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Gene: LIMK1 |
Gene summary for LIMK1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LIMK1 | Gene ID | 3984 |
| Gene name | LIM domain kinase 1 | |
| Gene Alias | LIMK | |
| Cytomap | 7q11.23 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | P53667 |
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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 |
| 3984 | LIMK1 | C04 | Human | Oral cavity | OSCC | 1.32e-03 | 2.46e-01 | 0.2633 |
| 3984 | LIMK1 | C21 | Human | Oral cavity | OSCC | 1.06e-03 | 2.62e-01 | 0.2678 |
| 3984 | LIMK1 | C30 | Human | Oral cavity | OSCC | 2.38e-22 | 7.65e-01 | 0.3055 |
| 3984 | LIMK1 | C38 | Human | Oral cavity | OSCC | 1.44e-02 | 4.08e-01 | 0.172 |
| 3984 | LIMK1 | C51 | Human | Oral cavity | OSCC | 1.24e-09 | 4.40e-01 | 0.2674 |
| 3984 | LIMK1 | C57 | Human | Oral cavity | OSCC | 2.12e-02 | 1.73e-01 | 0.1679 |
| 3984 | LIMK1 | C06 | Human | Oral cavity | OSCC | 6.77e-06 | 7.30e-01 | 0.2699 |
| 3984 | LIMK1 | C08 | Human | Oral cavity | OSCC | 4.19e-04 | 1.91e-01 | 0.1919 |
| 3984 | LIMK1 | SYSMH1 | Human | Oral cavity | OSCC | 3.14e-18 | 3.32e-01 | 0.1127 |
| 3984 | LIMK1 | SYSMH2 | Human | Oral cavity | OSCC | 4.67e-04 | 1.80e-01 | 0.2326 |
| 3984 | LIMK1 | SYSMH3 | Human | Oral cavity | OSCC | 1.80e-07 | 2.33e-01 | 0.2442 |
| 3984 | LIMK1 | male-WTA | Human | Thyroid | PTC | 1.84e-14 | 1.81e-01 | 0.1037 |
| 3984 | LIMK1 | PTC04 | Human | Thyroid | PTC | 1.78e-07 | 1.39e-01 | 0.1927 |
| 3984 | LIMK1 | PTC05 | Human | Thyroid | PTC | 4.95e-07 | 3.37e-01 | 0.2065 |
| 3984 | LIMK1 | PTC06 | Human | Thyroid | PTC | 2.69e-16 | 4.01e-01 | 0.2057 |
| 3984 | LIMK1 | PTC07 | Human | Thyroid | PTC | 2.97e-07 | 2.07e-01 | 0.2044 |
| 3984 | LIMK1 | ATC09 | Human | Thyroid | ATC | 3.99e-11 | 4.67e-01 | 0.2871 |
| 3984 | LIMK1 | ATC12 | Human | Thyroid | ATC | 1.68e-12 | 2.66e-01 | 0.34 |
| 3984 | LIMK1 | ATC13 | Human | Thyroid | ATC | 2.41e-17 | 3.12e-01 | 0.34 |
| 3984 | LIMK1 | ATC1 | Human | Thyroid | ATC | 1.81e-11 | 4.74e-01 | 0.2878 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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). |
| 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:190332020 | Oral cavity | OSCC | regulation of protein modification by small protein conjugation or removal | 165/7305 | 242/18723 | 2.52e-20 | 3.99e-18 | 165 |
| GO:003139620 | Oral cavity | OSCC | regulation of protein ubiquitination | 143/7305 | 210/18723 | 1.01e-17 | 9.80e-16 | 143 |
| GO:005134820 | Oral cavity | OSCC | negative regulation of transferase activity | 165/7305 | 268/18723 | 5.02e-14 | 2.74e-12 | 165 |
| GO:001604917 | Oral cavity | OSCC | cell growth | 268/7305 | 482/18723 | 6.55e-14 | 3.51e-12 | 268 |
| GO:190290520 | Oral cavity | OSCC | positive regulation of supramolecular fiber organization | 131/7305 | 209/18723 | 3.18e-12 | 1.27e-10 | 131 |
| GO:000155816 | Oral cavity | OSCC | regulation of cell growth | 228/7305 | 414/18723 | 1.74e-11 | 6.09e-10 | 228 |
| GO:190290320 | Oral cavity | OSCC | regulation of supramolecular fiber organization | 211/7305 | 383/18723 | 9.45e-11 | 2.88e-09 | 211 |
