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Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity.

Burniston JG, Kenyani J, Gray D, Guadagnin E, Jarman IH, Cobley JN, Cuthbertson DJ, Chen YW, Wastling JM, Lisboa PJ, Koch LG, Britton SL - J Proteomics (2014)

Bottom Line: Forty protein species were differentially (P<0.05, FDR<10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation.Instead we found that noncanonical STAT3 signalling may be associated with low exercise capacity and skeletal muscle insulin resistance.Moreover, we demonstrate that this novel approach can be applied to 2D gel analysis, which is unsurpassed in its ability to profile protein species but currently has few dedicated bioinformatic tools.

View Article: PubMed Central - PubMed

Affiliation: Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK. Electronic address: j.burniston@ljmu.ac.uk.

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Bibliometric network of PDIA3. A gene model representing the bibliometric network of PDIA3 was constructed by automated text-mining (data redrawn from iHOP; information hyperlinked over proteins; www.ihop-net. org). Nodes (genes) are connected by edges, which represent co-occurrence within sentences of peer-reviewed published literature. Edge thickness approximates the number of supporting sentences. The majority of associations (CANX, calnexin; CALR, calreticulin, TAPBP, tapsin; HLA-E/HLA-C, major histocompatibility complex IE/C; HSPA5, glucose regulated protein 78; P4HB, prolyl-4-hydroxylase beta) were related to protein folding or assembly of protein complexes within the endoplasmic reticulum. PDIA3 was also reported to interact (TUBB3, class III beta tubulin) or be co-expressed with mitogen activated protein kinase kinase kinase 5 (MAP3K5) and gene differentially expressed in prostate (GDEP) in malignant stages of prostate cancer. Fourteen sentences reported interaction or colocalisation of PDIA3 with STAT3.
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Figure 4: Bibliometric network of PDIA3. A gene model representing the bibliometric network of PDIA3 was constructed by automated text-mining (data redrawn from iHOP; information hyperlinked over proteins; www.ihop-net. org). Nodes (genes) are connected by edges, which represent co-occurrence within sentences of peer-reviewed published literature. Edge thickness approximates the number of supporting sentences. The majority of associations (CANX, calnexin; CALR, calreticulin, TAPBP, tapsin; HLA-E/HLA-C, major histocompatibility complex IE/C; HSPA5, glucose regulated protein 78; P4HB, prolyl-4-hydroxylase beta) were related to protein folding or assembly of protein complexes within the endoplasmic reticulum. PDIA3 was also reported to interact (TUBB3, class III beta tubulin) or be co-expressed with mitogen activated protein kinase kinase kinase 5 (MAP3K5) and gene differentially expressed in prostate (GDEP) in malignant stages of prostate cancer. Fourteen sentences reported interaction or colocalisation of PDIA3 with STAT3.

Mentions: A bibliometric network was constructed as an unbiased means to explore literature evidence of proteins that have been associated with PDIA3 (Fig. 4). The majority of citations were related to protein–protein interactions between PDIA3 and the ER chaperones calnexin and calreticulin. Second to these interactions was strong evidence of the association of PDIA3 with the signal transducer and activator of transcription 3 (STAT3), which encompassed evidence from co-expression, co-localisation, protein–protein interaction and gain/loss of function studies.


Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity.

Burniston JG, Kenyani J, Gray D, Guadagnin E, Jarman IH, Cobley JN, Cuthbertson DJ, Chen YW, Wastling JM, Lisboa PJ, Koch LG, Britton SL - J Proteomics (2014)

Bibliometric network of PDIA3. A gene model representing the bibliometric network of PDIA3 was constructed by automated text-mining (data redrawn from iHOP; information hyperlinked over proteins; www.ihop-net. org). Nodes (genes) are connected by edges, which represent co-occurrence within sentences of peer-reviewed published literature. Edge thickness approximates the number of supporting sentences. The majority of associations (CANX, calnexin; CALR, calreticulin, TAPBP, tapsin; HLA-E/HLA-C, major histocompatibility complex IE/C; HSPA5, glucose regulated protein 78; P4HB, prolyl-4-hydroxylase beta) were related to protein folding or assembly of protein complexes within the endoplasmic reticulum. PDIA3 was also reported to interact (TUBB3, class III beta tubulin) or be co-expressed with mitogen activated protein kinase kinase kinase 5 (MAP3K5) and gene differentially expressed in prostate (GDEP) in malignant stages of prostate cancer. Fourteen sentences reported interaction or colocalisation of PDIA3 with STAT3.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150023&req=5

Figure 4: Bibliometric network of PDIA3. A gene model representing the bibliometric network of PDIA3 was constructed by automated text-mining (data redrawn from iHOP; information hyperlinked over proteins; www.ihop-net. org). Nodes (genes) are connected by edges, which represent co-occurrence within sentences of peer-reviewed published literature. Edge thickness approximates the number of supporting sentences. The majority of associations (CANX, calnexin; CALR, calreticulin, TAPBP, tapsin; HLA-E/HLA-C, major histocompatibility complex IE/C; HSPA5, glucose regulated protein 78; P4HB, prolyl-4-hydroxylase beta) were related to protein folding or assembly of protein complexes within the endoplasmic reticulum. PDIA3 was also reported to interact (TUBB3, class III beta tubulin) or be co-expressed with mitogen activated protein kinase kinase kinase 5 (MAP3K5) and gene differentially expressed in prostate (GDEP) in malignant stages of prostate cancer. Fourteen sentences reported interaction or colocalisation of PDIA3 with STAT3.
Mentions: A bibliometric network was constructed as an unbiased means to explore literature evidence of proteins that have been associated with PDIA3 (Fig. 4). The majority of citations were related to protein–protein interactions between PDIA3 and the ER chaperones calnexin and calreticulin. Second to these interactions was strong evidence of the association of PDIA3 with the signal transducer and activator of transcription 3 (STAT3), which encompassed evidence from co-expression, co-localisation, protein–protein interaction and gain/loss of function studies.

Bottom Line: Forty protein species were differentially (P<0.05, FDR<10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation.Instead we found that noncanonical STAT3 signalling may be associated with low exercise capacity and skeletal muscle insulin resistance.Moreover, we demonstrate that this novel approach can be applied to 2D gel analysis, which is unsurpassed in its ability to profile protein species but currently has few dedicated bioinformatic tools.

View Article: PubMed Central - PubMed

Affiliation: Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK. Electronic address: j.burniston@ljmu.ac.uk.

Show MeSH
Related in: MedlinePlus