1. Future Plans for the HGNC Elspeth Bruford

2. HGNC Team Elspeth Bruford Susan Tweedie* Ruth Seal Kris Gray Welcome to Susan * starting 8.12.2014 Beth Yates

3. 1.continue naming of human protein-coding genes, pseudogenes & RNA genes 2.continue reassignment of uninformative symbols based on functional data 3.coordinate gene naming across vertebrates 4.assign gene names within complex families across vertebrate species (olfactory receptors, cytochrome P450s) Funded Aims (2012-2017)

4. Human Gene Naming Locus types: complex cases segregating pseudogenes: pseudogene/protein coding pseudogenes/lncRNAs smORFs: lncRNA/protein coding MT-RNR2: rRNA/protein coding Continue to display only one locus type per symbol?

5. Proteogenomics Proposed workshop with NextProt, UniProt, Havana, RefSeq, HPA, Peptide Atlas etc. (Tress, Pandey, Rinn, Ponting, smORFs) Discuss complex cases and genes encoding Uniprot PE3/4/5 NB we currently have 316 entries of locus type “unknown” Protein nomenclature – separate field? e.g. TACR3, “tachykinin receptor 3” vs “neuromedin K receptor ”

6. Bidirectional promoters Grzechnik et al 2014, TiBS lncRNA lies “head to head” (TSSs < 1 kb) with protein coding gene on antisense strand implications for transcription of both loci currently denoted in gene name, e.g. FOXG1-AS1, “FOXG1 antisense RNA 1 (head to head)” have proposed naming these as GENE1-AU1, “gene 1 antisense upstream RNA 1”

7. Human Phenotype Naming Historically HGNC maintained symbols for mapped phenotypes where causative gene was unknown Many of these fall into series, e.g. MRX#, DFN#, JBTS# Now only approve new phenotypic symbols upon request, usually via direct contact from researchers Allows researchers to reserve provisional symbols that can be confirmed upon acceptance of ms In the last decade OMIM have started assigning new members to these series without notification/consultation Many have been added retrospectively Some confusion caused, attempts made to minimise this but… …OMIM have told us they want to take over assignment

8. Human Phenotype Ontology Being developed by Peter Robinson et al in Berlin Standardized vocabulary of phenotypic abnormalities encountered in human disease ~10,000 terms, over 50,000 annotations to inherited diseases Created using information from literature, Orphanet, Decipher & OMIM

9. Human Phenotype Ontology CEP290: mutations can cause multiple phenotypes

10. Human Phenotype Ontology

11. CEP290 has 143 HPO terms HPO PhenExplorer How/where to display 143 terms? Likewise, should we include GO terms?

12. Renaming Literature searches Comparison with UniProt names CFAP# genes example – working with expert: 19 genes renamed, 19 aliased

13. Gene Naming Across Vertebrates What species? chimp > dog > cow > pig > horse > ? GeneFam – website branding Database ID format: e.g. HGNCGF:#, GeneFam:#, HGNC:PTRO# ?

14. Gene Naming Across Vertebrates Semi-automated naming of consensus 1:1 orthologs as identified by 4 comprehensive orthology resources: Ensembl Compara Homologene OMA Panther HCOP – HGNC Comparison of Orthology Predictions tool compares human to 17 species: chimp, macaque, mouse, rat, dog, horse, cow, pig, opossum, platypus, chicken, Anole lizard, Xenopus, zebrafish, C. elegans, Drosophila and S. cerevisiae using data from 12 resources:

15. Text mining Recent study by EBI Literature Services team Looked at gene symbol usage in full text articles in EuropePMC In 2006 Tamames & Valencia article estimated usage at 30% HGNC symbols vs 70% synonyms In 2014 -70% HGNC symbols vs 30% synonyms Awaiting data on the recalcitrant 30% can we update to what is being used?

16. Journals HGNC have checked manuscripts for Genomics since 1990s (or earlier?) 113 mss in the last year impact factor in 1994: 5.037 > now: 2.793 possible alternatives: PLOS One? (IF 2013 = 3.534) publishes ncRNA papers e.g. in June, PMID 24905231 cited AK096725 (LBX2-AS1) and ENST00000453068 (now CYP51A1-AS1) in May, PMID 24879036 cited lincRNA-ENST00000515084 (now LINC01373) - NB ENST00000515084 is a retired ID BUT huge no. of submissions, how to filter/identify, speed, logistics etc other suggestions?

17. Creative Commons? Public copyright licence, now on version 4.0 Different types allow adaptations of your work to be shared? yes no yes, as long as others share alike CC0 – public domain mark

18. Computing http://hgnc.github.io/reveal-talks/it-future- plans-sab2014.html

19. Complex Gene Families Olfactory receptors – Tsviya Cytochrome P450s – Jed & David