The iProXpress Knowledge System for Proteomic Data Analysis

1
The iProXpress Knowledge System for Proteomic
Data Analysis
Hongzhan Huang, Zhang-Zhi Hu, Peter McGarvey and
Cathy H. Wu Protein Information Resource,
Georgetown University, Washington, DC 20007
Figure 1. An Overview of the iProXpress System
IP/2D/MS Proteomic Data
Gene Expression
iProXpress integrated Protein eXpression Analysis
System
Gene/Protein ID list Peptide Sequence
UniProt
Protein Mapping
iProClass
Functional Annotation
Protein Information Matrix
Expression Profiling
Protein Information Matrix
GO tree visualization
Pathway Map
Interaction Map
Function Categorization Chart
Two-Way Comparison Matrix
Sorting of data sets and display of protein
information matrix
NIAID Biodefense Proteomics Program
Functional categorization based on Gene Ontology
Master Protein Diretory from NIAID Biodefence
Proteomic Research Centers.
Two-way comparative matrix
Browsing selected complete proteome(s) with
protein links to the Proteomic Center data.
Table 1. Mapping of mouse color genes to human
melanosome proteins
Table 2. Partial list of stage-specific
melanosome proteins
Human Disease (OMIM)
Human Melanosome Proteins
Function in Pigmentation
Murine Locus
Gene Symbol
MNT1 Stage I (77)
P36955 Pigment epithelium-derived factor
precursor (PEDF) Q14254 Flotillin-2 (Epidermal
surface antigen) P07093 Glia derived nexin
precursor (GDN) P24390 ER lumen protein
retaining receptor 1 (KDEL receptor 1)
(TM) O14880 Microsomal glutathione
S-transferase 3 (TM)
Waardenburg-shah syndrome 277580
P24530 ET-B (Common stage1 MNT1 stage2)
melanoblast differentiation
piebald spotting (s)
Ednrb
Q9H9B4 Sideroflexin-1(Common early stage)
Tricarboxylate carrier
flexed tail
Sfxn1
MNT1 Stage II (112)
Q12846 Syntaxin-4 (TM) (interact with O75379
Vesicle-associated membrane protein 4 Q15836
Vesicle-associated membrane protein 3) Q04656
Copper-transporting ATPase 1 (mouse
Atp7a) Adaptor proteins O95782 AP-2 (mouse
Ap3bl) (also Skmel) Q96EL6 Adaptin (mouse
Ap3d) Vacuolar protein sorting Q96A65 Exocyst
complex component Sec8 P46459 Vesicle-fusing
ATPase (EC 3.6.4.6) (interact) P14415
Sodium/potassium-transporting ATPase beta-2 chain
(TM)
606281
P57729 Ras-related protein Rab-38.
(uniqueSkmel28)
Targeting of Tyrp1 protein to the melanosome
chocolate (cht)
Rab38
Oculocutaneous albinism 155550
P40967 Pmel 17 precursor (Common all stage)
melanosomal matrix protein
silver (si)
si
OCA1 203100 OCA1B 606952
P14679 Tyrosinase precursor (Unique MNT1)
melanogenic enzyme
albino, color (c)
Tyr
MNT4 Stage IV (267)
Adaptor protein Q9Y6Q5 Adaptor protein
complex AP-1 mu-2 subunit, (interact with P63010
AP2B1) Motor poteins Q14203 Dynactin-1
(Progressive lower motor neuron disease
OMIM607641) (interact with P18669
Phosphoglycerate mutase 1) Q9H193
KINESIN-13A2 Transport Q99747 Gamma-soluble
NSF attachment protein (also Skmel) Q99698
Lysosomal trafficking regulator (mouse
Lyst) Vacuolar protein sorting Q9H444 VPS32
(mouse Vps33a) (interact) (also Skmel) Q9NZZ3
VPS60 (mouse Vps33a)
Rufous albinism, ROCA 115501 OCA3
203290 Precocious graying of hair 278400
P17643 5,6-dihydroxyindole-2-carboxylic acid
oxidase precursor. (Unique MNT1)
melanosomal enzyme/stabilizing factor
brown (b)
Tyrp1
A Case Study
Table 3. Summary of the comparison of organellar
proteomes
Glaucoma-related pigment dispersion syndrome-1
604368
Q14956 Transmembrane glycoprotein NMB precursor
(Common all stage)
Apparent melanosomal component
iris pigment dispersion (ipd)
Gpnmb
References
Common with melanosome
Entries mapped
Protein reported
Organelle

