Difference between revisions of "FF:11741-123F4"

Revision as of 13:37, 27 June 2012

Name:	Mouse Neurons - striatal, donor2
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	{{{sample_category}}}
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	corpus striatum
dev stage	NA
sex	NA
age	NA
cell type	neuron
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	RNAMNS1
catalog number	custom
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

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

CNhs12360

MCL coexpression id	Coexpression dpi cluster scores median value
0	0
1	0.423
10	0
100	0.423
1000	0
1001	--0.0668
1002	0.0456
1003	0.0293
1004	0.0717
1005	0
1006	0.37
1007	--0.0312
1008	0
1009	--0.2
101	--0.163
1010	0
1011	0.198
1012	0
1013	--0.0266
1014	0.0503
1015	0.444
1016	0.236
1017	0
1018	0
1019	0
102	0
1020	0.552
1021	0.135
1022	--0.0704
1023	0
1024	--0.14
1025	0
1026	0
1027	0.375
1028	0
1029	--0.115
103	--0.0709
1030	0
1031	--0.568
1032	0.01
1033	0.0234
1034	0
1035	0
1036	--0.225
1037	0
1038	0.108
1039	--0.213
104	0
1040	--0.271
1041	0

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family 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 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 this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon

link to dataset.
data

library id: CNhs12360

Jaspar motif	Logo	P-value
MA0002.2	MA0002.2	0.00164
MA0003.1	MA0003.1	0.173
MA0004.1	MA0004.1	0.604
MA0006.1	MA0006.1	0.085
MA0007.1	MA0007.1	0.154
MA0009.1	MA0009.1	0.805
MA0014.1	MA0014.1	0.424
MA0017.1	MA0017.1	1.64739e-5
MA0018.2	MA0018.2	0.0154
MA0019.1	MA0019.1	0.429
MA0024.1	MA0024.1	0.953
MA0025.1	MA0025.1	0.533
MA0027.1	MA0027.1	0.533
MA0028.1	MA0028.1	0.679
MA0029.1	MA0029.1	0.62
MA0030.1	MA0030.1	0.339
MA0031.1	MA0031.1	0.0575
MA0035.2	MA0035.2	0.0873
MA0038.1	MA0038.1	0.427
MA0039.2	MA0039.2	0.0173
MA0040.1	MA0040.1	0.688
MA0041.1	MA0041.1	0.253
MA0042.1	MA0042.1	0.539
MA0043.1	MA0043.1	0.0696
MA0046.1	MA0046.1	2.65618e-8
MA0047.2	MA0047.2	0.00146
MA0048.1	MA0048.1	0.396
MA0050.1	MA0050.1	6.31981e-9
MA0051.1	MA0051.1	1.53189e-4
MA0052.1	MA0052.1	0.0453
MA0055.1	MA0055.1	0.485
MA0057.1	MA0057.1	0.115
MA0058.1	MA0058.1	0.566
MA0059.1	MA0059.1	0.372
MA0060.1	MA0060.1	0.00769
MA0061.1	MA0061.1	0.0565
MA0062.2	MA0062.2	0.207
MA0065.2	MA0065.2	1.78908e-5
MA0066.1	MA0066.1	0.201
MA0067.1	MA0067.1	0.767
MA0068.1	MA0068.1	0.887
MA0069.1	MA0069.1	0.124
MA0070.1	MA0070.1	0.453
MA0071.1	MA0071.1	0.208
MA0072.1	MA0072.1	0.143
MA0073.1	MA0073.1	0.891
MA0074.1	MA0074.1	0.355
MA0076.1	MA0076.1	0.63
MA0077.1	MA0077.1	0.0134
MA0078.1	MA0078.1	0.0945
MA0079.2	MA0079.2	0.613
MA0080.2	MA0080.2	3.50162e-10
MA0081.1	MA0081.1	0.363
MA0083.1	MA0083.1	0.0061
MA0084.1	MA0084.1	0.696
MA0087.1	MA0087.1	0.528
MA0088.1	MA0088.1	0.224
MA0090.1	MA0090.1	0.0084
MA0091.1	MA0091.1	0.191
MA0092.1	MA0092.1	0.138
MA0093.1	MA0093.1	0.621
MA0099.2	MA0099.2	1.13922e-4
MA0100.1	MA0100.1	0.821
MA0101.1	MA0101.1	0.0577
MA0102.2	MA0102.2	0.923
MA0103.1	MA0103.1	0.168
MA0104.2	MA0104.2	0.623
MA0105.1	MA0105.1	0.0541
MA0106.1	MA0106.1	0.12
MA0107.1	MA0107.1	0.0518
MA0108.2	MA0108.2	0.0681
MA0111.1	MA0111.1	0.99
MA0112.2	MA0112.2	8.5774e-5
MA0113.1	MA0113.1	0.295
MA0114.1	MA0114.1	1.05204e-4
MA0115.1	MA0115.1	0.0102
MA0116.1	MA0116.1	0.0848
MA0117.1	MA0117.1	0.821
MA0119.1	MA0119.1	0.0418
MA0122.1	MA0122.1	0.677
MA0124.1	MA0124.1	0.813
MA0125.1	MA0125.1	0.208
MA0131.1	MA0131.1	0.842
MA0135.1	MA0135.1	0.128
MA0136.1	MA0136.1	7.65572e-8
MA0137.2	MA0137.2	0.0233
MA0138.2	MA0138.2	0.21
MA0139.1	MA0139.1	0.304
MA0140.1	MA0140.1	0.00174
MA0141.1	MA0141.1	0.00903
MA0142.1	MA0142.1	0.0977
MA0143.1	MA0143.1	0.0119
MA0144.1	MA0144.1	0.0208
MA0145.1	MA0145.1	0.0416
MA0146.1	MA0146.1	0.0458
MA0147.1	MA0147.1	0.712
MA0148.1	MA0148.1	1.06855e-5
MA0149.1	MA0149.1	0.0575
MA0150.1	MA0150.1	0.0195
MA0152.1	MA0152.1	0.0768
MA0153.1	MA0153.1	1.77314e-7
MA0154.1	MA0154.1	0.023
MA0155.1	MA0155.1	0.698
MA0156.1	MA0156.1	2.66772e-5
MA0157.1	MA0157.1	0.0584
MA0159.1	MA0159.1	0.003
MA0160.1	MA0160.1	0.0766
MA0162.1	MA0162.1	0.319
MA0163.1	MA0163.1	0.00311
MA0164.1	MA0164.1	0.996
MA0258.1	MA0258.1	0.00769
MA0259.1	MA0259.1	0.56

