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MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle.

Huang Z, Ma L, Wang Y, Pan Z, Ren J, Liu Z, Xue Y - Nucleic Acids Res. (2014)

Bottom Line: In total, 87,983 unique proteins with corresponding localization information were integrated into the database.The primary references of experimentally identified localizations were provided and the fluorescence microscope figures for the localizations of human proteins were shown.The orthologous relations between predicted and experimental localizations were also present.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

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The heatmap about the distribution of MiCroKiTS proteins in the MiCroKiTS 4.0 database for different localizations among 144 eukaryotic species from different kingdoms. The upper part was the results for the 66 animals, and the lower section was the results for the 33 plants and 45 fungi.
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Figure 4: The heatmap about the distribution of MiCroKiTS proteins in the MiCroKiTS 4.0 database for different localizations among 144 eukaryotic species from different kingdoms. The upper part was the results for the 66 animals, and the lower section was the results for the 33 plants and 45 fungi.

Mentions: In this study, we updated the database of MiCroKit 3.0 into MiCroKiTS 4.0 for more organisms and more types of subcellular positions including spindle apparatus and telomere. In total, 1872 experimentally identified MiCroKiTS proteins with 2277 localizations were collected in eight model organisms. Furthermore, homologous detections were performed to find orthologs in species beyond the eight model organisms for experimentally identified MiCroKiTS proteins to search potential MiCroKiTS proteins, which were also integrated into the database. The distribution of proteins in centrosome, kinetochore, spindle apparatus, midbody and telomere were summarized and presented in Figure 4. Because the reference proteome for X. laevis was unavailable, only known MiCroKiTS proteins were collected (Figure 4). From the result, it was observed that the centrosome has most proteins, while there were more proteins localized in kinetochore and midbody than spindle apparatus and telomere (Figure 4). Also, the numbers of MiCroKiTS proteins per localization vary greatly among different kingdoms, but are similar in the same kingdom (Figure 4). However, further experimental studies are still needed to verify the observations, while orthologs among distantly related species, such as organisms in different kingdoms, should be carefully considered. Taken together, here we updated the MiCroKit 3.0 database, which only contains proteins for three super-complexes in seven organisms, to MiCroKiTS 4.0 database for subcellular positions in 144 species. We believed that the update will make the database more helpful for the further computational or experimental studies. The MiCroKiTS database will be routinely updated to maintain more information for systematic understanding of the molecular mechanisms and function roles of the MiCroKiTS proteins during cell cycle.


MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle.

Huang Z, Ma L, Wang Y, Pan Z, Ren J, Liu Z, Xue Y - Nucleic Acids Res. (2014)

The heatmap about the distribution of MiCroKiTS proteins in the MiCroKiTS 4.0 database for different localizations among 144 eukaryotic species from different kingdoms. The upper part was the results for the 66 animals, and the lower section was the results for the 33 plants and 45 fungi.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383938&req=5

Figure 4: The heatmap about the distribution of MiCroKiTS proteins in the MiCroKiTS 4.0 database for different localizations among 144 eukaryotic species from different kingdoms. The upper part was the results for the 66 animals, and the lower section was the results for the 33 plants and 45 fungi.
Mentions: In this study, we updated the database of MiCroKit 3.0 into MiCroKiTS 4.0 for more organisms and more types of subcellular positions including spindle apparatus and telomere. In total, 1872 experimentally identified MiCroKiTS proteins with 2277 localizations were collected in eight model organisms. Furthermore, homologous detections were performed to find orthologs in species beyond the eight model organisms for experimentally identified MiCroKiTS proteins to search potential MiCroKiTS proteins, which were also integrated into the database. The distribution of proteins in centrosome, kinetochore, spindle apparatus, midbody and telomere were summarized and presented in Figure 4. Because the reference proteome for X. laevis was unavailable, only known MiCroKiTS proteins were collected (Figure 4). From the result, it was observed that the centrosome has most proteins, while there were more proteins localized in kinetochore and midbody than spindle apparatus and telomere (Figure 4). Also, the numbers of MiCroKiTS proteins per localization vary greatly among different kingdoms, but are similar in the same kingdom (Figure 4). However, further experimental studies are still needed to verify the observations, while orthologs among distantly related species, such as organisms in different kingdoms, should be carefully considered. Taken together, here we updated the MiCroKit 3.0 database, which only contains proteins for three super-complexes in seven organisms, to MiCroKiTS 4.0 database for subcellular positions in 144 species. We believed that the update will make the database more helpful for the further computational or experimental studies. The MiCroKiTS database will be routinely updated to maintain more information for systematic understanding of the molecular mechanisms and function roles of the MiCroKiTS proteins during cell cycle.

Bottom Line: In total, 87,983 unique proteins with corresponding localization information were integrated into the database.The primary references of experimentally identified localizations were provided and the fluorescence microscope figures for the localizations of human proteins were shown.The orthologous relations between predicted and experimental localizations were also present.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

Show MeSH