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Gene: CUX2 |
Gene summary for CUX2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CUX2 | Gene ID | 23316 |
| Gene name | cut like homeobox 2 | |
| Gene Alias | CDP2 | |
| Cytomap | 12q24.11-q24.12 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | O14529 |
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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 |
| 23316 | CUX2 | 047563_1562-all-cells | Human | Prostate | BPH | 4.38e-05 | 3.01e-01 | 0.0791 |
| 23316 | CUX2 | 048752_1579-all-cells | Human | Prostate | BPH | 7.06e-55 | 8.87e-01 | 0.1008 |
| 23316 | CUX2 | 052095_1628-all-cells | Human | Prostate | BPH | 3.17e-39 | 7.70e-01 | 0.1032 |
| 23316 | CUX2 | 052097_1595-all-cells | Human | Prostate | BPH | 1.11e-25 | 5.34e-01 | 0.0972 |
| 23316 | CUX2 | 052099_1652-all-cells | Human | Prostate | BPH | 8.19e-55 | 9.42e-01 | 0.1038 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:002260417 | Prostate | BPH | regulation of cell morphogenesis | 99/3107 | 309/18723 | 1.30e-11 | 9.72e-10 | 99 |
| GO:001076916 | Prostate | BPH | regulation of cell morphogenesis involved in differentiation | 40/3107 | 96/18723 | 5.08e-09 | 1.86e-07 | 40 |
| GO:003432910 | Prostate | BPH | cell junction assembly | 114/3107 | 420/18723 | 2.52e-08 | 7.49e-07 | 114 |
| GO:00109759 | Prostate | BPH | regulation of neuron projection development | 118/3107 | 445/18723 | 5.85e-08 | 1.57e-06 | 118 |
| GO:00107208 | Prostate | BPH | positive regulation of cell development | 86/3107 | 298/18723 | 7.11e-08 | 1.85e-06 | 86 |
| GO:00313469 | Prostate | BPH | positive regulation of cell projection organization | 98/3107 | 353/18723 | 7.34e-08 | 1.88e-06 | 98 |
| GO:00609966 | Prostate | BPH | dendritic spine development | 37/3107 | 99/18723 | 5.22e-07 | 1.04e-05 | 37 |
| GO:00163589 | Prostate | BPH | dendrite development | 71/3107 | 243/18723 | 5.73e-07 | 1.14e-05 | 71 |
| GO:19018888 | Prostate | BPH | regulation of cell junction assembly | 62/3107 | 204/18723 | 6.71e-07 | 1.30e-05 | 62 |
| GO:001077010 | Prostate | BPH | positive regulation of cell morphogenesis involved in differentiation | 31/3107 | 79/18723 | 1.27e-06 | 2.22e-05 | 31 |
| GO:00609985 | Prostate | BPH | regulation of dendritic spine development | 25/3107 | 61/18723 | 5.31e-06 | 7.84e-05 | 25 |
| GO:00507695 | Prostate | BPH | positive regulation of neurogenesis | 63/3107 | 225/18723 | 1.11e-05 | 1.51e-04 | 63 |
| GO:00507678 | Prostate | BPH | regulation of neurogenesis | 92/3107 | 364/18723 | 1.36e-05 | 1.78e-04 | 92 |
| GO:00488136 | Prostate | BPH | dendrite morphogenesis | 45/3107 | 146/18723 | 1.46e-05 | 1.88e-04 | 45 |
| GO:01060278 | Prostate | BPH | neuron projection organization | 32/3107 | 93/18723 | 2.19e-05 | 2.65e-04 | 32 |
| GO:00508087 | Prostate | BPH | synapse organization | 103/3107 | 426/18723 | 3.19e-05 | 3.61e-04 | 103 |
| GO:00991736 | Prostate | BPH | postsynapse organization | 49/3107 | 168/18723 | 3.20e-05 | 3.61e-04 | 49 |
| GO:00970617 | Prostate | BPH | dendritic spine organization | 29/3107 | 84/18723 | 4.86e-05 | 5.07e-04 | 29 |
| GO:00991752 | Prostate | BPH | regulation of postsynapse organization | 29/3107 | 90/18723 | 1.96e-04 | 1.61e-03 | 29 |
| GO:00610015 | Prostate | BPH | regulation of dendritic spine morphogenesis | 18/3107 | 47/18723 | 3.00e-04 | 2.32e-03 | 18 |
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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 |
| CUX2 | ECM | Colorectum | Healthy | KCNIP4,SGCZ,DPP10, etc. | 1.79e-01 |  |
| CUX2 | LYMEND | Liver | Cirrhotic | NNMT,GLT1D1,PLG, etc. | 3.99e-01 |  |
| CUX2 | LYMEND | Liver | Healthy | NNMT,GLT1D1,PLG, etc. | 1.46e-01 |  |
| CUX2 | LYMEND | Liver | NAFLD | NNMT,GLT1D1,PLG, etc. | 1.49e-01 |  |
| ∗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 |
| CUX2 | SNV | Missense_Mutation | c.3799N>C | p.Asp1267His | p.D1267H | O14529 | protein_coding | deleterious(0) | possibly_damaging(0.781) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CUX2 | SNV | Missense_Mutation | rs372685449 | c.4007C>T | p.Pro1336Leu | p.P1336L | O14529 | protein_coding | tolerated_low_confidence(0.56) | benign(0) | TCGA-AO-A12D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| CUX2 | insertion | Frame_Shift_Ins | novel | c.3295_3296insATCTCCTA | p.Gly1099AspfsTer24 | p.G1099Dfs*24 | O14529 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| CUX2 | insertion | In_Frame_Ins | novel | c.3296_3297insGAGTAAAGAACCTCTTAAATTAAAAAA | p.Gly1099_Arg1100insSerLysGluProLeuLysLeuLysLys | p.G1099_R1100insSKEPLKLKK | O14529 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| CUX2 | SNV | Missense_Mutation | novel | c.4022T>C | p.Leu1341Pro | p.L1341P | O14529 | protein_coding | tolerated_low_confidence(0.09) | benign(0) | TCGA-C5-A901-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CUX2 | SNV | Missense_Mutation | c.1034N>G | p.Lys345Arg | p.K345R | O14529 | protein_coding | tolerated(0.06) | probably_damaging(0.985) | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CUX2 | SNV | Missense_Mutation | c.4318N>A | p.Asp1440Asn | p.D1440N | O14529 | protein_coding | tolerated_low_confidence(0.07) | benign(0.001) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| CUX2 | SNV | Missense_Mutation | rs747760741 | c.3551N>A | p.Arg1184Gln | p.R1184Q | O14529 | protein_coding | deleterious(0) | benign(0.013) | TCGA-VS-A8EC-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | carboplatin | CR |
| CUX2 | SNV | Missense_Mutation | rs199740303 | c.892N>T | p.Arg298Trp | p.R298W | O14529 | protein_coding | deleterious(0) | probably_damaging(0.913) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CUX2 | SNV | Missense_Mutation | rs751335439 | c.220N>A | p.Glu74Lys | p.E74K | O14529 | protein_coding | deleterious(0.03) | benign(0.307) | TCGA-VS-A9V3-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
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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 |
| 23316 | CUX2 | TRANSCRIPTION FACTOR | rifampin | RIFAMPIN |
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