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Tsapogas et al.
Supplementary data.
These supplements are composed of two major groups of data, the first display the full
dCHIP analysis and the second part display tables containing the probabilistic state
analysis.
dCHIP analysis of B cell lines.
Hierarchical tree clusters were generated using the dChip program (Li and Wong,
http://biosun1.harvard.edu/complab/dchip/). The pro-B, pre-B, B and plasma cell lines
were treated as replicates. Expression values were calculated according to the PM-only
model and genes were filtered according to 0,50 < standard deviation/mean between <
10,00 and presence (P) call in the array used >= 10%. The full cluster analysis has been
split manually into 4 figures, each one displaying genes found over expressed at a defined
stage. The colour range is from blue (-3) to red (3).
Tsapogas et al.
Supplementary tables:
The data are generated by the probabilistic state analysis. Classification of genes with
apparently restricted expression pattern in the analysis into functional groups was
performed manually using the NCBI database. Non-defined genes in the data set were
resubmitted in a Blast search into Genebank allowing for the identification of most of
these entries. The tables are organized based on expression patterns as indicated in
legends. Table VII contains a summary of the data obtained.
pro-B cells
Present
pre-B cells
Absent
Proba
bility
0.934
0.934
Proba
bility 2
0.019
0.019
Pattern
2
MAAA
MAAA
GeneBankTM
Accession No
U01530
AI553024
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
L09600
X15763
AB000096
M97200
M21829
M31885
AI850893
X80638
L18868
U36488
AF087687
AF033655
AI851258
Z31362
M17979
U90435
AW046032
L03529
AW060556
AB012808
J04634
AI596094
AA967194
L04678
U45980
AA824102
AB013850
AI840198
B cells
Absent
plasma cells
Absent
Gene
T-cell acute lymphocytic leukemia 1/SCL
similar to: mPLZF(B)=promyelocytic leukemia zinc finger protein {alternatively
spliced}
Nuclear factor, erythroid derived 2
GATA-binding protein 1
GATA-binding protein 2
Erythroid Kruppel-like factor
Ecotropic viral integration site 1 (Evi-1)
Inhibitor of DNA binding 1 (Id1)
General transcription factor III A (Gtf3a)
rhoC
Thromboxane A synthase 1, platelet
Embryonic stem cell phosphatase(Esp)
calcium-binding protein S100A1
PFTAIRE protein kinase 1
dual-specificity Rho- and Arf-GTPase activating protein1 (Drag1)
Tx01
Epidermal growth factor binding protein type A
flotillin
thrombin receptor (Cf2r)
thrombin receptor mRNA
stabilin-1
mBOCT
Lymphocyte antigen 64
transferrin receptor 2 (Trfr2)
similar to aquaporin 9
Integrin beta 4
alpha (1,3) fucosyltransferase Fuc-TVII
3 beta-hydroxy-delta 5-C27-steroid oxidoreductase
peptidylarginine deiminase type IV
-N-acetyltransferase 6 (Nat6)
Protein
type
TF
TF
TF
TF
TF
TF
TF
TF
TF
STP
STP
STP
STP
STP
STP
STP
STP
MP
MP
MP
MP
MP
MP
MP
MP
MP
ME
ME
ME
ME
Tsapogas et al.
0.934
0.934
0.934
0.019
0.019
0.019
MAAA
MAAA
MAAA
AB027125
AW121619
AV092014
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.791
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.019
0.157
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
MAAA
PAMA
U83509
U49513
AF076482
X54542
V00743
AA867778
U04354
V00714
AA690863
AI848723
AI181346
AW229127
AI646638
AI853444
-hyaluronoglucosaminidase 1 (Hya1), fusion 2 (Fus2), and
hyaluronoglucosaminidase 3 (Hyl3)
AKR1C13 mRNA for aldo-keto reductase AKR1C13
cytochrome P450 side chain cleavage enzyme 11a1 (Cyp11a)
-peptidoglycan recognition protein (Pglyrp)
-TAG7-like protein
angiopoietin-1
Small inducible cytokine A9
Tumor necrosis factor super family 3-like
Interleukin 6
Alpha fetoprotein
actinin, alpha 1 (Actn1)
ADSEVERIN mRNA
Hemoglobin alpha, adult chain 1
similar to rat putative UA20 protein (Ua20) mRNA
Table I: List of genes with expression restricted to the pro-B cell
compartment.
