Circos plot has been widely used to display genomic element interactions along with annotations. In RISE database we also visualise RNA-RNA interactions in this format.
Here is how we retrieve data from mysql database, process the data into specific format and plot with Circos tool.
login to mysql and check the database information:
[zhangqf5@loginview02 bin]$ ./mysql -h bio04 -uzhangqf5
Warning: Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 1
Server version: 5.6.34-log MySQL Community Server (GPL)
Copyright (c) 2000, 2016, Oracle and/or its affiliates. All rights reserved.
Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
list available databases:
mysql> show DATABASES;
+--------------------+
| Database |
+--------------------+
| information_schema |
| RISE |
| test |
+--------------------+
3 rows in set (0.24 sec)
use RISE database and list tables:
mysql> use RISE;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
mysql> show tables;
+-----------------------------------------+
| Tables_in_RISE |
+-----------------------------------------+
| auth_group |
| auth_group_permissions |
| auth_permission |
| auth_user |
| auth_user_groups |
| auth_user_user_permissions |
| biomart_hg38 |
| biomart_hg38_mm10_longest |
| biomart_hg38_mm10_longest_chr |
| biomart_mm10 |
| conservation |
| datas_conservation |
| datas_rri |
| django_admin_log |
| django_content_type |
| django_migrations |
| django_session |
| expressionaltasCellLine_mouse |
| gencode_biomart_hg38_mm10_yeast |
| gencode_biomart_hg38_mm10_yeast_repeats |
| gencode_hg38_mm10 |
| human_DARNED |
| human_RADAR |
| human_RMBaseNm |
| human_RMBaseOthers |
| human_RMBasePseudoU |
| human_RMBasem5C |
| human_RMBasem6A |
| human_clipdb |
| human_editing |
| human_modification |
| human_pancan |
| human_ucscSnp142 |
| mouse_clipdb |
| mouse_editing |
| mouse_modification |
| mouse_ucscSnp142 |
| proteinaltasCellLine_human |
| rri |
| rri_bk |
+-----------------------------------------+
40 rows in set (0.00 sec)
columns of specific tables:
mysql> describe rri;
+-----------------------------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-----------------------------+-------------+------+-----+---------+-------+
| index | bigint(20) | YES | MUL | NULL | |
| chr1 | varchar(10) | YES | | NULL | |
| start1 | varchar(10) | YES | | NULL | |
| end1 | varchar(10) | YES | | NULL | |
| chr2 | varchar(10) | YES | | NULL | |
| start2 | varchar(10) | YES | | NULL | |
| end2 | varchar(10) | YES | | NULL | |
| rise_id | varchar(13) | YES | | NULL | |
| score | varchar(15) | YES | | NULL | |
| strand1 | varchar(1) | YES | | NULL | |
| strand2 | varchar(1) | YES | | NULL | |
| ensembl_gene_id1 | varchar(40) | YES | | NULL | |
| ensembl_gene_name1 | varchar(40) | YES | | NULL | |
| ensembl_gene_id2 | varchar(40) | YES | | NULL | |
| ensembl_gene_name2 | varchar(40) | YES | | NULL | |
