Reference - PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.

Reference summary

PubMed ID: PMID:37787768
Title: Broad functional profiling of fission yeast proteins using phenomics and machine learning.
Authors: Rodríguez-López M, Bordin N, Lees J, Scholes H, Hassan S, Saintain Q, Kamrad S, Orengo C, Bähler J
Citation: Elife 2023 Oct 03;12
Publication year: 2023
Abstract: Many proteins remain poorly characterized even in well-studied organisms, presenting a bottleneck for research. We applied phenomics and machine-learning approaches with Schizosaccharomyces pombe for broad cues on protein functions. We assayed colony-growth phenotypes to measure the fitness of deletion mutants for 3509 non-essential genes in 131 conditions with different nutrients, drugs, and stresses. These analyses exposed phenotypes for 3492 mutants, including 124 mutants of 'priority unstudied' proteins conserved in humans, providing varied functional clues. For example, over 900 proteins were newly implicated in the resistance to oxidative stress. Phenotype-correlation networks suggested roles for poorly characterized proteins through 'guilt by association' with known proteins. For complementary functional insights, we predicted Gene Ontology (GO) terms using machine learning methods exploiting protein-network and protein-homology data (NET-FF). We obtained 56,594 high-scoring GO predictions, of which 22,060 also featured high information content. Our phenotype-correlation data and NET-FF predictions showed a strong concordance with existing PomBase GO annotations and protein networks, with integrated analyses revealing 1675 novel GO predictions for 783 genes, including 47 predictions for 23 priority unstudied proteins. Experimental validation identified new proteins involved in cellular aging, showing that these predictions and phenomics data provide a rich resource to uncover new protein functions.

Annotation

Single locus phenotype

FYPO:0000082 - decreased cell population growth at high temperature

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FYPO:0000080 - decreased cell population growth at low temperature

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FYPO:0003743 - decreased cell population growth during glucose starvation

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FYPO:0009078 - decreased cell population growth on ethanol carbon source

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FYPO:0009075 - decreased cell population growth on fructose carbon source

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FYPO:0000251 - decreased cell population growth on galactose carbon source

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FYPO:0009053 - decreased cell population growth on glutamate nitrogen source

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FYPO:0009100 - decreased cell population growth on glycerol and galactose carbon source

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FYPO:0000684 - decreased cell population growth on glycerol carbon source

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FYPO:0009091 - decreased cell population growth on lysine and proline nitrogen source

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FYPO:0009092 - decreased cell population growth on lysine and serine nitrogen source

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FYPO:0009073 - decreased cell population growth on lysine nitrogen source

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FYPO:0002924 - decreased cell population growth on maltose carbon source

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FYPO:0009099 - decreased cell population growth on mannitol carbon source

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FYPO:0000250 - decreased cell population growth on proline nitrogen source

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FYPO:0007562 - decreased cell population growth on serine nitrogen source

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FYPO:0001176 - decreased cell population growth on sucrose carbon source

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FYPO:0009097 - decreased cell population growth on xylose carbon source

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FYPO:0001355 - decreased vegetative cell population growth

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FYPO:0005258 - increased cell population growth at high temperature

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FYPO:0003938 - increased cell population growth during glucose starvation

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FYPO:0009077 - increased cell population growth on ethanol carbon source

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FYPO:0009095 - increased cell population growth on fructose carbon source

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FYPO:0005261 - increased cell population growth on galactose carbon source

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FYPO:0009052 - increased cell population growth on glutamate nitrogen source

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FYPO:0009101 - increased cell population growth on glycerol and galactose carbon source

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FYPO:0004167 - increased cell population growth on glycerol carbon source

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FYPO:0009094 - increased cell population growth on lysine and proline nitrogen source

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FYPO:0009093 - increased cell population growth on lysine and serine nitrogen source

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FYPO:0009072 - increased cell population growth on lysine nitrogen source

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FYPO:0005262 - increased cell population growth on maltose carbon source

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FYPO:0009098 - increased cell population growth on mannitol carbon source

