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Gene: LIMS1 |
Gene summary for LIMS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LIMS1 | Gene ID | 3987 |
| Gene name | LIM zinc finger domain containing 1 | |
| Gene Alias | PINCH | |
| Cytomap | 2q12.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | P48059 |
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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 |
| 3987 | LIMS1 | AEH-subject3 | Human | Endometrium | AEH | 4.82e-02 | -1.98e-01 | -0.2576 |
| 3987 | LIMS1 | EEC-subject1 | Human | Endometrium | EEC | 4.71e-03 | 6.95e-02 | -0.2682 |
| 3987 | LIMS1 | EEC-subject2 | Human | Endometrium | EEC | 6.57e-06 | -3.53e-01 | -0.2607 |
| 3987 | LIMS1 | EEC-subject3 | Human | Endometrium | EEC | 2.48e-22 | -3.67e-01 | -0.2525 |
| 3987 | LIMS1 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 6.90e-22 | -5.55e-01 | -0.1869 |
| 3987 | LIMS1 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 1.99e-26 | -6.42e-01 | -0.1875 |
| 3987 | LIMS1 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 1.07e-21 | -5.25e-01 | -0.1883 |
| 3987 | LIMS1 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 5.38e-27 | -4.57e-01 | -0.1934 |
| 3987 | LIMS1 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 5.53e-50 | -6.98e-01 | -0.1917 |
| 3987 | LIMS1 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 1.17e-43 | -7.64e-01 | -0.1916 |
| 3987 | LIMS1 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 8.90e-16 | -4.93e-01 | -0.1269 |
| 3987 | LIMS1 | LZE2D | Human | Esophagus | HGIN | 2.29e-03 | 4.43e-01 | 0.0642 |
| 3987 | LIMS1 | LZE2T | Human | Esophagus | ESCC | 1.66e-05 | 9.74e-01 | 0.082 |
| 3987 | LIMS1 | LZE3D | Human | Esophagus | HGIN | 1.12e-05 | 8.33e-01 | 0.0668 |
| 3987 | LIMS1 | LZE4T | Human | Esophagus | ESCC | 9.91e-45 | 1.51e+00 | 0.0811 |
| 3987 | LIMS1 | LZE7T | Human | Esophagus | ESCC | 4.63e-13 | 7.30e-01 | 0.0667 |
| 3987 | LIMS1 | LZE8T | Human | Esophagus | ESCC | 5.57e-14 | 4.05e-01 | 0.067 |
| 3987 | LIMS1 | LZE20T | Human | Esophagus | ESCC | 2.61e-04 | 1.89e-01 | 0.0662 |
| 3987 | LIMS1 | LZE22D1 | Human | Esophagus | HGIN | 4.17e-02 | 7.00e-02 | 0.0595 |
| 3987 | LIMS1 | LZE22T | Human | Esophagus | ESCC | 1.43e-02 | 2.96e-01 | 0.068 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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). |
| 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:009010931 | Lung | MIAC | regulation of cell-substrate junction assembly | 17/967 | 66/18723 | 2.64e-08 | 1.13e-05 | 17 |
| GO:000195231 | Lung | MIAC | regulation of cell-matrix adhesion | 24/967 | 128/18723 | 3.46e-08 | 1.37e-05 | 24 |
| GO:001081032 | Lung | MIAC | regulation of cell-substrate adhesion | 33/967 | 221/18723 | 3.79e-08 | 1.39e-05 | 33 |
| GO:004804131 | Lung | MIAC | focal adhesion assembly | 19/967 | 87/18723 | 7.35e-08 | 2.36e-05 | 19 |
| GO:015011631 | Lung | MIAC | regulation of cell-substrate junction organization | 17/967 | 71/18723 | 8.51e-08 | 2.57e-05 | 17 |
| GO:003158931 | Lung | MIAC | cell-substrate adhesion | 44/967 | 363/18723 | 1.30e-07 | 3.56e-05 | 44 |
| GO:003432931 | Lung | MIAC | cell junction assembly | 48/967 | 420/18723 | 2.13e-07 | 4.11e-05 | 48 |
| GO:000704431 | Lung | MIAC | cell-substrate junction assembly | 19/967 | 95/18723 | 3.20e-07 | 5.66e-05 | 19 |
| GO:002260432 | Lung | MIAC | regulation of cell morphogenesis | 38/967 | 309/18723 | 6.47e-07 | 9.76e-05 | 38 |
| GO:004308721 | Lung | MIAC | regulation of GTPase activity | 41/967 | 348/18723 | 7.39e-07 | 1.08e-04 | 41 |
| GO:015011531 | Lung | MIAC | cell-substrate junction organization | 19/967 | 101/18723 | 8.64e-07 | 1.23e-04 | 19 |
| GO:004578523 | Lung | MIAC | positive regulation of cell adhesion | 47/967 | 437/18723 | 1.62e-06 | 2.10e-04 | 47 |
| GO:004354721 | Lung | MIAC | positive regulation of GTPase activity | 31/967 | 255/18723 | 8.63e-06 | 7.38e-04 | 31 |
| GO:004521623 | Lung | MIAC | cell-cell junction organization | 26/967 | 200/18723 | 1.38e-05 | 9.86e-04 | 26 |
| GO:190188831 | Lung | MIAC | regulation of cell junction assembly | 25/967 | 204/18723 | 5.46e-05 | 2.75e-03 | 25 |
| GO:007155922 | Lung | MIAC | response to transforming growth factor beta | 28/967 | 256/18723 | 1.51e-04 | 5.95e-03 | 28 |
| GO:001081123 | Lung | MIAC | positive regulation of cell-substrate adhesion | 17/967 | 123/18723 | 1.96e-04 | 7.07e-03 | 17 |
| GO:007156022 | Lung | MIAC | cellular response to transforming growth factor beta stimulus | 26/967 | 250/18723 | 5.59e-04 | 1.42e-02 | 26 |
| GO:000195422 | Lung | MIAC | positive regulation of cell-matrix adhesion | 10/967 | 58/18723 | 7.02e-04 | 1.60e-02 | 10 |
| GO:20010442 | Lung | MIAC | regulation of integrin-mediated signaling pathway | 5/967 | 16/18723 | 9.85e-04 | 2.04e-02 | 5 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| LIMS1 | SNV | Missense_Mutation | novel | c.61N>T | p.Arg21Cys | p.R21C | P48059 | protein_coding | deleterious_low_confidence(0.01) | benign(0.348) | TCGA-AC-A2FE-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| LIMS1 | SNV | Missense_Mutation | novel | c.473N>T | p.Arg158Leu | p.R158L | P48059 | protein_coding | tolerated(0.39) | benign(0.015) | TCGA-BH-A1FC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LIMS1 | SNV | Missense_Mutation | c.1127G>T | p.Arg376Ile | p.R376I | P48059 | protein_coding | tolerated(0.06) | probably_damaging(0.991) | TCGA-D8-A1X6-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| LIMS1 | SNV | Missense_Mutation | rs149119038 | c.67N>A | p.Asp23Asn | p.D23N | P48059 | protein_coding | tolerated_low_confidence(0.48) | benign(0) | TCGA-EA-A3QE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LIMS1 | SNV | Missense_Mutation | c.247N>A | p.Glu83Lys | p.E83K | P48059 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| LIMS1 | SNV | Missense_Mutation | c.874C>T | p.Arg292Cys | p.R292C | P48059 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| LIMS1 | SNV | Missense_Mutation | rs200004487 | c.220N>T | p.Arg74Cys | p.R74C | P48059 | protein_coding | deleterious(0.02) | probably_damaging(0.953) | TCGA-D5-6930-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| LIMS1 | insertion | Nonsense_Mutation | novel | c.892_893insTTTGAGACA | p.Gly298delinsValTerAspSer | p.G298delinsV*DS | P48059 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| LIMS1 | SNV | Missense_Mutation | novel | c.556N>T | p.Arg186Cys | p.R186C | P48059 | protein_coding | deleterious(0.01) | possibly_damaging(0.901) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LIMS1 | SNV | Missense_Mutation | rs377342624 | c.794N>A | p.Arg265His | p.R265H | P48059 | protein_coding | deleterious(0.04) | probably_damaging(0.918) | TCGA-AJ-A3OK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | CR |
| Page: 1 2 3 |
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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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