| ensembl_gene_type1 | varchar(50) | YES | | NULL | |
| ensembl_gene_type2 | varchar(50) | YES | | NULL | |
| ensembl_gene_abstract_type1 | varchar(20) | YES | | NULL | |
| ensembl_gene_abstract_type2 | varchar(20) | YES | | NULL | |
| method | varchar(15) | YES | | NULL | |
| species | varchar(20) | YES | | NULL | |
| cell_line | varchar(20) | YES | | NULL | |
| cell_line2 | varchar(20) | YES | | NULL | |
| pubmed_id | text | YES | | NULL | |
| reference | text | YES | | NULL | |
| pos1 | varchar(25) | YES | | NULL | |
| pos2 | varchar(25) | YES | | NULL | |
| chr1_fill | varchar(10) | YES | | NULL | |
| start1_fill | varchar(10) | YES | | NULL | |
| end1_fill | varchar(10) | YES | | NULL | |
| chr2_fill | varchar(10) | YES | | NULL | |
| start2_fill | varchar(10) | YES | | NULL | |
| end2_fill | varchar(10) | YES | | NULL | |
| genomic_context1 | varchar(10) | YES | | NULL | |
| genomic_context2 | varchar(10) | YES | | NULL | |
| pos1_phastCons | varchar(15) | YES | | NULL | |
| pos1_phyloP | varchar(15) | YES | | NULL | |
| pos2_phastCons | varchar(15) | YES | | NULL | |
| pos2_phyloP | varchar(15) | YES | | NULL | |
+-----------------------------+-------------+------+-----+---------+-------+
39 rows in set (0.06 sec)
mysql> describe gencode_biomart_hg38_mm10_yeast_repeats;
+------------------+------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+------------------+------------+------+-----+---------+-------+
| index | bigint(20) | YES | MUL | NULL | |
| gene_id | text | YES | | NULL | |
| gene_name | text | YES | | NULL | |
| gene_start | bigint(20) | YES | | NULL | |
| gene_end | bigint(20) | YES | | NULL | |
| gene_type | text | YES | | NULL | |
| tx_id | text | YES | | NULL | |
| tx_start | bigint(20) | YES | | NULL | |
| tx_end | bigint(20) | YES | | NULL | |
| tx_type | text | YES | | NULL | |
| tx_abstract_type | text | YES | | NULL | |
| sequence_type | text | YES | | NULL | |
| chr | text | YES | | NULL | |
| start | bigint(20) | YES | | NULL | |
| end | bigint(20) | YES | | NULL | |
+------------------+------------+------+-----+---------+-------+
15 rows in set (0.01 sec)
run script RISE_circos_plot.py to generate the circos plot:
/Share/home/zhangqf/usr/anaconda/bin/python RISE_circos_plot.py
output files
[zhangqf5@loginview02 duplex_test]$ lt
total 11K
-rw-rw---- 1 zhangqf5 zhangqf 394K May 16 21:26 ENSG00000100320.convert.png
-rw-rw---- 1 zhangqf5 zhangqf 133K May 16 21:26 ENSG00000100320.convert.resize.html
-rw-rw---- 1 zhangqf5 zhangqf 135K May 16 21:26 ENSG00000100320.convert.svg
-rw-rw---- 1 zhangqf5 zhangqf 369K May 16 21:26 ENSG00000100320.log
-rw-rw---- 1 zhangqf5 zhangqf 258K May 16 21:26 ENSG00000100320.convert.html
-rw-rw---- 1 zhangqf5 zhangqf 42K May 16 21:26 ENSG00000100320.anno.convert
-rw-rw---- 1 zhangqf5 zhangqf 37K May 16 21:26 ENSG00000100320.genestructure.convert
-rw-rw---- 1 zhangqf5 zhangqf 17K May 16 21:26 ENSG00000100320.link.convert
