IPD - ESTDAB Database

ESTDAB Database Dictionary Version 1.3

The dictionary represents a detailed list of all markers and the acceptable values for each of their associated fields. Where possible the accepted values have been listed, for example Gender can be M, F or Unknown. Within the list of acceptable values a comma separates the entries, so in the above example Gender is listed as M, F, Unknown. Some fields may contain a numerical value or a text string, in these cases a simple description has been provided.

Cell Source

Name	Field	Group
Cell Type	B-LCL, Melanoma, Uveal Melanoma, Unknown	Pawelec
Tissue of Origin	Axillary Lymph Node, Lymph Node, Primary Tumour, Secondary Tumour, Skin, Unknown	Pawelec
Gender	M, F, Unknown	Pawelec
Ethnic Origin	Description of ethnic origin	Pawelec
Morphology	Epithelial, Fibroblast, Unknown	Pawelec
Medium Used	RPMI 1640 10%FBS	Pawelec
Mycoplasma Status	Negative, Positive, Unknown	Pawelec
Comments	Free Text Comments	Pawelec

Primary Search Determinants

High Resolution HLA Typing

HLA RSCA Typing Data
Marker	Allele 1	Allele 2	Group
HLA-A	ND, Allele String	ND, Allele String	Marsh
HLA-B	ND, Allele String	ND, Allele String	Marsh
HLA-C	ND, Allele String	ND, Allele String	Marsh
HLA-DRB1	ND, Allele String	ND, Allele String	Marsh
HLA-DRB3	ND, Allele String	ND, Allele String	Marsh
HLA-DRB4	ND, Allele String	ND, Allele String	Marsh
HLA-DRB5	ND, Allele String	ND, Allele String	Marsh
HLA-DQA1	ND, Allele String	ND, Allele String	Marsh
HLA-DQB1	ND, Allele String	ND, Allele String	Marsh
HLA-DPA1	ND, Allele String	ND, Allele String	Marsh
HLA-DPB1	ND, Allele String	ND, Allele String	Marsh

HLA and Related Genes, Surface Expression

FACS Data
Marker	Conditions	Normalised Score	Intensity	Group
HLA-A, B, C	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-A	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-B	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-C	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-Bw4	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-Bw6	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-DR	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-DQ	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-DP	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-E	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
HLA-G	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido
MICA	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
MICB	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
MICA/B	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
Beta2Microglobulin	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Garrido

Tumour Associated Antigens

Real Time PCR Data
Marker	Score	Group
BAGE	ND, -, +, ++, +++	Straten
BUC1	ND, -, +, ++, +++	Straten
GAGE	ND, -, +, ++, +++	Straten
gp100	ND, -, +, ++, +++	Straten
MAGE1	ND, -, +, ++, +++	Straten
MAGE2	ND, -, +, ++, +++	Straten
MAGE3	ND, -, +, ++, +++	Straten
MAGE4	ND, -, +, ++, +++	Straten
MAGE6	ND, -, +, ++, +++	Straten
MAGE10	ND, -, +, ++, +++	Straten
MTA1	ND, -, +, ++, +++	Straten
NA17-A	ND, -, +, ++, +++	Straten
NMP-2	ND, -, +, ++, +++	Straten
T17	ND, -, +, ++, +++	Straten
T128	ND, -, +, ++, +++	Straten
T21	ND, -, +, ++, +++	Straten
TACC1D	ND, -, +, ++, +++	Straten
Chromium Release Assay Data
Marker	Specificity	Ratio	Lysis (%)	Group
MART1(-27-35)	ND, HLA Type	Numerical Ratio	Percentage	Straten
gp100 (-209-217)	ND, HLA Type	Numerical Ratio	Percentage	Straten
gp100 (-154-162)	ND, HLA Type	Numerical Ratio	Percentage	Straten
Immunohistochemistry Data
Marker	Score	Group
gp100	ND, -, +, ++, +++	Straten

