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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 |
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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 |
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 |
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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. |
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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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0051651110 | Oral cavity | LP | maintenance of location in cell | 74/4623 | 214/18723 | 7.18e-04 | 6.41e-03 | 74 |
GO:007138319 | Oral cavity | LP | cellular response to steroid hormone stimulus | 71/4623 | 204/18723 | 7.42e-04 | 6.62e-03 | 71 |
GO:003196019 | Oral cavity | LP | response to corticosteroid | 60/4623 | 167/18723 | 7.51e-04 | 6.69e-03 | 60 |
GO:0051101110 | Oral cavity | LP | regulation of DNA binding | 45/4623 | 118/18723 | 8.04e-04 | 7.06e-03 | 45 |
GO:004352316 | Oral cavity | LP | regulation of neuron apoptotic process | 73/4623 | 212/18723 | 8.87e-04 | 7.64e-03 | 73 |
GO:004276913 | Oral cavity | LP | DNA damage response, detection of DNA damage | 9/4623 | 13/18723 | 8.93e-04 | 7.64e-03 | 9 |
GO:007067012 | Oral cavity | LP | response to interleukin-4 | 18/4623 | 36/18723 | 9.03e-04 | 7.72e-03 | 18 |
GO:000599613 | Oral cavity | LP | monosaccharide metabolic process | 86/4623 | 257/18723 | 9.13e-04 | 7.79e-03 | 86 |
GO:003286817 | Oral cavity | LP | response to insulin | 88/4623 | 264/18723 | 9.19e-04 | 7.82e-03 | 88 |
GO:003286917 | Oral cavity | LP | cellular response to insulin stimulus | 70/4623 | 203/18723 | 1.07e-03 | 8.96e-03 | 70 |
GO:001046619 | Oral cavity | LP | negative regulation of peptidase activity | 87/4623 | 262/18723 | 1.12e-03 | 9.19e-03 | 87 |
GO:007137515 | Oral cavity | LP | cellular response to peptide hormone stimulus | 95/4623 | 290/18723 | 1.12e-03 | 9.19e-03 | 95 |
GO:190437717 | Oral cavity | LP | positive regulation of protein localization to cell periphery | 29/4623 | 69/18723 | 1.15e-03 | 9.40e-03 | 29 |
GO:005134619 | Oral cavity | LP | negative regulation of hydrolase activity | 120/4623 | 379/18723 | 1.16e-03 | 9.48e-03 | 120 |
GO:004214713 | Oral cavity | LP | retrograde transport, endosome to Golgi | 36/4623 | 91/18723 | 1.20e-03 | 9.67e-03 | 36 |
GO:0072521110 | Oral cavity | LP | purine-containing compound metabolic process | 130/4623 | 416/18723 | 1.30e-03 | 1.05e-02 | 130 |
GO:000257315 | Oral cavity | LP | myeloid leukocyte differentiation | 71/4623 | 208/18723 | 1.35e-03 | 1.08e-02 | 71 |
GO:004300113 | Oral cavity | LP | Golgi to plasma membrane protein transport | 19/4623 | 40/18723 | 1.44e-03 | 1.14e-02 | 19 |
GO:000991315 | Oral cavity | LP | epidermal cell differentiation | 69/4623 | 202/18723 | 1.53e-03 | 1.19e-02 | 69 |
GO:003052219 | Oral cavity | LP | intracellular receptor signaling pathway | 87/4623 | 265/18723 | 1.63e-03 | 1.25e-02 | 87 |
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 |
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 |
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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 |
∗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 |
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 |
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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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