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Gene: LMX1B |
Gene summary for LMX1B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LMX1B | Gene ID | 4010 |
| Gene name | LIM homeobox transcription factor 1 beta | |
| Gene Alias | FSGS10 | |
| Cytomap | 9q33.3 | |
| Gene Type | protein-coding | GO ID | GO:0001701 | UniProtAcc | B7ZLH2 |
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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 |
| 4010 | LMX1B | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.87e-02 | 1.42e-01 | -0.1808 |
| 4010 | LMX1B | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.73e-09 | 2.74e-01 | -0.0811 |
| 4010 | LMX1B | HTA11_78_2000001011 | Human | Colorectum | AD | 4.96e-02 | 1.04e-01 | -0.1088 |
| 4010 | LMX1B | HTA11_347_2000001011 | Human | Colorectum | AD | 6.35e-08 | 1.94e-01 | -0.1954 |
| 4010 | LMX1B | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.90e-02 | 3.35e-01 | -0.2196 |
| 4010 | LMX1B | HTA11_3361_2000001011 | Human | Colorectum | AD | 4.57e-06 | 2.00e-01 | -0.1207 |
| 4010 | LMX1B | HTA11_696_2000001011 | Human | Colorectum | AD | 9.02e-22 | 3.83e-01 | -0.1464 |
| 4010 | LMX1B | HTA11_866_2000001011 | Human | Colorectum | AD | 3.61e-02 | 8.69e-02 | -0.1001 |
| 4010 | LMX1B | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.96e-05 | 1.86e-01 | -0.059 |
| 4010 | LMX1B | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.52e-10 | 4.42e-01 | -0.1706 |
| 4010 | LMX1B | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.67e-10 | 4.00e-01 | -0.2061 |
| 4010 | LMX1B | HTA11_5216_2000001011 | Human | Colorectum | SER | 1.39e-19 | 8.54e-01 | -0.1462 |
| 4010 | LMX1B | HTA11_546_2000001011 | Human | Colorectum | AD | 2.42e-10 | 4.13e-01 | -0.0842 |
| 4010 | LMX1B | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 3.42e-04 | 3.77e-01 | 0.3487 |
| 4010 | LMX1B | HTA11_99999974143_84620 | Human | Colorectum | MSS | 9.04e-05 | 1.23e-01 | 0.3005 |
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| 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 |
| ∗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:0001701 | Colorectum | AD | in utero embryonic development | 110/3918 | 367/18723 | 2.36e-05 | 4.62e-04 | 110 |
| GO:00017011 | Colorectum | SER | in utero embryonic development | 77/2897 | 367/18723 | 2.77e-03 | 2.48e-02 | 77 |
| GO:00017012 | Colorectum | MSS | in utero embryonic development | 99/3467 | 367/18723 | 3.71e-05 | 7.10e-04 | 99 |
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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 |
| LMX1B | SNV | Missense_Mutation | rs772632723 | c.1090N>A | p.Asp364Asn | p.D364N | O60663 | protein_coding | deleterious(0.04) | possibly_damaging(0.477) | TCGA-A2-A04U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| LMX1B | SNV | Missense_Mutation | novel | c.1144G>C | p.Val382Leu | p.V382L | O60663 | protein_coding | tolerated(0.78) | benign(0.011) | TCGA-A2-A3XS-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | PD |
| LMX1B | SNV | Missense_Mutation | c.467T>G | p.Phe156Cys | p.F156C | O60663 | protein_coding | tolerated(0.13) | benign(0.276) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| LMX1B | SNV | Missense_Mutation | rs776839118 | c.463N>A | p.Glu155Lys | p.E155K | O60663 | protein_coding | deleterious(0.03) | possibly_damaging(0.814) | TCGA-MY-A913-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LMX1B | SNV | Missense_Mutation | novel | c.1028N>T | p.Pro343Leu | p.P343L | O60663 | protein_coding | tolerated(0.09) | benign(0.203) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LMX1B | SNV | Missense_Mutation | novel | c.347N>C | p.Ser116Thr | p.S116T | O60663 | protein_coding | tolerated(0.12) | possibly_damaging(0.669) | TCGA-ZJ-AAXD-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| LMX1B | SNV | Missense_Mutation | c.455A>G | p.Lys152Arg | p.K152R | O60663 | protein_coding | tolerated(0.17) | benign(0.307) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LMX1B | SNV | Missense_Mutation | c.460N>A | p.Asp154Asn | p.D154N | O60663 | protein_coding | deleterious(0) | possibly_damaging(0.736) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LMX1B | SNV | Missense_Mutation | c.571N>T | p.Asp191Tyr | p.D191Y | O60663 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| LMX1B | SNV | Missense_Mutation | rs767072869 | c.469N>A | p.Val157Met | p.V157M | O60663 | protein_coding | tolerated(0.06) | possibly_damaging(0.889) | TCGA-AA-3693-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | 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 |
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