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Gene: LEMD2 |
Gene summary for LEMD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LEMD2 | Gene ID | 221496 |
| Gene name | LEM domain nuclear envelope protein 2 | |
| Gene Alias | CTRCT42 | |
| Cytomap | 6p21.31 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q8NC56 |
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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 |
| 221496 | LEMD2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.33e-04 | 1.50e-01 | 0.0155 |
| 221496 | LEMD2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.19e-04 | 2.73e-01 | -0.0811 |
| 221496 | LEMD2 | HTA11_78_2000001011 | Human | Colorectum | AD | 6.00e-05 | 2.57e-01 | -0.1088 |
| 221496 | LEMD2 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.78e-14 | 3.54e-01 | -0.1954 |
| 221496 | LEMD2 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.60e-07 | 8.72e-01 | -0.2602 |
| 221496 | LEMD2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.89e-03 | 1.91e-01 | -0.1207 |
| 221496 | LEMD2 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.02e-02 | 2.43e-01 | -0.1526 |
| 221496 | LEMD2 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.64e-05 | 2.70e-01 | -0.1464 |
| 221496 | LEMD2 | HTA11_866_2000001011 | Human | Colorectum | AD | 6.46e-05 | 2.31e-01 | -0.1001 |
| 221496 | LEMD2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 8.07e-11 | 3.95e-01 | -0.059 |
| 221496 | LEMD2 | HTA11_546_2000001011 | Human | Colorectum | AD | 4.62e-04 | 3.39e-01 | -0.0842 |
| 221496 | LEMD2 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.03e-06 | 2.32e-01 | 0.096 |
| 221496 | LEMD2 | HTA11_7663_2000001011 | Human | Colorectum | SER | 9.50e-03 | 3.70e-01 | 0.0131 |
| 221496 | LEMD2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.14e-02 | 2.16e-01 | 0.0674 |
| 221496 | LEMD2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.87e-07 | 3.09e-01 | 0.281 |
| 221496 | LEMD2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.99e-04 | 3.29e-01 | 0.3859 |
| 221496 | LEMD2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 6.01e-04 | 3.43e-01 | 0.2585 |
| 221496 | LEMD2 | LZE24T | Human | Esophagus | ESCC | 3.16e-08 | 2.69e-01 | 0.0596 |
| 221496 | LEMD2 | P1T-E | Human | Esophagus | ESCC | 3.04e-12 | 5.86e-01 | 0.0875 |
| 221496 | LEMD2 | P2T-E | Human | Esophagus | ESCC | 1.13e-50 | 7.44e-01 | 0.1177 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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 | ||
| 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 |
| ∗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:0043409 | Colorectum | AD | negative regulation of MAPK cascade | 57/3918 | 180/18723 | 4.61e-04 | 5.14e-03 | 57 |
| GO:0007178 | Colorectum | AD | transmembrane receptor protein serine/threonine kinase signaling pathway | 99/3918 | 355/18723 | 9.92e-04 | 9.28e-03 | 99 |
| GO:00434091 | Colorectum | SER | negative regulation of MAPK cascade | 45/2897 | 180/18723 | 5.81e-04 | 7.98e-03 | 45 |
| GO:00434092 | Colorectum | MSS | negative regulation of MAPK cascade | 50/3467 | 180/18723 | 1.45e-03 | 1.35e-02 | 50 |
| GO:00071781 | Colorectum | MSS | transmembrane receptor protein serine/threonine kinase signaling pathway | 86/3467 | 355/18723 | 4.04e-03 | 2.95e-02 | 86 |
| GO:000699713 | Esophagus | ESCC | nucleus organization | 96/8552 | 133/18723 | 4.66e-10 | 1.21e-08 | 96 |
| GO:003450211 | Esophagus | ESCC | protein localization to chromosome | 70/8552 | 92/18723 | 2.54e-09 | 5.64e-08 | 70 |
| GO:000699811 | Esophagus | ESCC | nuclear envelope organization | 39/8552 | 47/18723 | 1.48e-07 | 2.35e-06 | 39 |
