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Gene: IRX3 |
Gene summary for IRX3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | IRX3 | Gene ID | 79191 |
Gene name | iroquois homeobox 3 | |
Gene Alias | IRX-1 | |
Cytomap | 16q12.2 | |
Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | P78415 |
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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 |
79191 | IRX3 | GSM4909281 | Human | Breast | IDC | 6.62e-04 | 2.02e-01 | 0.21 |
79191 | IRX3 | GSM4909285 | Human | Breast | IDC | 9.66e-04 | 2.20e-02 | 0.21 |
79191 | IRX3 | GSM4909293 | Human | Breast | IDC | 9.71e-13 | 2.66e-01 | 0.1581 |
79191 | IRX3 | GSM4909297 | Human | Breast | IDC | 4.65e-06 | -2.04e-01 | 0.1517 |
79191 | IRX3 | GSM4909298 | Human | Breast | IDC | 2.92e-15 | 4.25e-01 | 0.1551 |
79191 | IRX3 | GSM4909299 | Human | Breast | IDC | 1.84e-05 | 3.00e-01 | 0.035 |
79191 | IRX3 | GSM4909301 | Human | Breast | IDC | 8.35e-24 | 6.43e-01 | 0.1577 |
79191 | IRX3 | GSM4909306 | Human | Breast | IDC | 5.36e-11 | 4.39e-01 | 0.1564 |
79191 | IRX3 | GSM4909311 | Human | Breast | IDC | 5.93e-13 | 1.54e-02 | 0.1534 |
79191 | IRX3 | GSM4909312 | Human | Breast | IDC | 1.51e-04 | 2.19e-01 | 0.1552 |
79191 | IRX3 | GSM4909319 | Human | Breast | IDC | 6.98e-29 | 3.18e-01 | 0.1563 |
79191 | IRX3 | GSM4909321 | Human | Breast | IDC | 3.74e-03 | -7.06e-02 | 0.1559 |
79191 | IRX3 | brca2 | Human | Breast | Precancer | 1.38e-02 | 1.07e-01 | -0.024 |
79191 | IRX3 | M1 | Human | Breast | IDC | 6.28e-04 | 3.86e-01 | 0.1577 |
79191 | IRX3 | M2 | Human | Breast | IDC | 1.52e-04 | 3.60e-01 | 0.21 |
79191 | IRX3 | NCCBC14 | Human | Breast | DCIS | 8.71e-06 | 2.56e-01 | 0.2021 |
79191 | IRX3 | NCCBC2 | Human | Breast | DCIS | 2.29e-12 | 7.31e-01 | 0.1554 |
79191 | IRX3 | NCCBC5 | Human | Breast | DCIS | 1.11e-03 | -1.40e-01 | 0.2046 |
79191 | IRX3 | P1 | Human | Breast | IDC | 4.55e-07 | 6.62e-02 | 0.1527 |
79191 | IRX3 | DCIS2 | Human | Breast | DCIS | 1.36e-32 | 3.05e-01 | 0.0085 |
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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:000704312 | Liver | HCC | cell-cell junction assembly | 76/7958 | 146/18723 | 1.23e-02 | 4.47e-02 | 76 |
GO:00018388 | Oral cavity | OSCC | embryonic epithelial tube formation | 66/7305 | 121/18723 | 3.70e-04 | 2.26e-03 | 66 |
GO:003514810 | Oral cavity | OSCC | tube formation | 78/7305 | 148/18723 | 4.82e-04 | 2.85e-03 | 78 |
GO:00163315 | Oral cavity | OSCC | morphogenesis of embryonic epithelium | 77/7305 | 147/18723 | 6.63e-04 | 3.72e-03 | 77 |
GO:00016558 | Oral cavity | OSCC | urogenital system development | 160/7305 | 338/18723 | 1.03e-03 | 5.31e-03 | 160 |
GO:00721758 | Oral cavity | OSCC | epithelial tube formation | 69/7305 | 132/18723 | 1.32e-03 | 6.56e-03 | 69 |
GO:00605378 | Oral cavity | OSCC | muscle tissue development | 185/7305 | 403/18723 | 2.60e-03 | 1.14e-02 | 185 |
GO:004521618 | Oral cavity | OSCC | cell-cell junction organization | 97/7305 | 200/18723 | 3.83e-03 | 1.57e-02 | 97 |
GO:00426927 | Oral cavity | OSCC | muscle cell differentiation | 175/7305 | 384/18723 | 4.79e-03 | 1.92e-02 | 175 |
GO:003432916 | Oral cavity | OSCC | cell junction assembly | 190/7305 | 420/18723 | 4.99e-03 | 1.96e-02 | 190 |
GO:00147067 | Oral cavity | OSCC | striated muscle tissue development | 174/7305 | 384/18723 | 6.45e-03 | 2.40e-02 | 174 |
