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Gene: RHBDD2 |
Gene summary for RHBDD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RHBDD2 | Gene ID | 57414 |
| Gene name | rhomboid domain containing 2 | |
| Gene Alias | NPD007 | |
| Cytomap | 7q11.23 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | Q6NTF9 |
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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 |
| 57414 | RHBDD2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.56e-06 | 1.60e-01 | 0.0155 |
| 57414 | RHBDD2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.09e-12 | 3.54e-01 | -0.1808 |
| 57414 | RHBDD2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 7.42e-06 | 2.71e-01 | -0.0811 |
| 57414 | RHBDD2 | HTA11_78_2000001011 | Human | Colorectum | AD | 6.83e-03 | 1.79e-01 | -0.1088 |
| 57414 | RHBDD2 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.72e-10 | 2.43e-01 | -0.1954 |
| 57414 | RHBDD2 | HTA11_411_2000001011 | Human | Colorectum | SER | 9.92e-10 | 8.05e-01 | -0.2602 |
| 57414 | RHBDD2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.64e-04 | 5.11e-01 | -0.2196 |
| 57414 | RHBDD2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.83e-07 | 3.70e-01 | -0.1207 |
| 57414 | RHBDD2 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.98e-02 | 3.11e-01 | -0.1526 |
| 57414 | RHBDD2 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.91e-14 | 4.41e-01 | -0.1464 |
| 57414 | RHBDD2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.37e-17 | 5.58e-01 | -0.059 |
| 57414 | RHBDD2 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.48e-06 | 4.78e-01 | -0.1706 |
| 57414 | RHBDD2 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.16e-06 | 3.15e-01 | -0.2061 |
| 57414 | RHBDD2 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.20e-06 | 3.40e-01 | -0.0842 |
| 57414 | RHBDD2 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.84e-07 | 2.87e-01 | 0.096 |
| 57414 | RHBDD2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.12e-03 | 2.89e-01 | 0.0338 |
| 57414 | RHBDD2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 5.96e-05 | 2.84e-01 | 0.0674 |
| 57414 | RHBDD2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.85e-08 | 3.19e-01 | 0.294 |
| 57414 | RHBDD2 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 3.55e-02 | 4.88e-01 | 0.3487 |
| 57414 | RHBDD2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 7.69e-08 | 3.02e-01 | 0.281 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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:0010498113 | Thyroid | PTC | proteasomal protein catabolic process | 297/5968 | 490/18723 | 4.58e-40 | 9.63e-37 | 297 |
| GO:0043161113 | Thyroid | PTC | proteasome-mediated ubiquitin-dependent protein catabolic process | 254/5968 | 412/18723 | 3.91e-36 | 4.54e-33 | 254 |
| GO:0034976113 | Thyroid | PTC | response to endoplasmic reticulum stress | 161/5968 | 256/18723 | 1.14e-24 | 3.27e-22 | 161 |
| GO:0035966113 | Thyroid | PTC | response to topologically incorrect protein | 101/5968 | 159/18723 | 2.00e-16 | 1.66e-14 | 101 |
| GO:0006986113 | Thyroid | PTC | response to unfolded protein | 87/5968 | 137/18723 | 2.46e-14 | 1.57e-12 | 87 |
| GO:00365038 | Thyroid | PTC | ERAD pathway | 71/5968 | 107/18723 | 2.37e-13 | 1.22e-11 | 71 |
| GO:003043315 | Thyroid | PTC | ubiquitin-dependent ERAD pathway | 59/5968 | 85/18723 | 1.30e-12 | 5.91e-11 | 59 |
| GO:0035967113 | Thyroid | PTC | cellular response to topologically incorrect protein | 73/5968 | 116/18723 | 5.62e-12 | 2.41e-10 | 73 |
| GO:0034620113 | Thyroid | PTC | cellular response to unfolded protein | 60/5968 | 96/18723 | 6.36e-10 | 1.97e-08 | 60 |