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FYPO:0009028 - increased cell population growth on proline nitrogen source

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FYPO:0009074 - increased cell population growth on serine nitrogen source

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FYPO:0009076 - increased cell population growth on sucrose carbon source

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FYPO:0009096 - increased cell population growth on xylose carbon source

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FYPO:0004557 - increased vegetative cell population growth

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FYPO:0009041 - resistance to 2,2′-dipyridyl

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FYPO:0009030 - resistance to amitrole

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FYPO:0009066 - resistance to amorolfine

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FYPO:0009036 - resistance to benzamidine

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FYPO:0009031 - resistance to bleomycin

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FYPO:0009032 - resistance to bortezomib

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FYPO:0000067 - resistance to brefeldin A

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FYPO:0000763 - resistance to cadmium

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FYPO:0000073 - resistance to caffeine

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FYPO:0009079 - resistance to calcofluor and sodium dodecyl sulfate

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FYPO:0001884 - resistance to Calcofluor White

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FYPO:0009068 - resistance to ciclopirox olamine

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FYPO:0002634 - resistance to cobalt

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FYPO:0001450 - resistance to cold

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FYPO:0000764 - resistance to cycloheximide

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FYPO:0002693 - resistance to diamide

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FYPO:0009038 - resistance to egtazic acid

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FYPO:0001453 - resistance to ethanol

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FYPO:0009034 - resistance to ethylenediaminetetraacetic acid

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FYPO:0009035 - resistance to formamide

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FYPO:0001103 - resistance to hydrogen peroxide

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FYPO:0002578 - resistance to hydroxyurea

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FYPO:0009070 - resistance to itraconazole

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FYPO:0001583 - resistance to lithium

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FYPO:0009083 - resistance to lithium chloride and methyl methanesulfonate

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FYPO:0009085 - resistance to lithium chloride and sodium dodecyl sulfate

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FYPO:0005969 - resistance to magnesium chloride

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FYPO:0009087 - resistance to magnesium chloride and sodium dodecyl sulfate

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FYPO:0000725 - resistance to methyl methanesulfonate

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FYPO:0009039 - resistance to potassium chloride

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FYPO:0009081 - resistance to potassium chloride and methyl methanesulfonate

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FYPO:0009043 - resistance to potassium chloride and sodium dodecyl sulfate

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FYPO:0000077 - resistance to rapamycin

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FYPO:0005968 - resistance to sodium chloride

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FYPO:0009089 - resistance to sodium chloride and sodium dodecyl sulfate

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FYPO:0005266 - resistance to sodium dodecyl sulfate

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FYPO:0009040 - resistance to tea tree oil

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FYPO:0002767 - resistance to terbinafine

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FYPO:0003383 - resistance to tert-butyl hydroperoxide

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FYPO:0005193 - resistance to torin1

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FYPO:0000327 - resistance to trichostatin A

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FYPO:0001034 - resistance to tunicamycin

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FYPO:0007808 - resistance to valproic acid

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FYPO:0000830 - resistance to vanadate

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FYPO:0009065 - resistance to X-rays and rapamycin during vegetative growth

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FYPO:0009062 - resistance to X-rays during vegetative growth

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FYPO:0007933 - sensitive to 2,2′-dipyridyl

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FYPO:0001097 - sensitive to amitrole

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FYPO:0009067 - sensitive to amorolfine

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FYPO:0007921 - sensitive to benzamidine

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FYPO:0000095 - sensitive to bleomycin

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FYPO:0001701 - sensitive to bortezomib

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FYPO:0001501 - sensitive to brefeldin A

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FYPO:0000096 - sensitive to cadmium

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FYPO:0000097 - sensitive to caffeine during vegetative growth

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FYPO:0009080 - sensitive to calcofluor and sodium dodecyl sulfate

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FYPO:0001188 - sensitive to Calcofluor White

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FYPO:0009069 - sensitive to ciclopirox olamine

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FYPO:0001245 - sensitive to cobalt

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FYPO:0000104 - sensitive to cycloheximide

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FYPO:0000799 - sensitive to diamide

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