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Gene: LIMD2 |
Gene summary for LIMD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LIMD2 | Gene ID | 80774 |
| Gene name | LIM domain containing 2 | |
| Gene Alias | LIMD2 | |
| Cytomap | 17q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | A0A140VJN0 |
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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 |
| 80774 | LIMD2 | LZE4T | Human | Esophagus | ESCC | 7.12e-15 | 4.85e-01 | 0.0811 |
| 80774 | LIMD2 | LZE7T | Human | Esophagus | ESCC | 1.31e-23 | 1.02e+00 | 0.0667 |
| 80774 | LIMD2 | LZE8T | Human | Esophagus | ESCC | 1.31e-04 | 3.14e-01 | 0.067 |
| 80774 | LIMD2 | LZE20T | Human | Esophagus | ESCC | 3.98e-03 | 1.29e-01 | 0.0662 |
| 80774 | LIMD2 | LZE22T | Human | Esophagus | ESCC | 1.51e-05 | 4.52e-01 | 0.068 |
| 80774 | LIMD2 | LZE24T | Human | Esophagus | ESCC | 2.11e-17 | 5.04e-01 | 0.0596 |
| 80774 | LIMD2 | LZE21T | Human | Esophagus | ESCC | 8.19e-03 | 3.08e-01 | 0.0655 |
| 80774 | LIMD2 | LZE6T | Human | Esophagus | ESCC | 6.72e-18 | 7.38e-01 | 0.0845 |
| 80774 | LIMD2 | P1T-E | Human | Esophagus | ESCC | 2.03e-25 | 1.15e+00 | 0.0875 |
| 80774 | LIMD2 | P2T-E | Human | Esophagus | ESCC | 2.23e-26 | 6.45e-01 | 0.1177 |
| 80774 | LIMD2 | P4T-E | Human | Esophagus | ESCC | 2.59e-22 | 4.89e-01 | 0.1323 |
| 80774 | LIMD2 | P5T-E | Human | Esophagus | ESCC | 3.69e-02 | 1.13e-01 | 0.1327 |
| 80774 | LIMD2 | P8T-E | Human | Esophagus | ESCC | 5.64e-22 | 4.31e-01 | 0.0889 |
| 80774 | LIMD2 | P9T-E | Human | Esophagus | ESCC | 1.27e-10 | 2.64e-01 | 0.1131 |
| 80774 | LIMD2 | P10T-E | Human | Esophagus | ESCC | 2.07e-14 | 3.12e-01 | 0.116 |
| 80774 | LIMD2 | P11T-E | Human | Esophagus | ESCC | 7.13e-11 | 6.05e-01 | 0.1426 |
| 80774 | LIMD2 | P12T-E | Human | Esophagus | ESCC | 8.07e-23 | 5.34e-01 | 0.1122 |
| 80774 | LIMD2 | P15T-E | Human | Esophagus | ESCC | 2.42e-21 | 3.38e-01 | 0.1149 |
| 80774 | LIMD2 | P16T-E | Human | Esophagus | ESCC | 1.35e-53 | 1.09e+00 | 0.1153 |
| 80774 | LIMD2 | P17T-E | Human | Esophagus | ESCC | 1.57e-03 | 2.40e-01 | 0.1278 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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 |
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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 |
| LIMD2 | SNV | Missense_Mutation | rs367901623 | c.61A>G | p.Ser21Gly | p.S21G | Q9BT23 | protein_coding | tolerated(0.57) | benign(0) | TCGA-CM-5861-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| LIMD2 | SNV | Missense_Mutation | rs367901623 | c.61A>G | p.Ser21Gly | p.S21G | Q9BT23 | protein_coding | tolerated(0.57) | benign(0) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| LIMD2 | SNV | Missense_Mutation | novel | c.298G>A | p.Gly100Ser | p.G100S | Q9BT23 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-B5-A1MX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD |
| LIMD2 | SNV | Missense_Mutation | rs867751332 | c.28N>A | p.Ala10Thr | p.A10T | Q9BT23 | protein_coding | tolerated_low_confidence(0.58) | benign(0) | TCGA-EO-A22T-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIMD2 | SNV | Missense_Mutation | c.128N>A | p.Cys43Tyr | p.C43Y | Q9BT23 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-22-5478-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LIMD2 | SNV | Missense_Mutation | novel | c.361N>C | p.Asp121His | p.D121H | Q9BT23 | protein_coding | tolerated(0.05) | benign(0.121) | TCGA-85-A4CL-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| LIMD2 | SNV | Missense_Mutation | novel | c.151N>A | p.Glu51Lys | p.E51K | Q9BT23 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CR-6481-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | paclitaxel | SD |
| LIMD2 | deletion | Frame_Shift_Del | novel | c.36delN | p.Ser13LeufsTer24 | p.S13Lfs*24 | Q9BT23 | protein_coding | TCGA-CV-6956-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
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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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