deidrey langat shinen lo mahmoud rezaei carissa tudor

PROBLEM 4: BIOINFORMATICS-IDENTIFYING CPG

ISLANDS

Deidrey Langat

Shinen Lo

Mahmoud Rezaei

Carissa Tudor

Hypothesis

Where probes present an overexpression after demethylation treatment there will be a significantly higher occurance of CpG Islands around those probes than around probes that do not have an overexpression following demethylation.

i.e. Probe overexpression is correlated with the number of CpG Islands in existence 10,000 base pairs upstream of the Probe.

Sample0.010 mRNA chr5:42836013-42826013 00.021 mRNA chr11:74594777-74584777 00.021 mRNA chr21:45130327-45120327 00.022 mRNA chr22:20444866-20434866 00.023 mRNA chr2:68477967-68467967 0

0.023 ncRNA chr6:160020430-160010430 00.032 ncRNA chr16:24135824-24125824 00.033 ncRNA chr2:160837124-160827124 10.036 ncRNA chr1:42738071-42728071 00.036 ncRNA chr1:144346199-144336199 0

111.544 mRNA chr18:59323230-59313230 0115.002 mRNA chr4:6746670-6736670 0118.500 mRNA chr7:72884859-72874859 1124.146 mRNA chr2:172672477-172662477 2308.952 mRNA chr7:93354113-93344113 0

63.900 ncRNA chr7:41691439-41681439 077.180 ncRNA chr13:105827406-105817406 0

125.522 ncRNA chr18:53866484-53856484 1345.396 ncRNA chr6:25808985-25798985 0498.672 ncRNA chr16:2455344-2445344 1

Perl: Pseudocode1. Open xls file and sort using Perl2. Read in data of top and lowest Expression levels based on demethylation treatment 3. Navigate to Genome Browser database with parameters set as follows:* Groups - "All Tracks"* Track - "CpG Islands"4. Submit each of the chromosomal location from xls file as strings to the genome browser database5. Click on 'Get output' to locate CpG islands6. Count # of results7. Record # or results for each sample data

Perl: Step 1-Reading Excel file

Code:

#!/usr/bin/perl –w

use strict;

use Win32::OLE qw(in with);

useWin32::OLE::Const 'Microsoft Excel';

$Win32::OLE::Warn = 3;

# die on errors...# get already active Excel application or open newmy $Excel = Win32::OLE->GetActiveObject('Excel.Application') || Win32::OLE->new('Excel.Application', 'Quit');

# open Excel filemy $Book = $Excel->Workbooks->Open("C:/Documents and Settings/Mahmoud/Desktop/Claremont/forfirst1000highmRNA.xls");

# You can dynamically obtain the number of worksheets, rows, and columns

# through the Excel OLE interface. Excel's Visual Basic Editor has more

# information on the Excel OLE interface. Here we just use the first# worksheet, rows 1 through 4 and columns 1 through 3.

# select worksheet number 1 (you can also select a worksheet by name)my $Sheet = $Book->Worksheets(1);

my $newvalue = 10000;

foreach my $row (1..1000)

{ foreach my $col (55)

{ # skip empty cells next unless defined $Sheet->Cells($row,$col)->{'Value'};

# print out the contents of a cell

printf "At ($row, $col) the value is %s and we looked at upstream from %s to %s\n",

$Sheet->Cells($row,$col)->{'Value'},

$Sheet->Cells($row,$col)->{'Formula'}-$newvalue,

$Sheet->Cells($row,$col)->{'Value'}; }}

# clean up

$Book->Close;

Perl: Step 1-Reading Excel file

Output:At (1, 55) the value is 65370390 and we looked at upstream

from 65360390 to 65370390

At (2, 55) the value is 30769374 and we looked at upstream from 30759374 to 30769374



Step 2-4

Step 5

FASTA Format Code:#!/bin/perl -w

use Bio::Seq;use Bio::SeqIO;

$seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt", -display_id => "#12345", -desc => "example 1", -alphabet => "dna" );

