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Gene: HKDC1 |
Gene summary for HKDC1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HKDC1 | Gene ID | 80201 |
| Gene name | hexokinase domain containing 1 | |
| Gene Alias | HKDC1 | |
| Cytomap | 10q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0001678 | UniProtAcc | B3KT70 |
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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 |
| 80201 | HKDC1 | AEH-subject1 | Human | Endometrium | AEH | 2.03e-26 | 6.40e-01 | -0.3059 |
| 80201 | HKDC1 | AEH-subject2 | Human | Endometrium | AEH | 3.70e-05 | 2.74e-01 | -0.2525 |
| 80201 | HKDC1 | AEH-subject4 | Human | Endometrium | AEH | 2.30e-10 | 4.30e-01 | -0.2657 |
| 80201 | HKDC1 | EEC-subject2 | Human | Endometrium | EEC | 2.41e-21 | 6.09e-01 | -0.2607 |
| 80201 | HKDC1 | EEC-subject3 | Human | Endometrium | EEC | 5.95e-03 | 2.86e-01 | -0.2525 |
| 80201 | HKDC1 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 4.49e-03 | 2.17e-01 | -0.1269 |
| 80201 | HKDC1 | HCC1_Meng | Human | Liver | HCC | 3.69e-57 | 1.25e-01 | 0.0246 |
| 80201 | HKDC1 | HCC2_Meng | Human | Liver | HCC | 3.54e-19 | 1.02e-01 | 0.0107 |
| 80201 | HKDC1 | cirrhotic2 | Human | Liver | Cirrhotic | 4.22e-04 | 1.40e-01 | 0.0201 |
| 80201 | HKDC1 | HCC2 | Human | Liver | HCC | 9.32e-26 | 6.06e+00 | 0.5341 |
| 80201 | HKDC1 | Pt13.b | Human | Liver | HCC | 4.87e-13 | 2.17e-01 | 0.0251 |
| 80201 | HKDC1 | Pt14.a | Human | Liver | HCC | 6.41e-04 | 2.61e-01 | 0.0169 |
| 80201 | HKDC1 | S027 | Human | Liver | HCC | 5.56e-11 | 1.16e+00 | 0.2446 |
| 80201 | HKDC1 | S028 | Human | Liver | HCC | 1.03e-30 | 1.22e+00 | 0.2503 |
| 80201 | HKDC1 | S029 | Human | Liver | HCC | 3.25e-25 | 1.65e+00 | 0.2581 |
| 80201 | HKDC1 | Pat01-B | Human | Stomach | GC | 3.50e-62 | 1.09e+00 | 0.5754 |
| 80201 | HKDC1 | Pat02-B | Human | Stomach | GC | 6.72e-11 | 3.08e-01 | 0.0368 |
| 80201 | HKDC1 | Pat03-B | Human | Stomach | GC | 1.60e-37 | 7.90e-01 | 0.3693 |
| 80201 | HKDC1 | Pat04-B | Human | Stomach | GC | 4.99e-06 | 2.13e-01 | -0.1483 |
| 80201 | HKDC1 | Pat05-B | Human | Stomach | GC | 1.48e-04 | 2.52e-01 | -0.0353 |
| Page: 1 2 3 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:0046034 | Colorectum | AD | ATP metabolic process | 142/3918 | 277/18723 | 2.64e-29 | 8.26e-26 | 142 |
| GO:0006091 | Colorectum | AD | generation of precursor metabolites and energy | 209/3918 | 490/18723 | 3.17e-28 | 6.61e-25 | 209 |
| GO:0009150 | Colorectum | AD | purine ribonucleotide metabolic process | 142/3918 | 368/18723 | 4.29e-15 | 1.17e-12 | 142 |
| GO:0006163 | Colorectum | AD | purine nucleotide metabolic process | 149/3918 | 396/18723 | 1.08e-14 | 2.80e-12 | 149 |
| GO:0072521 | Colorectum | AD | purine-containing compound metabolic process | 153/3918 | 416/18723 | 4.34e-14 | 1.01e-11 | 153 |
| GO:0009259 | Colorectum | AD | ribonucleotide metabolic process | 144/3918 | 385/18723 | 5.25e-14 | 1.13e-11 | 144 |
| GO:0019693 | Colorectum | AD | ribose phosphate metabolic process | 145/3918 | 396/18723 | 3.01e-13 | 5.71e-11 | 145 |
| GO:0009117 | Colorectum | AD | nucleotide metabolic process | 168/3918 | 489/18723 | 2.20e-12 | 3.36e-10 | 168 |
