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Gene: ABLIM3 |
Gene summary for ABLIM3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ABLIM3 | Gene ID | 22885 |
| Gene name | actin binding LIM protein family member 3 | |
| Gene Alias | HMFN1661 | |
| Cytomap | 5q32 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | O94929 |
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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 |
| 22885 | ABLIM3 | NAFLD1 | Human | Liver | NAFLD | 2.30e-18 | 1.60e+00 | -0.04 |
| 22885 | ABLIM3 | S43 | Human | Liver | Cirrhotic | 2.02e-04 | -2.09e-01 | -0.0187 |
| 22885 | ABLIM3 | HCC1_Meng | Human | Liver | HCC | 2.87e-79 | -2.18e-01 | 0.0246 |
| 22885 | ABLIM3 | HCC2_Meng | Human | Liver | HCC | 2.19e-23 | -2.94e-01 | 0.0107 |
| 22885 | ABLIM3 | cirrhotic1 | Human | Liver | Cirrhotic | 4.85e-08 | -3.00e-01 | 0.0202 |
| 22885 | ABLIM3 | cirrhotic2 | Human | Liver | Cirrhotic | 6.33e-14 | -1.98e-01 | 0.0201 |
| 22885 | ABLIM3 | cirrhotic3 | Human | Liver | Cirrhotic | 1.02e-11 | -2.47e-01 | 0.0215 |
| 22885 | ABLIM3 | HCC1 | Human | Liver | HCC | 8.48e-06 | 1.14e+00 | 0.5336 |
| 22885 | ABLIM3 | Pt13.a | Human | Liver | HCC | 3.98e-07 | -2.96e-01 | 0.021 |
| 22885 | ABLIM3 | Pt13.b | Human | Liver | HCC | 3.29e-13 | -2.48e-01 | 0.0251 |
| 22885 | ABLIM3 | Pt14.a | Human | Liver | HCC | 3.68e-02 | -1.60e-01 | 0.0169 |
| 22885 | ABLIM3 | Pt14.d | Human | Liver | HCC | 9.47e-08 | -3.17e-01 | 0.0143 |
| 22885 | ABLIM3 | S016 | Human | Liver | HCC | 2.31e-04 | -2.90e-01 | 0.2243 |
| 22885 | ABLIM3 | S027 | Human | Liver | HCC | 3.49e-04 | 5.27e-01 | 0.2446 |
| 22885 | ABLIM3 | S028 | Human | Liver | HCC | 1.18e-04 | 3.76e-01 | 0.2503 |
| 22885 | ABLIM3 | S029 | Human | Liver | HCC | 8.29e-12 | 7.36e-01 | 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:00512227 | Liver | NAFLD | positive regulation of protein transport | 55/1882 | 303/18723 | 1.07e-05 | 3.35e-04 | 55 |
| GO:19049517 | Liver | NAFLD | positive regulation of establishment of protein localization | 55/1882 | 319/18723 | 4.79e-05 | 1.14e-03 | 55 |
| GO:00975816 | Liver | NAFLD | lamellipodium organization | 22/1882 | 90/18723 | 6.25e-05 | 1.37e-03 | 22 |
| GO:00300324 | Liver | NAFLD | lamellipodium assembly | 18/1882 | 72/18723 | 2.09e-04 | 3.60e-03 | 18 |
| GO:00903166 | Liver | NAFLD | positive regulation of intracellular protein transport | 29/1882 | 160/18723 | 1.24e-03 | 1.41e-02 | 29 |
| GO:00725947 | Liver | NAFLD | establishment of protein localization to organelle | 62/1882 | 422/18723 | 1.48e-03 | 1.64e-02 | 62 |
| GO:00331576 | Liver | NAFLD | regulation of intracellular protein transport | 37/1882 | 229/18723 | 2.55e-03 | 2.36e-02 | 37 |
| GO:00323866 | Liver | NAFLD | regulation of intracellular transport | 49/1882 | 337/18723 | 5.34e-03 | 4.11e-02 | 49 |
| GO:00323886 | Liver | NAFLD | positive regulation of intracellular transport | 32/1882 | 202/18723 | 6.42e-03 | 4.69e-02 | 32 |
| GO:19038297 | Liver | NAFLD | positive regulation of cellular protein localization | 41/1882 | 276/18723 | 7.11e-03 | 4.95e-02 | 41 |
| GO:007259412 | Liver | Cirrhotic | establishment of protein localization to organelle | 189/4634 | 422/18723 | 1.01e-19 | 2.45e-17 | 189 |