Table shows genes that were found to be expressed exclusively in pro-B cells. Genes
were considered as "Present" (P) or "Absent" (A) depending on their expression or
lack of expression, respectively, in all four cell lines representing a particular B cell
developmental stage. Genes that were not found to be uniformly Present or Absent
within a stage-specific cell line group were classified as "Mixed" (M). The list
includes only the genes that were found to have a pro-B cell specific
expression/presence pattern (PAAA) with a probability higher than 0.7, following
Present/Absent statistical analysis. For every gene, the second highest probability to
have another expression pattern is indicated (Probability 2), as well as the
corresponding pattern (Pattern 2). Abbreviations used: TF: Transcription Factor, STP:
Signal Transduction Protein, MP: Membrane Protein, ME: Metabolic Enzyme, Cy:
Cytokine, SP: Secreted Protein, CP: Cytoplasmic Protein.
ME
ME
Cy
Cy
Cy
Cy
Cy
SP
CP
CP
CP
Tsapogas et al.
pro-B cells
Absent
Proba
bility
0.790
0.790
0.934
0.712
0.712
0.934
0.790
0.790
0.790
0.790
0.790
0.790
0.712
0.790
0.934
0.712
0.712
0.934
0.934
0.934
0.934
0.934
0.934
0.934
0.790
0.790
0.790
0.790
0.790
0.790
0.790
0.790
0.712
0.712
0.712
Proba
bility 2
0.157
0.157
0.021
0.243
0.243
0.021
0.157
0.157
0.157
0.157
0.157
0.157
0.243
0.157
0.021
0.243
0.243
0.021
0.021
0.021
0.021
0.021
0.021
0.021
0.157
0.157
0.157
0.157
0.157
0.157
0.157
0.157
0.243
0.243
0.243
Pattern
2
APMA
APMA
AMAA
AMAA
AMAA
AMAA
APMA
APMA
APMA
APMA
APMA
APMA
AMAA
APMA
AMAA
AMAA
AMAA
AMAA
AMAA
AMAA
AMAA
AMAA
AMAA
AMAA
APMA
APMA
APMA
APMA
APMA
APMA
APMA
APMA
AMAA
AMAA
AMAA
pre-B cells
Present
GeneBankTM
Accession No
D16503
D16503
X70298
U58972
AW209414
M60474
AJ236881
AI853706
U10551
AV012348
U12620
X98471
AF002701
M29961
AV371846
U08373
M29475
L33954
M12376
AF036736
X02466
X02463
AF036738
L28059
AF042086
AF025445
U62386
U10410
AF059706
AF042798
X05557
X04748
X02468
AF036737
AF099973
B cells
Absent
plasma cells
Absent
Gene
Lymphoid enhancer binding factor 1
Lymphoid enhancer binding factor 1
SRY-box containing gene 4 (sox-4)
Growth factor independence 1 (Gfi1)
Kruppel-type zinc finger protein KROX-25
Myristoylated alanine rich protein kinase C substrate
SIT protein
Rho guanine nucleotide exchange factor (GEF) 3 (Arhgef3)
GTP binding protein (gene over-expressed in skeletal muscle)
potassium channel beta 2 subunit (I2RF5)
Dipeptidylpeptidase 4
Epithelial membrane protein 1
Glial cell line derived neurotrophic factor family receptor alpha 2
Glutamyl aminopeptidase
Similar to Ena-vasodilator stimulated phosphoprotein (Evl)
Calmegin
Recombination activating gene 1
clone BPS3.23 germline Ig variable region heavy chain precursor gene
immunoglobulin H-chain V-region pseudogene
clone BPS3.19 immunoglobulin heavy chain variable region precursor gene
germline immunoglobulin V(H)II gene H17
germline immunoglobulin V(H)II gene H8
clone BPS5.16 immunoglobulin heavy chain variable region precursor gene
Ig B cell antigen receptor gene
immunoglobulin heavy chain V DSP2.7-JH2 region (Igh) gene
clone BHS2.19 immunoglobulin heavy chain variable region precursor gene
immunoglobulin heavy and light chain variable region mRNA,
recombinant antineuraminidase single chain Ig VH and VL domains mRNA
clone N1.1.b immunoglobulin heavy chain VDJ region gene
immunoglobulin heavy chain gene, CDR3 region
V(preB)1 gene 4.6 kb upstream of lambda5 locus
Immunoglobulin lambda chain 5
germline immunoglobulin V(H)II gene H18
clone BPS3.26 immunoglobulin heavy chain variable region precursor, gene
schlafen2 (Slfn2) mRNA
Table II: List of genes with expression restricted to pre-B cells.
Table shows genes that were found to be expressed exclusively in pre-B cells.
