The Yoyo Has Stopped: Reviewing the Evidence for a Low Basal Human Protein Number

The Yoyo Has Stopped Reviewing the Evidence for a Low Basal Human Protein Number In Silico Analysis of Proteins: Celebrating the 20 th Anniversary of Swiss-Prot Fortaleza, Brazil, August 2006 Christopher Southan Molecular Pharmacology, AstraZeneca R&D, M ölndal

Presentation Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

So Who Cares About Human Protein Coding Gene Number? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Definitions ,[object Object],[object Object],[object Object]

Identifying Protein Coding Genes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Historical Arguments and Estimates for High Gene Numbers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Genesweep 2000 Literature estimates

Model Eukaryotes: No Significant Post-Completion Gene Increases ,[object Object],[object Object],[object Object],[object Object],[object Object]

Human Transcripts: Post-genomic mRNA Growth in UniGene ,[object Object],[object Object],[object Object]

Ensembl Human Gene Number ,[object Object],[object Object],[object Object],[object Object],[object Object]

Addressing the smORF Question: Protein Size Distributions in Human SPTr Pre Oct-01 6.3% > 100aa Post Oct-01 5.5% > 100aa “ Novel” in title 3.4% > 100aa

Summarising the smORF Question ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Release History of the International Protein Index: Only Slow Increases in the Non-redundant Protein Sets 56537 Entries

Experimental Transcript Skimming as Evidence for High Protein Numbers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Gene Numbers for Individual Completed Chromosomes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Disappearing Novelty ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],AK091256 15-JUL-2002 √ NP_060123 ENSG00000141627 BK000950 26-FEB-2003 Dymeclin AF063599 02-JAN-2001 √ XP_166119 ENSG00000075407 AY184389 28-JAN-2003 Zinc finger ZZaPK BC030506 20-MAY-2002 √ NP_689998 ENSG00000174500 AF521911 14-JAN-2003 HGAL-IL4 inducible L15344 25-MAY-1995 √ NP_787048 ENSG00000084652 AF516206 17-FEB-2003 Taxilin _ _ _ _ AF512521 12-JAN-2003 Ligand-gated channel subunit AK092564 15-JUL-2002 √ _ ENSG00000163126 AF492401 18-JAN-2003 Diabetes related ankyrin repeat BC026194 09-APR-2002 √ NP_786887 ENSG00000164304 AF414185 27-FEB-2003 CAGE-1 AB051553 07-FEB-2001 √ XP_049218 ENSG00000133812 AY234241 20-MAR-2003 SBF2 _ √ _ _ AY191416 22-JAN-2003 Zygote arrest-1 BC041376 24-DEC-2002 √ XP_171208 ENSG00000172159 AY1377 03-MAR-2003 4.10 gene _ √ XP_072027 _ AY101377 01-MAR-2003 Testicular OR-4 associated Earlier sequence EST NCBI 31 Ens 31 Accession and date Name

Human Proteome Sampling by MS/MS Identification: A Paucity of Novel Genes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Updates ,[object Object],[object Object],[object Object],[object Object]

Acknowledgments and Reference ,[object Object],[object Object],[object Object],[object Object],[object Object]

The Yoyo Has Stopped: Reviewing the Evidence for a Low Basal Human Protein Number

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The Yoyo Has Stopped: Reviewing the Evidence for a Low Basal Human Protein Number