• Organellar proteomes of various stages of
  melanosomes from human melanoma cell lines
• Mapping to known mouse coat color genes led to
  identification of 17 human melanosome related
  proteins
• Identification of possible stage-specific
  melanosome proteins for validation
• Comparison of melanosome proteome with those of
  several other organelles.

Knoblach et al, 2003
57 (M51, S36) -19(33) all stage
131
141
Mouse ER (ER)
OCA4 606574
Q9UMX9 Melanoma antigen AIM1 Q6P2P0
Membrane-associated transporter protein, isoform
b (MNT1 stage1 2)
transporter
underwhite (uw)
Matp
Skmel28 unique (143)
Both melanosome-specific proteins Tyrosinase and
TYRP1 are absent in Skmel28 data set, suggesting
that their absence can partially account for the
lack of melanin production in Skmel28. P57729
Ras-related protein Rab-38 (mouse Rab38) P51810
G-protein coupled receptor 143 (mouse Gpr143)
P53794 Sodium/myo-inositol cotransporter
(Na()/myo-inositol cotransporter)
Tribl et al, 2005
43 (M38, S36) -22(51) all stages
72
72
Human neuromelanin granules (NG)
Griscelli syndrome, type 2 607624
Q6IAS8 RAB27A protein P51159 Ras-related
protein Rab-27A (Common all stage)
melanosome transport
ashen (ash)
Rab27a
Witzmann et al, 2005
43 (M35, S27) -14(33) all stages
88
200
Rat synaptosome (SY)
All stage IV-specific membrane protein P50443
Sulfate transporter (Solute carrier family 26
member 2) (OMIM 600972) Q9NZ45 Protein
C10orf70 P33121 Long-chain-fatty-acid--CoA
ligase 1 (LACS 1) (OMIM 152425) (also in
ER) Q8NCC2 Hypothetical protein FLJ90355
(Solute carrier family 2 Q8IWB8 CCR4-NOT
transcription complex, subunit 1, isoform
b P27449 Vacuolar ATP synthase 16 kDa
proteolipid subunit (EC 3.6.3.14) (OMIM
108745) Q71RS6 Ion transporter JSX Homo
sapiens human skin color gene Q6ZTT7
Hypothetical protein FLJ44232 Homo
sapiens Q16444 Phosphoglycerate kinase
(Fragment) Homo sapiens (47 aa)
Bagshaw et al, 2005
49 (M40, S38) -13(27) all stages
116
215
Rat lysosome (LY)
SLC24A5, a human skin color gene Science 16
December 2005 1754-1755.
Q71RS6Ion transporter JSX (Unique late stage)
Causes delayed and reduced development of melanin
pigmentation
golden (gdn)
gdn
Martens et al, 2005
33 (M26, S22) -6(18) all stages
71
93
Human platelet (PL)
Mears et al, 2004
42 (M42, S32) -18(43) all stages
55
56
Human exosome (EX)
This is a partial list of total 17 mapped genes.
The others include Lyst, Ostm1, Dct, Atp7a,
Gpr143, Myo5a and Krt2-17. For complete list, go
to http//pir.georgetown.edu/huz/datamining/prote
omics/
Contact pirmail_at_georgetown.edu
http//pir.georgetown.edu/iproxpress