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Gene: LHX9 |
Gene summary for LHX9 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LHX9 | Gene ID | 56956 |
| Gene name | LIM homeobox 9 | |
| Gene Alias | LHX9 | |
| Cytomap | 1q31.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q9NQ69 |
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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 |
| 56956 | LHX9 | ATC13 | Human | Thyroid | ATC | 2.18e-22 | 5.44e-01 | 0.34 |
| 56956 | LHX9 | ATC5 | Human | Thyroid | ATC | 9.23e-23 | 5.69e-01 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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:006156423 | Thyroid | ATC | axon development | 220/6293 | 467/18723 | 6.85e-10 | 1.80e-08 | 220 |
| GO:000740919 | Thyroid | ATC | axonogenesis | 197/6293 | 418/18723 | 5.09e-09 | 1.13e-07 | 197 |
| GO:006145827 | Thyroid | ATC | reproductive system development | 193/6293 | 427/18723 | 3.32e-07 | 4.92e-06 | 193 |
| GO:004860825 | Thyroid | ATC | reproductive structure development | 190/6293 | 424/18723 | 8.40e-07 | 1.11e-05 | 190 |
| GO:004654621 | Thyroid | ATC | development of primary male sexual characteristics | 72/6293 | 142/18723 | 1.85e-05 | 1.69e-04 | 72 |
| GO:000858421 | Thyroid | ATC | male gonad development | 71/6293 | 141/18723 | 2.83e-05 | 2.38e-04 | 71 |
| GO:004666112 | Thyroid | ATC | male sex differentiation | 77/6293 | 165/18723 | 3.27e-04 | 2.04e-03 | 77 |
| GO:000840613 | Thyroid | ATC | gonad development | 96/6293 | 221/18723 | 1.40e-03 | 7.25e-03 | 96 |
| GO:00451374 | Thyroid | ATC | development of primary sexual characteristics | 97/6293 | 227/18723 | 2.47e-03 | 1.14e-02 | 97 |
| GO:00074113 | Thyroid | ATC | axon guidance | 96/6293 | 227/18723 | 3.74e-03 | 1.63e-02 | 96 |
| GO:00974853 | Thyroid | ATC | neuron projection guidance | 96/6293 | 228/18723 | 4.36e-03 | 1.81e-02 | 96 |
| GO:00466603 | Thyroid | ATC | female sex differentiation | 51/6293 | 114/18723 | 8.62e-03 | 3.28e-02 | 51 |
| GO:00085853 | Thyroid | ATC | female gonad development | 43/6293 | 95/18723 | 1.19e-02 | 4.22e-02 | 43 |
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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 |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| LHX9 | CLUB | Lung | IAC | HMGN3,PIGR,MAP1B, etc. | 2.54e-01 |  |
| LHX9 | iATC | Thyroid | PTC | NPPC,CHODL,PTPRT, etc. | 1.46e-02 |  |
| ∗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 |
| LHX9 | SNV | Missense_Mutation | novel | c.1051N>A | p.Gly351Arg | p.G351R | Q9NQ69 | protein_coding | deleterious(0.03) | benign(0.387) | TCGA-A8-A07G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| LHX9 | SNV | Missense_Mutation | novel | c.1097N>G | p.Thr366Ser | p.T366S | Q9NQ69 | protein_coding | tolerated(0.24) | benign(0.23) | TCGA-AC-A2FE-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| LHX9 | SNV | Missense_Mutation | c.673N>A | p.Gly225Arg | p.G225R | Q9NQ69 | protein_coding | deleterious(0.04) | benign(0.062) | TCGA-AN-A0AS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| LHX9 | SNV | Missense_Mutation | c.370T>C | p.Tyr124His | p.Y124H | Q9NQ69 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AN-A0FV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LHX9 | SNV | Missense_Mutation | c.777G>T | p.Gln259His | p.Q259H | Q9NQ69 | protein_coding | tolerated(0.21) | possibly_damaging(0.77) | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | |
| LHX9 | SNV | Missense_Mutation | novel | c.244N>C | p.Tyr82His | p.Y82H | Q9NQ69 | protein_coding | deleterious(0.01) | probably_damaging(0.992) | TCGA-LD-A9QF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxol | SD |
| LHX9 | insertion | In_Frame_Ins | novel | c.666_667insCCCTCTTTTTATTTTAAATGGTTTTTA | p.Val222_Gln223insProSerPheTyrPheLysTrpPheLeu | p.V222_Q223insPSFYFKWFL | Q9NQ69 | protein_coding | TCGA-A8-A09E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD | ||
| LHX9 | insertion | In_Frame_Ins | novel | c.575_576insGAATCATGGCCTCCAAAATTC | p.Gln192_Gly193insAsnHisGlyLeuGlnAsnSer | p.Q192_G193insNHGLQNS | Q9NQ69 | protein_coding | TCGA-AO-A03O-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | SD | ||
| LHX9 | deletion | Frame_Shift_Del | c.53delC | p.Pro18GlnfsTer76 | p.P18Qfs*76 | Q9NQ69 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| LHX9 | deletion | Frame_Shift_Del | novel | c.1104delC | p.Thr369LeufsTer4 | p.T369Lfs*4 | Q9NQ69 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | 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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