Cytokine Secretions

Cytokine Secretion Data
Marker	Substrate - Plastic	Substrate - Matrigel	Group
Interleukin 6	Numerical value picograms/ml	Numerical value picograms/ml	Kiessling
Interleukin 8	Numerical value picograms/ml	Numerical value picograms/ml	Kiessling
Interleukin 10	Numerical value picograms/ml	Numerical value picograms/ml	Kiessling
Interferon Gamma	Numerical value picograms/ml	Numerical value picograms/ml	Kiessling
TGF Beta	Numerical value picograms/ml	Numerical value picograms/ml	Kiessling
TNF Alpha	Numerical value picograms/ml	Numerical value picograms/ml	Kiessling

Secondary Search Determinants

Antigen Processing

Western Blot Data
Marker	Conditions	Presence	Group
Heavy Chain	Initial Conditions, After 72 hours, IFN-Gamma Induced	ND, -, +, ++, +++, ++++	Kiessling
LMP2	Initial Conditions, After 72 hours, IFN-Gamma Induced	ND, -, +, ++, +++, ++++	Kiessling
LMP7	Initial Conditions, After 72 hours, IFN-Gamma Induced	ND, -, +, ++, +++, ++++	Kiessling
MECL1	Initial Conditions, After 72 hours, IFN-Gamma Induced	ND, -, +, ++, +++, ++++	Kiessling
TAP1	Initial Conditions, After 72 hours, IFN-Gamma Induced	ND, -, +, ++, +++, ++++	Kiessling
TAP2	Initial Conditions, After 72 hours, IFN-Gamma Induced	ND, -, +, ++, +++, ++++	Kiessling

Apoptosis

FACS Data
Marker	Conditions	Normalised Score	Intensity	Group
B7H1	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD11a	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Solano
CD11b	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Solano
CD48	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Solano
CD49d	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Solano
CD56	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Solano
CD57	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Solano
CD95	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD95L	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD112	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD155	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
gp100	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
PD-1	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
TRAIL-R1	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
TRAIL-R2	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
TRAIL-R3	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
TRAIL-R4	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
RNA Protection Assay
Marker	Score	Group
caspase-8	ND, -, +/-, +, ++, +++	Garrido
cIAP1	ND, -, +/-, +, ++, +++	Garrido
cIAP2	ND, -, +/-, +, ++, +++	Garrido
DR3 TRAMP APO3	ND, -, +/-, +, ++, +++	Garrido
FADD	ND, -, +/-, +, ++, +++	Garrido
FAF	ND, -, +/-, +, ++, +++	Garrido
FAP	ND, -, +/-, +, ++, +++	Garrido
Fas	ND, -, +/-, +, ++, +++	Garrido
FasL	ND, -, +/-, +, ++, +++	Garrido
NAIP	ND, -, +/-, +, ++, +++	Garrido
RIP	ND, -, +/-, +, ++, +++	Garrido
TNFRp55	ND, -, +/-, +, ++, +++	Garrido
TRADD	ND, -, +/-, +, ++, +++	Garrido
TRAF1	ND, -, +/-, +, ++, +++	Garrido
TRAF2	ND, -, +/-, +, ++, +++	Garrido
TRAF3	ND, -, +/-, +, ++, +++	Garrido
TRAF4	ND, -, +/-, +, ++, +++	Garrido
TRAIL	ND, -, +/-, +, ++, +++	Garrido
TRPM2	ND, -, +/-, +, ++, +++	Garrido
XIAP	ND, -, +/-, +, ++, +++	Garrido
Western Blot Data
Marker	Score	Group
APAF1	ND, -, +, ++	Pawelec
BAX	ND, -, +, ++	Pawelec
Bcl 2	ND, -, +, ++	Pawelec
Bcl w	ND, -, +, ++	Pawelec
Bcl xL	ND, -, +, ++	Pawelec
Bcl xS	ND, -, +, ++	Pawelec
Bid	ND, -, +, ++	Pawelec
FliP	ND, -, +, ++	Pawelec