GO:00605629 | Oral cavity | OSCC | epithelial tube morphogenesis | 149/7305 | 325/18723 | 6.73e-03 | 2.50e-02 | 149 |
GO:00106447 | Oral cavity | OSCC | cell communication by electrical coupling | 19/7305 | 32/18723 | 1.56e-02 | 5.00e-02 | 19 |
GO:003432910 | Prostate | BPH | cell junction assembly | 114/3107 | 420/18723 | 2.52e-08 | 7.49e-07 | 114 |
GO:19018888 | Prostate | BPH | regulation of cell junction assembly | 62/3107 | 204/18723 | 6.71e-07 | 1.30e-05 | 62 |
GO:00605628 | Prostate | BPH | epithelial tube morphogenesis | 87/3107 | 325/18723 | 2.05e-06 | 3.39e-05 | 87 |
GO:004521616 | Prostate | BPH | cell-cell junction organization | 59/3107 | 200/18723 | 3.57e-06 | 5.54e-05 | 59 |
GO:00016557 | Prostate | BPH | urogenital system development | 88/3107 | 338/18723 | 6.05e-06 | 8.83e-05 | 88 |
GO:00605377 | Prostate | BPH | muscle tissue development | 100/3107 | 403/18723 | 1.35e-05 | 1.76e-04 | 100 |
GO:00720737 | Prostate | BPH | kidney epithelium development | 42/3107 | 136/18723 | 2.62e-05 | 3.10e-04 | 42 |
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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 |
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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 |
∗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 |
IRX3 | deletion | Frame_Shift_Del | c.379delG | p.Asp127ThrfsTer16 | p.D127Tfs*16 | P78415 | protein_coding | TCGA-AN-A0FT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
IRX3 | deletion | Frame_Shift_Del | novel | c.362_363delGC | p.Gly121AlafsTer69 | p.G121Afs*69 | P78415 | protein_coding | TCGA-OL-A5D8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
IRX3 | SNV | Missense_Mutation | rs567541390 | c.952N>T | p.Ala318Ser | p.A318S | P78415 | protein_coding | tolerated(0.67) | benign(0.028) | TCGA-VS-A8QH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | gemcitabine | PD |
IRX3 | SNV | Missense_Mutation | rs376056612 | c.332N>T | p.Pro111Leu | p.P111L | P78415 | protein_coding | deleterious_low_confidence(0.01) | benign(0.012) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
IRX3 | SNV | Missense_Mutation | c.818N>T | p.Ala273Val | p.A273V | P78415 | protein_coding | tolerated(0.18) | benign(0) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
IRX3 | SNV | Missense_Mutation | rs758083649 | c.161C>T | p.Ser54Leu | p.S54L | P78415 | protein_coding | tolerated(0.17) | probably_damaging(0.968) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
IRX3 | SNV | Missense_Mutation | novel | c.661G>A | p.Asp221Asn | p.D221N | P78415 | protein_coding | tolerated(0.33) | benign(0.113) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
IRX3 | SNV | Missense_Mutation | c.391C>T | p.Pro131Ser | p.P131S | P78415 | protein_coding | deleterious(0.01) | possibly_damaging(0.867) | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
IRX3 | SNV | Missense_Mutation | c.824N>A | p.Arg275His | p.R275H | P78415 | protein_coding | tolerated(0.34) | benign(0) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
IRX3 | SNV | Missense_Mutation | novel | c.775N>G | p.Leu259Val | p.L259V | P78415 | protein_coding | tolerated(0.32) | benign(0.028) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <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 |
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