-rw-rw---- 1 zhangqf5 zhangqf 5.3K May 16 21:26 ENSG00000100320.linkgenes.convert
-rw-rw---- 1 zhangqf5 zhangqf 2.8K May 16 21:26 ENSG00000100320.linkgenes.txt.convert
-rw-rw---- 1 zhangqf5 zhangqf 349K May 16 21:26 ENSG00000100320.png
-rw-rw---- 1 zhangqf5 zhangqf 135K May 16 21:26 ENSG00000100320.svg
-rw-rw---- 1 zhangqf5 zhangqf 232K May 16 21:26 ENSG00000100320.html
-rw-rw---- 1 zhangqf5 zhangqf 42K May 16 21:26 ENSG00000100320.anno
-rw-rw---- 1 zhangqf5 zhangqf 37K May 16 21:26 ENSG00000100320.genestructure
-rw-rw---- 1 zhangqf5 zhangqf 22K May 16 21:26 ENSG00000100320.genestructure.introns
-rw-rw---- 1 zhangqf5 zhangqf 19K May 16 21:26 ENSG00000100320.genestructure.introns.txt
-rw-rw---- 1 zhangqf5 zhangqf 17K May 16 21:26 ENSG00000100320.link
-rw-rw---- 1 zhangqf5 zhangqf 5.3K May 16 21:26 ENSG00000100320.linkgenes
-rw-rw---- 1 zhangqf5 zhangqf 2.8K May 16 21:26 ENSG00000100320.linkgenes.txt
-rw-rw---- 1 zhangqf5 zhangqf 1.9K May 16 21:26 ENSG00000100320.linkgenes.zooms
-rw-rw---- 1 zhangqf5 zhangqf 2.1K May 16 21:26 ENSG00000100320.linkgenes.zooms2
Note:
ENSG00000100320.convert.png/svg is the final plot correspond to the figure above or in the database for RNA RBFOX2
track files (before log2 transformed): desired file formats are here ENSG00000100320(RBFOX2) as an example
file gene structure:
[zhangqf5@loginview02 duplex_test]$ head -5 ENSG00000100320.genestructure
hs9 94175952 94176043 gene_id=ENSG00000199165,gene_name=MIRLET7A1,gene_type=miRNA,tx_id=ENST00000362295,sequence_type=Exon,id=ENSG00000199165|MIRLET7A1|94175952|94176043|miRNA|ENST00000362295|94175952|94176043|miRNA|miRNA|Exon|9|94175952|94176043
hs10 133246478 133247050 gene_id=ENSG00000166917,gene_name=MIR202HG,gene_type=ncRNA,tx_id=ENST00000553459,sequence_type=Exon,id=ENSG00000166917|MIR202HG|133246478|133247891|antisense|ENST00000553459|133246478|133247891|antisense|ncRNA|Exon|10|133246478|133247050
hs10 133247791 133247891 gene_id=ENSG00000166917,gene_name=MIR202HG,gene_type=ncRNA,tx_id=ENST00000553459,sequence_type=Exon,id=ENSG00000166917|MIR202HG|133246478|133247891|antisense|ENST00000553459|133246478|133247891|antisense|ncRNA|Exon|10|133247791|133247891
hs17 77319515 77320326 gene_id=ENSG00000184640,gene_name=SEPT9,gene_type=protein_coding,tx_id=ENST00000329047,sequence_type=5UTR,id=ENSG00000184640|SEPT9|77280569|77500596|protein_coding|ENST00000329047|77319515|77500592|protein_coding|protein_coding|5UTR|17|77319515|77320326
hs17 77498656 77500592 gene_id=ENSG00000184640,gene_name=SEPT9,gene_type=protein_coding,tx_id=ENST00000329047,sequence_type=3UTR,id=ENSG00000184640|SEPT9|77280569|77500596|protein_coding|ENST00000329047|77319515|77500592|protein_coding|protein_coding|3UTR|17|77498656|77500592
file annotations:
[zhangqf5@loginview02 duplex_test]$ head -5 ENSG00000100320.anno