Cytokine Polymorphisms

Cytokine Polymorphism Data
Marker	Position	Polymorphism	Polymorphsim	Group
Interleukin 6	-174 (Promoter)	A,C,G,T	A,C,G,T	Naumova
Interleukin 10	-1082	A,C,G,T	A,C,G,T	Naumova
Interleukin 10	-819	A,C,G,T	A,C,G,T	Naumova
Interleukin 10	-592	A,C,G,T	A,C,G,T	Naumova
Interleukin 10	+571	A,C,G,T	A,C,G,T	Naumova
Interferon Gamma	-333	A,C,G,T	A,C,G,T	Naumova
Interferon Gamma	-+874 (intron 1)	A,C,G,T	A,C,G,T	Naumova
TGF Beta	-988	A,C,G,T	A,C,G,T	Naumova
TGF Beta	-800	A,C,G,T	A,C,G,T	Naumova
TGF Beta	-509	A,C,G,T	A,C,G,T	Naumova
TGF Beta	+652	A,C,G,T	A,C,G,T	Naumova
TGF Beta	+653	A,C,G,T	A,C,G,T	Naumova
TGF Beta	+713	A,C,G,T	A,C,G,T	Naumova
TGF Beta	+788	A,C,G,T	A,C,G,T	Naumova
TGF Beta	+869	A,C,G,T	A,C,G,T	Naumova
TGF Beta	+915	A,C,G,T	A,C,G,T	Naumova
TGF Beta	codon 10	A,C,G,T	A,C,G,T	Naumova
TGF Beta	codon 25	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-1031	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-863	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-857	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-851	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-574	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-376	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-308	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	-238	A,C,G,T	A,C,G,T	Naumova
TNF Alpha	+488	A,C,G,T	A,C,G,T	Naumova

DNA Profile

DNA Profile Data
Marker	Score	Score	Group
Amelogenin	X,Y, Unknown		Pawelec
CSF1PO	6, 7, 8, 9, 10, 10.3, 11, 12, 13, 14, 15	6, 7, 8, 9, 10, 10.3, 11, 12, 13, 14, 15	Pawelec
D13S317	5, 8, 9, 10, 11, 12, 13, 14, 15	5, 8, 9, 10, 11, 12, 13, 14, 15	Pawelec
D3S1358	9, 11, 12, 13, 14,15, 15.2, 16, 17, 18, 19, 20	9, 11, 12, 13, 14,15, 15.2, 16, 17, 18, 19, 20	Pawelec
D5S818	7, 8, 9, 10, 11,12, 13, 14, 15, 16	7, 8, 9, 10, 11,12, 13, 14, 15, 16	Pawelec
D7S820	6,6.3, 7, 8, 9, 10, 11, 12, 13, 14, 15	6,6.3, 7, 8, 9, 10, 11, 12, 13, 14, 15	Pawelec
FGA	15, 16, 16.2,17, 18, 18.2, 19, 19.2, 20, 20.2, 21, 21.2, 22, 22.2, 22.3, 23, 23.2,24, 24.2, 25, 25.2, 26, 26.2, 27, 27.2, 28, 28.2, 29 30, 30.2, 34.2, 46.2	15, 16, 16.2,17, 18, 18.2, 19, 19.2, 20, 20.2, 21, 21.2, 22, 22.2, 22.3, 23, 23.2,24, 24.2, 25, 25.2, 26, 26.2, 27, 27.2, 28, 28.2, 29, 30, 30.2, 34.2, 46.2	Pawelec
THO1	4, 5, 6, 6.1, 7, 7.1, 7.3, 8, 8.3, 9,9.3, 10, 11, 13.3	4, 5, 6, 6.1, 7, 7.1, 7.3, 8, 8.3, 9,9.3, 10, 11, 13.3	Pawelec
TPOX	6, 7, 8, 9, 10, 11,12, 13	6, 7, 8, 9, 10, 11,12, 13	Pawelec
vWA	11,12, 13, 14, 15, 15.2, 16, 17, 18, 19, 20, 21, 22	11,12, 13, 14, 15, 15.2, 16, 17, 18, 19, 20, 21, 22	Pawelec