| GO:0006753 | Colorectum | AD | nucleoside phosphate metabolic process | 169/3918 | 497/18723 | 4.99e-12 | 6.98e-10 | 169 |
| GO:0009135 | Colorectum | AD | purine nucleoside diphosphate metabolic process | 47/3918 | 103/18723 | 1.61e-08 | 9.22e-07 | 47 |
| GO:0009179 | Colorectum | AD | purine ribonucleoside diphosphate metabolic process | 47/3918 | 103/18723 | 1.61e-08 | 9.22e-07 | 47 |
| GO:0006090 | Colorectum | AD | pyruvate metabolic process | 47/3918 | 106/18723 | 4.85e-08 | 2.55e-06 | 47 |
| GO:0009185 | Colorectum | AD | ribonucleoside diphosphate metabolic process | 47/3918 | 106/18723 | 4.85e-08 | 2.55e-06 | 47 |
| GO:0046031 | Colorectum | AD | ADP metabolic process | 41/3918 | 90/18723 | 1.37e-07 | 6.42e-06 | 41 |
| GO:0006096 | Colorectum | AD | glycolytic process | 38/3918 | 81/18723 | 1.52e-07 | 6.78e-06 | 38 |
| GO:0006757 | Colorectum | AD | ATP generation from ADP | 38/3918 | 82/18723 | 2.26e-07 | 9.37e-06 | 38 |
| GO:0009132 | Colorectum | AD | nucleoside diphosphate metabolic process | 49/3918 | 124/18723 | 1.75e-06 | 5.31e-05 | 49 |
| GO:0046939 | Colorectum | AD | nucleotide phosphorylation | 42/3918 | 101/18723 | 1.99e-06 | 5.92e-05 | 42 |
| GO:0016052 | Colorectum | AD | carbohydrate catabolic process | 56/3918 | 154/18723 | 7.01e-06 | 1.73e-04 | 56 |
| GO:0006165 | Colorectum | AD | nucleoside diphosphate phosphorylation | 40/3918 | 99/18723 | 8.02e-06 | 1.93e-04 | 40 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05131 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
| hsa01200 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
| hsa00010 | Colorectum | AD | Glycolysis / Gluconeogenesis | 34/2092 | 67/8465 | 3.63e-06 | 4.34e-05 | 2.77e-05 | 34 |
| hsa04066 | Colorectum | AD | HIF-1 signaling pathway | 48/2092 | 109/8465 | 7.25e-06 | 7.84e-05 | 5.00e-05 | 48 |
| hsa05230 | Colorectum | AD | Central carbon metabolism in cancer | 33/2092 | 70/8465 | 3.61e-05 | 3.19e-04 | 2.03e-04 | 33 |
| hsa00051 | Colorectum | AD | Fructose and mannose metabolism | 17/2092 | 34/8465 | 1.25e-03 | 8.02e-03 | 5.12e-03 | 17 |
| hsa051311 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
| hsa012001 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
| hsa000101 | Colorectum | AD | Glycolysis / Gluconeogenesis | 34/2092 | 67/8465 | 3.63e-06 | 4.34e-05 | 2.77e-05 | 34 |
| hsa040661 | Colorectum | AD | HIF-1 signaling pathway | 48/2092 | 109/8465 | 7.25e-06 | 7.84e-05 | 5.00e-05 | 48 |
| hsa052301 | Colorectum | AD | Central carbon metabolism in cancer | 33/2092 | 70/8465 | 3.61e-05 | 3.19e-04 | 2.03e-04 | 33 |
| hsa000511 | Colorectum | AD | Fructose and mannose metabolism | 17/2092 | 34/8465 | 1.25e-03 | 8.02e-03 | 5.12e-03 | 17 |
| hsa051312 | Colorectum | SER | Shigellosis | 87/1580 | 247/8465 | 3.07e-10 | 7.27e-09 | 5.28e-09 | 87 |
| hsa012002 | Colorectum | SER | Carbon metabolism | 40/1580 | 115/8465 | 2.77e-05 | 3.41e-04 | 2.47e-04 | 40 |
| hsa040662 | Colorectum | SER | HIF-1 signaling pathway | 36/1580 | 109/8465 | 2.27e-04 | 2.15e-03 | 1.56e-03 | 36 |
| hsa052302 | Colorectum | SER | Central carbon metabolism in cancer | 25/1580 | 70/8465 | 5.43e-04 | 4.51e-03 | 3.27e-03 | 25 |
| hsa000102 | Colorectum | SER | Glycolysis / Gluconeogenesis | 24/1580 | 67/8465 | 6.62e-04 | 5.36e-03 | 3.89e-03 | 24 |
| hsa051313 | Colorectum | SER | Shigellosis | 87/1580 | 247/8465 | 3.07e-10 | 7.27e-09 | 5.28e-09 | 87 |
| hsa012003 | Colorectum | SER | Carbon metabolism | 40/1580 | 115/8465 | 2.77e-05 | 3.41e-04 | 2.47e-04 | 40 |
| hsa040663 | Colorectum | SER | HIF-1 signaling pathway | 36/1580 | 109/8465 | 2.27e-04 | 2.15e-03 | 1.56e-03 | 36 |
| Page: 1 2 3 4 5 |
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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 |
| HKDC1 | SNV | Missense_Mutation | novel | c.885N>C | p.Lys295Asn | p.K295N | Q2TB90 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| HKDC1 | SNV | Missense_Mutation | c.859A>C | p.Asn287His | p.N287H | Q2TB90 | protein_coding | deleterious(0.03) | possibly_damaging(0.594) | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | |
| HKDC1 | SNV | Missense_Mutation | novel | c.720N>T | p.Glu240Asp | p.E240D | Q2TB90 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| HKDC1 | SNV | Missense_Mutation | novel | c.2367C>G | p.Ile789Met | p.I789M | Q2TB90 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-GM-A2DO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | CR |
| HKDC1 | SNV | Missense_Mutation | novel | c.1597N>T | p.Leu533Phe | p.L533F | Q2TB90 | protein_coding | deleterious(0.01) | probably_damaging(0.962) | TCGA-LL-A5YP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| HKDC1 | insertion | Nonsense_Mutation | novel | c.1795_1796insAGCTGGGACTACAGGCGCCCAGCACCACACCCGGA | p.Phe599Ter | p.F599* | Q2TB90 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| HKDC1 | insertion | Frame_Shift_Ins | novel | c.782_783insCAAGCTGCTTCCCTCAGCGAGA | p.Trp261CysfsTer23 | p.W261Cfs*23 | Q2TB90 | protein_coding | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| HKDC1 | insertion | Nonsense_Mutation | novel | c.307_308insACTGTGCCCAGCCCCCACCTTTCAATTAATGGCATCTGTCTTGG | p.Arg103HisfsTer10 | p.R103Hfs*10 | Q2TB90 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| HKDC1 | SNV | Missense_Mutation | c.1099N>A | p.Asp367Asn | p.D367N | Q2TB90 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| HKDC1 | SNV | Missense_Mutation | novel | c.464N>G | p.Ser155Cys | p.S155C | Q2TB90 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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 |
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | SJ000044511 | CHEMBL592124 | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | OXOPURPUREINE | OXOPURPUREINE | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | DNDI1417874 | CHEMBL1865517 | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | 2,6-DIMETHOXYQUINONE | 2,6-DIMETHOXYQUINONE | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | ALEXIDINE HYDROCHLORIDE | ALEXIDINE HYDROCHLORIDE | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | DEOXYVASICINONE | DEOXYVASICINONE | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | NSC-95397 | CHEMBL429095 | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | SJ000032153 | CHEMBL600862 | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | CHLORHEXIDINE | CHLORHEXIDINE | ||
| 80201 | HKDC1 | DRUGGABLE GENOME, KINASE | NSC-37642 | CHEMBL1707907 |
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