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 in 169 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: CNhs12360

Novel motif	Logo	P-value
1	1	0.141
10	10	0.104
100	100	0.795
101	101	0.9
102	102	0.978
103	103	0.137
104	104	0.914
105	105	0.173
106	106	0.00488
107	107	0.0329
108	108	0.42
109	109	0.00459
11	11	0.112
110	110	0.0966
111	111	0.167
112	112	0.00951
113	113	0.942
114	114	0.341
115	115	0.999
116	116	0.555
117	117	0.0616
118	118	0.499
119	119	0.115
12	12	0.603
120	120	0.746
121	121	0.383
122	122	0.821
123	123	0.123
124	124	0.676
125	125	0.371
126	126	0.242
127	127	0.0906
128	128	0.0184
129	129	0.245
13	13	6.65885e-6
130	130	0.25
131	131	0.295
132	132	0.957
133	133	0.356
134	134	0.293
135	135	0.941
136	136	0.222
137	137	0.295
138	138	0.709
139	139	0.154
14	14	0.618
140	140	0.094
141	141	0.245
142	142	0.027
143	143	0.598
144	144	0.982
145	145	0.0166
146	146	0.384
147	147	0.938
148	148	0.409
149	149	0.178
15	15	0.181
150	150	0.127
151	151	0.41
152	152	0.0407
153	153	0.45
154	154	0.609
155	155	0.72
156	156	0.00657
157	157	0.0785
158	158	0.14
159	159	0.103
160	160	0.209
161	161	0.42
162	162	0.873
163	163	0.43
164	164	0.0164
165	165	0.0439
166	166	0.763
167	167	0.911
168	168	0.541
169	169	0.00281
17	17	0.0256
18	18	0.686
19	19	0.0458
2	2	0.889
20	20	0.577
21	21	0.481
22	22	0.0762
23	23	0.256
24	24	0.0402
25	25	0.616
26	26	7.1553e-4
27	27	0.898
28	28	0.368
29	29	0.111
3	3	0.0915
30	30	0.713
31	31	0.948
32	32	0.524
33	33	0.147
34	34	0.489
35	35	0.512
36	36	0.321
37	37	0.0114
38	38	0.319
39	39	0.207
4	4	0.585
40	40	0.271
41	41	0.752
42	42	0.202
43	43	0.136
44	44	0.817
45	45	0.518
46	46	0.139
47	47	0.197
48	48	0.14
49	49	0.155
5	5	0.126
50	50	0.27
51	51	0.515
52	52	0.0948
53	53	0.658
54	54	0.629
55	55	0.875
56	56	0.329
57	57	0.568
58	58	0.219
59	59	0.0889
6	6	0.607
60	60	0.0128
61	61	0.145
62	62	0.108
63	63	0.0989
64	64	0.944
65	65	0.242
66	66	0.621
67	67	0.769
68	68	0.291
69	69	0.505
7	7	0.0192
70	70	0.0248
71	71	0.0138
72	72	0.364
73	73	0.0203
74	74	0.358
75	75	0.126
76	76	0.775
77	77	0.281
78	78	0.0162
79	79	0.59
8	8	0.161
80	80	0.704
81	81	0.515
82	82	0.102
83	83	0.155
84	84	0.844
85	85	0.143
86	86	0.259
87	87	0.256
88	88	0.306
89	89	0.378
9	9	0.288
90	90	0.106
91	91	0.25
92	92	0.322
93	93	0.0112
94	94	0.752
95	95	0.0598
96	96	0.292
97	97	0.886
98	98	0.82
99	99	0.36