| GO:003139720 | Oral cavity | OSCC | negative regulation of protein ubiquitination | 61/7305 | 83/18723 | 1.78e-10 | 5.17e-09 | 61 |
| GO:005149518 | Oral cavity | OSCC | positive regulation of cytoskeleton organization | 135/7305 | 226/18723 | 1.98e-10 | 5.66e-09 | 135 |
| GO:00072659 | Oral cavity | OSCC | Ras protein signal transduction | 185/7305 | 337/18723 | 1.95e-09 | 4.60e-08 | 185 |
| GO:190332120 | Oral cavity | OSCC | negative regulation of protein modification by small protein conjugation or removal | 65/7305 | 95/18723 | 5.88e-09 | 1.26e-07 | 65 |
| GO:000701520 | Oral cavity | OSCC | actin filament organization | 230/7305 | 442/18723 | 1.37e-08 | 2.77e-07 | 230 |
| GO:003297020 | Oral cavity | OSCC | regulation of actin filament-based process | 209/7305 | 397/18723 | 1.89e-08 | 3.72e-07 | 209 |
| GO:003253519 | Oral cavity | OSCC | regulation of cellular component size | 201/7305 | 383/18723 | 4.80e-08 | 8.88e-07 | 201 |
| GO:003295620 | Oral cavity | OSCC | regulation of actin cytoskeleton organization | 189/7305 | 358/18723 | 6.81e-08 | 1.21e-06 | 189 |
| GO:011005320 | Oral cavity | OSCC | regulation of actin filament organization | 150/7305 | 278/18723 | 2.68e-07 | 4.15e-06 | 150 |
| GO:00107209 | Oral cavity | OSCC | positive regulation of cell development | 159/7305 | 298/18723 | 3.06e-07 | 4.66e-06 | 159 |
| GO:005143810 | Oral cavity | OSCC | regulation of ubiquitin-protein transferase activity | 37/7305 | 53/18723 | 5.37e-06 | 6.04e-05 | 37 |
| GO:00507696 | Oral cavity | OSCC | positive regulation of neurogenesis | 120/7305 | 225/18723 | 8.45e-06 | 9.02e-05 | 120 |
| GO:00303079 | Oral cavity | OSCC | positive regulation of cell growth | 92/7305 | 166/18723 | 1.27e-05 | 1.29e-04 | 92 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513520 | Oral cavity | OSCC | Yersinia infection | 94/3704 | 137/8465 | 2.85e-09 | 3.08e-08 | 1.57e-08 | 94 |
| hsa0517027 | Oral cavity | OSCC | Human immunodeficiency virus 1 infection | 133/3704 | 212/8465 | 1.42e-08 | 1.40e-07 | 7.12e-08 | 133 |
| hsa0481026 | Oral cavity | OSCC | Regulation of actin cytoskeleton | 129/3704 | 229/8465 | 7.14e-05 | 2.74e-04 | 1.40e-04 | 129 |
| hsa0466618 | Oral cavity | OSCC | Fc gamma R-mediated phagocytosis | 60/3704 | 97/8465 | 2.35e-04 | 7.72e-04 | 3.93e-04 | 60 |
| hsa0436014 | Oral cavity | OSCC | Axon guidance | 97/3704 | 182/8465 | 5.59e-03 | 1.33e-02 | 6.76e-03 | 97 |
| hsa05135110 | Oral cavity | OSCC | Yersinia infection | 94/3704 | 137/8465 | 2.85e-09 | 3.08e-08 | 1.57e-08 | 94 |
| hsa05170111 | Oral cavity | OSCC | Human immunodeficiency virus 1 infection | 133/3704 | 212/8465 | 1.42e-08 | 1.40e-07 | 7.12e-08 | 133 |
| hsa04810111 | Oral cavity | OSCC | Regulation of actin cytoskeleton | 129/3704 | 229/8465 | 7.14e-05 | 2.74e-04 | 1.40e-04 | 129 |
| hsa0466619 | Oral cavity | OSCC | Fc gamma R-mediated phagocytosis | 60/3704 | 97/8465 | 2.35e-04 | 7.72e-04 | 3.93e-04 | 60 |
| hsa0436015 | Oral cavity | OSCC | Axon guidance | 97/3704 | 182/8465 | 5.59e-03 | 1.33e-02 | 6.76e-03 | 97 |
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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 |
