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Gene: DDX3X |
Gene summary for DDX3X |
Gene summary. |
Gene information | Species | Human | Gene symbol | DDX3X | Gene ID | 1654 |
Gene name | DEAD-box helicase 3 X-linked | |
Gene Alias | CAP-Rf | |
Cytomap | Xp11.4 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O00571 |
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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 |
1654 | DDX3X | GSM4909282 | Human | Breast | IDC | 1.60e-08 | -4.66e-01 | -0.0288 |
1654 | DDX3X | GSM4909285 | Human | Breast | IDC | 2.26e-03 | -3.03e-01 | 0.21 |
1654 | DDX3X | GSM4909286 | Human | Breast | IDC | 1.38e-07 | -2.68e-01 | 0.1081 |
1654 | DDX3X | GSM4909293 | Human | Breast | IDC | 7.56e-05 | 2.20e-01 | 0.1581 |
1654 | DDX3X | GSM4909294 | Human | Breast | IDC | 3.00e-05 | -2.81e-01 | 0.2022 |
1654 | DDX3X | GSM4909296 | Human | Breast | IDC | 1.49e-15 | -4.01e-01 | 0.1524 |
1654 | DDX3X | GSM4909297 | Human | Breast | IDC | 1.39e-14 | -1.92e-01 | 0.1517 |
1654 | DDX3X | GSM4909301 | Human | Breast | IDC | 1.01e-02 | -3.16e-01 | 0.1577 |
1654 | DDX3X | GSM4909311 | Human | Breast | IDC | 5.10e-37 | -5.06e-01 | 0.1534 |
1654 | DDX3X | GSM4909312 | Human | Breast | IDC | 9.85e-13 | -2.67e-01 | 0.1552 |
1654 | DDX3X | GSM4909313 | Human | Breast | IDC | 1.09e-04 | 1.49e-01 | 0.0391 |
1654 | DDX3X | GSM4909317 | Human | Breast | IDC | 4.79e-07 | 3.61e-01 | 0.1355 |
1654 | DDX3X | GSM4909319 | Human | Breast | IDC | 8.78e-39 | -6.57e-01 | 0.1563 |
1654 | DDX3X | GSM4909320 | Human | Breast | IDC | 1.57e-05 | -5.09e-01 | 0.1575 |
1654 | DDX3X | GSM4909321 | Human | Breast | IDC | 1.04e-15 | -2.05e-01 | 0.1559 |
1654 | DDX3X | brca1 | Human | Breast | Precancer | 6.61e-04 | -3.33e-01 | -0.0338 |
1654 | DDX3X | brca10 | Human | Breast | Precancer | 4.37e-07 | -4.79e-01 | -0.0029 |
1654 | DDX3X | NCCBC14 | Human | Breast | DCIS | 3.00e-06 | -1.85e-01 | 0.2021 |
1654 | DDX3X | NCCBC5 | Human | Breast | DCIS | 5.30e-12 | -3.22e-01 | 0.2046 |
1654 | DDX3X | P1 | Human | Breast | IDC | 1.12e-23 | 2.15e-02 | 0.1527 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:003011131 | Oral cavity | NEOLP | regulation of Wnt signaling pathway | 70/2005 | 328/18723 | 1.17e-08 | 5.67e-07 | 70 |
GO:200124332 | Oral cavity | NEOLP | negative regulation of intrinsic apoptotic signaling pathway | 31/2005 | 98/18723 | 1.57e-08 | 7.25e-07 | 31 |
GO:200011632 | Oral cavity | NEOLP | regulation of cysteine-type endopeptidase activity | 55/2005 | 235/18723 | 1.59e-08 | 7.25e-07 | 55 |
GO:001907933 | Oral cavity | NEOLP | viral genome replication | 37/2005 | 131/18723 | 2.07e-08 | 9.31e-07 | 37 |
GO:200011732 | Oral cavity | NEOLP | negative regulation of cysteine-type endopeptidase activity | 28/2005 | 86/18723 | 3.84e-08 | 1.60e-06 | 28 |
GO:004315432 | Oral cavity | NEOLP | negative regulation of cysteine-type endopeptidase activity involved in apoptotic process | 26/2005 | 78/18723 | 6.80e-08 | 2.61e-06 | 26 |
GO:004328132 | Oral cavity | NEOLP | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 49/2005 | 209/18723 | 8.94e-08 | 3.36e-06 | 49 |
GO:001604931 | Oral cavity | NEOLP | cell growth | 90/2005 | 482/18723 | 9.23e-08 | 3.43e-06 | 90 |
GO:005134631 | Oral cavity | NEOLP | negative regulation of hydrolase activity | 75/2005 | 379/18723 | 9.98e-08 | 3.66e-06 | 75 |
GO:000020931 | Oral cavity | NEOLP | protein polyubiquitination | 53/2005 | 236/18723 | 1.22e-07 | 4.38e-06 | 53 |
GO:001046632 | Oral cavity | NEOLP | negative regulation of peptidase activity | 57/2005 | 262/18723 | 1.32e-07 | 4.65e-06 | 57 |
GO:003497632 | Oral cavity | NEOLP | response to endoplasmic reticulum stress | 56/2005 | 256/18723 | 1.39e-07 | 4.84e-06 | 56 |
GO:001095132 | Oral cavity | NEOLP | negative regulation of endopeptidase activity | 55/2005 | 252/18723 | 1.94e-07 | 6.52e-06 | 55 |
GO:006082831 | Oral cavity | NEOLP | regulation of canonical Wnt signaling pathway | 55/2005 | 253/18723 | 2.23e-07 | 7.28e-06 | 55 |
GO:000644631 | Oral cavity | NEOLP | regulation of translational initiation | 25/2005 | 79/18723 | 3.75e-07 | 1.15e-05 | 25 |
GO:006007031 | Oral cavity | NEOLP | canonical Wnt signaling pathway | 62/2005 | 303/18723 | 3.79e-07 | 1.15e-05 | 62 |
GO:004572732 | Oral cavity | NEOLP | positive regulation of translation | 35/2005 | 136/18723 | 5.91e-07 | 1.74e-05 | 35 |
GO:004225534 | Oral cavity | NEOLP | ribosome assembly | 21/2005 | 61/18723 | 6.65e-07 | 1.93e-05 | 21 |
GO:003425033 | Oral cavity | NEOLP | positive regulation of cellular amide metabolic process | 39/2005 | 162/18723 | 8.79e-07 | 2.37e-05 | 39 |
GO:009026331 | Oral cavity | NEOLP | positive regulation of canonical Wnt signaling pathway | 29/2005 | 106/18723 | 1.40e-06 | 3.56e-05 | 29 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa052036 | Breast | Precancer | Viral carcinogenesis | 27/684 | 204/8465 | 7.19e-03 | 4.06e-02 | 3.11e-02 | 27 |
hsa0520312 | Breast | Precancer | Viral carcinogenesis | 27/684 | 204/8465 | 7.19e-03 | 4.06e-02 | 3.11e-02 | 27 |
hsa0520322 | Breast | IDC | Viral carcinogenesis | 34/867 | 204/8465 | 2.82e-03 | 1.86e-02 | 1.39e-02 | 34 |
hsa0520332 | Breast | IDC | Viral carcinogenesis | 34/867 | 204/8465 | 2.82e-03 | 1.86e-02 | 1.39e-02 | 34 |
hsa0520341 | Breast | DCIS | Viral carcinogenesis | 34/846 | 204/8465 | 1.88e-03 | 1.27e-02 | 9.33e-03 | 34 |
hsa052035 | Breast | DCIS | Viral carcinogenesis | 34/846 | 204/8465 | 1.88e-03 | 1.27e-02 | 9.33e-03 | 34 |
hsa052039 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
hsa0520315 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa051619 | Esophagus | ESCC | Hepatitis B | 108/4205 | 162/8465 | 7.68e-06 | 4.15e-05 | 2.12e-05 | 108 |
hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa0516114 | Esophagus | ESCC | Hepatitis B | 108/4205 | 162/8465 | 7.68e-06 | 4.15e-05 | 2.12e-05 | 108 |
hsa05203 | Liver | Cirrhotic | Viral carcinogenesis | 76/2530 | 204/8465 | 1.34e-02 | 4.20e-02 | 2.59e-02 | 76 |
hsa052031 | Liver | Cirrhotic | Viral carcinogenesis | 76/2530 | 204/8465 | 1.34e-02 | 4.20e-02 | 2.59e-02 | 76 |
hsa052032 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
hsa051612 | Liver | HCC | Hepatitis B | 91/4020 | 162/8465 | 1.56e-02 | 3.76e-02 | 2.09e-02 | 91 |
hsa052033 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
hsa0516111 | Liver | HCC | Hepatitis B | 91/4020 | 162/8465 | 1.56e-02 | 3.76e-02 | 2.09e-02 | 91 |
hsa051618 | Oral cavity | OSCC | Hepatitis B | 103/3704 | 162/8465 | 2.34e-07 | 1.51e-06 | 7.69e-07 | 103 |
hsa052038 | Oral cavity | OSCC | Viral carcinogenesis | 124/3704 | 204/8465 | 5.57e-07 | 3.28e-06 | 1.67e-06 | 124 |
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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 |
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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 |
DDX3X | SNV | Missense_Mutation | c.1675N>A | p.Leu559Ile | p.L559I | O00571 | protein_coding | tolerated(0.31) | benign(0.182) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
DDX3X | SNV | Missense_Mutation | novel | c.878C>A | p.Ser293Tyr | p.S293Y | O00571 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
DDX3X | SNV | Missense_Mutation | c.425N>T | p.Pro142Leu | p.P142L | O00571 | protein_coding | tolerated(0.11) | benign(0.179) | TCGA-AO-A03L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | |
DDX3X | SNV | Missense_Mutation | novel | c.536N>C | p.Ile179Thr | p.I179T | O00571 | protein_coding | deleterious(0.03) | benign(0.336) | TCGA-B6-A402-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | PD |
DDX3X | SNV | Missense_Mutation | c.203C>T | p.Ala68Val | p.A68V | O00571 | protein_coding | tolerated(0.15) | benign(0) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
DDX3X | SNV | Missense_Mutation | c.1907N>A | p.Gly636Glu | p.G636E | O00571 | protein_coding | tolerated(0.09) | probably_damaging(0.994) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
DDX3X | SNV | Missense_Mutation | c.81N>C | p.Gln27His | p.Q27H | O00571 | protein_coding | deleterious(0.04) | possibly_damaging(0.462) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
DDX3X | SNV | Missense_Mutation | novel | c.1321G>C | p.Asp441His | p.D441H | O00571 | protein_coding | deleterious(0.02) | possibly_damaging(0.749) | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
DDX3X | SNV | Missense_Mutation | novel | c.1873N>A | p.Gly625Arg | p.G625R | O00571 | protein_coding | deleterious(0.04) | benign(0.009) | TCGA-E2-A1B0-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
DDX3X | SNV | Missense_Mutation | novel | c.577N>A | p.Gly193Arg | p.G193R | O00571 | protein_coding | tolerated(0.4) | benign(0.272) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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