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Gene: PGRMC1 |
Gene summary for PGRMC1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PGRMC1 | Gene ID | 10857 |
| Gene name | progesterone receptor membrane component 1 | |
| Gene Alias | Dap1 | |
| Cytomap | Xq24 | |
| Gene Type | protein-coding | GO ID | GO:0006725 | UniProtAcc | O00264 |
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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 |
| 10857 | PGRMC1 | CA_HPV_1 | Human | Cervix | CC | 2.24e-05 | -2.37e-01 | 0.0264 |
| 10857 | PGRMC1 | CA_HPV_3 | Human | Cervix | CC | 2.10e-02 | 1.36e-01 | 0.0414 |
| 10857 | PGRMC1 | CCII_1 | Human | Cervix | CC | 6.03e-05 | -3.40e-01 | 0.3249 |
| 10857 | PGRMC1 | Tumor | Human | Cervix | CC | 1.08e-31 | 6.69e-01 | 0.1241 |
| 10857 | PGRMC1 | sample3 | Human | Cervix | CC | 3.51e-35 | 6.66e-01 | 0.1387 |
| 10857 | PGRMC1 | H2 | Human | Cervix | HSIL_HPV | 4.88e-03 | 3.19e-01 | 0.0632 |
| 10857 | PGRMC1 | T2 | Human | Cervix | CC | 7.20e-04 | 4.47e-01 | 0.0709 |
| 10857 | PGRMC1 | T3 | Human | Cervix | CC | 1.31e-34 | 6.84e-01 | 0.1389 |
| 10857 | PGRMC1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.42e-02 | 3.09e-01 | -0.1808 |
| 10857 | PGRMC1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.26e-12 | 5.42e-01 | -0.1088 |
| 10857 | PGRMC1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.75e-13 | 3.67e-01 | -0.1954 |
| 10857 | PGRMC1 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.53e-05 | 2.54e-01 | -0.1526 |
| 10857 | PGRMC1 | HTA11_2992_2000001011 | Human | Colorectum | SER | 7.12e-07 | 3.72e-01 | -0.1706 |
| 10857 | PGRMC1 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.96e-04 | 2.52e-01 | 0.096 |
| 10857 | PGRMC1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.35e-23 | 6.77e-01 | 0.294 |
| 10857 | PGRMC1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.16e-04 | 3.72e-01 | 0.281 |
| 10857 | PGRMC1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.33e-08 | 3.03e-01 | 0.3859 |
| 10857 | PGRMC1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.60e-03 | 1.55e-01 | 0.3005 |
| 10857 | PGRMC1 | AEH-subject1 | Human | Endometrium | AEH | 1.23e-41 | -8.09e-01 | -0.3059 |
| 10857 | PGRMC1 | AEH-subject2 | Human | Endometrium | AEH | 1.11e-45 | -9.89e-01 | -0.2525 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00067791 | Esophagus | ESCC | porphyrin-containing compound biosynthetic process | 23/8552 | 31/18723 | 1.20e-03 | 5.88e-03 | 23 |
| GO:00330141 | Esophagus | ESCC | tetrapyrrole biosynthetic process | 23/8552 | 31/18723 | 1.20e-03 | 5.88e-03 | 23 |
| GO:00461482 | Esophagus | ESCC | pigment biosynthetic process | 40/8552 | 62/18723 | 2.14e-03 | 9.54e-03 | 40 |
| GO:00067832 | Esophagus | ESCC | heme biosynthetic process | 20/8552 | 27/18723 | 2.61e-03 | 1.11e-02 | 20 |
| GO:00330132 | Esophagus | ESCC | tetrapyrrole metabolic process | 37/8552 | 59/18723 | 6.23e-03 | 2.29e-02 | 37 |
| GO:00424401 | Esophagus | ESCC | pigment metabolic process | 50/8552 | 84/18723 | 7.34e-03 | 2.64e-02 | 50 |
| GO:00421681 | Esophagus | ESCC | heme metabolic process | 27/8552 | 42/18723 | 1.16e-02 | 3.90e-02 | 27 |
| GO:0033013 | Liver | Cirrhotic | tetrapyrrole metabolic process | 24/4634 | 59/18723 | 5.06e-03 | 2.62e-02 | 24 |
| GO:0006778 | Liver | Cirrhotic | porphyrin-containing compound metabolic process | 20/4634 | 49/18723 | 9.60e-03 | 4.35e-02 | 20 |
| GO:0042168 | Liver | HCC | heme metabolic process | 30/7958 | 42/18723 | 1.40e-04 | 1.13e-03 | 30 |
| GO:00330131 | Liver | HCC | tetrapyrrole metabolic process | 39/7958 | 59/18723 | 2.14e-04 | 1.63e-03 | 39 |
| GO:00067781 | Liver | HCC | porphyrin-containing compound metabolic process | 33/7958 | 49/18723 | 3.86e-04 | 2.62e-03 | 33 |
| GO:0042440 | Liver | HCC | pigment metabolic process | 51/7958 | 84/18723 | 5.74e-04 | 3.65e-03 | 51 |
| GO:0006783 | Liver | HCC | heme biosynthetic process | 19/7958 | 27/18723 | 3.18e-03 | 1.47e-02 | 19 |
| GO:0006779 | Liver | HCC | porphyrin-containing compound biosynthetic process | 21/7958 | 31/18723 | 4.01e-03 | 1.76e-02 | 21 |
| GO:0033014 | Liver | HCC | tetrapyrrole biosynthetic process | 21/7958 | 31/18723 | 4.01e-03 | 1.76e-02 | 21 |
| GO:0046148 | Liver | HCC | pigment biosynthetic process | 37/7958 | 62/18723 | 4.73e-03 | 2.02e-02 | 37 |
| GO:00461481 | Oral cavity | OSCC | pigment biosynthetic process | 36/7305 | 62/18723 | 1.82e-03 | 8.57e-03 | 36 |
| GO:00067831 | Oral cavity | OSCC | heme biosynthetic process | 17/7305 | 27/18723 | 1.01e-02 | 3.49e-02 | 17 |
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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 |
| PGRMC1 | SNV | Missense_Mutation | c.562N>A | p.Asp188Asn | p.D188N | O00264 | protein_coding | tolerated(0.13) | benign(0.007) | TCGA-BH-A1EW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| PGRMC1 | SNV | Missense_Mutation | c.70N>A | p.Glu24Lys | p.E24K | O00264 | protein_coding | deleterious(0) | possibly_damaging(0.625) | TCGA-C8-A274-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| PGRMC1 | SNV | Missense_Mutation | c.32N>A | p.Ala11Asp | p.A11D | O00264 | protein_coding | tolerated(0.36) | benign(0) | TCGA-E2-A1LA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | |
| PGRMC1 | SNV | Missense_Mutation | c.325N>T | p.Pro109Ser | p.P109S | O00264 | protein_coding | deleterious(0) | possibly_damaging(0.816) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| PGRMC1 | SNV | Missense_Mutation | c.218N>G | p.Phe73Cys | p.F73C | O00264 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AA-3660-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PGRMC1 | SNV | Missense_Mutation | c.43N>A | p.Asp15Asn | p.D15N | O00264 | protein_coding | tolerated(0.23) | benign(0.003) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| PGRMC1 | SNV | Missense_Mutation | novel | c.103N>A | p.Leu35Ile | p.L35I | O00264 | protein_coding | tolerated(0.06) | benign(0.177) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| PGRMC1 | SNV | Missense_Mutation | novel | c.181G>A | p.Glu61Lys | p.E61K | O00264 | protein_coding | tolerated(0.3) | benign(0.018) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PGRMC1 | SNV | Missense_Mutation | c.23C>T | p.Ala8Val | p.A8V | O00264 | protein_coding | tolerated(0.14) | benign(0.042) | TCGA-FI-A2D0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PGRMC1 | insertion | In_Frame_Ins | novel | c.584_585insATTGTTTGTGTG | p.Asp195delinsGluLeuPheValCys | p.D195delinsELFVC | O00264 | protein_coding | TCGA-BS-A0UJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | 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 |
| 10857 | PGRMC1 | NA | OPC-14523 |
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