MitoCarta2.0 list and Maestro rankings of mitochondrial localization for all human genes This spreadsheet contains tabs with specfic datasets: A: Human MitoCarta2.0 "Data for all 1,158 mouse genes with high confidence of mitochondrial localization (based on integrated proteomics, computation, and microscopy)" B: Human All Genes "Maestro rankings of mitochondrial localization for all 20,629 mouse Entrez genes with RefSeq proteins, including:" "1) Training sets (Tmito, Tpossible_mito, and Tnot_mito)" 2) Proteomics data for genes detected in fourteen tissues "3) Auxilliary data, including values for each of seven dataset integrated by Maestro, chromosomal locations, etc" "Below are descriptions for the columns (in tables A,B):" TrainingDataset "Tmito, Tnot_mito, or T_possible_mito (indicating evidence based on NCBI GO mitochondrial annotation or MitoP2 database, but not in Tmito)" HumanGeneID "NCBI Entrez Gene ID for human ortholog of mouse gene (based on reciprocal BLASTP hit, expect<1e-3)" MouseOrthologGeneID NCBI Entrez Gene ID for mouse gene Symbol Official Entrez gene symbol Synonyms NCBI Entrez gene synonyms Description NCBI Entrez gene description EnsemblGeneID Ensembl Gene Identifier (based on Ensembl mapper) ProteinLength Length of longest RefSeq protein isoform TargetP_Score "TargetP confidence score (1-5, 1 is most confident) of mitochondrial targeting signal. Score 0 indicates no mitochondrial prediction" MitoDomain_Score MitoDomain indicates exclusively mito domain; SharedDomain indicates shared mito & non-mito domain; NonMitoDomain indicates exclusively non-mito domain; NA indicates unknown CoexpressionGnfN50_Score N50 score for coexpression across mouse GNFv3 tissue atlas (N50 = number of 50 nearest neighbors that are in Tmito) PGC_Induction_Score "Foldchange in transcript induction following overexpression of PGC1a, known to induce mitochondrial biogenesis" YeastMitoHomolog_Score "OrthologMitoHighConf (HomologMitoHighConf) if yeast ortholog (homolog) is annotated mitochondrial in SGD with high confidence; OrthologMitoLowConf (HomologMitoLowConf) if yeast ortholog (homolog) is annotated mitochondrial in SGD with low confidence (dual localized or only based on high throughput data), NoMitoHomolog indicates no yeast homolog or homolog is not annotated mitochondrial in SGD" RickettsiaHomolog_Score "Ortholog if 1:1 ortholog between mouse and Rickettsia prowazekii; Homolog if homology between mouse and Rickettsia prowazekii, otherwise NoHomolog" MSMS_Score "Category indicating MS/MS abundance (coverage) and enrichment in subtractive proteomics (either pure-enriched, crude-enriched, or ambiguous)" MitoCarta2_score Naïve Bayes score (sum of log-likelihood ratios for each of 7 above features) MitoCarta2_FDR Estimated corrected false discovery rate for all predictions >= given score MitoCarta2_List 1 if gene is on final MitoCarta2.0 list MitoCarta2_Evidence Type of experimental support hg19_Chromosome Chromosome (hg19 assembly) hg19_Start Start position (hg19) hg19_Stop Stop position (hg19) MSMS_NUM_TISSUES Number 0-14 tissues where gene products were found by MS/MS MSMS_NUM_PEPTIDES_UNIQUE "Number of unique peptides, based on pooling spectra from 14 tissues" MSMS_NUM_SPECTRA "Number of spectra corresponding to this gene, based on pooling spectra from 14 tissues" MSMS_TOTAL_INTENSITY "total peak intensity, based on pooling spectra from 14 tissues" MSMS_PERCENT_COVERAGE "Coverage (percent of amino acids covered by MS/MS spectra), based on pooling spectra from 14 tissues" Tissues "List of tissues with evidence of protein, based on 14 tissues" cerebrum_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) cerebellum_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) brainstem_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) spinalcord_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) kidney_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) liver_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) heart_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) skeletalmuscle_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) adipose_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) smallintestine_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) largeintestine_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) stomach_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) placenta_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) testis_total_peak_intensity_log10 Total peak intensity of spectra found in this tissue (log base 10) HPA_PrimarySubcellularLocalization_2015 Human Protein Atlas [September 2015] designation of primary subcellular localization based on immunofluorescence of antibodies in 3 human cell lines; Text in parenthesis indicates antibody reliability (where APE=antibody protein expression)