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Gene: CSMD1 |
Gene summary for CSMD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CSMD1 | Gene ID | 64478 |
| Gene name | CUB and Sushi multiple domains 1 | |
| Gene Alias | PPP1R24 | |
| Cytomap | 8p23.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A0U1RQY1 |
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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 |
| 64478 | CSMD1 | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.53e-02 | 2.46e-01 | 0.0216 |
| 64478 | CSMD1 | HTA11_347_2000001011 | Human | Colorectum | AD | 8.64e-04 | 5.36e-02 | -0.1954 |
| 64478 | CSMD1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.58e-08 | 4.53e-01 | -0.1207 |
| 64478 | CSMD1 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.20e-03 | 1.17e-01 | -0.1464 |
| 64478 | CSMD1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.42e-03 | 2.20e-01 | -0.059 |
| 64478 | CSMD1 | HTA11_546_2000001011 | Human | Colorectum | AD | 2.30e-04 | 1.23e-01 | -0.0842 |
| 64478 | CSMD1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.46e-04 | 2.80e-01 | 0.281 |
| 64478 | CSMD1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.43e-08 | 4.92e-02 | 0.3005 |
| 64478 | CSMD1 | A015-C-203 | Human | Colorectum | FAP | 1.07e-57 | 1.31e+00 | -0.1294 |
| 64478 | CSMD1 | A015-C-204 | Human | Colorectum | FAP | 4.46e-16 | 9.14e-01 | -0.0228 |
| 64478 | CSMD1 | A014-C-040 | Human | Colorectum | FAP | 1.08e-08 | 1.02e+00 | -0.1184 |
| 64478 | CSMD1 | A002-C-201 | Human | Colorectum | FAP | 2.68e-19 | 9.00e-01 | 0.0324 |
| 64478 | CSMD1 | A002-C-116 | Human | Colorectum | FAP | 4.53e-23 | 9.33e-01 | -0.0452 |
| 64478 | CSMD1 | CRC-1-8810 | Human | Colorectum | CRC | 3.64e-05 | 4.12e-01 | 0.6257 |
| 64478 | CSMD1 | CRC-3-11773 | Human | Colorectum | CRC | 2.01e-35 | 1.06e+00 | 0.2564 |
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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:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
| GO:0030879 | Colorectum | AD | mammary gland development | 53/3918 | 137/18723 | 1.46e-06 | 4.58e-05 | 53 |
| GO:0033500 | Colorectum | AD | carbohydrate homeostasis | 84/3918 | 259/18723 | 9.10e-06 | 2.15e-04 | 84 |
| GO:0042593 | Colorectum | AD | glucose homeostasis | 83/3918 | 258/18723 | 1.44e-05 | 3.11e-04 | 83 |
| GO:0061180 | Colorectum | AD | mammary gland epithelium development | 28/3918 | 67/18723 | 8.74e-05 | 1.35e-03 | 28 |
| GO:0022612 | Colorectum | AD | gland morphogenesis | 42/3918 | 118/18723 | 1.62e-04 | 2.23e-03 | 42 |
| GO:0060562 | Colorectum | AD | epithelial tube morphogenesis | 93/3918 | 325/18723 | 5.65e-04 | 6.00e-03 | 93 |
| GO:0061458 | Colorectum | AD | reproductive system development | 116/3918 | 427/18723 | 1.11e-03 | 1.01e-02 | 116 |
| GO:0060443 | Colorectum | AD | mammary gland morphogenesis | 18/3918 | 43/18723 | 1.51e-03 | 1.27e-02 | 18 |
| GO:0048608 | Colorectum | AD | reproductive structure development | 114/3918 | 424/18723 | 1.78e-03 | 1.47e-02 | 114 |
| GO:0001763 | Colorectum | AD | morphogenesis of a branching structure | 56/3918 | 196/18723 | 6.60e-03 | 4.09e-02 | 56 |
| GO:00487322 | Colorectum | MSS | gland development | 143/3467 | 436/18723 | 3.85e-13 | 8.01e-11 | 143 |
| GO:00308792 | Colorectum | MSS | mammary gland development | 51/3467 | 137/18723 | 1.88e-07 | 8.26e-06 | 51 |
| GO:00611802 | Colorectum | MSS | mammary gland epithelium development | 28/3467 | 67/18723 | 8.47e-06 | 2.11e-04 | 28 |
| GO:00614582 | Colorectum | MSS | reproductive system development | 115/3467 | 427/18723 | 9.86e-06 | 2.39e-04 | 115 |
| GO:00335002 | Colorectum | MSS | carbohydrate homeostasis | 76/3467 | 259/18723 | 1.37e-05 | 3.14e-04 | 76 |
| GO:00486082 | Colorectum | MSS | reproductive structure development | 113/3467 | 424/18723 | 1.94e-05 | 4.18e-04 | 113 |
| GO:00226122 | Colorectum | MSS | gland morphogenesis | 41/3467 | 118/18723 | 2.02e-05 | 4.30e-04 | 41 |
| GO:00425932 | Colorectum | MSS | glucose homeostasis | 75/3467 | 258/18723 | 2.22e-05 | 4.69e-04 | 75 |
| GO:00605621 | Colorectum | MSS | epithelial tube morphogenesis | 88/3467 | 325/18723 | 8.45e-05 | 1.37e-03 | 88 |
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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. |
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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 |
| CSMD1 | SNV | Missense_Mutation | c.5548N>A | p.Glu1850Lys | p.E1850K | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| CSMD1 | SNV | Missense_Mutation | novel | c.1369T>G | p.Phe457Val | p.F457V | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR | |
| CSMD1 | SNV | Missense_Mutation | c.1733C>A | p.Pro578His | p.P578H | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A076-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| CSMD1 | SNV | Missense_Mutation | c.8060T>A | p.Val2687Glu | p.V2687E | protein_coding | deleterious(0) | possibly_damaging(0.731) | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| CSMD1 | SNV | Missense_Mutation | rs371336619 | c.5431N>C | p.Gly1811Arg | p.G1811R | protein_coding | deleterious(0.01) | probably_damaging(0.975) | TCGA-A8-A08F-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| CSMD1 | SNV | Missense_Mutation | c.6422G>A | p.Arg2141Lys | p.R2141K | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| CSMD1 | SNV | Missense_Mutation | rs768149539 | c.9419N>A | p.Arg3140His | p.R3140H | protein_coding | tolerated(0.05) | benign(0) | TCGA-A8-A09K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CSMD1 | SNV | Missense_Mutation | c.690N>A | p.Asn230Lys | p.N230K | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-A8-A09Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD | ||
| CSMD1 | SNV | Missense_Mutation | novel | c.9170N>C | p.Lys3057Thr | p.K3057T | protein_coding | tolerated(0.15) | benign(0.036) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CSMD1 | SNV | Missense_Mutation | novel | c.7374N>G | p.Phe2458Leu | p.F2458L | protein_coding | tolerated(0.5) | benign(0.036) | TCGA-AN-A046-01 | Breast | breast invasive 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 |
| 64478 | CSMD1 | NA | oxaliplatin | OXALIPLATIN | 24444404 | |
| 64478 | CSMD1 | NA | hydrochlorothiazide | HYDROCHLOROTHIAZIDE |
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