DOI: 10.5281/zenodo.7551929
title: Vertebrate gene family trees

description: This is a dataset of phylogenies for 118 vertebrate gene families, used in two papers published by James Cotton and Roderic Page in 2002. The folder named "genes.zip" contains FASTA and NEXUS sequence files, and Newick-format tree files for each gene family. There is a PDF file "suppl.pdf" listing the names of each family. The file "final_dataset.gml" contains a graph of the taxonomic overlap in the gene trees. All 118 gene trees have been combined into the file "final_dataset.gtr" which is a NEXUS file with custom blocks recognised by GeneTree. HOVERGEN FAMILY CODE GENE FAMILY NAME FAM000030A wnt 5 FAM000030B wnt 7 FAM000030C wnt 11 FAM000030D wnt/int 1 FAM000030E wnt 4 FAM000030F wnt 10/12 FAM000030G wnt 3 FAM000030H wnt 2 FAM000030I wnt 8 FAM000105 rhodopsin FAM000214 beta-B globin FAM000033 protamine 1 FAM000370 PrP a prion-protein FAM000014 growth hormone FAM000556 Rag-1 recombination activation gene FAM001493 c-mos proto-oncogene FAM001462 tyrosine kinase / yes / fyn / src / lck FAM001041 metallothionein FAM000364 Ldh-2 lactate dehydrogenase-B (EC FAM000215 alpha globin FAM000016 placental lactogen - prolactin FAM000008 insulin FAM000824 phosphoglycerate kinase FAM000550 neurotrophin-4 (NT-4) FAM001478 tyrosine kinase receptor, c-fms oncogene FAM000173A guanine nucleotide-binding protein FAM000173B transducin alpha FAM000502 cytochrome P-450 aromatase FAM000192 alpha-fetoprotein / serum albumin FAM000627 neurone-specific enolase FAM001232 preprotrypsin (ta) FAM000664 complement component 3 (C3) FAM000175 Ras FAM000248 alpha B-crystallin FAM000006 insulin-like growth factor II FAM000639 transthyretin (prealbumin) FAM001303 butylcholinesterase (BCHE) FAM000242 connexin / gap junction protein FAM000058 dopamine D1 receptor FAM000055 beta-3-adrenergic receptor . FAM000131 ATPase (Na+K+, H+K+) FAM003983 preprogastrin FAM000353 vasopressin FAM000152 acetylcholine receptor FAM001327 peripherin, desmin, vimentin, GFAP FAM003199 (C57BL/6J) FAM002881 cytochrome P-450, 17a-hydroxylase (CYP17) FAM002789 (MUAHRB-1) Ah-receptor (Ah) FAM001461 tropomyosin FAM000385 Y3 peptide supply factor FAM000378 pancreatic polypeptide, neuropeptide Y FAM001329 cytokeratin FAM001619 amelogenin (enamel-specific protein) FAM000286 glucagon FAM000330 tissue inhibitor of FAM000475 lipophilin FAM001060 ornithine carbamoyltransferase FAM001328 neurofilament FAM001370 peroxisome proliferator FAM000371 somatostatin FAM001607 Wilms tumor assocated protein (WT1) FAM000495 aldolase A, B, C FAM001365 liver receptor homologous protein (LRH-1) FAM000672 ribosomal protein S4, FAM000135 Na, K-ATPase beta-1 subunit FAM000271 enkephalin : 1 2. FAM000799 RING10 FAM001664 glutamate decarboxylase FAM000617 creatine kinase FAM001337 amyloid beta protein precursor FAM000274 basic fibroblast growth factor (bFGF) FAM001108 Sl-d mutant allele kit ligand (KL) FAM000504 anion exchange protein 3 FAM001239 prothrombin FAM001360 high mobility group proteins HMG1 and HMG2 FAM000534 glutamine synthetase FAM001053 nucleoside diphosphate kinase FAM001390 low density lipoprotein receptor LDLR FAM001464 Cek6 receptor tyrosine kinase FAM000801 manganese-containing superoxide FAM003946 Six2 / Six1 mRNA FAM001606 Ikaros binding protein (Ikaros) FAM000350 SPARC protein FAM001339 calcium-binding protein FAM000553 pyruvate kinase FAM000604 t complex polypeptide 1 (Tcp-1-a) FAM002988 mSlo FAM001266 transcription factor / hepatocyte nuclear factor FAM000453 terminal deoxynucleotidyltransferase FAM001642 transformation associated protein p53 FAM000300A glucose-regulated protein 78 / HSP70 PART A FAM000300B glucose-regulated protein 78 / HSP70 PART B FAM000492A alpha actin etc FAM000492B beta actin etc FAM000649 Myelin Basic Protein FAM000843 ribosomal protein S4 FAM000170 atrial natriuretic protein FAM000871A tyrosinase FAM000871B tyrosinase related protein 1 FAM001605 ZFX put. transcription activator FAM001479 fibroblast growth factor FAM000160 pro-opiomelanocortin (POMC) FAM001644 fibrinogen alpha subunit FAM000564 SNAP-25 FAM000266 nitric oxide synthase FAM004159 chondroitin-6 sulfotransferase FAM000800 Lmp-2 (LMPq) proteasome subunit FAM001595 factor B FAM001134 zona pellucida (ZP) FAM001632 stromelysin-3 FAM001366 steroid receptor (TR2-9) FAM000526 c-ski protein FAM002463 thymosin beta 4 peptide FAM000904 sequence-specific DNA-binding protein (AP-2) FAM001465 T-cell specific tyrosine kinase (ltk) FAM000567 triosephosphate isomerase FAM006113 DNA-dependent RNA polymerase III, large subunit FAM001733 DNA-dependent RNA polymerase II
description: {"references": ["Cotton James A. and Page Roderic D. M. 2002Going nuclear: gene family evolution and vertebrate phylogeny reconciledProc. R. Soc. Lond. B.2691555\u20131561 http://doi.org/10.1098/rspb.2002.2074", "Page, R. D. M., & Cotton, J. A. (2001). Vertebrate phylogenomics: Reconciled trees and gene duplications. Biocomputing 2002, 536\u2013547. https://doi.org/10.1142/9789812799623_0050", "R D Page, GeneTree: comparing gene and species phylogenies using reconciled trees., Bioinformatics, Volume 14, Issue 9, 1998, Pages 819\u2013820, https://doi.org/10.1093/bioinformatics/14.9.819"]}