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Gene: LMO4 |
Gene summary for LMO4 |
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Gene information | Species | Human | Gene symbol | LMO4 | Gene ID | 8543 |
Gene name | LIM domain only 4 | |
Gene Alias | LMO4 | |
Cytomap | 1p22.3 | |
Gene Type | protein-coding | GO ID | GO:0001708 | UniProtAcc | P61968 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
8543 | LMO4 | cSCC_p10 | Human | Skin | cSCC | 4.27e-13 | 5.58e-01 | -0.2095 |
8543 | LMO4 | cSCC_p3 | Human | Skin | cSCC | 6.63e-06 | 3.48e-01 | -0.2085 |
8543 | LMO4 | cSCC_p7 | Human | Skin | cSCC | 1.91e-10 | 2.58e-01 | -0.2332 |
8543 | LMO4 | cSCC_p8 | Human | Skin | cSCC | 2.65e-09 | 2.55e-01 | -0.1971 |
8543 | LMO4 | cSCC_p9 | Human | Skin | cSCC | 7.19e-04 | 1.99e-01 | -0.1991 |
8543 | LMO4 | Pat02-B | Human | Stomach | GC | 1.82e-39 | 2.11e-01 | 0.0368 |
8543 | LMO4 | Pat03-B | Human | Stomach | GC | 2.34e-14 | 1.23e-01 | 0.3693 |
8543 | LMO4 | Pat04-B | Human | Stomach | GC | 1.60e-22 | 2.99e-01 | -0.1483 |
8543 | LMO4 | Pat05-B | Human | Stomach | GC | 1.31e-11 | 3.06e-01 | -0.0353 |
8543 | LMO4 | Pat06-B | Human | Stomach | GC | 3.86e-33 | 2.27e-01 | -0.1961 |
8543 | LMO4 | Pat11-B | Human | Stomach | GC | 9.67e-17 | 3.39e-01 | -0.182 |
8543 | LMO4 | Pat12-B | Human | Stomach | GC | 2.90e-22 | 2.67e-01 | 0.0325 |
8543 | LMO4 | Pat13-B | Human | Stomach | GC | 2.40e-04 | 1.65e-01 | 0.0555 |
8543 | LMO4 | Pat15-B | Human | Stomach | GC | 2.08e-13 | 2.50e-01 | -0.0778 |
8543 | LMO4 | Pat16-B | Human | Stomach | GC | 2.67e-02 | -8.80e-03 | 0.1918 |
8543 | LMO4 | Pat18-B | Human | Stomach | GC | 4.36e-13 | 2.00e-01 | -0.0432 |
8543 | LMO4 | Pat19-B | Human | Stomach | GC | 8.17e-16 | 4.16e-01 | 0.0826 |
8543 | LMO4 | Pat22-B | Human | Stomach | GC | 4.54e-32 | 3.27e-01 | -0.1042 |
8543 | LMO4 | Pat24-B | Human | Stomach | GC | 1.46e-14 | 3.18e-01 | -0.1184 |
8543 | LMO4 | Pat25-A | Human | Stomach | CAG with IM | 4.50e-35 | 3.09e-01 | -0.1648 |
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∗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 |
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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 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00432549 | Breast | Precancer | regulation of protein-containing complex assembly | 50/1080 | 428/18723 | 1.63e-06 | 5.97e-05 | 50 |
GO:00487329 | Breast | Precancer | gland development | 49/1080 | 436/18723 | 6.11e-06 | 1.73e-04 | 49 |
GO:00351486 | Breast | Precancer | tube formation | 19/1080 | 148/18723 | 8.79e-04 | 1.01e-02 | 19 |
GO:0048538 | Breast | Precancer | thymus development | 9/1080 | 45/18723 | 9.22e-04 | 1.05e-02 | 9 |
GO:00313338 | Breast | Precancer | negative regulation of protein-containing complex assembly | 18/1080 | 141/18723 | 1.27e-03 | 1.35e-02 | 18 |
GO:00336749 | Breast | Precancer | positive regulation of kinase activity | 42/1080 | 467/18723 | 2.94e-03 | 2.54e-02 | 42 |
GO:00018386 | Breast | Precancer | embryonic epithelial tube formation | 15/1080 | 121/18723 | 4.12e-03 | 3.24e-02 | 15 |
GO:00605625 | Breast | Precancer | epithelial tube morphogenesis | 31/1080 | 325/18723 | 4.21e-03 | 3.31e-02 | 31 |
GO:004873214 | Breast | IDC | gland development | 64/1434 | 436/18723 | 3.47e-07 | 1.74e-05 | 64 |
GO:004325414 | Breast | IDC | regulation of protein-containing complex assembly | 61/1434 | 428/18723 | 1.77e-06 | 7.31e-05 | 61 |
