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Gene: IRX5 |
Gene summary for IRX5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | IRX5 | Gene ID | 10265 |
| Gene name | iroquois homeobox 5 | |
| Gene Alias | HMMS | |
| Cytomap | 16q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P78411 |
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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 |
| 10265 | IRX5 | GSM4909298 | Human | Breast | IDC | 8.00e-08 | 2.78e-01 | 0.1551 |
| 10265 | IRX5 | GSM4909311 | Human | Breast | IDC | 2.45e-02 | -4.30e-02 | 0.1534 |
| 10265 | IRX5 | GSM4909319 | Human | Breast | IDC | 4.46e-04 | -6.50e-02 | 0.1563 |
| 10265 | IRX5 | M1 | Human | Breast | IDC | 4.19e-04 | 3.21e-01 | 0.1577 |
| 10265 | IRX5 | M5 | Human | Breast | IDC | 2.84e-03 | 5.28e-01 | 0.1598 |
| 10265 | IRX5 | P3 | Human | Breast | IDC | 1.26e-02 | 5.18e-01 | 0.1542 |
| 10265 | IRX5 | DCIS2 | Human | Breast | DCIS | 1.90e-19 | 1.26e-01 | 0.0085 |
| 10265 | IRX5 | S014 | Human | Liver | HCC | 3.33e-15 | 5.21e-01 | 0.2254 |
| 10265 | IRX5 | S015 | Human | Liver | HCC | 2.60e-11 | 3.83e-01 | 0.2375 |
| 10265 | IRX5 | S016 | Human | Liver | HCC | 2.44e-19 | 5.08e-01 | 0.2243 |
| 10265 | IRX5 | GSM5252132_BPH389PrGF | Human | Prostate | BPH | 3.12e-04 | 2.82e-01 | -0.2247 |
| 10265 | IRX5 | GSM5252136_BPH556PrGA1_Fcol | Human | Prostate | BPH | 3.49e-05 | 2.61e-01 | -0.23 |
| 10265 | IRX5 | GSM5252137_BPH556PrGA2_Fcol | Human | Prostate | BPH | 1.37e-06 | 3.01e-01 | -0.23 |
| 10265 | IRX5 | Dong_P1 | Human | Prostate | Tumor | 3.03e-04 | 1.45e-02 | 0.035 |
| 10265 | IRX5 | Dong_P3 | Human | Prostate | Tumor | 3.99e-05 | 8.13e-02 | 0.0278 |
| 10265 | IRX5 | GSM5353221_PA_PB2A_Pool_1_3_S25_L001 | Human | Prostate | Tumor | 4.80e-02 | 2.95e-01 | 0.1633 |
| 10265 | IRX5 | GSM5353224_PA_PR5186_Pool_1_2_3_S27_L001 | Human | Prostate | Tumor | 1.39e-04 | 4.08e-01 | 0.1621 |
| 10265 | IRX5 | GSM5353236_PA_PR5251_T1_S7_L001 | Human | Prostate | Tumor | 5.56e-03 | 4.96e-01 | 0.1608 |
| 10265 | IRX5 | GSM5353237_PA_PR5251_T2_S8_L001 | Human | Prostate | Tumor | 1.78e-05 | 7.06e-01 | 0.1622 |
| 10265 | IRX5 | GSM5353240_PA_PR5254_T1_S15_L001 | Human | Prostate | Tumor | 3.38e-10 | 5.29e-01 | 0.1575 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:004860812 | Breast | IDC | reproductive structure development | 60/1434 | 424/18723 | 2.71e-06 | 1.03e-04 | 60 |
| GO:006145813 | Breast | IDC | reproductive system development | 60/1434 | 427/18723 | 3.41e-06 | 1.24e-04 | 60 |
| GO:0008406 | Breast | IDC | gonad development | 32/1434 | 221/18723 | 3.64e-04 | 5.23e-03 | 32 |
| GO:0045137 | Breast | IDC | development of primary sexual characteristics | 32/1434 | 227/18723 | 5.85e-04 | 7.44e-03 | 32 |
| GO:0007548 | Breast | IDC | sex differentiation | 35/1434 | 276/18723 | 2.23e-03 | 2.07e-02 | 35 |
| GO:004860821 | Breast | DCIS | reproductive structure development | 57/1390 | 424/18723 | 9.06e-06 | 2.45e-04 | 57 |
| GO:006145822 | Breast | DCIS | reproductive system development | 57/1390 | 427/18723 | 1.12e-05 | 2.92e-04 | 57 |
| GO:00084061 | Breast | DCIS | gonad development | 29/1390 | 221/18723 | 1.96e-03 | 1.84e-02 | 29 |
| GO:00451371 | Breast | DCIS | development of primary sexual characteristics | 29/1390 | 227/18723 | 2.93e-03 | 2.52e-02 | 29 |
| GO:006145811 | Liver | HCC | reproductive system development | 205/7958 | 427/18723 | 1.16e-02 | 4.27e-02 | 205 |
| GO:006145810 | Prostate | BPH | reproductive system development | 126/3107 | 427/18723 | 1.35e-11 | 9.95e-10 | 126 |
| GO:004860810 | Prostate | BPH | reproductive structure development | 124/3107 | 424/18723 | 3.76e-11 | 2.43e-09 | 124 |
