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Gene: LDHD |
Gene summary for LDHD |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LDHD | Gene ID | 197257 |
| Gene name | lactate dehydrogenase D | |
| Gene Alias | DLACD | |
| Cytomap | 16q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | Q86WU2 |
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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 |
| 197257 | LDHD | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.00e-05 | 3.27e-01 | -0.1808 |
| 197257 | LDHD | HTA11_347_2000001011 | Human | Colorectum | AD | 2.81e-12 | 4.12e-01 | -0.1954 |
| 197257 | LDHD | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.43e-02 | 1.32e-01 | -0.059 |
| 197257 | LDHD | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.19e-07 | 5.13e-01 | -0.2061 |
| 197257 | LDHD | HCC1_Meng | Human | Liver | HCC | 4.17e-10 | -1.86e-03 | 0.0246 |
| 197257 | LDHD | HCC1 | Human | Liver | HCC | 2.29e-02 | 2.44e+00 | 0.5336 |
| 197257 | LDHD | HCC2 | Human | Liver | HCC | 3.16e-10 | 2.55e+00 | 0.5341 |
| 197257 | LDHD | S016 | Human | Liver | HCC | 2.31e-02 | 5.78e-02 | 0.2243 |
| 197257 | LDHD | S027 | Human | Liver | HCC | 3.31e-02 | 1.72e-01 | 0.2446 |
| 197257 | LDHD | S028 | Human | Liver | HCC | 4.77e-04 | 2.19e-01 | 0.2503 |
| 197257 | LDHD | S029 | Human | Liver | HCC | 6.26e-05 | 3.25e-01 | 0.2581 |
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| 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 | ||
| 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:0044282 | Colorectum | AD | small molecule catabolic process | 118/3918 | 376/18723 | 1.05e-06 | 3.55e-05 | 118 |
| GO:0072329 | Colorectum | AD | monocarboxylic acid catabolic process | 44/3918 | 122/18723 | 8.05e-05 | 1.28e-03 | 44 |
| GO:0016054 | Colorectum | AD | organic acid catabolic process | 73/3918 | 240/18723 | 3.20e-04 | 3.81e-03 | 73 |
| GO:0046395 | Colorectum | AD | carboxylic acid catabolic process | 70/3918 | 236/18723 | 9.06e-04 | 8.71e-03 | 70 |
| GO:00442821 | Colorectum | SER | small molecule catabolic process | 87/2897 | 376/18723 | 5.31e-05 | 1.27e-03 | 87 |
| GO:00723291 | Colorectum | SER | monocarboxylic acid catabolic process | 34/2897 | 122/18723 | 3.27e-04 | 5.22e-03 | 34 |
| GO:00160541 | Colorectum | SER | organic acid catabolic process | 53/2897 | 240/18723 | 4.04e-03 | 3.30e-02 | 53 |
| GO:004428221 | Liver | HCC | small molecule catabolic process | 225/7958 | 376/18723 | 6.50e-12 | 2.80e-10 | 225 |
| GO:001605421 | Liver | HCC | organic acid catabolic process | 152/7958 | 240/18723 | 5.11e-11 | 1.92e-09 | 152 |
| GO:00463952 | Liver | HCC | carboxylic acid catabolic process | 149/7958 | 236/18723 | 1.11e-10 | 3.87e-09 | 149 |
| GO:007232921 | Liver | HCC | monocarboxylic acid catabolic process | 80/7958 | 122/18723 | 2.18e-07 | 3.91e-06 | 80 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa00620 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
| hsa006201 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
| hsa006202 | Colorectum | SER | Pyruvate metabolism | 22/1580 | 47/8465 | 9.62e-06 | 1.33e-04 | 9.67e-05 | 22 |
| hsa006203 | Colorectum | SER | Pyruvate metabolism | 22/1580 | 47/8465 | 9.62e-06 | 1.33e-04 | 9.67e-05 | 22 |
| hsa0062021 | Liver | HCC | Pyruvate metabolism | 37/4020 | 47/8465 | 1.10e-05 | 8.03e-05 | 4.46e-05 | 37 |
| hsa0062031 | Liver | HCC | Pyruvate metabolism | 37/4020 | 47/8465 | 1.10e-05 | 8.03e-05 | 4.46e-05 | 37 |
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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 |
| LDHD | SNV | Missense_Mutation | c.1312N>T | p.Ala438Ser | p.A438S | Q86WU2 | protein_coding | tolerated(0.06) | benign(0.209) | TCGA-A2-A3XV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR | |
| LDHD | deletion | Frame_Shift_Del | novel | c.981delG | p.Glu327AspfsTer19 | p.E327Dfs*19 | Q86WU2 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| LDHD | SNV | Missense_Mutation | novel | c.1492N>A | p.Gln498Lys | p.Q498K | Q86WU2 | protein_coding | tolerated(1) | benign(0) | TCGA-A6-2683-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | irinotecan | PD |
| LDHD | SNV | Missense_Mutation | rs771707660 | c.1081N>A | p.Glu361Lys | p.E361K | Q86WU2 | protein_coding | deleterious(0.01) | probably_damaging(0.983) | TCGA-CA-6715-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR |
| LDHD | SNV | Missense_Mutation | c.1280N>C | p.Phe427Ser | p.F427S | Q86WU2 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-D5-6540-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LDHD | SNV | Missense_Mutation | c.880N>T | p.Val294Leu | p.V294L | Q86WU2 | protein_coding | tolerated(0.13) | possibly_damaging(0.447) | TCGA-D5-6932-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LDHD | SNV | Missense_Mutation | rs758295578 | c.814N>A | p.Ala272Thr | p.A272T | Q86WU2 | protein_coding | deleterious(0.02) | possibly_damaging(0.87) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LDHD | SNV | Missense_Mutation | novel | c.443N>A | p.Arg148Gln | p.R148Q | Q86WU2 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LDHD | SNV | Missense_Mutation | rs375943140 | c.695N>A | p.Arg232His | p.R232H | Q86WU2 | protein_coding | deleterious(0.01) | benign(0) | TCGA-A5-A0VP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LDHD | SNV | Missense_Mutation | novel | c.515N>T | p.Ala172Val | p.A172V | Q86WU2 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-A5-A0VP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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