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A systematic analysis of human lipocalin family and its expression in esophageal carcinoma.

Du ZP, Wu BL, Wu X, Lin XH, Qiu XY, Zhan XF, Wang SH, Shen JH, Zheng CP, Wu ZY, Xu LY, Wang D, Li EM - Sci Rep (2015)

Bottom Line: Lipocalins have been found to play important roles in many human diseases.In this study, human lipocalins were found to contain four structurally conserved regions (SCRs) and could be divided into two subgroups.Their subcellular distributions also suggested these lipocalins may transfer signals from the extracellular space to the nucleus using the pathway-like paths.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China.

ABSTRACT
The lipocalin proteins (lipocalins) are a large family of small proteins characterized by low sequence similarity and highly conserved crystal structures. Lipocalins have been found to play important roles in many human diseases. For this reason, a systemic analysis of the molecular properties of human lipocalins is essential. In this study, human lipocalins were found to contain four structurally conserved regions (SCRs) and could be divided into two subgroups. A human lipocalin protein-protein interaction network (PPIN) was constructed and integrated with their expression data in esophageal carcinoma. Many lipocalins showed obvious co-expression patterns in esophageal carcinoma. Their subcellular distributions also suggested these lipocalins may transfer signals from the extracellular space to the nucleus using the pathway-like paths. These analyses also expanded our knowledge about this human ancient protein family in the background of esophageal carcinoma.

No MeSH data available.


Related in: MedlinePlus

(A-B) The human lipocalin protein-protein interaction network and the lipocalins’ changes in expression in esophageal adenocarcinoma and esophageal squamous cell carcinoma are shown. The lipocalins are shown using triangles, and their interacting proteins are shown in circles. Red indicates upregulation and green indicates downregulation. The size of the node indicates the degree (the number of its interacting proteins) of the node. Bigger nodes have higher degrees. The connection between two nodes is indicated by an edge. Red edges indicate positive correlations in the expression of two proteins, and green edges indicate negative correlations. Correlation strength is shown by the edge width. (C) Expression levels of lipocalins in esophageal adenocarcinoma and esophageal squamous cell carcinoma. (D) The power law distribution of the node degree network and analysis of other network parameters. (E) Functional map of the lipocalins PPIN. Functionally grouped network with GO terms are represented as nodes, which were linked based on their kappa score level (≥0.3), suggesting overlapped enriched genes. The similar GO terms were labeled in the same color.
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f3: (A-B) The human lipocalin protein-protein interaction network and the lipocalins’ changes in expression in esophageal adenocarcinoma and esophageal squamous cell carcinoma are shown. The lipocalins are shown using triangles, and their interacting proteins are shown in circles. Red indicates upregulation and green indicates downregulation. The size of the node indicates the degree (the number of its interacting proteins) of the node. Bigger nodes have higher degrees. The connection between two nodes is indicated by an edge. Red edges indicate positive correlations in the expression of two proteins, and green edges indicate negative correlations. Correlation strength is shown by the edge width. (C) Expression levels of lipocalins in esophageal adenocarcinoma and esophageal squamous cell carcinoma. (D) The power law distribution of the node degree network and analysis of other network parameters. (E) Functional map of the lipocalins PPIN. Functionally grouped network with GO terms are represented as nodes, which were linked based on their kappa score level (≥0.3), suggesting overlapped enriched genes. The similar GO terms were labeled in the same color.

Mentions: A full screening of the lipocalins’ interactions with other proteins was performed to determine how they affect cellular activity. This may provide important clues of their functions. The PPI dataset from both acknowledged HPRD and BioGRID databases provided credible original data for subsequent analysis. The lipocalin PPIN was generated by mapping the lipocalins to the parental PPI network to extract the proteins that interacted directly and all their interactions, forming a sub-network for lipocalins containing 151 nodes and 569 edges (Fig. 3). Currently, the interactions of 23 human lipocalin proteins have been reported. An esophageal carcinoma expression profile GSE26886, containing clinical samples from normal esophageal squamous epithelium, esophageal adenocarcinoma (EAC), and esophageal squamous cell carcinoma (ESCC), was analyzed to determine the expression trends of lipocalins and the proteins with which they interact. The fold-changes of these proteins in EAC and ESCC and other important parameters were integrated into the PPIN (Fig. 3A,B). In Fig. 3A,B, the color of each node indicates the level of expression. The gradient from red to green indicates upregulation through downregulation, all relative to normal esophageal tissue. The size of the node indicates the degree of the node (the number of proteins with which it interacts directly). The bigger nodes indicate higher degrees of interactions, connecting with more proteins. Every two interacting nodes are linked by an edge. The correlations in the levels of expression of any two interacting proteins are here treated as edge weight. Red edges indicate positive correlations in the expression of two interacting proteins, and green edges indicate the negative expression correlation. The strength of the correlation is indicated by the width of the edge.