hs22 35744177 35744178 1 anno_category=modification,anno_source=RMBase,anno_type=m6A,anno_gene_info=chr22|35744164|35744204|RISE0255307_2|2|-|ENSG00000100320|RBFOX2|protein_coding|protein_coding,anno_full=chr22|35744177|35744178|m6A_site_86471|0|-|m6A_site_86471|m6A|1|GSE60213|25799998|RBFOX2&RBFOX2|retained_intron&protein_coding|exon&utr3|GTGAGACCCCTGCAAATGGGACAGCCCCCCAGTTCATGAGG|modification|RMBase|https://www.ncbi.nlm.nih.gov/pubmed/25799998|ENSG00000100320|ENST00000405409|3UTR|1,id=chr22|35744164|35744204|RISE0255307_2|2|-|ENSG00000100320|RBFOX2|protein_coding|protein_coding|chr22|35744177|35744178|m6A_site_86471|0|-|m6A_site_86471|m6A|1|GSE60213|25799998|RBFOX2&RBFOX2|retained_intron&protein_coding|exon&utr3|GTGAGACCCCTGCAAATGGGACAGCCCCCCAGTTCATGAGG|modification|RMBase|https://www.ncbi.nlm.nih.gov/pubmed/25799998|ENSG00000100320|ENST00000405409|3UTR|1
hs22 35744192 35744193 1 anno_category=modification,anno_source=RMBase,anno_type=m6A,anno_gene_info=chr22|35744164|35744204|RISE0255307_2|2|-|ENSG00000100320|RBFOX2|protein_coding|protein_coding,anno_full=chr22|35744192|35744193|m6A_site_86472|0|-|m6A_site_86472|m6A|1|GSE60213|25799998|RBFOX2&RBFOX2|retained_intron&protein_coding|exon&utr3|CCCTACTGAAGTGACGTGAGACCCCTGCAAATGGGACAGCC|modification|RMBase|https://www.ncbi.nlm.nih.gov/pubmed/25799998|ENSG00000100320|ENST00000405409|3UTR|1,id=chr22|35744164|35744204|RISE0255307_2|2|-|ENSG00000100320|RBFOX2|protein_coding|protein_coding|chr22|35744192|35744193|m6A_site_86472|0|-|m6A_site_86472|m6A|1|GSE60213|25799998|RBFOX2&RBFOX2|retained_intron&protein_coding|exon&utr3|CCCTACTGAAGTGACGTGAGACCCCTGCAAATGGGACAGCC|modification|RMBase|https://www.ncbi.nlm.nih.gov/pubmed/25799998|ENSG00000100320|ENST00000405409|3UTR|1
hs5 6668743 6668744 1 anno_category=RBP,anno_source=CLIPDB,anno_type=RBP,anno_gene_info=chr5|6668720|6668754|RISE0224410_1|2|+|ENSG00000145545|SRD5A1|protein_coding|protein_coding,anno_full=chr5|6668743|6668744|human_RBP_CLIPdb_iCLIP_CIMS_2234997|0|+|PTBP1|iCLIP&CIMS|HEK293T|GSE57278&GSM1378377|9|25219497|https://www.ncbi.nlm.nih.gov/pubmed/25219497|ENSG00000145545|ENST00000510531|3UTR|1|iCLIP|CIMS|human,id=chr5|6668720|6668754|RISE0224410_1|2|+|ENSG00000145545|SRD5A1|protein_coding|protein_coding|chr5|6668743|6668744|human_RBP_CLIPdb_iCLIP_CIMS_2234997|0|+|PTBP1|iCLIP&CIMS|HEK293T|GSE57278&GSM1378377|9|25219497|https://www.ncbi.nlm.nih.gov/pubmed/25219497|ENSG00000145545|ENST00000510531|3UTR|1|iCLIP|CIMS|human
hs5 6668704 6668725 1 anno_category=RBP,anno_source=CLIPDB,anno_type=RBP,anno_gene_info=chr5|6668720|6668754|RISE0224410_1|2|+|ENSG00000145545|SRD5A1|protein_coding|protein_coding,anno_full=chr5|6668704|6668725|human_RBP_CLIPdb_iCLIP_CIMS_4297059|0|+|TARDBP|iCLIP&CIMS|Brain|E-MTAB-530&ERR039849|4|21358640|https://www.ncbi.nlm.nih.gov/pubmed/21358640|ENSG00000145545|ENST00000510531|3UTR|5|iCLIP|CIMS|human,id=chr5|6668720|6668754|RISE0224410_1|2|+|ENSG00000145545|SRD5A1|protein_coding|protein_coding|chr5|6668704|6668725|human_RBP_CLIPdb_iCLIP_CIMS_4297059|0|+|TARDBP|iCLIP&CIMS|Brain|E-MTAB-530&ERR039849|4|21358640|https://www.ncbi.nlm.nih.gov/pubmed/21358640|ENSG00000145545|ENST00000510531|3UTR|5|iCLIP|CIMS|human
hs5 6668749 6668770 1 anno_category=RBP,anno_source=CLIPDB,anno_type=RBP,anno_gene_info=chr5|6668720|6668754|RISE0224410_1|2|+|ENSG00000145545|SRD5A1|protein_coding|protein_coding,anno_full=chr5|6668749|6668770|human_RBP_CLIPdb_iCLIP_CIMS_4435494|0|+|TIAL1|iCLIP&CIMS|HeLa|E-MTAB-432&ERR039780-ERR039783-ERR039784-ERR039785|7|21048981|https://www.ncbi.nlm.nih.gov/pubmed/21048981|ENSG00000145545|ENST00000510531|3UTR|5|iCLIP|CIMS|human,id=chr5|6668720|6668754|RISE0224410_1|2|+|ENSG00000145545|SRD5A1|protein_coding|protein_coding|chr5|6668749|6668770|human_RBP_CLIPdb_iCLIP_CIMS_4435494|0|+|TIAL1|iCLIP&CIMS|HeLa|E-MTAB-432&ERR039780-ERR039783-ERR039784-ERR039785|7|21048981|https://www.ncbi.nlm.nih.gov/pubmed/21048981|ENSG00000145545|ENST00000510531|3UTR|5|iCLIP|CIMS|human
file links (RRI):
[zhangqf5@loginview02 duplex_test]$ head -5 ENSG00000100320.link
hs5 6668720 6668754 hs22 35740046 35740082 category=GlobalAnalysis,method=PARIS,duplex=derived,gene_id1=ENSG00000145545,gene_name1=SRD5A1,gene_type1=protein_coding,gene_id2=ENSG00000100320,gene_name2=RBFOX2,gene_type2=protein_coding,id=chr5|6668720|6668754|chr22|35740046|35740082|RISE0224410|2|+|-|ENSG00000145545|SRD5A1|ENSG00000100320|RBFOX2|protein_coding|protein_coding|protein_coding|protein_coding|PARIS|human|Hela(highRNase)|Hela|27180905|https://www.ncbi.nlm.nih.gov/pubmed/27180905|chr5:6668720-6668754|chr22:35740046-35740082|chr5|6668720|6668754|chr22|35740046|35740082|3UTR|3UTR|0.000441176|-0.350088|0.0715833|0.0108889
hs22 35742350 35742375 hs17 41866974 41867001 category=GlobalAnalysis,method=PARIS,duplex=derived,gene_id1=ENSG00000100320,gene_name1=RBFOX2,gene_type1=protein_coding,gene_id2=ENSG00000131473,gene_name2=ACLY,gene_type2=protein_coding,id=chr22|35742350|35742375|chr17|41866974|41867001|RISE0233924|2|-|-|ENSG00000100320|RBFOX2|ENSG00000131473|ACLY|protein_coding|protein_coding|protein_coding|protein_coding|PARIS|human|Hela(highRNase)|Hela|27180905|https://www.ncbi.nlm.nih.gov/pubmed/27180905|chr22:35742350-35742375|chr17:41866974-41867001|chr22|35742350|35742375|chr17|41866974|41867001|3UTR|3UTR|0.2758|0.29404|0.733481|0.895222
hs22 35741848 35741867 hs8 101129130 101129157 category=GlobalAnalysis,method=PARIS,duplex=derived,gene_id1=ENSG00000100320,gene_name1=RBFOX2,gene_type1=protein_coding,gene_id2=ENSG00000253355,gene_name2=KB-1460A1,gene_type2=ncRNA,id=chr22|35741848|35741867|chr8|101129130|101129157|RISE0233925|2|-|+|ENSG00000100320|RBFOX2|ENSG00000253355|KB-1460A1|protein_coding|processed_transcript|protein_coding|ncRNA|PARIS|human|Hela(highRNase)|Hela|27180905|https://www.ncbi.nlm.nih.gov/pubmed/27180905|chr22:35741848-35741867|chr8:101129130-101129157|chr22|35741848|35741867|chr8|101129130|101129157|3UTR|Exon|0.000315789|-0.186737|0.0836296|0.0691481
