|
Gene: RP1 |
Gene summary for RP1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RP1 | Gene ID | 6101 |
Gene name | RP1 axonemal microtubule associated | |
Gene Alias | DCDC4A | |
Cytomap | 8q11.23-q12.1 | |
Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | P56715 |
Top |
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 |
6101 | RP1 | TD9 | Human | Lung | IAC | 1.99e-06 | 1.00e+00 | 0.088 |
6101 | RP1 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.35e-14 | 6.37e-01 | -0.2116 |
6101 | RP1 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 1.36e-03 | 4.77e-01 | -0.1941 |
6101 | RP1 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 4.20e-06 | 5.18e-01 | -0.2107 |
6101 | RP1 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.40e-11 | 6.14e-01 | -0.2119 |
Page: 1 |
Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Lung | AAH: Atypical adenomatous hyperplasia | |
AIS: Adenocarcinoma in situ | ||
IAC: Invasive lung adenocarcinoma | ||
MIA: Minimally invasive adenocarcinoma |
∗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. |
Top |
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:190165316 | Oral cavity | OSCC | cellular response to peptide | 194/7305 | 359/18723 | 4.31e-09 | 9.57e-08 | 194 |
GO:003109816 | Oral cavity | OSCC | stress-activated protein kinase signaling cascade | 141/7305 | 247/18723 | 5.74e-09 | 1.25e-07 | 141 |
GO:190332120 | Oral cavity | OSCC | negative regulation of protein modification by small protein conjugation or removal | 65/7305 | 95/18723 | 5.88e-09 | 1.26e-07 | 65 |
GO:005109920 | Oral cavity | OSCC | positive regulation of binding | 105/7305 | 173/18723 | 5.88e-09 | 1.26e-07 | 105 |
GO:003052218 | Oral cavity | OSCC | intracellular receptor signaling pathway | 149/7305 | 265/18723 | 8.69e-09 | 1.81e-07 | 149 |
GO:003166720 | Oral cavity | OSCC | response to nutrient levels | 245/7305 | 474/18723 | 1.02e-08 | 2.10e-07 | 245 |
GO:003461218 | Oral cavity | OSCC | response to tumor necrosis factor | 143/7305 | 253/18723 | 1.09e-08 | 2.23e-07 | 143 |
GO:190121420 | Oral cavity | OSCC | regulation of neuron death | 174/7305 | 319/18723 | 1.09e-08 | 2.23e-07 | 174 |
GO:000701520 | Oral cavity | OSCC | actin filament organization | 230/7305 | 442/18723 | 1.37e-08 | 2.77e-07 | 230 |
GO:001095019 | Oral cavity | OSCC | positive regulation of endopeptidase activity | 107/7305 | 179/18723 | 1.38e-08 | 2.78e-07 | 107 |
GO:190547516 | Oral cavity | OSCC | regulation of protein localization to membrane | 105/7305 | 175/18723 | 1.42e-08 | 2.85e-07 | 105 |
GO:20012389 | Oral cavity | OSCC | positive regulation of extrinsic apoptotic signaling pathway | 38/7305 | 48/18723 | 1.56e-08 | 3.12e-07 | 38 |
GO:00028317 | Oral cavity | OSCC | regulation of response to biotic stimulus | 177/7305 | 327/18723 | 1.73e-08 | 3.43e-07 | 177 |
GO:190165419 | Oral cavity | OSCC | response to ketone | 114/7305 | 194/18723 | 1.82e-08 | 3.60e-07 | 114 |
GO:003297020 | Oral cavity | OSCC | regulation of actin filament-based process | 209/7305 | 397/18723 | 1.89e-08 | 3.72e-07 | 209 |
GO:003158917 | Oral cavity | OSCC | cell-substrate adhesion | 193/7305 | 363/18723 | 2.48e-08 | 4.82e-07 | 193 |
GO:004873220 | Oral cavity | OSCC | gland development | 226/7305 | 436/18723 | 2.78e-08 | 5.39e-07 | 226 |
GO:001081019 | Oral cavity | OSCC | regulation of cell-substrate adhesion | 126/7305 | 221/18723 | 4.02e-08 | 7.55e-07 | 126 |
GO:00714788 | Oral cavity | OSCC | cellular response to radiation | 109/7305 | 186/18723 | 4.54e-08 | 8.45e-07 | 109 |
GO:003010016 | Oral cavity | OSCC | regulation of endocytosis | 121/7305 | 211/18723 | 4.74e-08 | 8.80e-07 | 121 |
Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
Page: 1 |
Top |
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 |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Breast | ADJ |
MDK | LRP1 | MDK_LRP1 | MK | Breast | DCIS |
SEMA4A | NRP1_PLXNA4 | SEMA4A_NRP1_PLXNA4 | SEMA4 | Breast | DCIS |
SEMA3C | NRP1_PLXNA4 | SEMA3C_NRP1_PLXNA4 | SEMA3 | Breast | DCIS |
SEMA3D | NRP1_PLXNA4 | SEMA3D_NRP1_PLXNA4 | SEMA3 | Breast | DCIS |
SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Breast | DCIS |
MDK | LRP1 | MDK_LRP1 | MK | Breast | Healthy |
SEMA3C | NRP1_PLXNA2 | SEMA3C_NRP1_PLXNA2 | SEMA3 | Breast | Healthy |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Breast | Healthy |
SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Breast | Healthy |
MDK | LRP1 | MDK_LRP1 | MK | Breast | IDC |
MDK | LRP1 | MDK_LRP1 | MK | Breast | Precancer |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | ADJ |
SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Cervix | ADJ |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | CC |
SEMA3C | NRP1_PLXNA2 | SEMA3C_NRP1_PLXNA2 | SEMA3 | Cervix | CC |
SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Cervix | CC |
SEMA4A | NRP1_PLXNA2 | SEMA4A_NRP1_PLXNA2 | SEMA4 | Cervix | CC |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | Healthy |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | Precancer |
Page: 1 |
Top |
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 |
∗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 |
Top |
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 |
RP1 | SNV | Missense_Mutation | novel | c.81G>C | p.Leu27Phe | p.L27F | P56715 | protein_coding | tolerated(0.65) | benign(0.007) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
RP1 | SNV | Missense_Mutation | rs747714373 | c.2978C>G | p.Ser993Cys | p.S993C | P56715 | protein_coding | deleterious(0.02) | possibly_damaging(0.781) | TCGA-5L-AAT0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
RP1 | SNV | Missense_Mutation | c.4362C>A | p.Ser1454Arg | p.S1454R | P56715 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-A2-A0CW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
RP1 | SNV | Missense_Mutation | novel | c.1138N>T | p.Pro380Ser | p.P380S | protein_coding | deleterious(0.04) | probably_damaging(0.923) | TCGA-A2-A3XV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR | |
RP1 | SNV | Missense_Mutation | novel | c.983N>G | p.Lys328Arg | p.K328R | protein_coding | deleterious(0.01) | probably_damaging(0.994) | TCGA-A7-A4SF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR | |
RP1 | SNV | Missense_Mutation | c.2516N>C | p.Gln839Pro | p.Q839P | P56715 | protein_coding | deleterious(0.03) | possibly_damaging(0.641) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RP1 | SNV | Missense_Mutation | novel | c.4466C>T | p.Ala1489Val | p.A1489V | P56715 | protein_coding | tolerated(0.22) | benign(0.01) | TCGA-A8-A092-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | CR |
RP1 | SNV | Missense_Mutation | c.2675N>T | p.Ala892Val | p.A892V | P56715 | protein_coding | tolerated(0.14) | benign(0.039) | TCGA-A8-A09B-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | SD | |
RP1 | SNV | Missense_Mutation | c.1895N>T | p.Ser632Leu | p.S632L | P56715 | protein_coding | tolerated(0.2) | benign(0.042) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
RP1 | SNV | Missense_Mutation | c.4027N>A | p.Asp1343Asn | p.D1343N | P56715 | protein_coding | tolerated(0.07) | benign(0) | TCGA-AN-A041-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 |
Top |
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 |
Page: 1 |