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Gene: ABCD1 |
Gene summary for ABCD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ABCD1 | Gene ID | 215 |
| Gene name | ATP binding cassette subfamily D member 1 | |
| Gene Alias | ABC42 | |
| Cytomap | Xq28 | |
| Gene Type | protein-coding | GO ID | GO:0000038 | UniProtAcc | P33897 |
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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 |
| 215 | ABCD1 | HCC1_Meng | Human | Liver | HCC | 3.38e-17 | 2.86e-02 | 0.0246 |
| 215 | ABCD1 | HCC2_Meng | Human | Liver | HCC | 5.21e-11 | 1.20e-01 | 0.0107 |
| 215 | ABCD1 | S014 | Human | Liver | HCC | 5.66e-14 | 4.13e-01 | 0.2254 |
| 215 | ABCD1 | S015 | Human | Liver | HCC | 1.71e-11 | 5.07e-01 | 0.2375 |
| 215 | ABCD1 | S016 | Human | Liver | HCC | 2.76e-19 | 5.43e-01 | 0.2243 |
| 215 | ABCD1 | S027 | Human | Liver | HCC | 1.74e-24 | 1.50e+00 | 0.2446 |
| 215 | ABCD1 | S028 | Human | Liver | HCC | 8.33e-51 | 1.59e+00 | 0.2503 |
| 215 | ABCD1 | S029 | Human | Liver | HCC | 2.68e-34 | 1.32e+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:000609122 | Liver | HCC | generation of precursor metabolites and energy | 340/7958 | 490/18723 | 4.04e-34 | 2.85e-31 | 340 |
| GO:000989622 | Liver | HCC | positive regulation of catabolic process | 335/7958 | 492/18723 | 3.83e-31 | 1.87e-28 | 335 |
| GO:003133122 | Liver | HCC | positive regulation of cellular catabolic process | 295/7958 | 427/18723 | 3.20e-29 | 1.45e-26 | 295 |
| GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
| GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
| GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
| GO:001943921 | Liver | HCC | aromatic compound catabolic process | 309/7958 | 467/18723 | 1.56e-25 | 4.94e-23 | 309 |
| GO:003465521 | Liver | HCC | nucleobase-containing compound catabolic process | 273/7958 | 407/18723 | 4.84e-24 | 1.23e-21 | 273 |
| GO:000906012 | Liver | HCC | aerobic respiration | 147/7958 | 189/18723 | 3.13e-23 | 6.61e-21 | 147 |
| GO:004533312 | Liver | HCC | cellular respiration | 171/7958 | 230/18723 | 6.35e-23 | 1.26e-20 | 171 |
| GO:004603422 | Liver | HCC | ATP metabolic process | 198/7958 | 277/18723 | 8.30e-23 | 1.55e-20 | 198 |
| GO:001598022 | Liver | HCC | energy derivation by oxidation of organic compounds | 221/7958 | 318/18723 | 1.02e-22 | 1.86e-20 | 221 |
| GO:000697922 | Liver | HCC | response to oxidative stress | 281/7958 | 446/18723 | 9.75e-19 | 1.24e-16 | 281 |
| GO:000611912 | Liver | HCC | oxidative phosphorylation | 110/7958 | 141/18723 | 6.58e-18 | 7.45e-16 | 110 |
| GO:000911722 | Liver | HCC | nucleotide metabolic process | 300/7958 | 489/18723 | 1.61e-17 | 1.71e-15 | 300 |
| GO:000675322 | Liver | HCC | nucleoside phosphate metabolic process | 304/7958 | 497/18723 | 1.78e-17 | 1.85e-15 | 304 |
| GO:001969322 | Liver | HCC | ribose phosphate metabolic process | 248/7958 | 396/18723 | 3.15e-16 | 2.70e-14 | 248 |
| GO:006219722 | Liver | HCC | cellular response to chemical stress | 216/7958 | 337/18723 | 6.86e-16 | 5.44e-14 | 216 |
| GO:000925922 | Liver | HCC | ribonucleotide metabolic process | 240/7958 | 385/18723 | 2.07e-15 | 1.51e-13 | 240 |
| GO:001593111 | Liver | HCC | nucleobase-containing compound transport | 150/7958 | 222/18723 | 3.17e-14 | 2.03e-12 | 150 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa041464 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
| hsa020102 | Liver | HCC | ABC transporters | 29/4020 | 45/8465 | 1.62e-02 | 3.88e-02 | 2.16e-02 | 29 |
| hsa041465 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
| hsa020103 | Liver | HCC | ABC transporters | 29/4020 | 45/8465 | 1.62e-02 | 3.88e-02 | 2.16e-02 | 29 |
| 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 |
| ABCD1 | SNV | Missense_Mutation | c.748N>A | p.Val250Met | p.V250M | P33897 | protein_coding | deleterious(0.02) | probably_damaging(0.998) | TCGA-E9-A295-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| ABCD1 | SNV | Missense_Mutation | c.951N>G | p.Ile317Met | p.I317M | P33897 | protein_coding | tolerated(1) | benign(0.048) | TCGA-GM-A2DO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | CR | |
| ABCD1 | SNV | Missense_Mutation | c.731N>T | p.Ser244Leu | p.S244L | P33897 | protein_coding | tolerated(0.7) | benign(0.099) | TCGA-C5-A1BF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| ABCD1 | SNV | Missense_Mutation | novel | c.1475N>A | p.Ser492Asn | p.S492N | P33897 | protein_coding | tolerated(0.13) | benign(0.005) | TCGA-C5-A8ZZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unspecific | Cisplatin | SD |
| ABCD1 | SNV | Missense_Mutation | novel | c.190N>C | p.Lys64Gln | p.K64Q | P33897 | protein_coding | tolerated(0.15) | benign(0.035) | TCGA-C5-A907-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| ABCD1 | SNV | Missense_Mutation | c.220C>T | p.Arg74Trp | p.R74W | P33897 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-EA-A411-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| ABCD1 | SNV | Missense_Mutation | c.455N>A | p.Arg152His | p.R152H | P33897 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| ABCD1 | SNV | Missense_Mutation | c.1372N>A | p.Glu458Lys | p.E458K | P33897 | protein_coding | tolerated(0.24) | benign(0.109) | TCGA-UC-A7PG-06 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | PD | |
| ABCD1 | SNV | Missense_Mutation | novel | c.2132N>T | p.Arg711Leu | p.R711L | P33897 | protein_coding | tolerated(0.06) | benign(0.007) | TCGA-VS-A8EC-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | carboplatin | CR |
| ABCD1 | SNV | Missense_Mutation | rs193922097 | c.421G>A | p.Ala141Thr | p.A141T | P33897 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A6-2681-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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