|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: AFM |
Gene summary for AFM |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AFM | Gene ID | 173 |
| Gene name | afamin | |
| Gene Alias | ALB2 | |
| Cytomap | 4q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | P43652 |
Top |
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 |
| 173 | AFM | NAFLD1 | Human | Liver | NAFLD | 5.60e-08 | 8.77e-01 | -0.04 |
| 173 | AFM | S41 | Human | Liver | Cirrhotic | 3.04e-03 | 3.77e-01 | -0.0343 |
| 173 | AFM | S43 | Human | Liver | Cirrhotic | 2.29e-07 | -1.63e-01 | -0.0187 |
| 173 | AFM | HCC1_Meng | Human | Liver | HCC | 1.79e-10 | -2.75e-01 | 0.0246 |
| 173 | AFM | HCC2_Meng | Human | Liver | HCC | 4.58e-11 | -2.78e-01 | 0.0107 |
| 173 | AFM | cirrhotic1 | Human | Liver | Cirrhotic | 1.16e-04 | -2.45e-01 | 0.0202 |
| 173 | AFM | cirrhotic2 | Human | Liver | Cirrhotic | 5.64e-06 | -2.37e-01 | 0.0201 |
| 173 | AFM | cirrhotic3 | Human | Liver | Cirrhotic | 6.39e-04 | -2.78e-01 | 0.0215 |
| 173 | AFM | HCC2 | Human | Liver | HCC | 2.50e-22 | 4.29e+00 | 0.5341 |
| 173 | AFM | Pt14.d | Human | Liver | HCC | 3.37e-02 | -2.02e-01 | 0.0143 |
| 173 | AFM | S016 | Human | Liver | HCC | 4.20e-03 | -2.78e-01 | 0.2243 |
| 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. |
Top |
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: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:0044270 | Colorectum | AD | cellular nitrogen compound catabolic process | 147/3918 | 451/18723 | 3.35e-09 | 2.23e-07 | 147 |
| GO:0046700 | Colorectum | AD | heterocycle catabolic process | 145/3918 | 445/18723 | 4.37e-09 | 2.84e-07 | 145 |
| GO:0019439 | Colorectum | AD | aromatic compound catabolic process | 146/3918 | 467/18723 | 7.48e-08 | 3.84e-06 | 146 |
| GO:1901361 | Colorectum | AD | organic cyclic compound catabolic process | 153/3918 | 495/18723 | 8.23e-08 | 4.18e-06 | 153 |
| GO:0044282 | Colorectum | AD | small molecule catabolic process | 118/3918 | 376/18723 | 1.05e-06 | 3.55e-05 | 118 |
| GO:1901293 | Colorectum | AD | nucleoside phosphate biosynthetic process | 80/3918 | 256/18723 | 6.31e-05 | 1.05e-03 | 80 |
| GO:0009165 | Colorectum | AD | nucleotide biosynthetic process | 79/3918 | 254/18723 | 8.33e-05 | 1.30e-03 | 79 |
| 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:0006520 | Colorectum | AD | cellular amino acid metabolic process | 81/3918 | 284/18723 | 1.37e-03 | 1.19e-02 | 81 |
| GO:00442702 | Colorectum | MSS | cellular nitrogen compound catabolic process | 141/3467 | 451/18723 | 2.95e-11 | 3.83e-09 | 141 |
| GO:00467002 | Colorectum | MSS | heterocycle catabolic process | 139/3467 | 445/18723 | 4.37e-11 | 5.05e-09 | 139 |
| GO:19013612 | Colorectum | MSS | organic cyclic compound catabolic process | 148/3467 | 495/18723 | 3.47e-10 | 3.18e-08 | 148 |
| GO:00194392 | Colorectum | MSS | aromatic compound catabolic process | 140/3467 | 467/18723 | 8.56e-10 | 6.85e-08 | 140 |
| GO:00091172 | Colorectum | MSS | nucleotide metabolic process | 144/3467 | 489/18723 | 1.87e-09 | 1.35e-07 | 144 |
| GO:00067532 | Colorectum | MSS | nucleoside phosphate metabolic process | 145/3467 | 497/18723 | 3.25e-09 | 2.23e-07 | 145 |
| GO:19012932 | Colorectum | MSS | nucleoside phosphate biosynthetic process | 71/3467 | 256/18723 | 1.80e-04 | 2.56e-03 | 71 |
| GO:00091652 | Colorectum | MSS | nucleotide biosynthetic process | 70/3467 | 254/18723 | 2.44e-04 | 3.34e-03 | 70 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| AFM | SNV | Missense_Mutation | c.1230N>T | p.Lys410Asn | p.K410N | P43652 | protein_coding | tolerated(0.1) | benign(0.198) | TCGA-A8-A097-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| AFM | SNV | Missense_Mutation | c.1515C>A | p.Phe505Leu | p.F505L | P43652 | protein_coding | tolerated(0.54) | probably_damaging(0.998) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| AFM | SNV | Missense_Mutation | c.931N>T | p.Gly311Cys | p.G311C | P43652 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-D8-A1XL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide+tamoxifen | SD | |
| AFM | insertion | Frame_Shift_Ins | novel | c.613_614insAT | p.Arg205AsnfsTer10 | p.R205Nfs*10 | P43652 | protein_coding | TCGA-A8-A0A9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| AFM | insertion | Nonsense_Mutation | novel | c.614_615insAAGTTGCCAGAAGGAACCCATTTGTCTTCGCCCCTACACTTCTAACTGTTGCTGTTCATTTTGAGGA | p.Ala206SerfsTer21 | p.A206Sfs*21 | P43652 | protein_coding | TCGA-A8-A0A9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| AFM | insertion | Nonsense_Mutation | novel | c.270_270+1insCTTTCTGCCGGTTAGGCACA | p.Asn91LeufsTer5 | p.N91Lfs*5 | P43652 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| AFM | SNV | Missense_Mutation | c.836N>T | p.Arg279Leu | p.R279L | P43652 | protein_coding | tolerated(0.11) | benign(0.066) | TCGA-EA-A411-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| AFM | SNV | Missense_Mutation | c.161N>G | p.Tyr54Cys | p.Y54C | P43652 | protein_coding | deleterious(0.01) | probably_damaging(0.989) | TCGA-AD-6965-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | PD | |
| AFM | SNV | Missense_Mutation | c.539C>T | p.Thr180Ile | p.T180I | P43652 | protein_coding | tolerated(0.14) | possibly_damaging(0.739) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| AFM | SNV | Missense_Mutation | c.770C>A | p.Ser257Tyr | p.S257Y | P43652 | protein_coding | deleterious(0.04) | probably_damaging(0.93) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |