RT Journal
A1 Reed, John C.
A1 Doctor, Kutbuddin
A1 Rojas, Ana
A1 Zapata, Juan M.
A1 Stehlik, Christian
A1 Fiorentino, Loredana
A1 Damiano, Jason
A1 Roth, Wilfried
A1 Matsuzawa, Shu-ichi
A1 Newman, Ruchi
A1 Takayama, Shinichi
A1 Marusawa, Hiroyuki
A1 Xu, Famming
A1 Salvesen, Guy
A1 RIKEN GER Group
A1 GSL Members
A1 Godzik, Adam
T1 Comparative Analysis of Apoptosis and Inflammation Genes of Mice and Humans
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6b 
SP 1376 
OP 1388 
DO 10.1101/gr.1053803 
UL http://genome.cshlp.org/content/13/6b/1376.abstract 
AB Apoptosis (programmed cell death) plays important roles in many facets of  normal mammalian physiology. Host-pathogen interactions have provided  evolutionary pressure for apoptosis as a defense mechanism against viruses and  microbes, sometimes linking apoptosis mechanisms with inflammatory responses  through NFκB induction. Proteins involved in apoptosis and NFκB  induction commonly contain evolutionarily conserved domains that can serve as  signatures for identification by bioinformatics methods. Using a combination  of public (NCBI) and private (RIKEN) databases, we compared the repertoire of  apoptosis and NFκB-inducing genes in humans and mice from  cDNA/EST/genomic data, focusing on the following domain families: (1) Caspase  proteases; (2) Caspase recruitment domains (CARD); (3) Death Domains (DD); (4)  Death Effector Domains (DED); (5) BIR domains of Inhibitor of Apoptosis  Proteins (IAPs); (6) Bcl-2 homology (BH) domains of Bcl-2 family proteins; (7)  Tumor Necrosis Factor (TNF)-family ligands; (8) TNF receptors (TNFR); (9) TIR  domains; (10) PAAD (PYRIN; PYD, DAPIN); (11) nucleotide-binding NACHT domains;  (12) TRAFs; (13) Hsp70-binding BAG domains; (14) endonuclease-associated CIDE  domains; and (15) miscellaneous additional proteins. After excluding  redundancy due to alternative splice forms, sequencing errors, and other  considerations, we identified cDNAs derived from a total of 227 human genes  among these domain families. Orthologous murine genes were found for 219  (96%); in addition, several unique murine genes were found, which appear not  to have human orthologs. This mismatch may be due to the still fragmentary  information about the mouse genome or genuine differences between mouse and  human repertoires of apoptotic genes. With this caveat, we discuss  similarities and differences in human and murine genes from these domain  families.