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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:GGA2-PRKCB

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GGA2-PRKCB
FusionPDB ID: 33002
FusionGDB2.0 ID: 33002
HgeneTgene
Gene symbol

GGA2

PRKCB

Gene ID

23062

5579

Gene namegolgi associated, gamma adaptin ear containing, ARF binding protein 2protein kinase C beta
SynonymsVEARPKC-beta|PKCB|PKCI(2)|PKCbeta|PRKCB1|PRKCB2
Cytomap

16p12.2

16p12.2-p12.1

Type of geneprotein-codingprotein-coding
DescriptionADP-ribosylation factor-binding protein GGA2VHS domain and ear domain of gamma-adaptinVHS domain and ear domain-containing proteingamma-adaptin-related protein 2golgi-localized, gamma ear-containing, ARF-binding protein 2protein kinase C beta typePKC-Bprotein kinase C, beta 1 polypeptide
Modification date2020031320200313
UniProtAcc

Q9UJY4

.
Ensembl transtripts involved in fusion geneENST idsENST00000309859, ENST00000567468, 
ENST00000569182, 
ENST00000482000, 
ENST00000498058, ENST00000303531, 
ENST00000321728, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 7 X 4=19620 X 15 X 13=3900
# samples 825
** MAII scorelog2(8/196*10)=-1.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(25/3900*10)=-3.96347412397489
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: GGA2 [Title/Abstract] AND PRKCB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GGA2(23502998)-PRKCB(23999829), # samples:3
Anticipated loss of major functional domain due to fusion event.GGA2-PRKCB seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
GGA2-PRKCB seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
GGA2-PRKCB seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
GGA2-PRKCB seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneGGA2

GO:0034394

protein localization to cell surface

27901063

HgeneGGA2

GO:0043001

Golgi to plasma membrane protein transport

27901063

TgenePRKCB

GO:0010827

regulation of glucose transmembrane transport

25982116

TgenePRKCB

GO:0035408

histone H3-T6 phosphorylation

20228790


check buttonFusion gene breakpoints across GGA2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across PRKCB (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LAMLTCGA-AB-2929-03AGGA2chr16

23478534

-PRKCBchr16

24230943

+
ChimerDB4LGGTCGA-HT-A5RC-01AGGA2chr16

23502998

-PRKCBchr16

23999829

+
ChimerDB4LGGTCGA-HT-A5RCGGA2chr16

23502998

-PRKCBchr16

23999829

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000309859GGA2chr1623502998-ENST00000321728PRKCBchr1623999829+2867558832368761
ENST00000309859GGA2chr1623502998-ENST00000303531PRKCBchr1623999829+8170558832374763
ENST00000567468GGA2chr1623502998-ENST00000321728PRKCBchr1623999829+2797488132298761
ENST00000567468GGA2chr1623502998-ENST00000303531PRKCBchr1623999829+8100488132304763

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000309859ENST00000321728GGA2chr1623502998-PRKCBchr1623999829+0.0014798270.9985202
ENST00000309859ENST00000303531GGA2chr1623502998-PRKCBchr1623999829+0.0006263140.99937373
ENST00000567468ENST00000321728GGA2chr1623502998-PRKCBchr1623999829+0.0012974960.9987025
ENST00000567468ENST00000303531GGA2chr1623502998-PRKCBchr1623999829+0.0005949990.999405

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>33002_33002_1_GGA2-PRKCB_GGA2_chr16_23502998_ENST00000309859_PRKCB_chr16_23999829_ENST00000303531_length(amino acids)=763AA_BP=158
MAATAVAAAVAGTESAQGPPGPAASLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCM
NHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQVCCFVVHKRCHEFVTFSCPGAD
KGPASDDPRSKHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCMMNVHKRCVMNVPSLCGTDHTERRGRIYIQAHIDRDVLIVLVRDA
KNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAS
VDGWFKLLSQEEGEYFNVPVPPEGSEANEELRQKFERAKISQGTKVPEEKTTNTVSKFDNNGNRDRMKLTDFNFLMVLGKGSFGKVMLSE
RKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEI
AIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKTFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAP
FEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKACGRNAENFD

--------------------------------------------------------------

>33002_33002_2_GGA2-PRKCB_GGA2_chr16_23502998_ENST00000309859_PRKCB_chr16_23999829_ENST00000321728_length(amino acids)=761AA_BP=158
MAATAVAAAVAGTESAQGPPGPAASLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCM
NHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQVCCFVVHKRCHEFVTFSCPGAD
KGPASDDPRSKHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCMMNVHKRCVMNVPSLCGTDHTERRGRIYIQAHIDRDVLIVLVRDA
KNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAS
VDGWFKLLSQEEGEYFNVPVPPEGSEANEELRQKFERAKISQGTKVPEEKTTNTVSKFDNNGNRDRMKLTDFNFLMVLGKGSFGKVMLSE
RKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEI
AIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKTFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAP
FEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKARDKRDTSNF

--------------------------------------------------------------

>33002_33002_3_GGA2-PRKCB_GGA2_chr16_23502998_ENST00000567468_PRKCB_chr16_23999829_ENST00000303531_length(amino acids)=763AA_BP=158
MAATAVAAAVAGTESAQGPPGPAASLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCM
NHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQVCCFVVHKRCHEFVTFSCPGAD
KGPASDDPRSKHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCMMNVHKRCVMNVPSLCGTDHTERRGRIYIQAHIDRDVLIVLVRDA
KNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAS
VDGWFKLLSQEEGEYFNVPVPPEGSEANEELRQKFERAKISQGTKVPEEKTTNTVSKFDNNGNRDRMKLTDFNFLMVLGKGSFGKVMLSE
RKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEI
AIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKTFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAP
FEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKACGRNAENFD

--------------------------------------------------------------

>33002_33002_4_GGA2-PRKCB_GGA2_chr16_23502998_ENST00000567468_PRKCB_chr16_23999829_ENST00000321728_length(amino acids)=761AA_BP=158
MAATAVAAAVAGTESAQGPPGPAASLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCM
NHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQVCCFVVHKRCHEFVTFSCPGAD
KGPASDDPRSKHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCMMNVHKRCVMNVPSLCGTDHTERRGRIYIQAHIDRDVLIVLVRDA
KNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAS
VDGWFKLLSQEEGEYFNVPVPPEGSEANEELRQKFERAKISQGTKVPEEKTTNTVSKFDNNGNRDRMKLTDFNFLMVLGKGSFGKVMLSE
RKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEI
AIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKTFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAP
FEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKARDKRDTSNF

--------------------------------------------------------------

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:23502998/chr16:23999829)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
GGA2

Q9UJY4

.
FUNCTION: Plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes. Mediates the ARF-dependent recruitment of clathrin to the TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster-dileucine (DXXLL) motif (PubMed:10747088). Mediates export of the GPCR receptor ADRA2B to the cell surface (PubMed:27901063). Regulates retrograde transport of phosphorylated form of BACE1 from endosomes to the trans-Golgi network (PubMed:15615712). {ECO:0000269|PubMed:10747088, ECO:0000269|PubMed:15615712, ECO:0000269|PubMed:27901063}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgenePRKCBchr16:23502998chr16:23999829ENST00000303531117158_27568.33333333333333674.0DomainC2
TgenePRKCBchr16:23502998chr16:23999829ENST00000303531117342_60068.33333333333333674.0DomainProtein kinase
TgenePRKCBchr16:23502998chr16:23999829ENST00000303531117601_67168.33333333333333674.0DomainAGC-kinase C-terminal
TgenePRKCBchr16:23502998chr16:23999829ENST00000321728117158_27568.33333333333333672.0DomainC2
TgenePRKCBchr16:23502998chr16:23999829ENST00000321728117342_60068.33333333333333672.0DomainProtein kinase
TgenePRKCBchr16:23502998chr16:23999829ENST00000321728117601_67168.33333333333333672.0DomainAGC-kinase C-terminal
TgenePRKCBchr16:23502998chr16:23999829ENST0000049805802158_275058.0DomainC2
TgenePRKCBchr16:23502998chr16:23999829ENST0000049805802342_600058.0DomainProtein kinase
TgenePRKCBchr16:23502998chr16:23999829ENST0000049805802601_671058.0DomainAGC-kinase C-terminal
TgenePRKCBchr16:23502998chr16:23999829ENST00000303531117348_35668.33333333333333674.0Nucleotide bindingATP
TgenePRKCBchr16:23502998chr16:23999829ENST00000321728117348_35668.33333333333333672.0Nucleotide bindingATP
TgenePRKCBchr16:23502998chr16:23999829ENST0000049805802348_356058.0Nucleotide bindingATP
TgenePRKCBchr16:23502998chr16:23999829ENST00000303531117101_15168.33333333333333674.0Zinc fingerPhorbol-ester/DAG-type 2
TgenePRKCBchr16:23502998chr16:23999829ENST00000321728117101_15168.33333333333333672.0Zinc fingerPhorbol-ester/DAG-type 2
TgenePRKCBchr16:23502998chr16:23999829ENST0000049805802101_151058.0Zinc fingerPhorbol-ester/DAG-type 2
TgenePRKCBchr16:23502998chr16:23999829ENST000004980580236_86058.0Zinc fingerPhorbol-ester/DAG-type 1

