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Gene: ROMO1 |
Gene summary for ROMO1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | ROMO1 | Gene ID | 140823 |
Gene name | reactive oxygen species modulator 1 | |
Gene Alias | C20orf52 | |
Cytomap | 20q11.22 | |
Gene Type | protein-coding | GO ID | GO:0000302 | UniProtAcc | P60602 |
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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 |
140823 | ROMO1 | GSM4909282 | Human | Breast | IDC | 6.21e-07 | 4.10e-01 | -0.0288 |
140823 | ROMO1 | GSM4909285 | Human | Breast | IDC | 5.08e-03 | -1.46e-01 | 0.21 |
140823 | ROMO1 | GSM4909287 | Human | Breast | IDC | 1.48e-04 | 3.42e-01 | 0.2057 |
140823 | ROMO1 | GSM4909290 | Human | Breast | IDC | 2.07e-07 | 4.35e-01 | 0.2096 |
140823 | ROMO1 | GSM4909291 | Human | Breast | IDC | 4.66e-06 | 4.26e-01 | 0.1753 |
140823 | ROMO1 | GSM4909293 | Human | Breast | IDC | 1.07e-09 | 3.28e-01 | 0.1581 |
140823 | ROMO1 | GSM4909294 | Human | Breast | IDC | 8.21e-10 | 3.48e-01 | 0.2022 |
140823 | ROMO1 | GSM4909296 | Human | Breast | IDC | 9.13e-13 | 3.29e-01 | 0.1524 |
140823 | ROMO1 | GSM4909297 | Human | Breast | IDC | 4.23e-08 | -3.25e-02 | 0.1517 |
140823 | ROMO1 | GSM4909298 | Human | Breast | IDC | 1.69e-06 | 3.24e-01 | 0.1551 |
140823 | ROMO1 | GSM4909299 | Human | Breast | IDC | 8.40e-05 | 2.82e-01 | 0.035 |
140823 | ROMO1 | GSM4909301 | Human | Breast | IDC | 3.37e-20 | 5.44e-01 | 0.1577 |
140823 | ROMO1 | GSM4909304 | Human | Breast | IDC | 2.07e-25 | 6.23e-01 | 0.1636 |
140823 | ROMO1 | GSM4909307 | Human | Breast | IDC | 6.91e-03 | 3.00e-01 | 0.1569 |
140823 | ROMO1 | GSM4909308 | Human | Breast | IDC | 6.62e-05 | 2.11e-01 | 0.158 |
140823 | ROMO1 | GSM4909309 | Human | Breast | IDC | 4.53e-10 | 3.72e-01 | 0.0483 |
140823 | ROMO1 | GSM4909311 | Human | Breast | IDC | 3.14e-37 | 2.49e-01 | 0.1534 |
140823 | ROMO1 | GSM4909312 | Human | Breast | IDC | 6.53e-08 | 1.35e-01 | 0.1552 |
140823 | ROMO1 | GSM4909315 | Human | Breast | IDC | 1.16e-23 | 6.34e-01 | 0.21 |
140823 | ROMO1 | GSM4909316 | Human | Breast | IDC | 2.38e-15 | 6.16e-01 | 0.21 |
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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:000660512 | Liver | HCC | protein targeting | 219/7958 | 314/18723 | 7.74e-23 | 1.49e-20 | 219 |
GO:000683912 | Liver | HCC | mitochondrial transport | 184/7958 | 254/18723 | 2.30e-22 | 3.83e-20 | 184 |
GO:000697922 | Liver | HCC | response to oxidative stress | 281/7958 | 446/18723 | 9.75e-19 | 1.24e-16 | 281 |
GO:007265512 | Liver | HCC | establishment of protein localization to mitochondrion | 98/7958 | 120/18723 | 1.18e-18 | 1.46e-16 | 98 |
GO:007058512 | Liver | HCC | protein localization to mitochondrion | 101/7958 | 125/18723 | 1.53e-18 | 1.86e-16 | 101 |
GO:000662612 | Liver | HCC | protein targeting to mitochondrion | 82/7958 | 100/18723 | 4.93e-16 | 4.05e-14 | 82 |
GO:006219722 | Liver | HCC | cellular response to chemical stress | 216/7958 | 337/18723 | 6.86e-16 | 5.44e-14 | 216 |
GO:001703811 | Liver | HCC | protein import | 140/7958 | 206/18723 | 1.12e-13 | 6.46e-12 | 140 |
GO:003459922 | Liver | HCC | cellular response to oxidative stress | 183/7958 | 288/18723 | 3.65e-13 | 1.93e-11 | 183 |
GO:009015012 | Liver | HCC | establishment of protein localization to membrane | 168/7958 | 260/18723 | 4.07e-13 | 2.13e-11 | 168 |
GO:004440322 | Liver | HCC | biological process involved in symbiotic interaction | 183/7958 | 290/18723 | 9.13e-13 | 4.59e-11 | 183 |
GO:199054212 | Liver | HCC | mitochondrial transmembrane transport | 78/7958 | 102/18723 | 2.73e-12 | 1.26e-10 | 78 |
GO:000030222 | Liver | HCC | response to reactive oxygen species | 144/7958 | 222/18723 | 1.24e-11 | 5.09e-10 | 144 |
GO:003461412 | Liver | HCC | cellular response to reactive oxygen species | 102/7958 | 155/18723 | 3.70e-09 | 9.89e-08 | 102 |
GO:007180611 | Liver | HCC | protein transmembrane transport | 47/7958 | 59/18723 | 5.82e-09 | 1.51e-07 | 47 |
GO:000700612 | Liver | HCC | mitochondrial membrane organization | 80/7958 | 116/18723 | 7.09e-09 | 1.81e-07 | 80 |
GO:006500211 | Liver | HCC | intracellular protein transmembrane transport | 41/7958 | 51/18723 | 3.41e-08 | 7.61e-07 | 41 |
GO:00447431 | Liver | HCC | protein transmembrane import into intracellular organelle | 29/7958 | 36/18723 | 3.42e-06 | 4.49e-05 | 29 |
GO:000756822 | Liver | HCC | aging | 185/7958 | 339/18723 | 4.28e-06 | 5.50e-05 | 185 |
GO:009015111 | Liver | HCC | establishment of protein localization to mitochondrial membrane | 25/7958 | 30/18723 | 5.25e-06 | 6.54e-05 | 25 |
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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 |
ROMO1 | SNV | Missense_Mutation | c.172N>G | p.Lys58Glu | p.K58E | P60602 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
ROMO1 | SNV | Missense_Mutation | novel | c.142C>T | p.Arg48Trp | p.R48W | P60602 | protein_coding | deleterious(0.04) | benign(0.007) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
ROMO1 | SNV | Missense_Mutation | novel | c.186N>C | p.Gln62His | p.Q62H | P60602 | protein_coding | deleterious(0.04) | benign(0.425) | TCGA-85-A4QQ-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
ROMO1 | SNV | Missense_Mutation | rs749056787 | c.193N>A | p.Gly65Ser | p.G65S | P60602 | protein_coding | tolerated(0.16) | benign(0.056) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | |
ROMO1 | SNV | Missense_Mutation | novel | c.37N>A | p.Pro13Thr | p.P13T | P60602 | protein_coding | deleterious(0) | possibly_damaging(0.887) | TCGA-VQ-AA68-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Chemotherapy | fluorouracil | CR |
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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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