Tissue | Expression Dynamics | Abbreviation |
Cervix | ![The image shows the 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.](images/deg_images/Cervix/RFX3_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
Colorectum (GSE201348) | ![The image shows the 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.](images/deg_images/Colorectum/Becker/RFX3_pca_on_diff_genes.png) | FAP: Familial adenomatous polyposis |
CRC: Colorectal cancer |
Colorectum (HTA11) | ![The image shows the 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.](images/deg_images/Colorectum/Chen/RFX3_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
Endometrium | ![The image shows the 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.](images/deg_images/Endometrium/RFX3_pca_on_diff_genes.png) | AEH: Atypical endometrial hyperplasia |
EEC: Endometrioid Cancer |
Lung | ![The image shows the 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.](images/deg_images/Lung/RFX3_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00300722 | Colorectum | FAP | peptide hormone secretion | 51/2622 | 236/18723 | 9.09e-04 | 9.19e-03 | 51 |
GO:00428862 | Colorectum | FAP | amide transport | 62/2622 | 301/18723 | 1.01e-03 | 9.93e-03 | 62 |
GO:0030856 | Colorectum | FAP | regulation of epithelial cell differentiation | 36/2622 | 154/18723 | 1.16e-03 | 1.11e-02 | 36 |
GO:00027902 | Colorectum | FAP | peptide secretion | 51/2622 | 242/18723 | 1.62e-03 | 1.43e-02 | 51 |
GO:0021700 | Colorectum | FAP | developmental maturation | 57/2622 | 280/18723 | 2.08e-03 | 1.72e-02 | 57 |
GO:0046883 | Colorectum | FAP | regulation of hormone secretion | 50/2622 | 249/18723 | 4.97e-03 | 3.32e-02 | 50 |
GO:0046879 | Colorectum | FAP | hormone secretion | 57/2622 | 295/18723 | 6.67e-03 | 4.12e-02 | 57 |
GO:00020645 | Colorectum | CRC | epithelial cell development | 55/2078 | 220/18723 | 4.63e-09 | 1.16e-06 | 55 |
GO:00107204 | Colorectum | CRC | positive regulation of cell development | 60/2078 | 298/18723 | 3.27e-06 | 1.47e-04 | 60 |
GO:00507084 | Colorectum | CRC | regulation of protein secretion | 49/2078 | 268/18723 | 3.00e-04 | 4.75e-03 | 49 |
GO:00093064 | Colorectum | CRC | protein secretion | 59/2078 | 359/18723 | 1.32e-03 | 1.48e-02 | 59 |
GO:00355924 | Colorectum | CRC | establishment of protein localization to extracellular region | 59/2078 | 360/18723 | 1.41e-03 | 1.54e-02 | 59 |
GO:00230611 | Colorectum | CRC | signal release | 72/2078 | 463/18723 | 1.95e-03 | 1.96e-02 | 72 |
GO:0002065 | Colorectum | CRC | columnar/cuboidal epithelial cell differentiation | 20/2078 | 91/18723 | 2.04e-03 | 2.03e-02 | 20 |
GO:00716924 | Colorectum | CRC | protein localization to extracellular region | 59/2078 | 368/18723 | 2.37e-03 | 2.27e-02 | 59 |
GO:00217001 | Colorectum | CRC | developmental maturation | 47/2078 | 280/18723 | 2.52e-03 | 2.38e-02 | 47 |
GO:00308561 | Colorectum | CRC | regulation of epithelial cell differentiation | 29/2078 | 154/18723 | 3.02e-03 | 2.71e-02 | 29 |
GO:00507964 | Colorectum | CRC | regulation of insulin secretion | 30/2078 | 165/18723 | 4.44e-03 | 3.48e-02 | 30 |
GO:00300734 | Colorectum | CRC | insulin secretion | 34/2078 | 195/18723 | 5.10e-03 | 3.91e-02 | 34 |
GO:00158334 | Colorectum | CRC | peptide transport | 43/2078 | 264/18723 | 6.47e-03 | 4.68e-02 | 43 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
RFX3 | FIB | Breast | ADJ | MIR181A1HG,ANKRD42,ANKRD44, etc. | 5.02e-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.](images/gene_regulatory/Breast/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
RFX3 | CD8TEXP | Endometrium | ADJ | ZBTB20,SIK3,ARHGAP15, etc. | 2.48e-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.](images/gene_regulatory/Endometrium/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