Genes were considered as "Present" (P), "Absent" (A) or "Mixed" (M) with the
same criteria as in Table I. The list includes only the genes that were found to have
a pre-B cell specific expression pattern (APAA) with a probability higher than 0.7,
following Present/Absent statistical analysis. For every gene, the second highest
Protein
type
TF
TF
TF
TF
TF
STP
STP
STP
STP
MP
MP
MP
MP
ME
CP
CP
CP
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Ig
Tsapogas et al.
probability to have another expression pattern is indicated (Probability 2), as well
as the corresponding pattern (Pattern 2). Abbreviations used: TF: Transcription
Factor, STP: Signal Transduction Protein, MP: Membrane Protein, ME: Metabolic
Enzyme, CP: Cytoplasmic Protein, Ig: Immunoglobulin Molecule.
pro-B cells
Absent
Proba
bility
0.709
0.709
0.709
0.709
0.709
0.709
0.709
0.709
0.709
Proba
bility 2
0.246
0.246
0.246
0.246
0.246
0.246
0.246
0.246
0.246
Pattern
2
AAMA
AAMA
AAMA
AAMA
AAMA
AAMA
AAMA
AAMA
AAMA
pre-B cells
Absent
GeneBankTM
Accession No
AF017021
U87620
U87619
AB020808
AF108020
AB009377
J00475
AA795198
AA986114
B cells
Present
plasma cells
Absent
Gene
B-ATF mRNA
Ets transcription factor Spi-B
129SV encoding transcription factor Spi-B form IA
TLR6
lysophospholipid receptor B2 (lpb2)
caspase-activated DNase (CAD)
germline IgH chain gene, DJC region- segment D-FL16.1
T-cell immunoglobulin and mucin domain containing 2 (Timd2)
T-cell immunoglobulin and mucin domain containing 2
Protein
type
TF
TF
TF
MP
MP
ME
Ig
Table III: List of genes with expression restricted to B cells.
Table shows genes that were found to be expressed exclusively in B cells. Genes were
considered as "Present" (P), "Absent" (A) or "Mixed" (M) with the same criteria as in
Table I. The list includes only the genes that were found to have a B cell specific
expression pattern (AAPA) with a probability higher than 0.7, following
Present/Absent statistical analysis. For every gene, the second highest probability to
have another expression pattern is indicated (Probability 2), as well as the
corresponding pattern (Pattern 2). Abbreviations used: TF: Transcription Factor, MP:
Membrane Protein, ME: Metabolic Enzyme, Ig: Immunoglobulin Molecule.
pro-B cells
Absent
Proba
Proba
Pattern
pre-B cells
Absent
GeneBankTM
B cells
Absent
Gene
plasma cells
Present
Protein
34
bility
0.927
0.927
0.927
0.927
0.927
0.927
0.927
0.927
0.927
0.927
0.927
0.772
0.927
0.927
0.927
0.927
0.927
bility 2
0.030
0.030
0.030
0.030
0.030
0.030
0.030
0.030
0.030
0.030
0.030
0.168
0.030
0.030
0.030
0.030
0.030
2
AAAM
AAAM
AAAM
AAAM
AAAM
AAAM
AAAM
AAAM
AAAM
AAAM
AAAM
MAAP
AAAM
AAAM
AAAM
AAAM
AAAM
Accession No
Y07686
Y07685
U79550
AF079535
AI850288
AJ002306
AF061505
AF029843
AW124433
AV345565
AB030316
AA408341
U43541
AF054819
AW122372
AI834849
AW047643
Tsapogas et al.
type
TF
TF
TF
STP
STP
MP
MP
ME
ME
ME
ME
ME
ECM
NfiB3-protein, splice variant (exon 9, 10 and 11 missing)
NfiB1-protein (exon 1-12)
Slug, chicken homolog
3-phosphoinositide dependent protein kinase-1
similar to GTP-RHO binding protein 1 (RHOPHILIN)
synaptogyrin 1b
B-cell maturation protein
phosphoglycerate mutase muscle-specific subunit
Similar to human adenosine deaminase, RNA-specific
Similar to human adenosine deaminase, RNA-specific
Pig-n gene for phosphatidylinositolglycan class N
phospholipase A2, group V
Laminin, beta 2
DNA Segment, Chr 6, human D12S2489E
Similar to KIAA0721 protein
Table IV: List of genes present only in plasma cells.
