Please cite our latest paper when using our TFmapper
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6216026/
- http://www.ijbs.com/v14p1724.htm
- http://www.tfmapper.org/
Jianming Zeng (PHD student in university of Macau) : jmzeng1314@163.com
First, make sure that the mysql client and server were installed successfully in your OS , and please remember the password for root user( the default user in mysql).
Then you can log in by mysql -u root -p
useful link ( once you forget the password ):
-
https://www.variphy.com/kb/mac-os-x-reset-mysql-root-password
-
https://stackoverflow.com/questions/6474775/setting-the-mysql-root-user-password-on-os-x
show databases;
create database tfmapperdb;
show databases;
CREATE USER tfmapperuser IDENTIFIED BY 'tfmapper_@Abc';
GRANT ALL PRIVILEGES ON tfmapperdb.* TO 'tfmapperuser'@'%' IDENTIFIED BY 'tfmapper_@Abc';
FLUSH PRIVILEGES;Now, you just need to use the tfmapperdb and tfmapperuser.
Firstly, we should download the information about genes in human and mouse from GENCODE
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz ## 38M
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz ## 25M
cat gencode.v29.annotation.gtf |perl -alne '{next unless $F[1] eq "HAVANA";next unless $F[2] eq "gene";/gene_id \"(.*?)\.\d+\"; gene_type \"(.*?)\"; gene_name \"(.*?)\"/;print "$3\t$2\t$1\t$F[0]\t$F[3]\t$F[4]"}' > gencode_v29_human_gene_info
cat gencode.vM20.annotation.gtf |perl -alne '{next unless $F[1] eq "HAVANA";next unless $F[2] eq "gene";/gene_id \"(.*?)\.\d+\"; gene_type \"(.*?)\"; gene_name \"(.*?)\"/;print "$3\t$2\t$1\t$F[0]\t$F[3]\t$F[4]"}' > gencode_vM20_mouse_gene_infoIt doesn't matter if you can't understand the perl scripts above, just check two files
Then we can upload these files into our datbase by R codes below:
library(RMySQL)
host <<- "127.0.0.1"
port <<- 3306
user <<- "tfmapperuser"
password <<- 'tfmapper_@Abc'
library(RMySQL)
con <- dbConnect(MySQL(), host=host, port=port, user=user, password=password)
sql="USE tfmapperdb;"
dbSendQuery(con, sql)
sql='show tables;'
dbGetQuery(con, sql)
options(stringsAsFactors = F)
# a simple example to upload one file into mysql .
a=read.table('files/gencode_v29_human_gene_info',sep = '\t')
head(a)
colnames(a)=c('symbol' , 'type' , 'ensembl' , 'chr' ,'start', 'end' )
dbWriteTable(con, 'gencode_v29_human_gene_info', a, append=F,row.names=F)
sql='show tables;'
dbGetQuery(con, sql) By this way, we should upload all the information for our web-tool into mysql.
Upload the txt files (I download those files from cistrome) in to cistrome_metadata:
TF_human_information.txt
TF_mouse_data_information.txt
ca_human_data_information.txt
ca_mouse_data_information.txt
histone_human_data_information.txt
histone_mouse_data_information.txt
other_human_data_information.txt
other_mouse_data_information.txt
Pay attention that the columns for this table:
sampleID GSM bs1 bs2 bs3 IP species type
gather all the GSM IDs and search the details by using GEOmetadb then upload them into cistrome_GSM_metadata Pay attention that the columns for this table:
[1] "ID" "title" "gsm"
[4] "series_id" "gpl" "status"
············
Upload the txt files (I download those files from ENCODE) in to encode_metadata:
human_TF_GRCh38.conservative.bed.list.txt
human_histone_GRCh38.replicated.peaks.bed.list.txt
mouse_TF_mm10.conservative.peaks.bed.list.txt
mouse_histone_mm10.replicated.peaks.bed.list.txt
Lastly, upload all the peaks annotation files to mysql ( extremely time consuming and really big size ), about 300 tables. (by chromosome, database,type,species)
You should read my codes from begin to end: upload_into_mysql.R
Please send me email to me to request those files ( about 100 Gb), you should read my paper to study the details for how to generate the files
We should create index for some tables in mysql to speed up the searching from user.
With the help of Xiaojie Sun, We create a beautiful ui framework, as below :
There are totally 4 pages in our tool, which are : home, statistics, more, help.
You can check the codes in UI
Please remember the IDs we create in UI page:
-
input values
- species(human or mouse )/IP(TF or histone)/database(cistrome or ENCODE)/cellline( too many )
- input_gene/genomic_feature
- position, such as '18:28176327,28178670'
-
output values
- DT::dataTableOutput('results')
- plotOutput('results_stat')
- DT::dataTableOutput('stat_table')
-
actionButton
-
do_gene
-
do_position/zoom_in/zoom_out
You can check the codes in server
check the codes in updateSelectizeInput
the gene choices depends on the species user choosed ( we should search all the genes from mysql)
the cellLine choices depends on the database and species and IP user choosed
check the codes in positions.R
Get the position of choosed gene according to GENCODE database. ( gencode_v29_human_gene_info and gencode_vM20_mouse_gene_info in mysql)
first the choosed gene will change the positon. Then zoom_in and zoom_out will also change the position.
Check the codes in search_by_gene.R
Once the user click the button for searching by gene, we should return the result table( the peaks information).
paste0(" select * from ",peaks_tab," where symbol=",shQuote(gene) ) Check the codes in search_by_position.R
The similar codes as above, this time we don't search peaks by gene, instead of position.
paste0("select * from ",peaks_tab," where start > ",start," and end < ",end)Check the codes in output_main_result_table.R
this table is a little complicate.
Check the codes in output_links.R
There are two files : downloadData_csv and downloadData_bed and one link : uiOutput('washUlink')
Check the codes in output_stat.R
we can download the free shiny-server from https://www.rstudio.com/products/shiny/download-server/
Then install shiny-server and use it to host our tool.
Also we should install all the R packages which required by our tool.
Then visit our tool by the public IP.
See help page.
Papers citing TFmapper
So far, no paper cite our tool.
What a pity !