Extra Cellular Matrix

Cell Adhesion Data
Marker	Score	Group
Collagen	ND, -, +, ++, +++, ++++	Laidler
Fibronectin	ND, -, +, ++, +++, ++++	Laidler
Laminin	ND, -, +, ++, +++, ++++	Laidler
Glycosyltranserase Data
Marker	Score	Group
FUT1	ND, +, -	Laidler
FUT4	ND, +, -	Laidler
MGAT5	ND, +, -	Laidler
SIAT3	ND, +, -	Laidler
SIAT4C	ND, +, -	Laidler

Lectin Data
Marker	Molecular Weight	Presence	Group
DSA	< 30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100, 101-110, 110-120, 121-130, 131-140, 141-150, 151-160, 161-170, 171-180, 181-190, 191-200, > 200	ND, -, +, ++, +++, ++++, +++++	Laidler
GNA	< 30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100, 101-110, 110-120, 121-130, 131-140, 141-150, 151-160, 161-170, 171-180, 181-190, 191-200, > 200	ND, -, +, ++, +++, ++++, +++++	Laidler
LTA	< 30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100, 101-110, 110-120, 121-130, 131-140, 141-150, 151-160, 161-170, 171-180, 181-190, 191-200, > 200	ND, -, +, ++, +++, ++++, +++++	Laidler
MAA	< 30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100, 101-110, 110-120, 121-130, 131-140, 141-150, 151-160, 161-170, 171-180, 181-190, 191-200, > 200	ND, -, +, ++, +++, ++++, +++++	Laidler
PHA-L	< 30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100, 101-110, 110-120, 121-130, 131-140, 141-150, 151-160, 161-170, 171-180, 181-190, 191-200, > 200	ND, -, +, ++, +++, ++++, +++++	Laidler
SBA	< 30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100, 101-110, 110-120, 121-130, 131-140, 141-150, 151-160, 161-170, 171-180, 181-190, 191-200, > 200	ND, -, +, ++, +++, ++++, +++++	Laidler
SNA	< 30, 31-40, 41-50, 51-60, 61-70, 71-80, 81-90, 91-100, 101-110, 110-120, 121-130, 131-140, 141-150, 151-160, 161-170, 171-180, 181-190, 191-200, > 200	ND, -, +, ++, +++, ++++, +++++	Laidler

Surface Markers

FACS Data
Marker	Conditions	Normalised Score	Intensity	Group
CD40	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD44	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD54	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD58	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD80	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD86	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD95	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
CD95L	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
ULBP1	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
ULBP2	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
ULBP3	Initial Conditions, After 48 hours, IFN-Gamma Induced	ND, -, +/-, +, ++, +++	Numerical Value	Pawelec
Immunohistochemistry Data
Marker	Score	Group
E-Cadherin	ND, -, +, ++	Pawelec
K-Cadherin	ND, -, +, ++	Pawelec
N-Cadherin	ND, -, +, ++	Pawelec
P-Cadherin	ND, -, +, ++	Pawelec
VE-Cadherin	ND, -, +, ++	Pawelec
Survivin	ND, -, +, ++	Pawelec

EpiGenetic Analysis

EpiGenetic Analysis Data
Marker	Genetic Event	Presence	Details of Event	Group
APC	Mutation, Deletion, Methylation	ND, +, -	Free Text Comments	Goldberg
brAF	Mutation	ND, +, -	Free Text Comments	Goldberg
CDK4	Mutation	ND, +, -	Free Text Comments	Goldberg
CTNNB1	Mutation	ND, +, -	Free Text Comments	Goldberg
NRAS	Mutation	ND, +, -	Free Text Comments	Goldberg
p16	Mutation, Deletion, Methylation	ND, +, -	Free Text Comments	Goldberg
p27	Mutation, Deletion, Methylation	ND, +, -	Free Text Comments	Goldberg
PTEN	Mutation, Methylation	ND, +, -	Free Text Comments	Goldberg
RASSF1A	Mutation, Deletion, Methylation	ND, +, -	Free Text Comments	Goldberg
RB1	Mutation, Methylation	ND, +, -	Free Text Comments	Goldberg
TP53	Mutation	ND, +, -	Free Text Comments	Goldberg

Information

For further information regarding the ESTDAB project please visit http://www.medizin.uni-tuebingen.de/estdab/.

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