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: CNhs12360

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000209 mouse striatal neuron 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)
0000540 (neuron)
0000055 (non-terminally differentiated cell)
0000047 (neuronal stem cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000034 (stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002319 (neural cell)
0000221 (ectodermal cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000031 (neuroblast)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002613 (striatum neuron)
0000133 (neurectodermal cell)
0000337 (neuroblast (sensu Vertebrata))

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000955 (brain)
0000483 (epithelium)
0000369 (corpus striatum)
0002435 (striatum)
0000033 (head)
0000479 (tissue)
0002346 (neurectoderm)
0000064 (organ part)
0000073 (regional part of nervous system)
0004121 (ectoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000025 (tube)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0002020 (gray matter)
0002791 (regional part of telencephalon)
0003528 (brain grey matter)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0002616 (regional part of brain)
0001062 (anatomical entity)
0000119 (cell layer)
0005291 (embryonic tissue)
0002420 (basal ganglion)
0002780 (regional part of forebrain)
0007245 (nuclear complex of neuraxis)
0006598 (presumptive structure)
0002532 (epiblast (generic))
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0001893 (telencephalon)
0001890 (forebrain)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
0003075 (neural plate)
0003056 (pre-chordal neural plate)
0001049 (neural tube)
0006238 (future brain)
0000454 (cerebral subcortex)
0010082 (future corpus striatum)
0006601 (presumptive ectoderm)
0005068 (neural rod)
0006241 (future spinal cord)
0003080 (anterior neural tube)
0006240 (future forebrain)
0007284 (presumptive neural plate)
0007135 (neural keel)

