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Gene: LMF2 |
Gene summary for LMF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LMF2 | Gene ID | 91289 |
| Gene name | lipase maturation factor 2 | |
| Gene Alias | TMEM112B | |
| Cytomap | 22q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0006807 | UniProtAcc | Q9BU23 |
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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 |
| 91289 | LMF2 | C30 | Human | Oral cavity | OSCC | 1.13e-45 | 1.73e+00 | 0.3055 |
| 91289 | LMF2 | C38 | Human | Oral cavity | OSCC | 1.11e-20 | 2.01e+00 | 0.172 |
| 91289 | LMF2 | C43 | Human | Oral cavity | OSCC | 8.89e-18 | 3.30e-01 | 0.1704 |
| 91289 | LMF2 | C46 | Human | Oral cavity | OSCC | 6.82e-64 | 1.24e+00 | 0.1673 |
| 91289 | LMF2 | C51 | Human | Oral cavity | OSCC | 1.67e-42 | 1.69e+00 | 0.2674 |
| 91289 | LMF2 | C57 | Human | Oral cavity | OSCC | 3.50e-17 | 4.89e-01 | 0.1679 |
| 91289 | LMF2 | C06 | Human | Oral cavity | OSCC | 1.59e-14 | 1.50e+00 | 0.2699 |
| 91289 | LMF2 | C07 | Human | Oral cavity | OSCC | 1.52e-07 | 1.19e+00 | 0.2491 |
| 91289 | LMF2 | C08 | Human | Oral cavity | OSCC | 5.99e-41 | 7.68e-01 | 0.1919 |
| 91289 | LMF2 | LN22 | Human | Oral cavity | OSCC | 1.88e-16 | 1.39e+00 | 0.1733 |
| 91289 | LMF2 | LN38 | Human | Oral cavity | OSCC | 3.54e-06 | 1.36e+00 | 0.168 |
| 91289 | LMF2 | LN46 | Human | Oral cavity | OSCC | 2.69e-30 | 1.01e+00 | 0.1666 |
| 91289 | LMF2 | LP15 | Human | Oral cavity | LP | 9.32e-16 | 1.81e+00 | 0.2174 |
| 91289 | LMF2 | LP17 | Human | Oral cavity | LP | 4.80e-12 | 9.60e-01 | 0.2349 |
| 91289 | LMF2 | SYSMH1 | Human | Oral cavity | OSCC | 3.57e-15 | 2.89e-01 | 0.1127 |
| 91289 | LMF2 | SYSMH2 | Human | Oral cavity | OSCC | 2.27e-23 | 5.05e-01 | 0.2326 |
| 91289 | LMF2 | SYSMH3 | Human | Oral cavity | OSCC | 1.07e-35 | 7.84e-01 | 0.2442 |
| 91289 | LMF2 | SYSMH5 | Human | Oral cavity | OSCC | 1.13e-25 | 5.76e-01 | 0.0647 |
| 91289 | LMF2 | SYSMH6 | Human | Oral cavity | OSCC | 2.77e-06 | 3.71e-01 | 0.1275 |
| 91289 | LMF2 | P5_S10_cSCC | Human | Skin | cSCC | 4.09e-09 | 1.98e-01 | -0.299 |
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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 | ||
| 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:005160417 | Esophagus | HGIN | protein maturation | 68/2587 | 294/18723 | 9.77e-06 | 2.86e-04 | 68 |
| GO:005160418 | Esophagus | ESCC | protein maturation | 189/8552 | 294/18723 | 7.64e-11 | 2.39e-09 | 189 |
| GO:00516046 | Liver | Cirrhotic | protein maturation | 121/4634 | 294/18723 | 3.54e-10 | 1.68e-08 | 121 |
| GO:005160412 | Liver | HCC | protein maturation | 171/7958 | 294/18723 | 3.80e-08 | 8.30e-07 | 171 |
| GO:005160410 | Oral cavity | OSCC | protein maturation | 170/7305 | 294/18723 | 3.97e-11 | 1.28e-09 | 170 |
| GO:005160416 | Oral cavity | LP | protein maturation | 122/4623 | 294/18723 | 1.37e-10 | 7.72e-09 | 122 |
| GO:005160419 | Skin | cSCC | protein maturation | 117/4864 | 294/18723 | 1.27e-07 | 2.93e-06 | 117 |
| GO:005160420 | Thyroid | PTC | protein maturation | 132/5968 | 294/18723 | 1.71e-06 | 2.39e-05 | 132 |
| GO:0051604110 | Thyroid | ATC | protein maturation | 136/6293 | 294/18723 | 4.00e-06 | 4.42e-05 | 136 |
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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 |
| LMF2 | SNV | Missense_Mutation | c.334N>A | p.Leu112Met | p.L112M | Q9BU23 | protein_coding | deleterious(0.02) | probably_damaging(0.94) | TCGA-E9-A22G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| LMF2 | insertion | Frame_Shift_Ins | novel | c.1147_1148insAACGTTTCTCTTTCTTTGAA | p.Ala383GlufsTer25 | p.A383Efs*25 | Q9BU23 | protein_coding | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| LMF2 | deletion | Frame_Shift_Del | novel | c.728delT | p.Phe243SerfsTer22 | p.F243Sfs*22 | Q9BU23 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| LMF2 | SNV | Missense_Mutation | rs375477419 | c.1325N>T | p.Ala442Val | p.A442V | Q9BU23 | protein_coding | tolerated(0.18) | benign(0.038) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LMF2 | SNV | Missense_Mutation | novel | c.2048N>A | p.Gly683Glu | p.G683E | Q9BU23 | protein_coding | tolerated(1) | benign(0.058) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| LMF2 | SNV | Missense_Mutation | novel | c.2051N>T | p.Ala684Val | p.A684V | Q9BU23 | protein_coding | tolerated(0.19) | benign(0.006) | TCGA-C5-A905-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LMF2 | SNV | Missense_Mutation | rs149785243 | c.908N>T | p.Thr303Met | p.T303M | Q9BU23 | protein_coding | tolerated(0.32) | benign(0.021) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| LMF2 | SNV | Missense_Mutation | novel | c.1046N>C | p.Arg349Thr | p.R349T | Q9BU23 | protein_coding | deleterious(0.03) | benign(0.018) | TCGA-VS-AA62-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| LMF2 | SNV | Missense_Mutation | rs752866373 | c.1360N>T | p.Leu454Phe | p.L454F | Q9BU23 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-ZJ-AB0H-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| LMF2 | insertion | In_Frame_Ins | novel | c.165_166insGTT | p.Gln55_Gln56insVal | p.Q55_Q56insV | Q9BU23 | protein_coding | TCGA-C5-A7X5-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | 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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