multiple filters in biomaRt
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Entering edit mode
Yijing • 0
@d0a8eb95
Last seen 7 months ago
Germany

Hello,

I try to follow biomaRt tutorial to Retrieve all HUGO gene symbols of genes that are located on chromosomes 17,20 or Y, and are associated with specific GO terms.

getBM(attributes = c('hgnc_symbol', 'chromosome_name'),
      filters = c('go', 'chromosome_name'),
      values = list(go, chrom),
      mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl"))

I only got three results:

hgnc_symbol chromosome_name
1        E2F1              20
2     RPS6KB1              17
3        CDK3              17

But if I want to add go_id into the attributes, then I got many results:

getBM(attributes = c('go_id', 'hgnc_symbol', 'chromosome_name'),
      filters = c('go', 'chromosome_name'),
      values = list(go, chrom),
      mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl"))

Results:

    go_id hgnc_symbol chromosome_name
1   GO:0006355        E2F1              20
2   GO:0006357        E2F1              20
3   GO:0005667        E2F1              20
4   GO:0046983        E2F1              20
5   GO:0000978        E2F1              20
6   GO:0005515        E2F1              20
7   GO:0010628        E2F1              20
8   GO:0005634        E2F1              20
9   GO:0032991        E2F1              20
10  GO:0007049        E2F1              20
11  GO:0005654        E2F1              20
12  GO:0003677        E2F1              20
13  GO:0006915        E2F1              20
14  GO:0003700        E2F1              20
15  GO:0005813        E2F1              20
16  GO:0043565        E2F1              20
17  GO:0006351        E2F1              20
18  GO:0045944        E2F1              20
19  GO:0000981        E2F1              20
20  GO:0045893        E2F1              20
21  GO:0000785        E2F1              20
22  GO:0000077        E2F1              20
23  GO:0000987        E2F1              20
24  GO:1990837        E2F1              20
25  GO:0090575        E2F1              20
26  GO:0043065        E2F1              20
27  GO:0045892        E2F1              20
28  GO:0000122        E2F1              20
29  GO:0060090        E2F1              20
30  GO:0045599        E2F1              20
31  GO:0001216        E2F1              20
32  GO:0070345        E2F1              20
33  GO:0000082        E2F1              20
34  GO:0140297        E2F1              20
35  GO:0008630        E2F1              20
36  GO:0048146        E2F1              20
37  GO:0043392        E2F1              20
38  GO:0043433        E2F1              20
39  GO:0071930        E2F1              20
40  GO:0035189        E2F1              20
41  GO:2000045        E2F1              20
42  GO:0048255        E2F1              20
43  GO:0000976        E2F1              20
44  GO:0019901        E2F1              20
45  GO:0000083        E2F1              20
46  GO:0007283        E2F1              20
47  GO:0030900        E2F1              20
48  GO:0043276        E2F1              20
49  GO:0051726        E2F1              20
50  GO:0060252        E2F1              20
51  GO:0071398        E2F1              20
52  GO:0071456        E2F1              20
53  GO:0071466        E2F1              20
54  GO:0072332        E2F1              20
55  GO:1990086        E2F1              20
56  GO:1990090        E2F1              20
57  GO:0000228        E2F1              20
58  GO:0005737        E2F1              20
59  GO:0005524     RPS6KB1              17
60  GO:0007165     RPS6KB1              17
61  GO:0006468     RPS6KB1              17
62  GO:0004674     RPS6KB1              17
63  GO:0004672     RPS6KB1              17
64  GO:0005634     RPS6KB1              17
65  GO:0005737     RPS6KB1              17
66  GO:0016020     RPS6KB1              17
67  GO:0000166     RPS6KB1              17
68  GO:0016301     RPS6KB1              17
69  GO:0016740     RPS6KB1              17
70  GO:0007049     RPS6KB1              17
71  GO:0016310     RPS6KB1              17
72  GO:0043066     RPS6KB1              17
73  GO:0005654     RPS6KB1              17
74  GO:0005739     RPS6KB1              17
75  GO:0006915     RPS6KB1              17
76  GO:0005741     RPS6KB1              17
77  GO:0006417     RPS6KB1              17
78  GO:0005515     RPS6KB1              17
79  GO:0043005     RPS6KB1              17
80  GO:0045202     RPS6KB1              17
81  GO:0106310     RPS6KB1              17
82  GO:0018105     RPS6KB1              17
