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Gene: PHKA2 |
Gene summary for PHKA2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PHKA2 | Gene ID | 5256 |
| Gene name | phosphorylase kinase regulatory subunit alpha 2 | |
| Gene Alias | GSD9A | |
| Cytomap | Xp22.13 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | P46019 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 5256 | PHKA2 | NAFLD1 | Human | Liver | NAFLD | 3.44e-18 | 1.31e+00 | -0.04 |
| 5256 | PHKA2 | HCC1_Meng | Human | Liver | HCC | 1.06e-43 | 3.54e-02 | 0.0246 |
| 5256 | PHKA2 | HCC2_Meng | Human | Liver | HCC | 2.53e-12 | -5.53e-02 | 0.0107 |
| 5256 | PHKA2 | HCC1 | Human | Liver | HCC | 1.16e-09 | 4.68e+00 | 0.5336 |
| 5256 | PHKA2 | HCC2 | Human | Liver | HCC | 4.91e-21 | 4.96e+00 | 0.5341 |
| 5256 | PHKA2 | S027 | Human | Liver | HCC | 8.47e-11 | 1.16e+00 | 0.2446 |
| 5256 | PHKA2 | S028 | Human | Liver | HCC | 1.85e-24 | 1.13e+00 | 0.2503 |
| 5256 | PHKA2 | S029 | Human | Liver | HCC | 6.37e-23 | 1.33e+00 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00060917 | Liver | NAFLD | generation of precursor metabolites and energy | 84/1882 | 490/18723 | 7.03e-07 | 3.95e-05 | 84 |
| GO:00442623 | Liver | NAFLD | cellular carbohydrate metabolic process | 55/1882 | 283/18723 | 1.27e-06 | 6.01e-05 | 55 |
| GO:0005976 | Liver | NAFLD | polysaccharide metabolic process | 24/1882 | 107/18723 | 1.28e-04 | 2.46e-03 | 24 |
| GO:0044264 | Liver | NAFLD | cellular polysaccharide metabolic process | 22/1882 | 96/18723 | 1.73e-04 | 3.08e-03 | 22 |
| GO:0005977 | Liver | NAFLD | glycogen metabolic process | 18/1882 | 72/18723 | 2.09e-04 | 3.60e-03 | 18 |
| GO:0006073 | Liver | NAFLD | cellular glucan metabolic process | 18/1882 | 73/18723 | 2.51e-04 | 4.12e-03 | 18 |
| GO:0044042 | Liver | NAFLD | glucan metabolic process | 18/1882 | 73/18723 | 2.51e-04 | 4.12e-03 | 18 |
| GO:0006112 | Liver | NAFLD | energy reserve metabolic process | 18/1882 | 84/18723 | 1.49e-03 | 1.64e-02 | 18 |
| GO:00159807 | Liver | NAFLD | energy derivation by oxidation of organic compounds | 48/1882 | 318/18723 | 2.78e-03 | 2.54e-02 | 48 |
| GO:000609122 | Liver | HCC | generation of precursor metabolites and energy | 340/7958 | 490/18723 | 4.04e-34 | 2.85e-31 | 340 |
| GO:001598022 | Liver | HCC | energy derivation by oxidation of organic compounds | 221/7958 | 318/18723 | 1.02e-22 | 1.86e-20 | 221 |
| GO:004426221 | Liver | HCC | cellular carbohydrate metabolic process | 153/7958 | 283/18723 | 5.27e-05 | 5.00e-04 | 153 |
| GO:00059772 | Liver | HCC | glycogen metabolic process | 46/7958 | 72/18723 | 2.02e-04 | 1.56e-03 | 46 |
| GO:00060732 | Liver | HCC | cellular glucan metabolic process | 46/7958 | 73/18723 | 3.23e-04 | 2.28e-03 | 46 |
| GO:00440422 | Liver | HCC | glucan metabolic process | 46/7958 | 73/18723 | 3.23e-04 | 2.28e-03 | 46 |
| GO:00061122 | Liver | HCC | energy reserve metabolic process | 49/7958 | 84/18723 | 2.46e-03 | 1.19e-02 | 49 |