RFX3 | BMEM | Endometrium | EEC | ZBTB20,SIK3,ARHGAP15, etc. | 1.22e-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.](images/gene_regulatory/Endometrium/Str/TF_EEC/regulons_activity_in_dotplot.png) |
RFX3 | TH17 | Endometrium | EEC | ZBTB20,SIK3,ARHGAP15, etc. | 5.09e-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.](images/gene_regulatory/Endometrium/Str/TF_EEC/regulons_activity_in_dotplot.png) |
RFX3 | CD8TEXP | Endometrium | EEC | ZBTB20,SIK3,ARHGAP15, etc. | 1.31e-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.](images/gene_regulatory/Endometrium/Str/TF_EEC/regulons_activity_in_dotplot.png) |
RFX3 | TREG | Lung | ADJ | ARHGAP15,SIK3,ZBTB20, etc. | 8.52e-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.](images/gene_regulatory/Lung/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
RFX3 | CD4TN | Lung | ADJ | ARHGAP15,SIK3,ZBTB20, etc. | 1.45e-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.](images/gene_regulatory/Lung/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
RFX3 | PANIN | Pancreas | ADJ | RFX2,LRRIQ1,EFCAB2, etc. | 6.24e-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.](images/gene_regulatory/Pancreas/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
RFX3 | CD4TN | Skin | ADJ | JUND,ZBTB20,SIK3, etc. | 1.94e-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.](images/gene_regulatory/Skin/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
RFX3 | CD8TEXP | Skin | cSCC | JUND,ZBTB20,SIK3, 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.](images/gene_regulatory/Skin/Str/TF_cSCC/regulons_activity_in_dotplot.png) |
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 |
RFX3 | SNV | Missense_Mutation | novel | c.1490N>A | p.Arg497Gln | p.R497Q | P48380 | protein_coding | deleterious(0.02) | possibly_damaging(0.639) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
RFX3 | SNV | Missense_Mutation | | c.209N>A | p.Gly70Glu | p.G70E | P48380 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AR-A1AX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
RFX3 | SNV | Missense_Mutation | novel | c.160C>T | p.Pro54Ser | p.P54S | P48380 | protein_coding | tolerated(0.35) | possibly_damaging(0.609) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD |
RFX3 | SNV | Missense_Mutation | | c.1129N>A | p.Glu377Lys | p.E377K | P48380 | protein_coding | deleterious(0) | benign(0.041) | TCGA-BH-A0W7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
RFX3 | SNV | Missense_Mutation | novel | c.581N>G | p.Ala194Gly | p.A194G | P48380 | protein_coding | deleterious(0.01) | possibly_damaging(0.842) | TCGA-D8-A13Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
RFX3 | SNV | Missense_Mutation | | c.1042N>A | p.Glu348Lys | p.E348K | P48380 | protein_coding | tolerated(0.13) | benign(0.101) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
RFX3 | SNV | Missense_Mutation | | c.1499C>A | p.Thr500Lys | p.T500K | P48380 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-E2-A159-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
RFX3 | insertion | Frame_Shift_Ins | novel | c.135_136insT | p.Val46CysfsTer50 | p.V46Cfs*50 | P48380 | protein_coding | | | TCGA-A7-A13E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | bevacizumab | PD |
RFX3 | insertion | Frame_Shift_Ins | novel | c.1747_1748insAAAGATTAAAAACAGCATTTATGACCTTTGTAGGT | p.Pro583GlnfsTer29 | p.P583Qfs*29 | P48380 | protein_coding | | | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | | SD |
RFX3 | SNV | Missense_Mutation | rs777692576 | c.190N>A | p.Asp64Asn | p.D64N | P48380 | protein_coding | deleterious(0.05) | benign(0.077) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |