr2:166888058..166888105,-!p2@Znfx1!0.59!10.75!Znfx1;;chr12:84828663..84828679,-!p1@Dpf3!0.58!26.54!Dpf3;;chr5:140267476..140267493,+!p1@Mafk!0.58!18.99!Mafk;;chr13:83663902..83663927,+!p1@Mef2c!0.57!82.13!Mef2c;;chr5:65194720..65194738,+!p2@Klf3!0.57!18.07!Klf3;;chr1:181733959..181733977,-!p4@Ahctf1!0.57!3.66!Ahctf1;;chr11:102180696..102180760,-!p2@Ubtf!0.56!16.24!Ubtf;;chr8:108583550..108583595,+!p2@Nfatc3!0.56!14.41!Nfatc3;;chr4:102792009..102792021,+!p6@Mier1!0.56!5.03!Mier1;;chr10:80598968..80599012,+!p5@Zbtb7a!0.56!3.66!Zbtb7a;;chr11:106134241..106134320,-!p2@Smarcd2!0.55!36.83!Smarcd2;;chr4:102791976..102792008,+!p2@Mier1!0.55!35.23!Mier1;;chr5:34163023..34163090,+!p2@Whsc1!0.55!20.59!Whsc1;;chr7:20214704..20214800,-!p1@Relb!0.55!10.07!Relb;;chr1:52176378..52176401,+!p3@Stat1!0.55!9.15!Stat1;;chr7:56137011..56137041,-!p2@E2f8!0.55!5.72!E2f8;;chr7:56136349..56136360,-!p5@E2f8!0.55!3.43!E2f8;;chr2:162880418..162880429,+!p4@Mybl2!0.55!3.43!Mybl2;;chr5:134720044..134720103,-!p6@Gtf2i!0.55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FF:1354-25G3: Difference between revisions

From FANTOM5_SSTAR

Revision as of 20:34, 29 June 2012

CNhs11099

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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