A systematic analysis of human lipocalin family and its expression in esophageal carcinoma.

Du ZP, Wu BL, Wu X, Lin XH, Qiu XY, Zhan XF, Wang SH, Shen JH, Zheng CP, Wu ZY, Xu LY, Wang D, Li EM - Sci Rep (2015)

(A-B) The human lipocalin protein-protein interaction network and the lipocalins’ changes in expression in esophageal adenocarcinoma and esophageal squamous cell carcinoma are shown. The lipocalins are shown using triangles, and their interacting proteins are shown in circles. Red indicates upregulation and green indicates downregulation. The size of the node indicates the degree (the number of its interacting proteins) of the node. Bigger nodes have higher degrees. The connection between two nodes is indicated by an edge. Red edges indicate positive correlations in the expression of two proteins, and green edges indicate negative correlations. Correlation strength is shown by the edge width. (C) Expression levels of lipocalins in esophageal adenocarcinoma and esophageal squamous cell carcinoma. (D) The power law distribution of the node degree network and analysis of other network parameters. (E) Functional map of the lipocalins PPIN. Functionally grouped network with GO terms are represented as nodes, which were linked based on their kappa score level (≥0.3), suggesting overlapped enriched genes. The similar GO terms were labeled in the same color.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4487233&req=5

f3: (A-B) The human lipocalin protein-protein interaction network and the lipocalins’ changes in expression in esophageal adenocarcinoma and esophageal squamous cell carcinoma are shown. The lipocalins are shown using triangles, and their interacting proteins are shown in circles. Red indicates upregulation and green indicates downregulation. The size of the node indicates the degree (the number of its interacting proteins) of the node. Bigger nodes have higher degrees. The connection between two nodes is indicated by an edge. Red edges indicate positive correlations in the expression of two proteins, and green edges indicate negative correlations. Correlation strength is shown by the edge width. (C) Expression levels of lipocalins in esophageal adenocarcinoma and esophageal squamous cell carcinoma. (D) The power law distribution of the node degree network and analysis of other network parameters. (E) Functional map of the lipocalins PPIN. Functionally grouped network with GO terms are represented as nodes, which were linked based on their kappa score level (≥0.3), suggesting overlapped enriched genes. The similar GO terms were labeled in the same color.
Mentions: A full screening of the lipocalins’ interactions with other proteins was performed to determine how they affect cellular activity. This may provide important clues of their functions. The PPI dataset from both acknowledged HPRD and BioGRID databases provided credible original data for subsequent analysis. The lipocalin PPIN was generated by mapping the lipocalins to the parental PPI network to extract the proteins that interacted directly and all their interactions, forming a sub-network for lipocalins containing 151 nodes and 569 edges (Fig. 3). Currently, the interactions of 23 human lipocalin proteins have been reported. An esophageal carcinoma expression profile GSE26886, containing clinical samples from normal esophageal squamous epithelium, esophageal adenocarcinoma (EAC), and esophageal squamous cell carcinoma (ESCC), was analyzed to determine the expression trends of lipocalins and the proteins with which they interact. The fold-changes of these proteins in EAC and ESCC and other important parameters were integrated into the PPIN (Fig. 3A,B). In Fig. 3A,B, the color of each node indicates the level of expression. The gradient from red to green indicates upregulation through downregulation, all relative to normal esophageal tissue. The size of the node indicates the degree of the node (the number of proteins with which it interacts directly). The bigger nodes indicate higher degrees of interactions, connecting with more proteins. Every two interacting nodes are linked by an edge. The correlations in the levels of expression of any two interacting proteins are here treated as edge weight. Red edges indicate positive correlations in the expression of two interacting proteins, and green edges indicate the negative expression correlation. The strength of the correlation is indicated by the width of the edge.

Bottom Line: Lipocalins have been found to play important roles in many human diseases.In this study, human lipocalins were found to contain four structurally conserved regions (SCRs) and could be divided into two subgroups.Their subcellular distributions also suggested these lipocalins may transfer signals from the extracellular space to the nucleus using the pathway-like paths.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou 515041, China.

ABSTRACT
The lipocalin proteins (lipocalins) are a large family of small proteins characterized by low sequence similarity and highly conserved crystal structures. Lipocalins have been found to play important roles in many human diseases. For this reason, a systemic analysis of the molecular properties of human lipocalins is essential. In this study, human lipocalins were found to contain four structurally conserved regions (SCRs) and could be divided into two subgroups. A human lipocalin protein-protein interaction network (PPIN) was constructed and integrated with their expression data in esophageal carcinoma. Many lipocalins showed obvious co-expression patterns in esophageal carcinoma. Their subcellular distributions also suggested these lipocalins may transfer signals from the extracellular space to the nucleus using the pathway-like paths. These analyses also expanded our knowledge about this human ancient protein family in the background of esophageal carcinoma.

No MeSH data available.


Related in: MedlinePlus