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Gene: OSTM1 |
Gene summary for OSTM1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | OSTM1 | Gene ID | 28962 |
Gene name | osteoclastogenesis associated transmembrane protein 1 | |
Gene Alias | GIPN | |
Cytomap | 6q21 | |
Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | Q86WC4 |
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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 |
28962 | OSTM1 | LZE4T | Human | Esophagus | ESCC | 1.14e-12 | 3.22e-01 | 0.0811 |
28962 | OSTM1 | LZE24T | Human | Esophagus | ESCC | 3.97e-08 | 3.56e-01 | 0.0596 |
28962 | OSTM1 | P2T-E | Human | Esophagus | ESCC | 6.29e-21 | 3.61e-01 | 0.1177 |
28962 | OSTM1 | P4T-E | Human | Esophagus | ESCC | 3.87e-18 | 3.22e-01 | 0.1323 |
28962 | OSTM1 | P5T-E | Human | Esophagus | ESCC | 3.12e-12 | 2.55e-01 | 0.1327 |
28962 | OSTM1 | P8T-E | Human | Esophagus | ESCC | 4.36e-07 | 1.45e-01 | 0.0889 |
28962 | OSTM1 | P9T-E | Human | Esophagus | ESCC | 1.95e-08 | 1.45e-01 | 0.1131 |
28962 | OSTM1 | P10T-E | Human | Esophagus | ESCC | 7.68e-17 | 4.40e-01 | 0.116 |
28962 | OSTM1 | P11T-E | Human | Esophagus | ESCC | 4.49e-13 | 5.65e-01 | 0.1426 |
28962 | OSTM1 | P12T-E | Human | Esophagus | ESCC | 2.68e-13 | 2.19e-01 | 0.1122 |
28962 | OSTM1 | P15T-E | Human | Esophagus | ESCC | 5.30e-13 | 4.36e-01 | 0.1149 |
28962 | OSTM1 | P16T-E | Human | Esophagus | ESCC | 8.04e-18 | 3.33e-01 | 0.1153 |
28962 | OSTM1 | P19T-E | Human | Esophagus | ESCC | 5.22e-06 | 4.96e-01 | 0.1662 |
28962 | OSTM1 | P20T-E | Human | Esophagus | ESCC | 3.57e-08 | 2.43e-01 | 0.1124 |
28962 | OSTM1 | P21T-E | Human | Esophagus | ESCC | 1.33e-33 | 7.11e-01 | 0.1617 |
28962 | OSTM1 | P22T-E | Human | Esophagus | ESCC | 4.46e-10 | 1.77e-01 | 0.1236 |
28962 | OSTM1 | P23T-E | Human | Esophagus | ESCC | 2.45e-20 | 4.50e-01 | 0.108 |
28962 | OSTM1 | P24T-E | Human | Esophagus | ESCC | 8.17e-11 | 2.70e-01 | 0.1287 |
28962 | OSTM1 | P26T-E | Human | Esophagus | ESCC | 3.70e-15 | 3.16e-01 | 0.1276 |
28962 | OSTM1 | P27T-E | Human | Esophagus | ESCC | 1.28e-12 | 1.56e-01 | 0.1055 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0030099111 | Esophagus | ESCC | myeloid cell differentiation | 232/8552 | 381/18723 | 1.22e-09 | 2.90e-08 | 232 |
GO:000257317 | Esophagus | ESCC | myeloid leukocyte differentiation | 128/8552 | 208/18723 | 2.75e-06 | 3.15e-05 | 128 |
GO:00303165 | Esophagus | ESCC | osteoclast differentiation | 54/8552 | 94/18723 | 1.43e-02 | 4.65e-02 | 54 |
GO:003009922 | Liver | HCC | myeloid cell differentiation | 200/7958 | 381/18723 | 4.64e-05 | 4.49e-04 | 200 |
GO:003009920 | Oral cavity | OSCC | myeloid cell differentiation | 213/7305 | 381/18723 | 1.24e-11 | 4.42e-10 | 213 |
GO:000257310 | Oral cavity | OSCC | myeloid leukocyte differentiation | 119/7305 | 208/18723 | 7.29e-08 | 1.29e-06 | 119 |
GO:00303164 | Oral cavity | OSCC | osteoclast differentiation | 48/7305 | 94/18723 | 1.16e-02 | 3.92e-02 | 48 |
GO:003009926 | Oral cavity | EOLP | myeloid cell differentiation | 91/2218 | 381/18723 | 2.87e-11 | 4.15e-09 | 91 |
GO:000257323 | Oral cavity | EOLP | myeloid leukocyte differentiation | 48/2218 | 208/18723 | 3.71e-06 | 7.88e-05 | 48 |
GO:003009932 | Oral cavity | NEOLP | myeloid cell differentiation | 83/2005 | 381/18723 | 1.79e-10 | 1.69e-08 | 83 |
GO:000257331 | Oral cavity | NEOLP | myeloid leukocyte differentiation | 41/2005 | 208/18723 | 8.21e-05 | 1.03e-03 | 41 |
GO:003009929 | Skin | cSCC | myeloid cell differentiation | 146/4864 | 381/18723 | 6.38e-08 | 1.61e-06 | 146 |
GO:000257324 | Skin | cSCC | myeloid leukocyte differentiation | 76/4864 | 208/18723 | 4.75e-04 | 3.60e-03 | 76 |
GO:0030099113 | Thyroid | PTC | myeloid cell differentiation | 160/5968 | 381/18723 | 1.75e-05 | 1.82e-04 | 160 |
GO:003009933 | Thyroid | ATC | myeloid cell differentiation | 170/6293 | 381/18723 | 4.26e-06 | 4.68e-05 | 170 |
GO:0002573110 | Thyroid | ATC | myeloid leukocyte differentiation | 86/6293 | 208/18723 | 1.15e-02 | 4.11e-02 | 86 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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. |
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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 |
OSTM1 | SNV | Missense_Mutation | novel | c.44C>A | p.Pro15Gln | p.P15Q | Q86WC4 | protein_coding | tolerated_low_confidence(0.12) | benign(0.039) | TCGA-CV-7253-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
OSTM1 | SNV | Missense_Mutation | novel | c.850N>T | p.Pro284Ser | p.P284S | Q86WC4 | protein_coding | tolerated(0.09) | possibly_damaging(0.594) | TCGA-CV-7434-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
OSTM1 | SNV | Missense_Mutation | rs779528585 | c.316G>A | p.Ala106Thr | p.A106T | Q86WC4 | protein_coding | deleterious(0) | probably_damaging(0.942) | TCGA-BR-6452-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
OSTM1 | SNV | Missense_Mutation | c.989N>G | p.Gln330Arg | p.Q330R | Q86WC4 | protein_coding | deleterious(0.01) | possibly_damaging(0.657) | TCGA-BR-7707-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
OSTM1 | SNV | Missense_Mutation | c.428N>T | p.Ala143Val | p.A143V | Q86WC4 | protein_coding | tolerated(0.19) | benign(0.412) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <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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