Table shows genes that were found to be expressed exclusively in plasma cells. Genes
were considered as "Present" (P), "Absent" (A) or "Mixed" (M) with the same criteria
as in Table I. The list includes only the genes that were found to have a plasma cell
specific expression pattern (AAAP) with a probability higher than 0.7, following
Present/Absent statistical analysis. For every gene, the second highest probability to
have another expression pattern is indicated (Probability 2), as well as the
corresponding pattern (Pattern 2). Abbreviations used: TF: Transcription Factor, STP:
Signal Transduction Protein, MP: Membrane Protein, ME: Metabolic Enzyme, ECM:
Extracellular Matrix Molecule.
pro-B cells
Present
pre-B cells
Present
Proba
bility
0.927
0.785
0.785
0.927
0.785
Proba
bility 2
0.021
0.156
0.156
0.021
0.156
Pattern
2
PMAA
PPMA
PPMA
PMAA
PPMA
GeneBankTM
Accession No
AF006492
AB017132
D26532
M80632
AW124359
0.927
0.785
0.785
0.021
0.156
0.156
PMAA
PPMA
PPMA
AI841654
AI850484
U18975
B cells
Absent
plasma cells
Absent
Gene
friend of GATA-1 (FOG)
Hex(prh) gene
Core binding factor alpha 2
Guanine nucleotide binding protein, alpha 15
Similar to: partial Pik3cd gene for phosphatidylinositol 3-kinase p110 delta, exon
22
G protein-coupled receptor 56 (Gpr56)
Rat putative potassium channel subunit protein (RCK3)
Ganglioside expression 2
Protein
type
TF
TF
TF
STP
STP
MP
MP
MP
Tsapogas et al.
0.785
0.785
0.785
0.785
0.707
0.785
0.785
0.785
0.785
0.156
0.156
0.156
0.156
0.241
0.156
0.156
0.156
0.156
PPMA
PPMA
PPMA
PPMA
PMAA
PPMA
PPMA
PPMA
PPMA
X13986
M16465
D88769
U87814
AA681862
X99805
AA921411
AA822174
AA833293
pro-B cells
Present
minopontin
Calpactin I light chain
latexin
PEST phosphatase interacting protein
spindlin (Spin)
Tectorin alpha
pre-B cells
Present
Proba
bility
0.917
Proba
bility 2
0.023
Pattern
2
PPMA
GeneBankTM
Accession No
AW121057
0.731
0.917
0.917
0.917
0.917
0.917
0.917
0.731
0.731
0.209
0.023
0.023
0.023
0.023
0.023
0.023
0.209
0.209
PPMA
PPMA
PPMA
PPMA
PPMA
PPMA
PPMA
PPMA
PPMA
AF087434
X55663
AI852578
U86405
U60884
AV336639
AA623483
Y15910
AI840868
0.917
0.917
0.917
0.917
0.917
0.917
0.917
0.731
0.023
0.023
0.023
0.023
0.023
0.023
0.023
0.209
PPMA
PPMA
PPMA
PPMA
PPMA
PPMA
PPMA
PPMA
AI835446
U38967
AW120727
AI152195
AW123599
AA222883
AW125453
AI851565
pro-B cells
Absent
Proba
bility 2
0.029
0.029
0.029
0.029
0.029
0.165
0.165
0.165
0.207
0.165
0.029
Pattern
2
APPM
APPM
APPM
APPM
APPM
MPPP
MPPP
MPPP
APMP
MPPP
APPM
GeneBankTM
Accession No
AF061972
Z54283
L13171
AF068182
AF068182
AW045474
AI835784
AW046747
AF029347
L42115
U57746
0.910
0.910
0.910
0.910
0.910
0.910
0.910
0.910
0.029
0.029
0.029
0.029
0.029
0.029
0.029
0.029
APPM
APPM
APPM
APPM
APPM
APPM
APPM
APPM
AF023463
U96746
U42443
D29639
M19436
Z46966
AW125480
AW120567
B cells
Present
plasma cells
Absent
Gene
similar to: nuclear receptor co-repressor 2; silencing mediator of retinoid acid and
thyroid hormone receptor
transcription factor NF-ATc isoform a (NF-ATca)
Cytoplasmic tyrosine kinase, Dscr28C related (Drosophila)
Similar to: Rat natural resistance-associated macrophage protein 2 (Nramp2)
brain amphiphysin 2
SH3P9
talin (Tln)
ribosomal protein L40
dia protein
neural precursor cell expressed, developmentally down-regulated gene 4b
(Nedd4b)
isocitrate dehydrogenase 3 (NAD+) alpha
Prothymosin beta 4
pre-B cells
Present
Proba
bility
0.910
0.910
0.910
0.910
0.910
0.757
0.757
0.757
0.726
0.757
0.910
SP
CP
CP
CP
CP
ECM
B cells
Present
Protein
type
TF
TF
STP
MP
CP
CP
CP
CP
CP
CP
ME
H
plasma cells
Present
Gene
Tat-interacting protein TIP30
B-cell-specific coactivator BOB.1
Myocyte enhancer factor 2C
B cell linker protein BLNK
B cell linker protein BLNK
Similar to: ADP-ribosylation-like 3 (Arl3) mRNA
sphingosine-1-phosphate phosphatase1
cation-transporting atpase (catp)
chloride channel protein 3 (CLCN3)
insulin-activated amino acid transporter
platelet-activating factor acetylhydrolase isoform Ib gamma subunit (PAF-AH
gamma)
peroxisomal phytanoyl-CoA alpha hydroxylase (PAHX)
antioxidant enzyme AOE372
MECA39 mRNA
embryonal carcinoma cell mRNA for 3-hydroxyacyl CoA dehydrogenase
Myosin light chain, alkali, cardiac atria
imogen 44
similar to 16.7Kd protein
homolog to sorting Nexin 9 (SH3 and PX domain-containing protein 1) (SDP1
protein)
Protein
type
TF
TF
TF
STP
STP
STP
STP
MP
MP
MP
ME
ME
ME
ME
ME
CP
MtP
Tsapogas et al.
