Cancer Guide

http://www.cancerguide.org/pathology.html

Boxplot

GP130 <- c(0.016, 0.023, 0.028, 0.030, 0.037, 0.040, 0.045, 0.051, 0.055, 0.070, 0.071, 0.075, 0.075, 0.076, 0.088, 0.092, 0.094, 0.095, 0.096, 0.097, 0.105, 0.114, 0.123, 0.135, 0.146, 0.163, 0.165, 0.176, 0.187, 0.199, 0.200, 0.214, 0.215, 0.249, 0.256, 0.263, 0.273, 0.302, 0.317, 0.330, 0.361, 0.364, 0.380, 0.386, 0.390, 0.392, 0.393, 0.449, 0.480, 0.494, 0.500, 0.514, 0.536, 0.541, 0.545, 0.562, 0.587, 0.647, 0.652, 0.662, 0.685, 0.696, 0.709, 0.718, 0.719, 0.741, 0.747, 0.799, 0.805, 0.805, 0.821, 0.870, 0.901, 0.988, 0.994, 0.008, 0.017, 0.017, 0.028, 0.030, 0.039, 0.045, 0.067, 0.085, 0.204, 0.223, 0.264, 0.276, 0.289, 0.290, 0.303, 0.314, 0.320, 0.346, 0.363, 0.365, 0.372, 0.380, 0.386, 0.389, 0.391, 0.408, 0.441, 0.446, 0.449, 0.460, 0.471, 0.472, 0.485, 0.492, 0.497, 0.498, 0.500, 0.501, 0.502, 0.508, 0.513, 0.527, 0.528, 0.529, 0.543, 0.585, 0.604, 0.612, 0.621, 0.628, 0.651, 0.652, 0.672, 0.688, 0.688, 0.702, 0.704, 0.704, 0.709, 0.716, 0.723, 0.727, 0.730, 0.736, 0.743, 0.749, 0.751, 0.758, 0.762, 0.764, 0.766, 0.772, 0.779, 0.780, 0.783, 0.784, 0.787, 0.800, 0.803, 0.814, 0.819, 0.824, 0.826, 0.831, 0.836, 0.837, 0.840, 0.843, 0.860, 0.903, 0.931, 0.948, 0.960, 0.968, 0.974, 0.983, 0.991, 0.999)



Lauren <- c("Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Diffuse", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal", "Intestinal")



p <- t.test(GP130~Lauren)$p.value



#p <- lapply(p, signif, 3)

p <- signif(p, 3)



 boxplot( as.numeric(GP130) ~ Lauren, col=c("#FFC000", "#0070C0"),  medlwd = 2, lwd = 2, outlwd=1, cex.axis=1.2, ylab="GP130 activation score")



legend(2.05,0.2, paste("p = ", p, sep=""), box.col ="white")



setwd('E:/Projects/GP130')



pdf(file='SG192.boxplot.pdf')



 boxplot( as.numeric(GP130) ~ Lauren, col=c("#FFC000", "#0070C0"),  medlwd = 2, lwd = 2, outlwd=1, cex.axis=1.2, ylab="GP130 activation score")



legend(2.05,0.2, paste("p = ", p, sep=""), box.col ="white")



dev.off()

GSM2Sample.pl

use lib 'E:/perl_lib';
use FileSystem;

my $work_dir = 'E:\CEL\GSE15460\GSE15460_RAW\GSE15460.SG.CEL';
my $output_file = 'E:\CEL\GSE15460\GSE15460_RAW\GSE15460.info.txt';

my @CellFiles = ();
@CellFiles = FileSystem::GetFileByPattern($work_dir, '\.CEL', @CellFiles);
foreach $cel (@CellFiles)
{
print "$cel\n";
my @CELContent = FileSystem::ReadFile($cel);
my $sample_info_line = $CELContent[13];
my @sample_info = split(/[\s:]/, $sample_info_line);
print "$sample_info[2]";

FileSystem::WriteFile($output_file, "$cel\t$sample_info[2]\n");


}

FileSystem::Close();

STANDARD TRID Tumors on mRNA (Affy U133P2) Reason for exclusion GEO NGCII011/LGE GC-011LGE-T.CEL Fail QC GSM387788.CEL NGCII035/PCC GC-035PCC-T.CEL Fail QC GSM387797.CEL NGCII038/LYC GC-038LYC-T.CEL Fail QC GSM387798.CEL TGCII021/LAH GC-021LAH-T.CEL Fail QC GSM387790.CEL 980327 GC-980327T.CEL called as "adenosquamous cancer", relapse also adenosquamous GSM387937.CEL 2000619 GC-2000619T.CEL squamous CA GSM387844.CEL TGCII026/GJK GC-026-GJK-T.CEL GIST/squamous GSM387793.CEL TGCII039/TSC GC-039-TSC-T.CEL GIST/squamous GSM387799.CEL

幽门螺杆菌（Hp）感染、肠上皮化生、萎缩性胃炎

幽门螺杆菌（Hp）感染、肠上皮化生、萎缩性胃炎

chipcomparer

http://chipcomparer.genome.duke.edu/

BFRM+NTP

top 1/3 vs bottom 1/3
use NTP and gene signature to predict the direction.

human gastric precancerous lesions

http://www.weibing.com.cn/html/mxqbxwy/
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1766652/pdf/v045p000I5.pdf
http://www.google.com.sg/url?sa=t&source=web&cd=2&ved=0CC0QFjAB&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC1146204%2F&ei=yNuWTtO4BsLsrAeSvqWbBA&usg=AFQjCNHwRAwFh8ipHDTFVBzNx-r7G-dbkg&sig2=kbm6v1zThHgCqzhCMyg13Q


chronic superficial gastritis (CSG, 16),
chronic atrophic gastritis (CAG, 16), intestinal metaplasia
(IM, 35), gastric epithelial dysplasia (GED, 23) and gastric
cancer (CA, 25), and conditions of H.pylori infection