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Gene: GAPDH |
Gene summary for GAPDH |
Gene summary. |
Gene information | Species | Human | Gene symbol | GAPDH | Gene ID | 2597 |
Gene name | glyceraldehyde-3-phosphate dehydrogenase | |
Gene Alias | G3PD | |
Cytomap | 12p13.31 | |
Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | P04406 |
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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 |
2597 | GAPDH | GSM4909321 | Human | Breast | IDC | 4.68e-09 | 1.28e-01 | 0.1559 |
2597 | GAPDH | ctrl6 | Human | Breast | Precancer | 1.76e-25 | 3.94e-01 | -0.0061 |
2597 | GAPDH | brca1 | Human | Breast | Precancer | 3.60e-08 | 2.02e-01 | -0.0338 |
2597 | GAPDH | brca3 | Human | Breast | Precancer | 1.80e-32 | 3.10e-01 | -0.0263 |
2597 | GAPDH | brca7 | Human | Breast | Precancer | 1.84e-19 | 4.90e-01 | -0.009 |
2597 | GAPDH | brca10 | Human | Breast | Precancer | 3.58e-61 | 4.22e-01 | -0.0029 |
2597 | GAPDH | M2 | Human | Breast | IDC | 1.13e-05 | 2.36e-01 | 0.21 |
2597 | GAPDH | NCCBC14 | Human | Breast | DCIS | 1.08e-05 | -3.39e-02 | 0.2021 |
2597 | GAPDH | NCCBC5 | Human | Breast | DCIS | 3.71e-36 | 3.58e-01 | 0.2046 |
2597 | GAPDH | P1 | Human | Breast | IDC | 1.40e-30 | -6.76e-01 | 0.1527 |
2597 | GAPDH | P2 | Human | Breast | IDC | 5.94e-54 | 4.70e-01 | 0.21 |
2597 | GAPDH | DCIS2 | Human | Breast | DCIS | 4.80e-25 | -1.74e-01 | 0.0085 |
2597 | GAPDH | CA_HPV_1 | Human | Cervix | CC | 5.31e-04 | -9.19e-02 | 0.0264 |
2597 | GAPDH | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 3.51e-11 | 2.10e-01 | 0.0208 |
2597 | GAPDH | N_HPV_2 | Human | Cervix | N_HPV | 1.28e-13 | 2.36e-01 | -0.0131 |
2597 | GAPDH | CCI_1 | Human | Cervix | CC | 2.77e-32 | -1.31e+00 | 0.528 |
2597 | GAPDH | CCI_2 | Human | Cervix | CC | 1.80e-09 | -2.41e-01 | 0.5249 |
2597 | GAPDH | CCI_3 | Human | Cervix | CC | 1.73e-25 | -8.47e-01 | 0.516 |
2597 | GAPDH | CCII_1 | Human | Cervix | CC | 5.40e-63 | -1.43e+00 | 0.3249 |
2597 | GAPDH | Tumor | Human | Cervix | CC | 2.99e-52 | 4.02e-01 | 0.1241 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00460349 | Breast | Precancer | ATP metabolic process | 82/1080 | 277/18723 | 1.94e-36 | 5.19e-33 | 82 |
GO:00060918 | Breast | Precancer | generation of precursor metabolites and energy | 94/1080 | 490/18723 | 1.54e-25 | 1.64e-22 | 94 |
GO:00525479 | Breast | Precancer | regulation of peptidase activity | 71/1080 | 461/18723 | 2.72e-14 | 6.94e-12 | 71 |
GO:00525489 | Breast | Precancer | regulation of endopeptidase activity | 67/1080 | 432/18723 | 1.06e-13 | 2.36e-11 | 67 |
GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
GO:00458619 | Breast | Precancer | negative regulation of proteolysis | 50/1080 | 351/18723 | 2.99e-09 | 2.39e-07 | 50 |
GO:00709979 | Breast | Precancer | neuron death | 50/1080 | 361/18723 | 7.75e-09 | 5.70e-07 | 50 |
GO:00514029 | Breast | Precancer | neuron apoptotic process | 38/1080 | 246/18723 | 2.68e-08 | 1.75e-06 | 38 |
GO:00444039 | Breast | Precancer | biological process involved in symbiotic interaction | 42/1080 | 290/18723 | 3.40e-08 | 2.11e-06 | 42 |
GO:00513468 | Breast | Precancer | negative regulation of hydrolase activity | 50/1080 | 379/18723 | 3.85e-08 | 2.34e-06 | 50 |
GO:00104668 | Breast | Precancer | negative regulation of peptidase activity | 38/1080 | 262/18723 | 1.46e-07 | 7.82e-06 | 38 |
GO:00109519 | Breast | Precancer | negative regulation of endopeptidase activity | 37/1080 | 252/18723 | 1.55e-07 | 8.05e-06 | 37 |
GO:00196938 | Breast | Precancer | ribose phosphate metabolic process | 49/1080 | 396/18723 | 3.81e-07 | 1.78e-05 | 49 |
GO:00091509 | Breast | Precancer | purine ribonucleotide metabolic process | 46/1080 | 368/18723 | 6.47e-07 | 2.71e-05 | 46 |
GO:00091179 | Breast | Precancer | nucleotide metabolic process | 56/1080 | 489/18723 | 7.40e-07 | 3.00e-05 | 56 |
GO:00092598 | Breast | Precancer | ribonucleotide metabolic process | 47/1080 | 385/18723 | 9.69e-07 | 3.84e-05 | 47 |
GO:00469398 | Breast | Precancer | nucleotide phosphorylation | 20/1080 | 101/18723 | 1.07e-06 | 4.18e-05 | 20 |
GO:00067539 | Breast | Precancer | nucleoside phosphate metabolic process | 56/1080 | 497/18723 | 1.24e-06 | 4.70e-05 | 56 |
GO:00508219 | Breast | Precancer | protein stabilization | 29/1080 | 191/18723 | 1.67e-06 | 6.08e-05 | 29 |
GO:00061639 | Breast | Precancer | purine nucleotide metabolic process | 47/1080 | 396/18723 | 2.14e-06 | 7.50e-05 | 47 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501016 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0541518 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
hsa0513218 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
hsa0513018 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
