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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SEC24C |
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Phenotypic Information for SEC24C(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SEC24C |
Familial Cancer Database: SEC24C |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: SEC24C |
MedGen: SEC24C (Human Medical Genetics with Condition) | |
ClinVar: SEC24C | |
Phenotype | MGI: SEC24C (International Mouse Phenotyping Consortium) |
PhenomicDB: SEC24C |
Mutations for SEC24C |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- For Intra-chromosomal Variations |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SEC24C related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BG998981 | FMNL2 | 1 | 196 | 2 | 153300488 | 153300686 | SEC24C | 187 | 404 | 10 | 75526109 | 75526544 | |
BE829581 | RILPL1 | 1 | 105 | 12 | 124013465 | 124013569 | SEC24C | 103 | 410 | 10 | 75519814 | 75520121 | |
BF815734 | SEC24C | 13 | 143 | 10 | 75531074 | 75531204 | SEC24C | 136 | 357 | 10 | 75531211 | 75531432 | |
BI049604 | DHDDS | 157 | 201 | 1 | 26765919 | 26766321 | SEC24C | 184 | 359 | 10 | 75521175 | 75521350 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=63) | (# total SNVs=15) |
(# total SNVs=4) | (# total SNVs=1) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr10:75506596-75506596 | p.N2N | 3 |
chr10:75520491-75520491 | p.G291S | 3 |
chr10:75530798-75530798 | p.S1077C | 3 |
chr10:75526586-75526586 | p.I623T | 2 |
chr10:75530509-75530509 | p.R1033* | 2 |
chr10:75526174-75526174 | p.F558L | 2 |
chr10:75530738-75530738 | p.K1057R | 2 |
chr10:75506674-75506674 | p.Y28Y | 2 |
chr10:75530754-75530754 | p.F1062F | 2 |
chr10:75506695-75506696 | p.A36fs*139 | 2 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 5 |   | 9 |   |   | 1 |   | 2 |   |   | 8 | 5 |   |   | 1 | 10 | 6 |   | 12 |
# mutation | 1 | 6 |   | 7 |   |   | 1 |   | 2 |   |   | 10 | 5 |   |   | 1 | 10 | 6 |   | 14 |
nonsynonymous SNV |   | 4 |   | 5 |   |   | 1 |   | 1 |   |   | 7 | 3 |   |   | 1 | 7 | 5 |   | 11 |
synonymous SNV | 1 | 2 |   | 2 |   |   |   |   | 1 |   |   | 3 | 2 |   |   |   | 3 | 1 |   | 3 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr10:75506596 | p.N2N,SEC24C | 3 |
chr10:75519797 | p.P244P,SEC24C | 1 |
chr10:75527676 | p.V510I,SEC24C | 1 |
chr10:75520491 | p.D786G,SEC24C | 1 |
chr10:75529384 | p.S1012N,SEC24C | 1 |
chr10:75525908 | p.M260K,SEC24C | 1 |
chr10:75530502 | p.R516M,SEC24C | 1 |
chr10:75519806 | p.D797A,SEC24C | 1 |
chr10:75527697 | p.K1030K,SEC24C | 1 |
chr10:75520505 | p.P263P,SEC24C | 1 |
Other DBs for Point Mutations |
Copy Number for SEC24C in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for SEC24C |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
AGAP5,ANXA7,AP3M1,ASCC1,BEST3,BMS1P4,CAMK2G, MICU1,ECD,FAM149B1,ZSWIM8,MRPS16,NDST2,NUDT13, OR10J5,P4HA1,PPP3CB,SEC24C,TSG1,USP54,VDAC2 | ATP13A1,HID1,CCDC57,CUL9,DIS3L2,ESRP2,GTPBP1, HYOU1,ILDR1,ITPR3,KDM5C,KIAA0556,MARK2,MST1R, PIAS4,PIGO,SEC16A,SEC24C,SIPA1L3,TJP3,ZNF687 |
BRDT,CT47A2,CT47A6,DCAF8L2,DUPD1,FAM9B,GAGE2C, LOC100287704,NF1P1,NKX2-4,NOBOX,OR4N4,OR51B6,OR51F2, OR52E6,POM121L12,SEC24C,SEPT14,STRA8,TNP1,TUBA3C | AP3D1,ATP2A2,BIRC6,COPG1,DHX38,DHX8,EIF4G1, GBF1,GOLGA2,CCAR2,NCOR1,PATL1,SAP130,SEC16A, SEC24C,SEC61A1,SLC39A7,TMEM214,TRIP12,UGGT1,VCP |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for SEC24C |
There's no related Drug. |
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Cross referenced IDs for SEC24C |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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