| GO:00066057 | Liver | Cirrhotic | protein targeting | 148/4634 | 314/18723 | 3.86e-18 | 6.20e-16 | 148 |
| GO:003238611 | Liver | Cirrhotic | regulation of intracellular transport | 147/4634 | 337/18723 | 1.84e-14 | 1.72e-12 | 147 |
| GO:003315711 | Liver | Cirrhotic | regulation of intracellular protein transport | 108/4634 | 229/18723 | 1.23e-13 | 1.04e-11 | 108 |
| GO:190382912 | Liver | Cirrhotic | positive regulation of cellular protein localization | 123/4634 | 276/18723 | 4.06e-13 | 3.22e-11 | 123 |
| GO:190495112 | Liver | Cirrhotic | positive regulation of establishment of protein localization | 135/4634 | 319/18723 | 3.20e-12 | 2.28e-10 | 135 |
| GO:00068397 | Liver | Cirrhotic | mitochondrial transport | 112/4634 | 254/18723 | 1.03e-11 | 6.66e-10 | 112 |
| GO:00705857 | Liver | Cirrhotic | protein localization to mitochondrion | 65/4634 | 125/18723 | 4.91e-11 | 2.77e-09 | 65 |
| GO:00726557 | Liver | Cirrhotic | establishment of protein localization to mitochondrion | 63/4634 | 120/18723 | 5.70e-11 | 3.19e-09 | 63 |
| GO:005122212 | Liver | Cirrhotic | positive regulation of protein transport | 126/4634 | 303/18723 | 6.85e-11 | 3.77e-09 | 126 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| ABLIM3 | SNV | Missense_Mutation | rs764090826 | c.1705N>T | p.Arg569Trp | p.R569W | O94929 | protein_coding | deleterious(0.05) | possibly_damaging(0.487) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| ABLIM3 | SNV | Missense_Mutation | novel | c.1624N>C | p.Trp542Arg | p.W542R | O94929 | protein_coding | deleterious(0.02) | possibly_damaging(0.736) | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ABLIM3 | SNV | Missense_Mutation | novel | c.1214N>T | p.Ser405Ile | p.S405I | O94929 | protein_coding | deleterious(0) | probably_damaging(0.951) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ABLIM3 | SNV | Missense_Mutation | c.577N>T | p.Asp193Tyr | p.D193Y | O94929 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-C8-A1HN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| ABLIM3 | SNV | Missense_Mutation | c.765N>T | p.Glu255Asp | p.E255D | O94929 | protein_coding | tolerated(0.12) | possibly_damaging(0.524) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| ABLIM3 | insertion | Frame_Shift_Ins | novel | c.1647_1648insTCCTTTAAAATGGTTAATTTGA | p.Ser551PhefsTer18 | p.S551Ffs*18 | O94929 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| ABLIM3 | insertion | Nonsense_Mutation | novel | c.1649_1650insTTAAGTAATTTTCAC | p.Ser550_Ser551insTer | p.S550_S551ins* | O94929 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| ABLIM3 | insertion | Frame_Shift_Ins | novel | c.1065_1066insACTAGAATAGGAGCACTCAGGAAGCTGCTGCACTG | p.Tyr356ThrfsTer34 | p.Y356Tfs*34 | O94929 | protein_coding | TCGA-A8-A08S-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| ABLIM3 | SNV | Missense_Mutation | novel | c.8C>T | p.Thr3Ile | p.T3I | O94929 | protein_coding | deleterious(0.04) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ABLIM3 | SNV | Missense_Mutation | novel | c.1061N>T | p.Ser354Phe | p.S354F | O94929 | protein_coding | deleterious(0.01) | benign(0.073) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | 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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