Tissue | Expression Dynamics | Abbreviation |
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/THRA_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/THRA_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
Esophagus | ![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/Esophagus/THRA_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
Liver | ![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/Liver/THRA_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:004802616 | Oral cavity | LP | positive regulation of mRNA splicing, via spliceosome | 14/4623 | 22/18723 | 1.23e-04 | 1.44e-03 | 14 |
GO:006101317 | Oral cavity | LP | regulation of mRNA catabolic process | 62/4623 | 166/18723 | 1.87e-04 | 2.06e-03 | 62 |
GO:004348717 | Oral cavity | LP | regulation of RNA stability | 62/4623 | 170/18723 | 3.94e-04 | 3.82e-03 | 62 |
GO:000038117 | Oral cavity | LP | regulation of alternative mRNA splicing, via spliceosome | 27/4623 | 60/18723 | 4.71e-04 | 4.43e-03 | 27 |
GO:004348817 | Oral cavity | LP | regulation of mRNA stability | 58/4623 | 158/18723 | 4.93e-04 | 4.62e-03 | 58 |
GO:190236914 | Oral cavity | LP | negative regulation of RNA catabolic process | 29/4623 | 75/18723 | 5.06e-03 | 3.15e-02 | 29 |
GO:190331124 | Oral cavity | EOLP | regulation of mRNA metabolic process | 102/2218 | 288/18723 | 8.13e-26 | 2.44e-22 | 102 |
GO:004348426 | Oral cavity | EOLP | regulation of RNA splicing | 59/2218 | 148/18723 | 2.64e-18 | 5.27e-15 | 59 |
GO:000838025 | Oral cavity | EOLP | RNA splicing | 115/2218 | 434/18723 | 2.24e-17 | 3.04e-14 | 115 |
GO:005068424 | Oral cavity | EOLP | regulation of mRNA processing | 55/2218 | 137/18723 | 2.54e-17 | 3.04e-14 | 55 |
GO:000640224 | Oral cavity | EOLP | mRNA catabolic process | 74/2218 | 232/18723 | 3.36e-16 | 2.51e-13 | 74 |
GO:004802425 | Oral cavity | EOLP | regulation of mRNA splicing, via spliceosome | 42/2218 | 101/18723 | 3.41e-14 | 1.28e-11 | 42 |
GO:006101323 | Oral cavity | EOLP | regulation of mRNA catabolic process | 55/2218 | 166/18723 | 3.70e-13 | 1.11e-10 | 55 |
GO:000640124 | Oral cavity | EOLP | RNA catabolic process | 77/2218 | 278/18723 | 3.92e-13 | 1.12e-10 | 77 |
GO:004348823 | Oral cavity | EOLP | regulation of mRNA stability | 50/2218 | 158/18723 | 2.91e-11 | 4.15e-09 | 50 |
GO:000037725 | Oral cavity | EOLP | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 80/2218 | 320/18723 | 4.20e-11 | 5.60e-09 | 80 |
GO:000039825 | Oral cavity | EOLP | mRNA splicing, via spliceosome | 80/2218 | 320/18723 | 4.20e-11 | 5.60e-09 | 80 |
GO:000037525 | Oral cavity | EOLP | RNA splicing, via transesterification reactions | 80/2218 | 324/18723 | 8.11e-11 | 9.53e-09 | 80 |
GO:004348723 | Oral cavity | EOLP | regulation of RNA stability | 51/2218 | 170/18723 | 1.63e-10 | 1.68e-08 | 51 |
GO:190331323 | Oral cavity | EOLP | positive regulation of mRNA metabolic process | 40/2218 | 118/18723 | 2.69e-10 | 2.45e-08 | 40 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04919 | Colorectum | AD | Thyroid hormone signaling pathway | 51/2092 | 121/8465 | 1.71e-05 | 1.73e-04 | 1.10e-04 | 51 |
hsa049191 | Colorectum | AD | Thyroid hormone signaling pathway | 51/2092 | 121/8465 | 1.71e-05 | 1.73e-04 | 1.10e-04 | 51 |
hsa049192 | Colorectum | SER | Thyroid hormone signaling pathway | 40/1580 | 121/8465 | 1.02e-04 | 1.06e-03 | 7.67e-04 | 40 |
hsa049193 | Colorectum | SER | Thyroid hormone signaling pathway | 40/1580 | 121/8465 | 1.02e-04 | 1.06e-03 | 7.67e-04 | 40 |
hsa049194 | Colorectum | MSS | Thyroid hormone signaling pathway | 46/1875 | 121/8465 | 5.04e-05 | 4.97e-04 | 3.05e-04 | 46 |
hsa049195 | Colorectum | MSS | Thyroid hormone signaling pathway | 46/1875 | 121/8465 | 5.04e-05 | 4.97e-04 | 3.05e-04 | 46 |
hsa0491928 | Esophagus | ESCC | Thyroid hormone signaling pathway | 78/4205 | 121/8465 | 6.79e-04 | 2.23e-03 | 1.14e-03 | 78 |
hsa04919113 | Esophagus | ESCC | Thyroid hormone signaling pathway | 78/4205 | 121/8465 | 6.79e-04 | 2.23e-03 | 1.14e-03 | 78 |
hsa0491912 | Liver | HCC | Thyroid hormone signaling pathway | 75/4020 | 121/8465 | 8.76e-04 | 3.38e-03 | 1.88e-03 | 75 |
hsa0491913 | Liver | HCC | Thyroid hormone signaling pathway | 75/4020 | 121/8465 | 8.76e-04 | 3.38e-03 | 1.88e-03 | 75 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
THRA | CD8TEXINT | Colorectum | ADJ | SEMA3C,AGPAT4,NCEH1, etc. | 1.08e-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/Colorectum/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