hs22 35741792 35741815 hs6 123471015 123471034 category=GlobalAnalysis,method=PARIS,duplex=derived,gene_id1=ENSG00000100320,gene_name1=RBFOX2,gene_type1=protein_coding,gene_id2=ENSG00000235535,gene_name2=RP11-532N4,gene_type2=ncRNA,id=chr22|35741792|35741815|chr6|123471015|123471034|RISE0233926|2|-|+|ENSG00000100320|RBFOX2|ENSG00000235535|RP11-532N4|protein_coding|antisense|protein_coding|ncRNA|PARIS|human|Hela(highRNase)|Hela|27180905|https://www.ncbi.nlm.nih.gov/pubmed/27180905|chr22:35741792-35741815|chr6:123471015-123471034|chr22|35741792|35741815|chr6|123471015|123471034|3UTR|Exon|0.00156522|0.232348|0.0652632|0.296211
hs22 35740318 35740336 hs2 97735297 97735318 category=GlobalAnalysis,method=PARIS,duplex=derived,gene_id1=ENSG00000100320,gene_name1=RBFOX2,gene_type1=protein_coding,gene_id2=ENSG00000115085,gene_name2=ZAP70,gene_type2=protein_coding,id=chr22|35740318|35740336|chr2|97735297|97735318|RISE0233927|2|-|+|ENSG00000100320|RBFOX2|ENSG00000115085|ZAP70|protein_coding|protein_coding|protein_coding|protein_coding|PARIS|human|Hela(highRNase)|Hela|27180905|https://www.ncbi.nlm.nih.gov/pubmed/27180905|chr22:35740318-35740336|chr2:97735297-97735318|chr22|35740318|35740336|chr2|97735297|97735318|3UTR|CDS|0.895778|1.97189|0.903|4.62224
file link genes:
[zhangqf5@loginview02 duplex_test]$ head -5 ENSG00000100320.linkgenes
hs9 94175952 94176043 gene_id=ENSG00000199165,gene_name=MIRLET7A1,gene_type=miRNA,tx_id=ENST00000362295,id=ENSG00000199165|MIRLET7A1|94175952|94176043|miRNA|ENST00000362295|94175952|94176043|miRNA|miRNA|Exon|9|94175952|94176043
hs17 41866908 41918987 gene_id=ENSG00000131473,gene_name=ACLY,gene_type=protein_coding,tx_id=ENST00000352035,id=ENSG00000131473|ACLY|41866908|41930542|protein_coding|ENST00000352035|41866908|41918987|protein_coding|protein_coding|5UTR|17|41913874|41913896
hs10 133246478 133247891 gene_id=ENSG00000166917,gene_name=MIR202HG,gene_type=miRNA,tx_id=ENST00000553459,id=ENSG00000166917|MIR202HG|133246478|133247891|antisense|ENST00000553459|133246478|133247891|antisense|ncRNA|Exon|10|133246478|133247050
hs1 629640 630683 gene_id=ENSG00000225630,gene_name=MTND2P28,gene_type=pseudogene,tx_id=ENST00000457540,id=ENSG00000225630|MTND2P28|629640|630683|unprocessed_pseudogene|ENST00000457540|629640|630683|unprocessed_pseudogene|pseudogene|Exon|1|629640|630683
hsX 53556223 53556341 gene_id=ENSG00000271886,gene_name=MIR98,gene_type=miRNA,tx_id=ENST00000606724,id=ENSG00000271886|MIR98|53556223|53556341|miRNA|ENST00000606724|53556223|53556341|miRNA|miRNA|Exon|X|53556223|53556341
generated .conf file, which control the layout of whole plot, e.g., ENSG00000100320.conf
If you link this blog, please refer to this page, thanks!
Post link：https://tsinghua-gongjing.github.io/posts/RISE_circos_plot.html
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