hsa0406616 | Breast | Precancer | HIF-1 signaling pathway | 23/684 | 109/8465 | 1.51e-05 | 1.59e-04 | 1.22e-04 | 23 |
hsa0001010 | Breast | Precancer | Glycolysis / Gluconeogenesis | 13/684 | 67/8465 | 2.39e-03 | 1.51e-02 | 1.16e-02 | 13 |
hsa0120012 | Breast | Precancer | Carbon metabolism | 18/684 | 115/8465 | 4.79e-03 | 2.75e-02 | 2.11e-02 | 18 |
hsa0501017 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0541519 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
hsa0513219 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
hsa0513019 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
hsa0406617 | Breast | Precancer | HIF-1 signaling pathway | 23/684 | 109/8465 | 1.51e-05 | 1.59e-04 | 1.22e-04 | 23 |
hsa0001013 | Breast | Precancer | Glycolysis / Gluconeogenesis | 13/684 | 67/8465 | 2.39e-03 | 1.51e-02 | 1.16e-02 | 13 |
hsa0120013 | Breast | Precancer | Carbon metabolism | 18/684 | 115/8465 | 4.79e-03 | 2.75e-02 | 2.11e-02 | 18 |
hsa0501023 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
hsa0541523 | Breast | IDC | Diabetic cardiomyopathy | 67/867 | 203/8465 | 3.17e-19 | 8.59e-18 | 6.43e-18 | 67 |
hsa0513224 | Breast | IDC | Salmonella infection | 55/867 | 249/8465 | 2.07e-08 | 4.49e-07 | 3.36e-07 | 55 |
hsa0513024 | Breast | IDC | Pathogenic Escherichia coli infection | 42/867 | 197/8465 | 2.66e-06 | 3.92e-05 | 2.94e-05 | 42 |
hsa0406623 | Breast | IDC | HIF-1 signaling pathway | 22/867 | 109/8465 | 1.36e-03 | 1.00e-02 | 7.50e-03 | 22 |
hsa0501033 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
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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 |
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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. |
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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 |
GAPDH | SNV | Missense_Mutation | c.658N>C | p.Val220Leu | p.V220L | P04406 | protein_coding | deleterious_low_confidence(0.01) | benign(0.409) | TCGA-A2-A25B-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | PD | |
GAPDH | SNV | Missense_Mutation | novel | c.550A>G | p.Thr184Ala | p.T184A | P04406 | protein_coding | deleterious_low_confidence(0) | benign(0.1) | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD |
GAPDH | insertion | Frame_Shift_Ins | novel | c.536_537insT | p.Ala180CysfsTer19 | p.A180Cfs*19 | P04406 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
GAPDH | insertion | In_Frame_Ins | novel | c.538_539insCCCTTCTCCCCATTCCGTCTT | p.Ala180_Ile181insLeuLeuProIleProSerSer | p.A180_I181insLLPIPSS | P04406 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
GAPDH | insertion | Frame_Shift_Ins | novel | c.322_323insGGTGGGCTTGCCCTGTCCAGTTAATTTCTGAC | p.Ala108GlyfsTer39 | p.A108Gfs*39 | P04406 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
GAPDH | SNV | Missense_Mutation | c.274N>A | p.Ala92Thr | p.A92T | P04406 | protein_coding | deleterious_low_confidence(0.03) | benign(0.07) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
GAPDH | SNV | Missense_Mutation | c.599N>T | p.Arg200Leu | p.R200L | P04406 | protein_coding | tolerated_low_confidence(0.06) | benign(0.068) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
GAPDH | SNV | Missense_Mutation | c.306C>G | p.Phe102Leu | p.F102L | P04406 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.805) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
GAPDH | SNV | Missense_Mutation | novel | c.887A>G | p.Asp296Gly | p.D296G | P04406 | protein_coding | deleterious_low_confidence(0.01) | benign(0.423) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
GAPDH | SNV | Missense_Mutation | c.266N>G | p.Asp89Gly | p.D89G | P04406 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.615) | TCGA-AP-A0LP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Hormone Therapy | megace | 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 |
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | PURPUROGALLIN | PURPUROGALLIN | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | NSC-228155 | CHEMBL505670 | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | NSC-92207 | CHEMBL139935 | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | NSC-119911 | CHEMBL502775 | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | BISPHOSPHONATES | 8518293 | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | NSC-95397 | CHEMBL429095 | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | TCMDC-124224 | CHEMBL580421 | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | Omigapil | OMIGAPIL | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | 9,10-PHENANTHRENEQUINONE | 9,10-PHENANTHRENEQUINONE | ||
2597 | GAPDH | DRUGGABLE GENOME, ENZYME | ANESTHETICS | 17194030 |
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