THRA | INCAF | Colorectum | CRC | RABL2B,NDUFAF6,PIGN, etc. | 4.72e-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/Colorectum/Str/TF_CRC/regulons_activity_in_dotplot.png) |
THRA | ICAF | Colorectum | MSS | RABL2B,NDUFAF6,PIGN, etc. | 5.18e-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/Colorectum/Str/TF_MSS/regulons_activity_in_dotplot.png) |
THRA | M1MAC | Endometrium | Healthy | USF1,ZNF483,AL356234.2, etc. | 4.31e-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_Healthy/regulons_activity_in_dotplot.png) |
THRA | SMC | Endometrium | ADJ | GUCY1A3,BRSK2,AC097724.3, etc. | 2.73e-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) |
THRA | SMC | Endometrium | AEH | GUCY1A3,BRSK2,AC097724.3, 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/Endometrium/Str/TF_AEH/regulons_activity_in_dotplot.png) |
THRA | PERI | Liver | Cirrhotic | BAMBI,C2orf40,C15orf39, etc. | 1.40e-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/Liver/Str/TF_Cirrhotic/regulons_activity_in_dotplot.png) |
THRA | SMC | Liver | Cirrhotic | BAMBI,C2orf40,C15orf39, etc. | 1.58e-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/Liver/Str/TF_Cirrhotic/regulons_activity_in_dotplot.png) |
THRA | SMC | Liver | HCC | BAMBI,C2orf40,C15orf39, etc. | 3.49e-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/Liver/Str/TF_HCC/regulons_activity_in_dotplot.png) |
THRA | CD8TEREX | Lung | MIAC | PLPP3,ZNF683,TRAF3IP2-AS1, etc. | 4.57e-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_MIAC/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 |
THRA | SNV | Missense_Mutation | novel | c.1007N>G | p.Asp336Gly | p.D336G | P10827 | protein_coding | tolerated(0.13) | benign(0.133) | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD |
THRA | SNV | Missense_Mutation | novel | c.612N>T | p.Met204Ile | p.M204I | P10827 | protein_coding | tolerated(0.23) | benign(0.155) | TCGA-AC-A6IW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
THRA | SNV | Missense_Mutation | | c.32N>T | p.Gly11Val | p.G11V | P10827 | protein_coding | deleterious_low_confidence(0.01) | benign(0.08) | TCGA-E2-A14V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
THRA | insertion | In_Frame_Ins | novel | c.878_879insAAGGTCTGGCTGCTCTAAGAAATCAGC | p.Gly293_Val294insArgSerGlyCysSerLysLysSerAla | p.G293_V294insRSGCSKKSA | P10827 | protein_coding | | | TCGA-AN-A04A-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
THRA | SNV | Missense_Mutation | | c.1175N>T | p.Ser392Leu | p.S392L | P10827 | protein_coding | deleterious_low_confidence(0) | benign(0.039) | TCGA-EK-A2H0-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
THRA | SNV | Missense_Mutation | | c.1175N>T | p.Ser392Leu | p.S392L | P10827 | protein_coding | deleterious_low_confidence(0) | benign(0.039) | TCGA-ZJ-A8QQ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
THRA | SNV | Missense_Mutation | | c.871G>A | p.Gly291Ser | p.G291S | P10827 | protein_coding | deleterious(0.04) | probably_damaging(0.964) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
THRA | SNV | Missense_Mutation | | c.854A>G | p.Glu285Gly | p.E285G | P10827 | protein_coding | tolerated(0.23) | benign(0.012) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
THRA | SNV | Missense_Mutation | | c.473N>A | p.Pro158Gln | p.P158Q | P10827 | protein_coding | deleterious(0.02) | benign(0.077) | TCGA-DM-A1DA-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
THRA | SNV | Missense_Mutation | | c.709N>T | p.Pro237Ser | p.P237S | P10827 | protein_coding | deleterious(0.01) | possibly_damaging(0.85) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | | LEVOTHYROXINE | LEVOTHYROXINE | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 135651405 | TIRATRICOL | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 135651574 | LEVOTHYROXINE SODIUM | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | | Dextrothyroxine Sodium | | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 178103533 | DEXTROTHYROXINE | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | 135651573 | LIOTHYRONINE SODIUM | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | agonist | CHEMBL1544 | LIOTHYRONINE | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | | tiratricol | TIRATRICOL | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | | TRIIODOTHYRONINE (T3) | | |
7067 | THRA | DRUGGABLE GENOME, NUCLEAR HORMONE RECEPTOR | antagonist | 135650713 | | |