GO:006056212 | Breast | IDC | epithelial tube morphogenesis | 44/1434 | 325/18723 | 1.58e-04 | 2.73e-03 | 44 |
GO:003514812 | Breast | IDC | tube formation | 23/1434 | 148/18723 | 8.79e-04 | 1.02e-02 | 23 |
GO:003133313 | Breast | IDC | negative regulation of protein-containing complex assembly | 22/1434 | 141/18723 | 1.07e-03 | 1.17e-02 | 22 |
GO:00485381 | Breast | IDC | thymus development | 10/1434 | 45/18723 | 1.80e-03 | 1.74e-02 | 10 |
GO:000183812 | Breast | IDC | embryonic epithelial tube formation | 19/1434 | 121/18723 | 2.10e-03 | 1.97e-02 | 19 |
GO:00721756 | Breast | IDC | epithelial tube formation | 19/1434 | 132/18723 | 5.63e-03 | 4.08e-02 | 19 |
GO:004325424 | Breast | DCIS | regulation of protein-containing complex assembly | 61/1390 | 428/18723 | 6.32e-07 | 2.71e-05 | 61 |
GO:004873223 | Breast | DCIS | gland development | 60/1390 | 436/18723 | 2.50e-06 | 8.74e-05 | 60 |
GO:006056221 | Breast | DCIS | epithelial tube morphogenesis | 41/1390 | 325/18723 | 5.98e-04 | 7.60e-03 | 41 |
GO:003133322 | Breast | DCIS | negative regulation of protein-containing complex assembly | 22/1390 | 141/18723 | 7.08e-04 | 8.51e-03 | 22 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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. |
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Somatic mutation of malignant transformation related genes |
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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 |
LMO4 | SNV | Missense_Mutation | c.445N>T | p.His149Tyr | p.H149Y | P61968 | protein_coding | deleterious(0.01) | benign(0.284) | TCGA-B6-A0IJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LMO4 | SNV | Missense_Mutation | rs754509420 | c.371N>T | p.Pro124Leu | p.P124L | P61968 | protein_coding | tolerated(0.25) | probably_damaging(0.987) | TCGA-BH-A0E9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
LMO4 | SNV | Missense_Mutation | c.308N>T | p.Ala103Val | p.A103V | P61968 | protein_coding | tolerated(0.06) | benign(0.113) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
LMO4 | SNV | Missense_Mutation | rs771825798 | c.287N>T | p.Ala96Val | p.A96V | P61968 | protein_coding | deleterious(0.03) | probably_damaging(0.962) | TCGA-F4-6808-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LMO4 | SNV | Missense_Mutation | novel | c.380N>A | p.Arg127Gln | p.R127Q | P61968 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
LMO4 | SNV | Missense_Mutation | c.229T>C | p.Tyr77His | p.Y77H | P61968 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A0LE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LMO4 | SNV | Missense_Mutation | c.379N>T | p.Arg127Trp | p.R127W | P61968 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
LMO4 | SNV | Missense_Mutation | novel | c.395N>G | p.Asn132Ser | p.N132S | P61968 | protein_coding | tolerated(0.15) | benign(0.075) | TCGA-E6-A2P8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
LMO4 | SNV | Missense_Mutation | novel | c.362N>A | p.Arg121His | p.R121H | P61968 | protein_coding | deleterious(0.04) | possibly_damaging(0.667) | TCGA-EO-A3KX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LMO4 | SNV | Missense_Mutation | novel | c.325N>T | p.His109Tyr | p.H109Y | P61968 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EY-A1GU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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