| GO:0030968111 | Thyroid | PTC | endoplasmic reticulum unfolded protein response | 48/5968 | 74/18723 | 5.52e-09 | 1.41e-07 | 48 |
| GO:000698628 | Thyroid | goiters | response to unfolded protein | 17/497 | 137/18723 | 1.38e-07 | 1.10e-05 | 17 |
| GO:003596628 | Thyroid | goiters | response to topologically incorrect protein | 18/497 | 159/18723 | 2.42e-07 | 1.82e-05 | 18 |
| GO:003497628 | Thyroid | goiters | response to endoplasmic reticulum stress | 20/497 | 256/18723 | 1.77e-05 | 6.80e-04 | 20 |
| GO:0010498210 | Thyroid | goiters | proteasomal protein catabolic process | 27/497 | 490/18723 | 3.03e-04 | 7.94e-03 | 27 |
| GO:003462027 | Thyroid | goiters | cellular response to unfolded protein | 9/497 | 96/18723 | 1.02e-03 | 2.10e-02 | 9 |
| GO:003596728 | Thyroid | goiters | cellular response to topologically incorrect protein | 10/497 | 116/18723 | 1.05e-03 | 2.15e-02 | 10 |
| GO:003650316 | Thyroid | goiters | ERAD pathway | 9/497 | 107/18723 | 2.19e-03 | 3.62e-02 | 9 |
| GO:001049832 | Thyroid | ATC | proteasomal protein catabolic process | 309/6293 | 490/18723 | 1.78e-41 | 1.13e-37 | 309 |
| GO:0043161210 | Thyroid | ATC | proteasome-mediated ubiquitin-dependent protein catabolic process | 265/6293 | 412/18723 | 7.09e-38 | 1.49e-34 | 265 |
| GO:003497633 | Thyroid | ATC | response to endoplasmic reticulum stress | 167/6293 | 256/18723 | 2.62e-25 | 1.03e-22 | 167 |
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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 |
| 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 |
| RHBDD2 | SNV | Missense_Mutation | novel | c.722N>T | p.Ala241Val | p.A241V | Q6NTF9 | protein_coding | deleterious(0.03) | probably_damaging(0.994) | TCGA-E9-A1RG-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| RHBDD2 | SNV | Missense_Mutation | rs782231378 | c.293N>A | p.Arg98His | p.R98H | Q6NTF9 | protein_coding | deleterious(0) | probably_damaging(0.949) | TCGA-IR-A3LF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RHBDD2 | SNV | Missense_Mutation | c.335N>C | p.Ile112Thr | p.I112T | Q6NTF9 | protein_coding | deleterious(0.05) | benign(0.197) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RHBDD2 | SNV | Missense_Mutation | c.154N>C | p.Ser52Pro | p.S52P | Q6NTF9 | protein_coding | tolerated(0.42) | benign(0.007) | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RHBDD2 | SNV | Missense_Mutation | c.631G>A | p.Ala211Thr | p.A211T | Q6NTF9 | protein_coding | deleterious(0.01) | benign(0.186) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |
| RHBDD2 | SNV | Missense_Mutation | novel | c.873G>A | p.Met291Ile | p.M291I | Q6NTF9 | protein_coding | tolerated(0.28) | benign(0.003) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RHBDD2 | SNV | Missense_Mutation | novel | c.907C>A | p.Leu303Met | p.L303M | Q6NTF9 | protein_coding | tolerated(0.07) | benign(0.365) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RHBDD2 | SNV | Missense_Mutation | rs368476168 | c.613N>A | p.Asp205Asn | p.D205N | Q6NTF9 | protein_coding | tolerated(0.05) | benign(0.144) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RHBDD2 | SNV | Missense_Mutation | novel | c.998N>T | p.Pro333Leu | p.P333L | Q6NTF9 | protein_coding | tolerated_low_confidence(0.06) | benign(0) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RHBDD2 | SNV | Missense_Mutation | rs782696848 | c.823N>A | p.Ala275Thr | p.A275T | Q6NTF9 | protein_coding | tolerated(0.63) | benign(0) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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