CLIME is an algorithm that partitions an input gene set of interest into distinct, evolutionarily conserved modules (ECMs). It then expands each module with genes sharing an inferred evolutionary history. CLIME accepts as input (i) a binary species tree, (ii) an input gene set, and (iii) a phylogenetic matrix of all genes in a reference genome across the species. This website provides an interactive interface for performing CLIME analysis on a user-defined gene set from any of ten different model organisms. CLIME software is available for download at this site. Also available at this site are pre-computed CLIME analyses of ~1000 human pathways and full-genome analysis of P. falciparum, C. merolae, and S. cerevisiae.
New website (2022): login no longer required, and results will be emailed to users instead of stored on the server. The interactive visualizer is no longer available, so PDF and text results will be emailed to users.
Citing CLIME
Y. Li, S.E. Calvo, R. Gutman, J.S. Liu, and V.K. Mootha (2014) Expansion of biological pathways based on evolutionary inference, Cell 158, 213–225. Pubmed: 24995987
Y. Li, S. Ning, S.E. Calvo, V.K. Mootha and J.S. Liu (2018) Bayesian hidden Markov tree models for clustering genes with shared evolutionary history, The Annals of Applied Statistics, in press. arXiv: 1808.06109
Run CLIME
Downloads
CLIME software (including users' manual)
Pre-computed CLIME analyses of published gene sets
| TXT | Human complex I | |
| TXT | Human MICU1 | |
| TXT | Human ciliary genes | |
| TXT | Human mitochondrial genes | |
| TXT | All 5331 P. falciparum genes | |
| TXT | All 5013 C. merolae genes | |
| TXT | All 5882 S. cerevisiae genes | |
| 1025 human pathways from GO and KEGG | ||
Phylogenetic profile matrices for 10 model organisms across 138 eukaryotes (plus Prokaryote outgroup)
| hsa.matrix138.txt | H. sapiens phylogenetic matrix |
| mmu.matrix138.txt | M. musculus phylogenetic matrix |
| dme.matrix138.txt | D. melanogaster phylogenetic matrix |
| cel.matrix138.txt | C. elegans phylogenetic matrix |
| ncr.matrix138.txt | N. crassa phylogenetic matrix |
| sce.matrix138.txt | S. cerevisiae phylogenetic matrix |
| ath.matrix138.txt | A. thaliana phylogenetic matrix |
| cme.matrix138.txt | C. merolae phylogenetic matrix |
| pfa.matrix138.txt | P. falciparum phylogenetic matrix |
| tbr.matrix138.txt | T. brucei phylogenetic matrix |
| euk138.with_prok.nwk | Tree topology for 138 eukaryotes plus prokaryote outgroup, in Newick format |
Last updated 10/18/2022