| GO:000717810 | Esophagus | ESCC | transmembrane receptor protein serine/threonine kinase signaling pathway | 195/8552 | 355/18723 | 2.58e-04 | 1.58e-03 | 195 |
| GO:0043409110 | Esophagus | ESCC | negative regulation of MAPK cascade | 105/8552 | 180/18723 | 4.13e-04 | 2.35e-03 | 105 |
| GO:006053716 | Esophagus | ESCC | muscle tissue development | 211/8552 | 403/18723 | 3.84e-03 | 1.56e-02 | 211 |
| GO:0071168 | Esophagus | ESCC | protein localization to chromatin | 21/8552 | 31/18723 | 1.10e-02 | 3.70e-02 | 21 |
| GO:001470615 | Esophagus | ESCC | striated muscle tissue development | 197/8552 | 384/18723 | 1.46e-02 | 4.74e-02 | 197 |
| GO:00069971 | Liver | HCC | nucleus organization | 82/7958 | 133/18723 | 6.32e-06 | 7.72e-05 | 82 |
| GO:0006998 | Liver | HCC | nuclear envelope organization | 34/7958 | 47/18723 | 3.27e-05 | 3.29e-04 | 34 |
| GO:00345021 | Liver | HCC | protein localization to chromosome | 55/7958 | 92/18723 | 6.12e-04 | 3.82e-03 | 55 |
| GO:00434097 | Liver | HCC | negative regulation of MAPK cascade | 98/7958 | 180/18723 | 7.88e-04 | 4.74e-03 | 98 |
| GO:00069974 | Oral cavity | OSCC | nucleus organization | 85/7305 | 133/18723 | 5.12e-09 | 1.12e-07 | 85 |
| GO:00069982 | Oral cavity | OSCC | nuclear envelope organization | 37/7305 | 47/18723 | 3.19e-08 | 6.12e-07 | 37 |
| GO:004340917 | Oral cavity | OSCC | negative regulation of MAPK cascade | 105/7305 | 180/18723 | 1.10e-07 | 1.87e-06 | 105 |
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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 |
| LEMD2 | SNV | Missense_Mutation | novel | c.1003G>A | p.Gly335Ser | p.G335S | Q8NC56 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A7-A4SE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| LEMD2 | SNV | Missense_Mutation | c.1453G>C | p.Glu485Gln | p.E485Q | Q8NC56 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LEMD2 | SNV | Missense_Mutation | c.815T>C | p.Leu272Pro | p.L272P | Q8NC56 | protein_coding | deleterious(0) | possibly_damaging(0.757) | TCGA-E2-A14R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | |
| LEMD2 | insertion | In_Frame_Ins | novel | c.1008_1009insATGTTG | p.Ile336_Trp337insMetLeu | p.I336_W337insML | Q8NC56 | protein_coding | TCGA-A2-A0CU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| LEMD2 | insertion | In_Frame_Ins | novel | c.1006_1007insAGAATGATGACACTCACCTTT | p.Ile336delinsLysAsnAspAspThrHisLeuPhe | p.I336delinsKNDDTHLF | Q8NC56 | protein_coding | TCGA-A2-A0CU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| LEMD2 | insertion | In_Frame_Ins | novel | c.1182_1183insGAAATTAGAACAAGTGAA | p.Leu394_Ile395insGluIleArgThrSerGlu | p.L394_I395insEIRTSE | Q8NC56 | protein_coding | TCGA-AN-A0FW-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| LEMD2 | SNV | Missense_Mutation | novel | c.1261N>C | p.Val421Leu | p.V421L | Q8NC56 | protein_coding | deleterious(0.01) | possibly_damaging(0.769) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| LEMD2 | SNV | Missense_Mutation | c.1057G>A | p.Val353Met | p.V353M | Q8NC56 | protein_coding | deleterious(0) | possibly_damaging(0.867) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| LEMD2 | SNV | Missense_Mutation | rs768891530 | c.1103N>A | p.Arg368His | p.R368H | Q8NC56 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LEMD2 | SNV | Missense_Mutation | c.965N>T | p.Ala322Val | p.A322V | Q8NC56 | protein_coding | tolerated(0.38) | possibly_damaging(0.562) | TCGA-AP-A0LP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Hormone Therapy | megace | SD |
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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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