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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:003103222 | Liver | HCC | actomyosin structure organization | 109/7958 | 196/18723 | 1.39e-04 | 1.13e-03 | 109 |
GO:004504711 | Liver | HCC | protein targeting to ER | 30/7958 | 42/18723 | 1.40e-04 | 1.13e-03 | 30 |
GO:000975521 | Liver | HCC | hormone-mediated signaling pathway | 106/7958 | 190/18723 | 1.45e-04 | 1.17e-03 | 106 |
GO:001820911 | Liver | HCC | peptidyl-serine modification | 177/7958 | 338/18723 | 1.45e-04 | 1.17e-03 | 177 |
GO:00714782 | Liver | HCC | cellular response to radiation | 104/7958 | 186/18723 | 1.48e-04 | 1.19e-03 | 104 |
GO:00713461 | Liver | HCC | cellular response to interferon-gamma | 70/7958 | 118/18723 | 1.66e-04 | 1.32e-03 | 70 |
GO:005189321 | Liver | HCC | regulation of focal adhesion assembly | 43/7958 | 66/18723 | 1.69e-04 | 1.34e-03 | 43 |
GO:009010921 | Liver | HCC | regulation of cell-substrate junction assembly | 43/7958 | 66/18723 | 1.69e-04 | 1.34e-03 | 43 |
GO:004671812 | Liver | HCC | viral entry into host cell | 83/7958 | 144/18723 | 1.73e-04 | 1.36e-03 | 83 |
GO:001087621 | Liver | HCC | lipid localization | 228/7958 | 448/18723 | 1.80e-04 | 1.41e-03 | 228 |
GO:000920612 | Liver | HCC | purine ribonucleoside triphosphate biosynthetic process | 44/7958 | 68/18723 | 1.80e-04 | 1.41e-03 | 44 |
GO:003158922 | Liver | HCC | cell-substrate adhesion | 188/7958 | 363/18723 | 2.00e-04 | 1.55e-03 | 188 |
GO:190332122 | Liver | HCC | negative regulation of protein modification by small protein conjugation or removal | 58/7958 | 95/18723 | 2.01e-04 | 1.56e-03 | 58 |
GO:190303421 | Liver | HCC | regulation of response to wounding | 94/7958 | 167/18723 | 2.19e-04 | 1.66e-03 | 94 |
GO:190435621 | Liver | HCC | regulation of telomere maintenance via telomere lengthening | 40/7958 | 61/18723 | 2.30e-04 | 1.75e-03 | 40 |
GO:0009411 | Liver | HCC | response to UV | 85/7958 | 149/18723 | 2.34e-04 | 1.77e-03 | 85 |
GO:00467775 | Liver | HCC | protein autophosphorylation | 123/7958 | 227/18723 | 2.40e-04 | 1.80e-03 | 123 |
GO:005134622 | Liver | HCC | negative regulation of hydrolase activity | 195/7958 | 379/18723 | 2.44e-04 | 1.82e-03 | 195 |
GO:0016239 | Liver | HCC | positive regulation of macroautophagy | 41/7958 | 63/18723 | 2.47e-04 | 1.84e-03 | 41 |
GO:00075962 | Liver | HCC | blood coagulation | 118/7958 | 217/18723 | 2.63e-04 | 1.94e-03 | 118 |
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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