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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 |
| LIMK1 | SNV | Missense_Mutation | c.1567N>A | p.Gly523Ser | p.G523S | P53667 | protein_coding | deleterious(0.03) | probably_damaging(0.981) | TCGA-BH-A0WA-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LIMK1 | SNV | Missense_Mutation | novel | c.139N>T | p.Ala47Ser | p.A47S | P53667 | protein_coding | tolerated(0.87) | benign(0.007) | TCGA-PE-A5DD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | CR | |
| LIMK1 | insertion | Frame_Shift_Ins | novel | c.544_545insACCAGGAAGCTTCACTGAGCTTCAGCAGCCAGAGTTT | p.Ile182AsnfsTer14 | p.I182Nfs*14 | P53667 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| LIMK1 | insertion | Frame_Shift_Ins | novel | c.1712_1713insC | p.Asn574LysfsTer71 | p.N574Kfs*71 | P53667 | protein_coding | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| LIMK1 | SNV | Missense_Mutation | c.358G>A | p.Asp120Asn | p.D120N | P53667 | protein_coding | deleterious(0.03) | probably_damaging(0.998) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| LIMK1 | SNV | Missense_Mutation | c.1557N>C | p.Glu519Asp | p.E519D | P53667 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-EA-A43B-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| LIMK1 | SNV | Missense_Mutation | c.646N>A | p.Ser216Thr | p.S216T | P53667 | protein_coding | tolerated(0.11) | benign(0.117) | TCGA-EA-A556-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| LIMK1 | SNV | Missense_Mutation | rs782256257 | c.985C>T | p.Arg329Trp | p.R329W | P53667 | protein_coding | deleterious(0) | possibly_damaging(0.462) | TCGA-IR-A3LC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unspecific | Cisplatin | Complete Response |
| LIMK1 | SNV | Missense_Mutation | novel | c.1563N>G | p.Ile521Met | p.I521M | P53667 | protein_coding | tolerated(0.71) | benign(0.323) | TCGA-PN-A8MA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| LIMK1 | SNV | Missense_Mutation | novel | c.1864N>C | p.Glu622Gln | p.E622Q | P53667 | protein_coding | deleterious(0.04) | possibly_damaging(0.65) | TCGA-UC-A7PG-06 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | PD |
| Page: 1 2 3 4 5 6 7 8 |
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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 |
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | PAZOPANIB | PAZOPANIB | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | GO-6976 | GO-6976 | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | CENISERTIB | CENISERTIB | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | TAE-684 | TAE-684 | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | BMS-345541 | BMS-345541 | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | TCMDC-125758 | CHEMBL546797 | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | inhibitor | 249565797 | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | SB-220025 | SB-220025 | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | RG-1530 | RG-1530 | ||
| 3984 | LIMK1 | KINASE, DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE | inhibitor | 363894217 | VORUCICLIB |
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