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Gene: DEPDC5 |
Gene summary for DEPDC5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DEPDC5 | Gene ID | 9681 |
| Gene name | DEP domain containing 5, GATOR1 subcomplex subunit | |
| Gene Alias | DEP.5 | |
| Cytomap | 22q12.2-q12.3 | |
| Gene Type | protein-coding | GO ID | GO:0006914 | UniProtAcc | O75140 |
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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 |
| 9681 | DEPDC5 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.02e-11 | 2.37e-01 | 0.0155 |
| 9681 | DEPDC5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.43e-18 | 4.98e-01 | -0.1808 |
| 9681 | DEPDC5 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.34e-04 | 3.89e-01 | 0.0216 |
| 9681 | DEPDC5 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.53e-23 | 6.33e-01 | -0.0811 |
| 9681 | DEPDC5 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.86e-16 | 4.36e-01 | -0.1088 |
| 9681 | DEPDC5 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.69e-50 | 8.41e-01 | -0.1954 |
| 9681 | DEPDC5 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.35e-12 | 7.18e-01 | -0.2602 |
| 9681 | DEPDC5 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.08e-06 | 4.24e-01 | -0.2196 |
| 9681 | DEPDC5 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.93e-12 | 4.18e-01 | -0.1207 |
| 9681 | DEPDC5 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.68e-22 | 6.66e-01 | -0.1526 |
| 9681 | DEPDC5 | HTA11_696_2000001011 | Human | Colorectum | AD | 8.45e-42 | 7.89e-01 | -0.1464 |
| 9681 | DEPDC5 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.14e-33 | 5.83e-01 | -0.1001 |
| 9681 | DEPDC5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.25e-24 | 6.20e-01 | -0.059 |
| 9681 | DEPDC5 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.52e-10 | 5.85e-01 | -0.1706 |
| 9681 | DEPDC5 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.00e-07 | 3.82e-01 | -0.2061 |
| 9681 | DEPDC5 | HTA11_5216_2000001011 | Human | Colorectum | SER | 3.22e-05 | 3.36e-01 | -0.1462 |
| 9681 | DEPDC5 | HTA11_546_2000001011 | Human | Colorectum | AD | 4.57e-20 | 6.83e-01 | -0.0842 |
| 9681 | DEPDC5 | HTA11_9341_2000001011 | Human | Colorectum | SER | 1.20e-07 | 4.38e-01 | -0.00410000000000005 |
| 9681 | DEPDC5 | HTA11_7862_2000001011 | Human | Colorectum | AD | 7.36e-06 | 3.05e-01 | -0.0179 |
| 9681 | DEPDC5 | HTA11_866_3004761011 | Human | Colorectum | AD | 8.97e-15 | 3.40e-01 | 0.096 |
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| 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 |
| ∗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:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
| GO:0031667 | Colorectum | AD | response to nutrient levels | 138/3918 | 474/18723 | 1.22e-05 | 2.68e-04 | 138 |
| GO:0042594 | Colorectum | AD | response to starvation | 63/3918 | 197/18723 | 1.77e-04 | 2.38e-03 | 63 |
| GO:0071496 | Colorectum | AD | cellular response to external stimulus | 94/3918 | 320/18723 | 1.98e-04 | 2.64e-03 | 94 |
| GO:0009267 | Colorectum | AD | cellular response to starvation | 51/3918 | 156/18723 | 3.90e-04 | 4.44e-03 | 51 |
| GO:0031668 | Colorectum | AD | cellular response to extracellular stimulus | 71/3918 | 246/18723 | 1.86e-03 | 1.52e-02 | 71 |
| GO:0031669 | Colorectum | AD | cellular response to nutrient levels | 63/3918 | 215/18723 | 2.19e-03 | 1.73e-02 | 63 |
| GO:00316671 | Colorectum | SER | response to nutrient levels | 106/2897 | 474/18723 | 3.94e-05 | 1.00e-03 | 106 |
| GO:00105061 | Colorectum | SER | regulation of autophagy | 74/2897 | 317/18723 | 1.39e-04 | 2.77e-03 | 74 |
| GO:00425941 | Colorectum | SER | response to starvation | 47/2897 | 197/18723 | 1.31e-03 | 1.45e-02 | 47 |
| GO:00714961 | Colorectum | SER | cellular response to external stimulus | 70/2897 | 320/18723 | 1.40e-03 | 1.53e-02 | 70 |
| GO:00092671 | Colorectum | SER | cellular response to starvation | 38/2897 | 156/18723 | 2.45e-03 | 2.32e-02 | 38 |
| GO:00316681 | Colorectum | SER | cellular response to extracellular stimulus | 54/2897 | 246/18723 | 4.26e-03 | 3.45e-02 | 54 |
| GO:00316691 | Colorectum | SER | cellular response to nutrient levels | 48/2897 | 215/18723 | 4.82e-03 | 3.78e-02 | 48 |
| GO:00105062 | Colorectum | MSS | regulation of autophagy | 95/3467 | 317/18723 | 4.36e-07 | 1.71e-05 | 95 |
| GO:00316672 | Colorectum | MSS | response to nutrient levels | 125/3467 | 474/18723 | 1.24e-05 | 2.88e-04 | 125 |
| GO:00425942 | Colorectum | MSS | response to starvation | 56/3467 | 197/18723 | 4.25e-04 | 5.21e-03 | 56 |
| GO:00714962 | Colorectum | MSS | cellular response to external stimulus | 82/3467 | 320/18723 | 9.30e-04 | 9.44e-03 | 82 |
| GO:00092672 | Colorectum | MSS | cellular response to starvation | 44/3467 | 156/18723 | 1.96e-03 | 1.69e-02 | 44 |
| GO:00316692 | Colorectum | MSS | cellular response to nutrient levels | 56/3467 | 215/18723 | 3.80e-03 | 2.79e-02 | 56 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04150 | Colorectum | MSS | mTOR signaling pathway | 47/1875 | 156/8465 | 1.19e-02 | 3.99e-02 | 2.44e-02 | 47 |
| hsa041501 | Colorectum | MSS | mTOR signaling pathway | 47/1875 | 156/8465 | 1.19e-02 | 3.99e-02 | 2.44e-02 | 47 |
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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 |
| DEPDC5 | SNV | Missense_Mutation | c.4205T>A | p.Val1402Asp | p.V1402D | O75140 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A7-A26J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| DEPDC5 | SNV | Missense_Mutation | c.2983N>T | p.Arg995Cys | p.R995C | O75140 | protein_coding | tolerated(0.09) | possibly_damaging(0.88) | TCGA-AC-A3TN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| DEPDC5 | SNV | Missense_Mutation | rs200020310 | c.1153C>T | p.Arg385Trp | p.R385W | O75140 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| DEPDC5 | SNV | Missense_Mutation | rs760696765 | c.1814G>A | p.Arg605Gln | p.R605Q | O75140 | protein_coding | deleterious(0.02) | probably_damaging(0.959) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| DEPDC5 | SNV | Missense_Mutation | rs747454808 | c.3746N>A | p.Arg1249Gln | p.R1249Q | O75140 | protein_coding | tolerated(0.14) | probably_damaging(0.994) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| DEPDC5 | SNV | Missense_Mutation | c.3268N>A | p.Gly1090Arg | p.G1090R | O75140 | protein_coding | tolerated_low_confidence(0.16) | benign(0) | TCGA-BH-A1F8-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| DEPDC5 | SNV | Missense_Mutation | rs780509997 | c.4403G>A | p.Arg1468Gln | p.R1468Q | O75140 | protein_coding | deleterious(0) | benign(0.416) | TCGA-BH-A42V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| DEPDC5 | SNV | Missense_Mutation | c.3777N>T | p.Lys1259Asn | p.K1259N | O75140 | protein_coding | tolerated(0.16) | possibly_damaging(0.672) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| DEPDC5 | SNV | Missense_Mutation | c.1561N>A | p.Ser521Thr | p.S521T | O75140 | protein_coding | tolerated(0.15) | benign(0.219) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| DEPDC5 | SNV | Missense_Mutation | novel | c.4200G>T | p.Glu1400Asp | p.E1400D | O75140 | protein_coding | tolerated(0.52) | probably_damaging(0.978) | TCGA-E2-A574-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | 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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