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 36: / Line 36: @@
 |has_quality=
 |id=FF:11741-123F4
-|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000209
+|is_a=EFO:0002091;;FF:0000209
+|is_obsolete=
 |name=Mouse Neurons - striatal, donor2
 |namespace=FANTOM5
@@ Line 76: / Line 77: @@
 |sample_tissue=corpus striatum
 |top_motifs=LHX3,4:2.6557195051;TFDP1:2.36653233495;SOX2:2.34314178733;OCT4_SOX2{dimer}:2.31981795804;ALX1:2.28665150014;POU6F1:2.24658914749;ZFP161:2.24270598772;PAX6:2.21693126402;BREu{core}:2.20491835792;MED-1{core}:2.19633814711;ZIC1..3:2.11971984474;MZF1:2.08102670277;ZBTB6:1.98160428535;ADNP_IRX_SIX_ZHX:1.97955174479;UFEwm:1.97558087543;AHR_ARNT_ARNT2:1.95985531658;MTE{core}:1.94748670176;NKX6-1,2:1.94312547146;VSX1,2:1.90941149075;NRF1:1.8252023024;REST:1.78331287892;RFX1:1.75913213091;RREB1:1.74308478628;FOXQ1:1.73064759464;PRRX1,2:1.69400877659;PRDM1:1.67322899084;SOX{8,9,10}:1.66735023588;EGR1..3:1.66447245613;TFAP2B:1.63501140652;HIC1:1.62673799748;ONECUT1,2:1.61720010531;KLF4:1.61451765231;ZNF423:1.60536940983;LEF1_TCF7_TCF7L1,2:1.55779194303;FOXD3:1.51699867589;HMX1:1.46610433787;PATZ1:1.44383159225;POU3F1..4:1.39714539913;RFX2..5_RFXANK_RFXAP:1.39491230372;LMO2:1.34278859205;FOXM1:1.3169938444;DBP:1.28922604236;SOX17:1.27542183456;ZNF143:1.20876527395;NANOG:1.15809495594;YY1:1.15010130101;NFE2L1:1.12636748289;ATF2:1.09683568382;GTF2I:1.0710193664;NKX3-2:1.03784638762;HOXA9_MEIS1:0.98464246584;EN1,2:0.946304021829;NHLH1,2:0.943400724833;POU5F1:0.917659614526;SMAD1..7,9:0.913546498729;NR5A1,2:0.901080886149;TBX4,5:0.874801037937;JUN:0.866735286957;HOX{A5,B5}:0.789284209857;ELK1,4_GABP{A,B1}:0.786570576921;PAX5:0.785215058043;MTF1:0.77931185375;FOXL1:0.776665900144;GFI1B:0.776537534565;NANOG{mouse}:0.764394426138;MYFfamily:0.735749779343;EP300:0.721454657828;CDX1,2,4:0.69208037508;PAX8:0.665681372431;GATA4:0.66440506004;HES1:0.662814360484;POU2F1..3:0.662583604227;MAZ:0.651685411961;FOX{I1,J2}:0.63334807204;HOX{A4,D4}:0.621932369953;RBPJ:0.571271863131;TGIF1:0.567112064028;NKX2-3_NKX2-5:0.557622611695;CREB1:0.54822055058;RORA:0.520418811489;ATF5_CREB3:0.498982700792;CDC5L:0.494025979747;PAX4:0.466440706712;T:0.446440372012;RXR{A,B,G}:0.440200365841;CUX2:0.420360320094;HAND1,2:0.416193286892;HMGA1,2:0.403407146881;NKX2-1,4:0.397019234743;NKX3-1:0.369647962824;ZNF384:0.352232324651;SOX5:0.335621998472;MAFB:0.321204991369;HBP1_HMGB_SSRP1_UBTF:0.320961610757;PAX1,9:0.317042714577;EVI1:0.299765648323;GZF1:0.256263360458;FOXP3:0.245457718937;BPTF:0.243873813757;ARID5B:0.238501796572;NR3C1:0.228170936716;NFIX:0.227609059318;CRX:0.186576963924;STAT1,3:0.181879175529;NFY{A,B,C}:0.179286604449;PPARG:0.118849896132;PAX2:0.0492432414238;FOX{F1,F2,J1}:0.0201715494362;STAT5{A,B}:-0.00804064319542;IKZF2:-0.0253943297929;HSF1,2:-0.0382156136839;TFAP2{A,C}:-0.0519516492803;HIF1A:-0.0543056185779;ESR1:-0.0688154144015;TFAP4:-0.0818081847269;SP1:-0.12695336315;ZBTB16:-0.137923083085;GLI1..3:-0.160697980159;MYOD1:-0.163501060065;ZEB1:-0.205420030242;GTF2A1,2:-0.213343594403;ATF4:-0.213688522417;FOXN1:-0.243931748915;MYB:-0.248531920205;NFIL3:-0.30376250236;POU1F1:-0.331620143548;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.351048182954;AIRE:-0.360055140063;TAL1_TCF{3,4,12}:-0.372425490947;GCM1,2:-0.372966406991;SREBF1,2:-0.384411527645;PBX1:-0.394904805986;SNAI1..3:-0.404322622943;XCPE1{core}:-0.414320156464;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.44027582354;TEF:-0.444638225265;RUNX1..3:-0.467958480539;SPZ1:-0.468676439919;SPI1:-0.469216443242;IKZF1:-0.51355044102;bHLH_family:-0.541140065677;HNF4A_NR2F1,2:-0.556793286648;EBF1:-0.56236492292;TOPORS:-0.572891735325;FOXP1:-0.637021855334;ALX4:-0.654899876011;ESRRA:-0.656499721542;ATF6:-0.658748844044;TLX1..3_NFIC{dimer}:-0.66534271474;GFI1:-0.680737594257;TP53:-0.69223714451;MEF2{A,B,C,D}:-0.703680403078;NR1H4:-0.706404317406;GATA6:-0.711484759273;ZNF148:-0.719948193643;PITX1..3:-0.72251931732;HNF1A:-0.737242870848;NFKB1_REL_RELA:-0.751305071937;FOXA2:-0.765682679104;TLX2:-0.802449915312;SPIB:-0.838217044525;E2F1..5:-0.895706679998;CEBPA,B_DDIT3:-0.898036165065;ELF1,2,4:-0.943024624748;TBP:-0.95755303932;HLF:-0.976367990419;ZNF238:-1.04287366058;NFE2:-1.05788419169;AR:-1.10772324263;TFCP2:-1.10817790802;BACH2:-1.1700341839;NFE2L2:-1.18681871742;ETS1,2:-1.2100131367;TEAD1:-1.216812388;NKX2-2,8:-1.22804250323;MYBL2:-1.30644322749;FOSL2:-1.31732949305;RXRA_VDR{dimer}:-1.33001052;NFATC1..3:-1.39109463298;DMAP1_NCOR{1,2}_SMARC:-1.40317752259;FOS_FOS{B,L1}_JUN{B,D}:-1.42081195866;FOXO1,3,4:-1.55540709946;IRF7:-1.60161260325;PDX1:-1.65436891945;SRF:-1.67955310391;FOX{D1,D2}:-1.70334115224;IRF1,2:-1.74315306237;STAT2,4,6:-1.86883158162;NR6A1:-1.91763819772
+|xref=
 }}

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Revision as of 13:37, 27 June 2012

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