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mutLBSgeneDB |
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| Gene summary for APOD |
 Gene summary |
| Basic gene Info. | Gene symbol | APOD |
| Gene name | apolipoprotein D | |
| Synonyms | - | |
| Cytomap | UCSC genome browser: 3q29 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001647.3, | |
| Description | apo-D | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 107740 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000189058 | ||
| HPRD : 00134 | ||
| Vega : OTTHUMG00000155854 | ||
| Protein | UniProt: P05090 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_APOD | |
| BioGPS: 347 | ||
| Pathway | NCI Pathway Interaction Database: APOD | |
| KEGG: APOD | ||
| REACTOME: APOD | ||
| Pathway Commons: APOD | ||
| Context | iHOP: APOD | |
| ligand binding site mutation search in PubMed: APOD | ||
| UCL Cancer Institute: APOD | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0000302 | response to reactive oxygen species | 18419796 | GO:0006006 | glucose metabolic process | 19176353 | GO:0006629 | lipid metabolic process | 19176353 | GO:0010642 | negative regulation of platelet-derived growth factor receptor signaling pathway | 14551159 | GO:0042308 | negative regulation of protein import into nucleus | 14551159 | GO:0048662 | negative regulation of smooth muscle cell proliferation | 14551159 | GO:0060588 | negative regulation of lipoprotein lipid oxidation | 18419796 | GO:0071638 | negative regulation of monocyte chemotactic protein-1 production | 18842892 | GO:1900016 | negative regulation of cytokine production involved in inflammatory response | 18842892 | GO:2000405 | negative regulation of T cell migration | 18842892 |
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| Ligand binding site mutations for APOD |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | F109 | S110F | SKCM | 1 | T54 | P53Q | STAD | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
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| Protein structure related information for APOD |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | T54 | P53Q | -1.2558664 | F109 | S110F | -0.90955853 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for APOD from PDB |
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| Differential gene expression and gene-gene network for APOD |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for APOD |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0017638 | Glioma | 1 | Biomarker |
| umls:C0086439 | Hypokinesia | 1 | Biomarker |
| umls:C0023186 | Learning Disorders | 1 | Biomarker |
| umls:C0524851 | Neurodegenerative Diseases | 1 | Therapeutic |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for APOD |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of APOD go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of APOD |
| Multiple alignments for P05090 in multiple species |
| LBS | AA sequence | # species | Species | A64 | GNCIQANYSLM | 2 | Mus musculus, Rattus norvegicus | A64 | GRCIQANYSLM | 1 | Homo sapiens | A64 | GSCIQANYSLK | 1 | Bos taurus | F109 | KLEVKFSWFMP | 1 | Homo sapiens | F109 | KLEVQFFPLMP | 1 | Mus musculus | F109 | KLEVQFFSLMP | 1 | Rattus norvegicus | F109 | KLAVKFFWFMP | 1 | Bos taurus | N78 | KIKVLNQELRA | 1 | Homo sapiens | N78 | NIEVLNKELSP | 1 | Mus musculus | N78 | NIKVLNKELRP | 1 | Rattus norvegicus | N78 | NVEVINKELRA | 1 | Bos taurus | T54 | IEKIPVSFEKG | 2 | Rattus norvegicus, Bos taurus | T54 | IEKIPTTFENG | 1 | Homo sapiens | T54 | IEKIPASFEKG | 1 | Mus musculus | W147 | HVDFAWILARN | 1 | Homo sapiens | W147 | HVDFVWILGRN | 1 | Mus musculus | W147 | HVDYVWILGRN | 1 | Rattus norvegicus | W147 | HMDHVWILGRN | 1 | Bos taurus | Y66 | CIQANYSLMEN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y66 | CIQANYSLKEN | 1 | Bos taurus |
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