#!/bin/perl -w

use Bio::Seq;use Bio::SeqIO;

$seq_obj2 = Bio::Seq->new(-seq => "aaaatgggggggggggcccccccccc", -display_id => "#12346", -desc => "example 2", -alphabet => "dna" );

$seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'fasta' );

$seqio_obj->write_seq($seq_obj);

$seqio_obj = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'fasta' ); $seqio_obj->write_seq($seq_obj);

$seqio_obj->write_seq($seq_obj2);

FASTA Format

Output:

>#12345 example 1aaaatgggggggggggccccgtt>#12346 example2aaaatgggggggggggcccccccccc

BioperlCode:

#!/local/bin/perl –w

use Bio::DB::GenBank;my $gb =new Bio::DB::GenBank(-retrievaltype=>'tempfile',-format=>'Fasta');

my ($seq) = $seq =$gb->get_Seq_by_id("AB000460");

print $seq->id, "\n";

print $seq->desc(), "Sequence:\n";

print $seq->seq(), "\n";exit;

CACAATGACATGCAGACCTGCATATTGGAGCTGGACGGAGAAACTGGGCTAATGTGACAGACAGCAACAAGAGTAAGGCAGTTGCTTCGCTATTGAGAGAAAGAACCATATGAAGAAATTTCGGCAGAGGCGGACCGGGAACCTCAGCAGCTGCAGAACTACTGGTCAGAAGTGCGCTACACGGTGCGCTGCATCTACCGCCAGGCAGGAACCCCGCTGGCAGATGACCAGGACCAGTCTCTGGTGCCTGACAAGGAGGGAGTGAAGGAGCTCGTGGATAGGCTCTGCGAGAGGGACCCCTACCAGCTGTACCAGCGTCTGGAACAGCAAGCTCGAGAGTATGTGCTGGAGATGAAGGTCCGCCTGCTCCGGCAGCTGTCGGCTGCGGCCAAGGTGAAGGCACCATCTGGCCTGCAGGGCCCGCCGCAAGCGCACCAGTTCATCTCCCTCCTGCTTGAGGAGTACGGCGCCCTCTGCCAGGCCGCACGCTCCATCAGCACCTTCCTTGGCACTCTGGAAAATGAACACTTGAAAAAGTTCCAAGTGACGTGGGAACTGCATAATAAACACCTGTTTGAAAATCTGGTCTTTTCGGAGCCACTTCTTCAGAGCAACTTGCCCGCACTGGTGTCACAGATCAGGCTAGGAACCACCACACACGACACCTGCAGTGAGGACACATACAGTACCTTGCTGCAGAGGTACCAGCGTTCCGAGGAGGAGCTGCGCAGAGTCGCCGAGGAGTGGCTGGAGTGCCAGAAGAGGATCGACGCCTATGTCGACGAGCAGATGACAATGAAAACCAAGCAGCGCATGTTAACAGAAGACTGGGAGCTTTTTAAACAAAGAAGATTCATTGAAGAACAGTTAACCAATAAGAAAGCAGTTACTGGCGAGAACAACTTCACAGACACCATGAGGCACGTGTTATCGTCCCGGCTGAGCATGCCCGACTGCCCCAACTGCAACTACAGGAGAAGATGTGCTTGCGATGACTGCAGTCTCTCACACATCCTCACGTGTGGTATCATGGACCCCCCCGTCACTGATGACATCCACATTCACCAGCTCCCACTTCAAGTGGATCCTGCTCCTGACTATCTTGCTGAGAGGAGCCCGCCCAGTGTGTCATCTGCAAGCTCGGGGTCCGGCTCCAGCTCTCCCATCACAATTCAGCAGCACCCCAGGCTCATCCTCACAGACAGTGGCTCGGCACCAACTTTTTGTAGTGATGATGAAGATGTTGCACCATTGTCAGCCAAATTTGCTGATATTTATCCATTGAGTAATTATGATGATACCGAGGTGGTGGCCAACATGAATGGAATCCACAGCGAATTGAATGGTGGCGGGGAAAACATGGCCCTGAAGGATGAGTCTCCTCAGATAAGCAGTACCAGCAGTAGTTCCTCAGAAGCTGATGATGAAGAAGCGGACGGCGAGAGTAGTGGGGAGCCCCCAGGGGCCCCGAAGGAAGATGGAGTGCTGGGAAGCAGGAGCCCCAGGACAGAGGAGAGCAAAGCAGACAGTCCACCCCCATCCTACCCAACACAGCAGGCTGAACAAGCTCCAAACACTTGTGAATGTCATGTTTGTAAGCAAGAAGCTTCTGGACTGACACCATCTGCAATGACAGCCGGAGCCCTTCCTCCTGGCCATCAGTTCTTGAGCCCAGAGAAGCCCACACACCCTGCACTGCACCTTTACCCTCACATCCATGGACATGTGCCTTTGCACACTGTTCCACACCTGCCACGCCCTCTCATCCACCCCACCTTGTATGCAACGCCCCCCTTCACACACAGTAAGGCTTTACCGCCAGCACCTGTTCAGAATCACACAAATAAGCATCAGGTATTCAATGCATCTCTTCAAGACCATATTTATCCGAGCTGTTTTGGGAATACTCCAGAGTGGAATAGTTCTAAATTTATAAGTCTTTGGGGATCAGAAGTGATGAATGATAAGAACTGGAATCCTGGCACTTTCTTGCCAGATACAATTTCTGGGAGTGAAATATTAGGGCCAACACTCTCAGAAACAAGACCGGAAGCCCTTCCACCTCCATCTAGCAATGAAACACCTGCAGTCTCGGATAGTAAAGAGAAAAAGAATGCTGCAAAAAAGAAATGTTTATACAATTTCCAAGATGCTTTCATGGAAGCAAATAAAGTTGTCATGGCCACGTCATCAGCCACGTCCTCTGTGTCCTGCACAGCTACCACAGTGCAGTCCAGCAACAGCCAGTTCAGAGTGTCATCCAAGAGACCTCCTTCAGTAGGTGACGTGTTTCATGGCATCAGCAAGGAGGACCACAGACACTCGGCCCCAGCCGCCCCGAGGAATAGCCCCACGGGCTTGGCCCCCCTCCCAGCGCTCTCGCCTGCTGCGCTGTCACCTGCTGCGCTCTCACCTGCCTCCACACCTCACCTTGCAAATCTTGCAGCCCCATCATTCCCCAAAACAGCAACCACAACTCCTGGGTTTGTGGACACACGCAAGAGTTTCTGTCCTGCACCCCTACCCCCGGCCACAGATGGCTCCATTAGCGCCCCTCCAAGTGTCTGCAGTGACCCTGACTGCGAAGGGCACCGCTGCGAGAATGGTGTCTACGACCCACAGCAGGATGATGGGGACGAGAGTGCAGATGAGGACAGCTGCTCTGAGCACAGCTCCAGCACCTCGACCTCCACCAACCAGAAGGAGGGCAAGTACTGCGACTGCTGCTACTGCGAATTCTTTGGGCACGGCGGGCCTCCAGCTGCACCAACAAGTAGAAATTATGCAGAAATGAGGGAAAAGCTTCGCTTACGGCTGACCAAGAGGAAAGAGGAGCAACCTAAAAAAATGGACCAGATCTCAGAAAGGGAAAGCGTCGTTGACCATCGGAGGGTGGAGGATTTGTTGCAGTTTATAAATAGCTCCGAAACCAAACCAGTGAGCAGCACGCGTGCAGCGAAGCGAGCAAGGCATAAGCAAAGGAAGCTGGAGGAGAAAGCTCGCCTAGAAGCAGAGGCCAGGGCCCGGGAGCACCTGCACCTCCAGGAGGAGCAGAGGCGGCGGGAGGAGGAGGAGGATGAGGAAGAAGAGGAGGATCGTTTCAAGGAGGAATTTCAGCGGCTTCAGGAGCTTCAGAAGCTAAGAGCTGTAAAAAAGAAGAAGAAGGAGAGGCCAAGTAAAGACTGCCCCAAGTTGGACATGCTCACTAGAAATTTCCAGGCAGCAACAGAGTCTGTTCCTAACTCTGGAAACATCCACAATGGCTCACTAGAGCAAACTGAAGAACCAGAAACCTCTTCTCACTCCCCATCCAGGCATATGAACCACTCAGAGCCCAGGCCAGGGCTAGGGGCTGATGGGGATGCTGCAGACCCCGTCGACACCAGAGACTCCAAATTTCTCCTCCCCAAGGAGGTGAATGGGAAGCAGCATGAGCCACTCTCTTTTTTCTTCGACATCATGCAGCACCATAAAGAAGGAAATGGCAAGCAGAAGCTGAGGCAGACCAGCAAGGCCAGCAGCGAGCCAGCGAGGAGGCCCACAGAGCCCCCCAAGGCCACAGAGGGGCAGTCCAAGCCCCGGGCCCAGACTGAGTCAAAGGCTAAGGTGGTCGACCTCATGTCCATCACAGAGCAGAAAAGAGAGGAGAGAAAAGTCAACAGTAATAACAATAACAAAAAGCAGCTGAACCACATCAAGGACGAAAAGTCAAACCCAACCCCTATGGAGCCCACCTCTCCCGGTGAGCATCAGCAGAACAGCAAGCTGGTGCTGGCAGAGTCCCCTCAGCCAAAGGGCAAGAACAAGAAAAATAAGAAGAAGAAAGGAGACAGAGTCAACAATTCAATTGATGGAGTTTCGCTCTTGTTGCCCAGTCTGGGGTACAATGGTGCAATCTTGGCTCACTGCAACCTTCGCCTCCCAGGTTCAAGCGATTGTGCTGCCTCAGCCTCCCAAGTAGTTGGAATTACAGATGATGTCTTTCTACCTAAAGATATTGACCTAGACAGTGTGGATATGGATGAGACAGAGAGGGAAGTGGAATATTTCAAAAGGTTCTGCTTGGATTCTGCTAGACAGACCCGACAAAGACTGTCTATCAACTGGTCCAATTTTAGCTTGAAAAAAGCCACCTTTGCTGCCCACTGAATGAGGACTCCCTGGAGAGGGACACGCGAGAGGCAGGCCAGGCTGCACCACCCCAAGAGCCACGCCCCTCGCTGGCGCCCCAGAGCCGTGGTGCTTGCCAAGGGCTGTGCGGAGCTGGTGCTGCCTGAAACCCCAGACCGAGAAGTTGATGCTCGGCCCACGCCGTTAGCTCGTGTGCGTGTAGTCTGTGCGTGAGACTCCTTCGATTGTAGCTCTGTGCTGTCGGATTGGAACAGTAGTTCCCGCCAAGTCCTCCCACCACCGCGGCCTCGGAGGCCTGGGCCGTGGCCAGATAGGAGTTTGCATCATCCACGTGGCTCCGTTGCCTCTGCATTGCGCCCTGTCCTGTCATGTGTCCTCACCGGGGTATCGGCCGTCACTCAGCTCTCCTGTGCCCCTGCGTCTCACCCTAGGCGGGCTGGGCGGGGCAGGCCTCCTTTGTTCTCCACAATCTACTGTCTCCGAGTGTACACGTTGCGCTGTTTGTGTTTGATCCCCCTGACTTGTAGCCAGCTTGTGTAAGATCCCTTGCAGAACGAGAAAGTTAAAAACAAGCCCACCCAGTACTCACACCATCAAGTCTGTTATAGAGTGTACGACTGTATTAACACGGAGGCCTGCCTGGCTACTTTTTTAACATATTGTTAAGTAATATTAAAATCATGTCTTTCTTTTTGAAAGATG

Thank you!