| GO:00084063 | Prostate | BPH | gonad development | 58/3107 | 221/18723 | 1.73e-04 | 1.48e-03 | 58 |
| GO:00451373 | Prostate | BPH | development of primary sexual characteristics | 58/3107 | 227/18723 | 3.67e-04 | 2.71e-03 | 58 |
| GO:00075483 | Prostate | BPH | sex differentiation | 68/3107 | 276/18723 | 3.75e-04 | 2.76e-03 | 68 |
| GO:006145816 | Prostate | Tumor | reproductive system development | 133/3246 | 427/18723 | 1.24e-12 | 1.15e-10 | 133 |
| GO:004860815 | Prostate | Tumor | reproductive structure development | 131/3246 | 424/18723 | 3.48e-12 | 2.89e-10 | 131 |
| GO:000840612 | Prostate | Tumor | gonad development | 60/3246 | 221/18723 | 1.68e-04 | 1.50e-03 | 60 |
| GO:000754811 | Prostate | Tumor | sex differentiation | 71/3246 | 276/18723 | 2.70e-04 | 2.24e-03 | 71 |
| GO:004513712 | Prostate | Tumor | development of primary sexual characteristics | 60/3246 | 227/18723 | 3.65e-04 | 2.86e-03 | 60 |
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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 |
| IRX5 | MES | Cervix | HSIL_HPV | SOSTDC1,AC058791.1,CRNDE, etc. | 4.55e-01 |  |
| IRX5 | INCAF | Skin | AK | NOLC1,INTS14,PLRG1, etc. | 1.49e-01 |  |
| IRX5 | GOB | Stomach | ADJ | HRASLS2,PSAPL1,SUV420H1, etc. | 4.44e-16 |  |
| IRX5 | PARI | Stomach | CAG | HRASLS2,PSAPL1,SUV420H1, etc. | 1.14e-03 |  |
| IRX5 | A.X | Stomach | CAG | HRASLS2,PSAPL1,SUV420H1, etc. | 0.00e+00 | |
| IRX5 | MESC | Stomach | CSG | HRASLS2,PSAPL1,SUV420H1, etc. | 2.96e-03 |  |
| IRX5 | GOB | Stomach | GC | HRASLS2,PSAPL1,SUV420H1, etc. | 3.39e-03 |  |
| IRX5 | PMC | Stomach | SIM | HRASLS2,PSAPL1,SUV420H1, etc. | 4.54e-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 |
| IRX5 | SNV | Missense_Mutation | c.308C>T | p.Ala103Val | p.A103V | P78411 | protein_coding | deleterious(0) | possibly_damaging(0.842) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| IRX5 | SNV | Missense_Mutation | rs766917570 | c.652G>A | p.Ala218Thr | p.A218T | P78411 | protein_coding | tolerated(0.71) | benign(0) | TCGA-C5-A3HE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| IRX5 | SNV | Missense_Mutation | c.1238N>T | p.Thr413Met | p.T413M | P78411 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-EK-A3GN-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| IRX5 | SNV | Missense_Mutation | novel | c.137C>T | p.Ser46Leu | p.S46L | P78411 | protein_coding | deleterious(0.04) | possibly_damaging(0.669) | TCGA-VS-A8Q8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| IRX5 | SNV | Missense_Mutation | novel | c.530N>C | p.Met177Thr | p.M177T | P78411 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-VS-A8QH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | gemcitabine | PD |
| IRX5 | SNV | Missense_Mutation | c.325N>C | p.Tyr109His | p.Y109H | P78411 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| IRX5 | SNV | Missense_Mutation | c.280G>T | p.Ala94Ser | p.A94S | P78411 | protein_coding | tolerated(0.31) | benign(0.082) | TCGA-AA-3697-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| IRX5 | SNV | Missense_Mutation | novel | c.640N>A | p.Glu214Lys | p.E214K | P78411 | protein_coding | tolerated(0.52) | benign(0.151) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| IRX5 | SNV | Missense_Mutation | c.407N>A | p.Arg136His | p.R136H | P78411 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| IRX5 | SNV | Missense_Mutation | c.1258C>T | p.His420Tyr | p.H420Y | P78411 | protein_coding | deleterious(0.04) | possibly_damaging(0.747) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | 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 |
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