83  GO:0048015     RPS6KB1              17
84  GO:0031929     RPS6KB1              17
85  GO:0005829     RPS6KB1              17
86  GO:0004712     RPS6KB1              17
87  GO:0045727     RPS6KB1              17
88  GO:0045948     RPS6KB1              17
89  GO:0000082     RPS6KB1              17
90  GO:0045931     RPS6KB1              17
91  GO:0044539     RPS6KB1              17
92  GO:0032869     RPS6KB1              17
93  GO:0046627     RPS6KB1              17
94  GO:0071363     RPS6KB1              17
95  GO:0031667     RPS6KB1              17
96  GO:0004711     RPS6KB1              17
97  GO:0030165     RPS6KB1              17
98  GO:0042277     RPS6KB1              17
99  GO:0042802     RPS6KB1              17
100 GO:0051721     RPS6KB1              17
101 GO:0001662     RPS6KB1              17
102 GO:0003009     RPS6KB1              17
103 GO:0007281     RPS6KB1              17
104 GO:0007568     RPS6KB1              17
105 GO:0007584     RPS6KB1              17
106 GO:0007616     RPS6KB1              17
107 GO:0009408     RPS6KB1              17
108 GO:0009410     RPS6KB1              17
109 GO:0009611     RPS6KB1              17
110 GO:0009612     RPS6KB1              17
111 GO:0009636     RPS6KB1              17
112 GO:0009749     RPS6KB1              17
113 GO:0010033     RPS6KB1              17
114 GO:0010243     RPS6KB1              17
115 GO:0014070     RPS6KB1              17
116 GO:0014732     RPS6KB1              17
117 GO:0014878     RPS6KB1              17
118 GO:0014911     RPS6KB1              17
119 GO:0016477     RPS6KB1              17
120 GO:0032496     RPS6KB1              17
121 GO:0032868     RPS6KB1              17
122 GO:0032870     RPS6KB1              17
123 GO:0033574     RPS6KB1              17
124 GO:0033762     RPS6KB1              17
125 GO:0034612     RPS6KB1              17
126 GO:0043200     RPS6KB1              17
127 GO:0043201     RPS6KB1              17
128 GO:0043434     RPS6KB1              17
129 GO:0043491     RPS6KB1              17
130 GO:0045471     RPS6KB1              17
131 GO:0046324     RPS6KB1              17
132 GO:0048633     RPS6KB1              17
133 GO:0048661     RPS6KB1              17
134 GO:0050804     RPS6KB1              17
135 GO:0051384     RPS6KB1              17
136 GO:0071346     RPS6KB1              17
137 GO:0071407     RPS6KB1              17
138 GO:0071549     RPS6KB1              17
139 GO:2001237     RPS6KB1              17
140 GO:0009986     RPS6KB1              17
141 GO:0048471     RPS6KB1              17
142 GO:0098794     RPS6KB1              17
143 GO:0098978     RPS6KB1              17
144 GO:0005524        CDK3              17
145 GO:0006468        CDK3              17
146 GO:0004672        CDK3              17
147 GO:0000166        CDK3              17
148 GO:0004674        CDK3              17
149 GO:0016301        CDK3              17
150 GO:0016740        CDK3              17
151 GO:0007049        CDK3              17
152 GO:0016310        CDK3              17
153 GO:0051301        CDK3              17
154 GO:0005515        CDK3              17
155 GO:0106310        CDK3              17
156 GO:0051726        CDK3              17
157 GO:0005634        CDK3              17
158 GO:0004693        CDK3              17
159 GO:0000082        CDK3              17
160 GO:0006974        CDK3              17
161 GO:0008283        CDK3              17
162 GO:0000307        CDK3              17
163 GO:0045023        CDK3              17
164 GO:0045746        CDK3              17

Is it due to that one gene is related to several GO ID?

Besides, there is no Y chromosome result. Not sure if it is indeed no gene in Y or I missed something.

Thank you!

biomaRt • 849 views
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0
Entering edit mode
RuBBiT0 ▴ 10
@7fec931f
Last seen 7 months ago
United States

First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use.

Second, could you provide more context about the variable go and chrom? Maybe you want to make sure that chrom contains 17, 20, and Y. I believe this annotation has information about the genes that have GO terms associated and are on Y chromosome, and it is named as 'Y'. I double-checked this through the code below:

getBM(attributes = c('chromosome_name'),
      filters = c('with_go'),
      values = T,
      mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl"))

It outputs a long list of the names of chromosomes including Y.

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