|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for MAN2A1 |
Top |
Phenotypic Information for MAN2A1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: MAN2A1 |
Familial Cancer Database: MAN2A1 |
* This gene is included in those cancer gene databases. |
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: MAN2A1 |
MedGen: MAN2A1 (Human Medical Genetics with Condition) | |
ClinVar: MAN2A1 | |
Phenotype | MGI: MAN2A1 (International Mouse Phenotyping Consortium) |
PhenomicDB: MAN2A1 |
Mutations for MAN2A1 |
* 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 |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | MAN2A1 | chr5 | 109055821 | 109055841 | MAN2A1 | chr5 | 109066795 | 109066815 |
ovary | MAN2A1 | chr5 | 109124750 | 109124770 | MAN2A1 | chr5 | 109124865 | 109124885 |
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 MAN2A1 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 |
AI474018 | MAN2A1 | 1 | 73 | 5 | 109194057 | 109194129 | KCNH8 | 71 | 407 | 3 | 19390373 | 19390709 |
Other DBs for Structural Variants |
Top |
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 |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   | 1 |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   | |||
LOSS (# sample) |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   |
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) |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=99) | (# total SNVs=30) |
(# total SNVs=4) | (# total SNVs=1) |
Top |
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 |
chr5:109124646-109124646 | p.S591L | 3 |
chr5:109110611-109110611 | p.K440R | 3 |
chr5:109155490-109155490 | p.G744R | 3 |
chr5:109120589-109120589 | p.G574G | 3 |
chr5:109120470-109120470 | p.A535T | 3 |
chr5:109183456-109183456 | p.R981* | 3 |
chr5:109155562-109155562 | p.R768W | 3 |
chr5:109106195-109106195 | p.P383P | 2 |
chr5:109124642-109124642 | p.H590Y | 2 |
chr5:109181655-109181655 | p.H930Q | 2 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 | 5 | 5 |   | 16 |   |   | 3 |   | 3 |   |   | 17 | 6 | 3 |   |   | 7 | 5 |   | 19 |
# mutation | 5 | 5 |   | 16 |   |   | 3 |   | 3 |   |   | 20 | 6 | 3 |   |   | 11 | 6 |   | 25 |
nonsynonymous SNV | 5 | 3 |   | 14 |   |   | 2 |   | 3 |   |   | 16 | 5 | 2 |   |   | 8 | 5 |   | 16 |
synonymous SNV |   | 2 |   | 2 |   |   | 1 |   |   |   |   | 4 | 1 | 1 |   |   | 3 | 1 |   | 9 |
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]) |
Top |
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 |
chr5:109120589 | p.G574G | 3 |
chr5:109155562 | p.R768W | 3 |
chr5:109120509 | p.K410N | 2 |
chr5:109153015 | p.I641M | 2 |
chr5:109190857 | p.V652V | 2 |
chr5:109125208 | p.S662L | 2 |
chr5:109152986 | p.S998L | 2 |
chr5:109110522 | p.L548I | 2 |
chr5:109051935 | p.A937A | 1 |
chr5:109120470 | p.S12I | 1 |
Other DBs for Point Mutations |
Copy Number for MAN2A1 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] |
Top |
Gene Expression for MAN2A1 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
AFF4,APC,CCNT1,FER,GTF2A1,HMBOX1,LMBRD2, LNPEP,MAN2A1,MFAP3,NBEAL1,PJA2,POLK,RAPGEF6, REL,SCAF11,SLC25A46,TCP11L2,TTC37,UHMK1,UHRF1BP1L | CAMSAP2,DENND4A,DNAJB14,DNAJC13,HIPK1,ITCH,ITGAV, MAN2A1,MAP3K2,MOB1A,PIK3C2A,SETX,SLC30A6,SLK, STRN,TBCEL,TMOD3,TRIM44,VPS13C,WDFY3,XRN1 | ||||
AFF4,ASXL2,CCNT1,DDI2,DMXL1,GTF2A1,HIPK3, LMBRD2,LNPEP,MAN1A2,MAN2A1,PRKAR2A,PTPLB,RAPGEF6, RC3H2,REL,REST,SCYL2,SERINC5,TAOK1,UHMK1 | ADAM10,AP1G1,ARFGEF1,ARHGAP32,PRR14L,CNOT1,CPD, DSP,ITPR3,AREL1,LRRC16A,MAN2A1,MARCH6,MFSD9, MYO5B,OSBP,PTPLB,PTPRK,RREB1,TMPPE,UBE4A |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for MAN2A1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB02034 | mannosidase, alpha, class 2A, member 1 | experimental | Swainsonine | ||
DB02318 | mannosidase, alpha, class 2A, member 1 | experimental | 2-Deoxy-2-Fluoro-Alpha-D-Mannosyl Fluoride | ||
DB02492 | mannosidase, alpha, class 2A, member 1 | experimental | Ghavamiol | ||
DB02742 | mannosidase, alpha, class 2A, member 1 | experimental | Kifunensine | ||
DB03008 | mannosidase, alpha, class 2A, member 1 | experimental | 5-Fluoro-Beta-L-Gulosyl Fluoride | ||
DB03414 | mannosidase, alpha, class 2A, member 1 | experimental | 5-Thio-a/B-D-Mannopyranosylamine | ||
DB03955 | mannosidase, alpha, class 2A, member 1 | experimental | 1,5-Dideoxy-1,5-Imino-D-Mannitol | ||
DB06984 | mannosidase, alpha, class 2A, member 1 | experimental | (1R,2R,3R,4S,5R)-4-(BENZYLAMINO)-5-(METHYLTHIO)CYCLOPENTANE-1,2,3-TRIOL | ||
DB08321 | mannosidase, alpha, class 2A, member 1 | experimental | (1S,2S,3R,6R)-4-(hydroxymethyl)-6-(octylamino)cyclohex-4-ene-1,2,3-triol |
Top |
Cross referenced IDs for MAN2A1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |