Tamada et al. PSB 2009 Supplementary Information
This web page is Online Supplementary Information
for
UNRAVELING DYNAMIC ACTIVITIES OF AUTOCRINE
PATHWAYS THAT CONTROL DRUG-RESPONSE
TRANSCRIPTOME NETWORKS
by
YOSHINORI TAMADA,
HIROMITSU ARAKI,
SEIYA IMOTO,
MASAO NAGASAKI,
ATSUSHI, DOI,
YUKIKO NAKANISHI,
YUKI TOMIYASU,
KAORI YASUDA,
BEN DUNMORE,
DEBORAH SANDERS,
SALLY HUMPHREYS,
CRISTIN PRINT,
D. STEPHEN CHARNOCK-JONES,
KOUSUKE TASHIRO,
SATORU KUHARA, and
SATORU MIYANO,
Pacific Symposium on Biocomputing 14, 251-263, 2009 (PSB 2009).
Contact: Yoshinori Tamada <tamadasatpimsadotsu-tokyoadotmacsdotsjp>a(replace "at" with "@", "dot" with ".")
The original paper can be downloaded
from PSB Online.
Go back to my www site home page.
- PPI network: gnp_ppi.txt (Tab-separated text file: 519,767 bytes)
The file includes all the pairs of Entrez Gene IDs representing
protein-protein interactions extracted from Genome Network Platform
(http://genomenetwork.nig.ac.jp/index_e.html).
- Receptors and Ligands: receptor_ligand.txt (List of
Entrez Gene IDs).
- Active Gene Sets (Tab-separated text file. The columns corresponding to
CodeLink Probe ID, Entrez Gene ID, and Eztrez Gene Symbol).
- Node Sets (The format is the same as active gene sets).
- Dynamic Transcriptome Networks.
The gzipped CSML files can be viewed with Cell Illustrator 4.0 or later.
You can obtain one-month free license for online version CIO 4.0 and use it on
the CI Online web page.
The CSML 1.9 versions of the files are also available and can be viewed with
Cell Illustrator 3.0.
- G1 (2hr): G1-2hr.csml.gz (gzipped CSML file), G1-2hr.gon (CSML 1.9 file), G1-2hr.txt (Tab separated parent-child pair text file).
- G2 (2hr/4hr): G2-2hr4hr.csml.gz (gzipped CSML file), G2-2hr4hr.gon (CSML 1.9 file), G2-2hr4hr.txt (Tab separated parent child pair text file).
- G3 (4hr/6hr): G3-4hr6hr.csml.gz (gzipped CSML file), G3-4hr6hr.gon (CSML 1.9 file), G3-4hr6hr.txt (Tab separated parent child pair text file).
- G4 (6hr/8hr): G4-6hr8hr.csml.gz (gzipped CSML file), G4-6hr8hr.gon (CSML 1.9 file), G4-6hr8hr.txt (Tab separated parent child pair text file).
- G5 (8hr/18hr): G5-8hr18hr.csml.gz (gzipped CSML file), G5-8hr18hr.gon (CSML 1.9 file), G5-8hr18hr.txt (Tab separated parent child pair text file).
- G (Combined all): G.csml.gz (gzipped CSML file), G.gon (CSML 1.9 file), G.txt (Tab separeted parent child text file).
- Hub and their parent genes (Gene symbols and Entrez IDs).
- All the Extracted Significant Pathways.
Each line corresponds to one pathway. The columns are
p-value, first node (ligand or receptor), intermediate proteins, ..., the last node.
- Autocrine Ligand Pathways (ALPs) (The format is the same as the above files).
- Large version of Fig. 2: ALPs.pdf (PDF file)
Each figure for Gt is put on the separate page.
Copyright © 2008 - 2009 Yoshinori Tamada, Human Genome Center,
Institute of Medical Science, The University of Tokyo