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGGA2chr16:23502998chr16:23999829ENST00000309859-517188_315158.33333333333334614.0DomainGAT
HgeneGGA2chr16:23502998chr16:23999829ENST00000309859-51733_163158.33333333333334614.0DomainVHS
HgeneGGA2chr16:23502998chr16:23999829ENST00000309859-517484_605158.33333333333334614.0DomainGAE
HgeneGGA2chr16:23502998chr16:23999829ENST00000309859-517316_483158.33333333333334614.0RegionNote=Unstructured hinge
TgenePRKCBchr16:23502998chr16:23999829ENST0000030353111736_8668.33333333333333674.0Zinc fingerPhorbol-ester/DAG-type 1
TgenePRKCBchr16:23502998chr16:23999829ENST0000032172811736_8668.33333333333333672.0Zinc fingerPhorbol-ester/DAG-type 1


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1539_GGA2_23502998_PRKCB_23999829_ranked_0.pdbGGA22350299823502998ENST00000303531PRKCBchr1623999829+
MAATAVAAAVAGTESAQGPPGPAASLELWLNKATDPSMSEQDWSAIQNFCEQVNTDPNGPTHAPWLLAHKIQSPQEKEALYALTVLEMCM
NHCGEKFHSEVAKFRFLNELIKVLSPKYLGSWATGKVKGRVIEILFSWTVWFPEDIKIRDAYQMLKKQVCCFVVHKRCHEFVTFSCPGAD
KGPASDDPRSKHKFKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCMMNVHKRCVMNVPSLCGTDHTERRGRIYIQAHIDRDVLIVLVRDA
KNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAS
VDGWFKLLSQEEGEYFNVPVPPEGSEANEELRQKFERAKISQGTKVPEEKTTNTVSKFDNNGNRDRMKLTDFNFLMVLGKGSFGKVMLSE
RKGTDELYAVKILKKDVVIQDDDVECTMVEKRVLALPGKPPFLTQLHSCFQTMDRLYFVMEYVNGGDLMYHIQQVGRFKEPHAVFYAAEI
AIGLFFLQSKGIIYRDLKLDNVMLDSEGHIKIADFGMCKENIWDGVTTKTFCGTPDYIAPEIIAYQPYGKSVDWWAFGVLLYEMLAGQAP
FEGEDEDELFQSIMEHNVAYPKSMSKEAVAICKGLMTKHPGKRLGCGPEGERDIKEHAFFRYIDWEKLERKEIQPPYKPKACGRNAENFD
763


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
GGA2_pLDDT.png
all structure
all structure
PRKCB_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
GGA2
PRKCB


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to GGA2-PRKCB


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to GGA2-PRKCB


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource