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Gene: PREX1 |
Gene summary for PREX1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PREX1 | Gene ID | 57580 |
| Gene name | phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1 | |
| Gene Alias | P-REX1 | |
| Cytomap | 20q13.13 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q8TCU6 |
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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 |
| 57580 | PREX1 | GSM4909298 | Human | Breast | IDC | 1.86e-02 | 9.87e-02 | 0.1551 |
| 57580 | PREX1 | GSM4909301 | Human | Breast | IDC | 6.43e-13 | 4.54e-01 | 0.1577 |
| 57580 | PREX1 | GSM4909302 | Human | Breast | IDC | 2.63e-07 | 3.17e-01 | 0.1545 |
| 57580 | PREX1 | GSM4909304 | Human | Breast | IDC | 1.99e-69 | 1.05e+00 | 0.1636 |
| 57580 | PREX1 | GSM4909308 | Human | Breast | IDC | 4.05e-02 | 1.53e-01 | 0.158 |
| 57580 | PREX1 | GSM4909320 | Human | Breast | IDC | 2.72e-02 | 3.78e-01 | 0.1575 |
| 57580 | PREX1 | M1 | Human | Breast | IDC | 1.46e-22 | 6.54e-01 | 0.1577 |
| 57580 | PREX1 | NCCBC2 | Human | Breast | DCIS | 2.77e-04 | 6.22e-01 | 0.1554 |
| 57580 | PREX1 | P1 | Human | Breast | IDC | 3.78e-08 | 4.78e-01 | 0.1527 |
| 57580 | PREX1 | P3 | Human | Breast | IDC | 1.11e-05 | 5.71e-01 | 0.1542 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
| ∗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:004578514 | Breast | IDC | positive regulation of cell adhesion | 62/1434 | 437/18723 | 1.70e-06 | 7.16e-05 | 62 |
| GO:004325414 | Breast | IDC | regulation of protein-containing complex assembly | 61/1434 | 428/18723 | 1.77e-06 | 7.31e-05 | 61 |
| GO:007162111 | Breast | IDC | granulocyte chemotaxis | 26/1434 | 125/18723 | 2.36e-06 | 9.30e-05 | 26 |
| GO:005090011 | Breast | IDC | leukocyte migration | 54/1434 | 369/18723 | 3.10e-06 | 1.15e-04 | 54 |
| GO:009752911 | Breast | IDC | myeloid leukocyte migration | 37/1434 | 220/18723 | 4.65e-06 | 1.62e-04 | 37 |
| GO:003059511 | Breast | IDC | leukocyte chemotaxis | 38/1434 | 230/18723 | 5.36e-06 | 1.76e-04 | 38 |
| GO:003297014 | Breast | IDC | regulation of actin filament-based process | 56/1434 | 397/18723 | 6.37e-06 | 1.99e-04 | 56 |
| GO:003059311 | Breast | IDC | neutrophil chemotaxis | 22/1434 | 103/18723 | 8.82e-06 | 2.50e-04 | 22 |
| GO:190290314 | Breast | IDC | regulation of supramolecular fiber organization | 54/1434 | 383/18723 | 9.40e-06 | 2.66e-04 | 54 |
| GO:006032611 | Breast | IDC | cell chemotaxis | 46/1434 | 310/18723 | 1.13e-05 | 3.08e-04 | 46 |
| GO:004211012 | Breast | IDC | T cell activation | 64/1434 | 487/18723 | 1.49e-05 | 3.77e-04 | 64 |
| GO:009753011 | Breast | IDC | granulocyte migration | 27/1434 | 148/18723 | 1.98e-05 | 4.88e-04 | 27 |
| GO:199026611 | Breast | IDC | neutrophil migration | 23/1434 | 122/18723 | 4.67e-05 | 1.04e-03 | 23 |
| GO:007259313 | Breast | IDC | reactive oxygen species metabolic process | 36/1434 | 239/18723 | 7.16e-05 | 1.43e-03 | 36 |
| GO:003295614 | Breast | IDC | regulation of actin cytoskeleton organization | 48/1434 | 358/18723 | 1.03e-04 | 1.96e-03 | 48 |
| GO:000701514 | Breast | IDC | actin filament organization | 55/1434 | 442/18723 | 2.45e-04 | 3.84e-03 | 55 |
| GO:011005314 | Breast | IDC | regulation of actin filament organization | 37/1434 | 278/18723 | 7.01e-04 | 8.58e-03 | 37 |
| GO:00322719 | Breast | IDC | regulation of protein polymerization | 32/1434 | 233/18723 | 9.19e-04 | 1.05e-02 | 32 |
| GO:190313111 | Breast | IDC | mononuclear cell differentiation | 51/1434 | 426/18723 | 9.81e-04 | 1.11e-02 | 51 |
| GO:001081114 | Breast | IDC | positive regulation of cell-substrate adhesion | 20/1434 | 123/18723 | 1.05e-03 | 1.16e-02 | 20 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0516743 | Breast | DCIS | Kaposi sarcoma-associated herpesvirus infection | 38/846 | 194/8465 | 3.43e-05 | 3.69e-04 | 2.72e-04 | 38 |
| hsa0516753 | Breast | DCIS | Kaposi sarcoma-associated herpesvirus infection | 38/846 | 194/8465 | 3.43e-05 | 3.69e-04 | 2.72e-04 | 38 |
| 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 |
| PREX1 | SNV | Missense_Mutation | novel | c.1455N>G | p.Phe485Leu | p.F485L | Q8TCU6 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| PREX1 | SNV | Missense_Mutation | c.3696C>G | p.Ile1232Met | p.I1232M | Q8TCU6 | protein_coding | deleterious(0.01) | probably_damaging(0.968) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD | |
| PREX1 | SNV | Missense_Mutation | c.1030G>A | p.Gly344Arg | p.G344R | Q8TCU6 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A0D2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| PREX1 | SNV | Missense_Mutation | c.3133N>T | p.Leu1045Phe | p.L1045F | Q8TCU6 | protein_coding | deleterious_low_confidence(0.02) | benign(0.03) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| PREX1 | SNV | Missense_Mutation | c.1316N>A | p.Pro439His | p.P439H | Q8TCU6 | protein_coding | deleterious(0.02) | probably_damaging(0.98) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PREX1 | SNV | Missense_Mutation | rs755273231 | c.1295N>A | p.Arg432Gln | p.R432Q | Q8TCU6 | protein_coding | deleterious(0) | possibly_damaging(0.65) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PREX1 | SNV | Missense_Mutation | c.1484N>A | p.Arg495His | p.R495H | Q8TCU6 | protein_coding | deleterious(0.03) | probably_damaging(0.931) | TCGA-AR-A1AQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PREX1 | SNV | Missense_Mutation | c.3830N>A | p.Ser1277Asn | p.S1277N | Q8TCU6 | protein_coding | tolerated(0.42) | benign(0.003) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PREX1 | SNV | Missense_Mutation | rs201399202 | c.4178N>A | p.Arg1393Gln | p.R1393Q | Q8TCU6 | protein_coding | tolerated(0.58) | benign(0.025) | TCGA-BH-A203-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PREX1 | insertion | Frame_Shift_Ins | novel | c.3797_3798insGCCGGGCATGG | p.Cys1266TrpfsTer12 | p.C1266Wfs*12 | Q8TCU6 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 |
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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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