| GO:00442641 | Liver | HCC | cellular polysaccharide metabolic process | 52/7958 | 96/18723 | 1.38e-02 | 4.91e-02 | 52 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa049106 | Liver | NAFLD | Insulin signaling pathway | 29/1043 | 137/8465 | 2.23e-03 | 2.46e-02 | 1.99e-02 | 29 |
| hsa0492210 | Liver | NAFLD | Glucagon signaling pathway | 24/1043 | 107/8465 | 2.33e-03 | 2.46e-02 | 1.99e-02 | 24 |
| hsa0491011 | Liver | NAFLD | Insulin signaling pathway | 29/1043 | 137/8465 | 2.23e-03 | 2.46e-02 | 1.99e-02 | 29 |
| hsa0492211 | Liver | NAFLD | Glucagon signaling pathway | 24/1043 | 107/8465 | 2.33e-03 | 2.46e-02 | 1.99e-02 | 24 |
| hsa0491041 | Liver | HCC | Insulin signaling pathway | 95/4020 | 137/8465 | 1.53e-07 | 1.97e-06 | 1.10e-06 | 95 |
| hsa0492241 | Liver | HCC | Glucagon signaling pathway | 64/4020 | 107/8465 | 6.70e-03 | 1.87e-02 | 1.04e-02 | 64 |
| hsa0491051 | Liver | HCC | Insulin signaling pathway | 95/4020 | 137/8465 | 1.53e-07 | 1.97e-06 | 1.10e-06 | 95 |
| hsa0492251 | Liver | HCC | Glucagon signaling pathway | 64/4020 | 107/8465 | 6.70e-03 | 1.87e-02 | 1.04e-02 | 64 |
| Page: 1 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PHKA2 | SNV | Missense_Mutation | c.3609N>A | p.Ser1203Arg | p.S1203R | P46019 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-A2-A1G1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PHKA2 | SNV | Missense_Mutation | c.1715C>A | p.Thr572Lys | p.T572K | P46019 | protein_coding | tolerated(0.52) | benign(0.04) | TCGA-A2-A25E-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | PD | |
| PHKA2 | SNV | Missense_Mutation | c.1042N>T | p.Val348Phe | p.V348F | P46019 | protein_coding | deleterious(0) | benign(0.4) | TCGA-A7-A0CD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| PHKA2 | SNV | Missense_Mutation | c.709N>A | p.His237Asn | p.H237N | P46019 | protein_coding | deleterious(0.01) | possibly_damaging(0.762) | TCGA-A8-A081-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PHKA2 | SNV | Missense_Mutation | novel | c.3338N>G | p.Met1113Arg | p.M1113R | P46019 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PHKA2 | SNV | Missense_Mutation | rs374245493 | c.3332G>A | p.Arg1111Gln | p.R1111Q | P46019 | protein_coding | tolerated(0.69) | benign(0.001) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PHKA2 | SNV | Missense_Mutation | c.350N>G | p.Asn117Ser | p.N117S | P46019 | protein_coding | tolerated(0.85) | benign(0.034) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PHKA2 | SNV | Missense_Mutation | c.1243N>C | p.Glu415Gln | p.E415Q | P46019 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PHKA2 | SNV | Missense_Mutation | c.1171G>T | p.Asp391Tyr | p.D391Y | P46019 | protein_coding | deleterious(0) | possibly_damaging(0.903) | TCGA-C8-A1HK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PHKA2 | SNV | Missense_Mutation | rs191267737 | c.1397C>T | p.Ala466Val | p.A466V | P46019 | protein_coding | deleterious(0.03) | benign(0.117) | TCGA-E2-A15C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
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