0.726
0.910
0.910
0.910
0.910
0.207
0.029
0.029
0.029
0.029
APMP
APPM
APPM
APPM
APPM
AI153421
AW050059
AI426400
AA597220
AA473729
pro-B cells
Absent
Proba
bility
0.924
0.924
0.924
0.924
0.924
0.769
0.737
0.924
Proba
bility 2
0.024
0.024
0.024
0.024
0.024
0.167
0.210
0.024
Pattern
2
APMA
APMA
APMA
APMA
APMA
MPPA
APMA
APMA
Similar to: erythroid differentiation regulator
pre-B cells
Present
GeneBankTM
Accession No
M32489
X53532
X59274
M28240
AI153959
AI606951
AI838274
AI850090
B cells
Present
plasma cells
Absent
Gene
Protein
type
TF
STP
STP
MP
ME
Interferon concensus sequence binding protein
Protein kinase C, beta
brain protein kinase C beta-I
CD19 antigen
sialyltransferase 10 (alpha-2,3 sialyltransferaseVI)
similar to hypothetical protein DKFZp434A1319
solute carrier family 29 (nucleoside transporters), member 1
Table V: Lists of genes with continuous expression patterns.
Table shows genes that were found to be expressed in more than one B cell
developmental stages. Genes were considered as "Present" (P), "Absent" (A) or
"Mixed" (M) with the same criteria as in Table I. The lists include only the genes that
were found to have specific expression patterns with a probability higher than 0.7,
following Present/Absent statistical analysis. For every gene, the second highest
probability to have another expression pattern is indicated (Probability 2), as well as
the corresponding pattern (Pattern 2). Abbreviations used: TF: Transcription Factor,
STP: Signal Transduction Protein, MP: Membrane Protein, ME: Metabolic Enzyme,
CP: Cytoplasmic Protein, SP: Secreted Protein, ECM: Extracellular Matrix Molecule,
H: Hormone, MtP: Mitochondrial Protein.
pro-B cells
Absent
Proba
bility
0.920
0.920
0.779
Proba
bility 2
0.029
0.029
0.155
Pattern
2
APAM
APAM
APMP
pre-B cells
Present
GeneBankTM
Accession No
U05252
U20949
J02980
B cells
Absent
Gene
nuclear matrix attachment DNA-binding protein SATB1
lymphoid-specific interferon regulatory factor (LSIRF)
Alkaline phosphatase 2
plasma cells
Present
Protein
type
TF
TF
ME
Tsapogas et al.
pro-B cells
Present
Proba
bility
0.921
0.921
0.921
0.921
0.921
0.921
0.921
0.921
Proba
bility 2
0.029
0.029
0.029
0.029
0.029
0.029
0.029
0.029
Pattern
2
PAAM
PAAM
PAAM
PAAM
PAAM
PAAM
PAAM
PAAM
pre-B cells
Absent
GeneBankTM
Accession No
AF020200
D86563
AI840130
X66084
AF056187
X15788
U15635
AA981725
pro-B cells
Present
Proba
bility 2
0.153
Pattern
2
PPMP
GeneBankTM
Accession No
AA710439
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.773
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
0.153
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
PPMP
AB024005
Z11664
J05261
AI021421
AI851218
AI120844
X60672
AI851598
AW122935
AI850509
AI852704
AA266467
AW122973
AI838630
AI851614
pro-B cells
Present
Proba
bility
0.703
Proba
bility 2
0.244
Pattern
2
PAMA
Protein
type
TF
STP
STP
MP
MP
MP
CP
CP
transcription factor PBX3b (PBX3b)
RAB4A, member RAS oncogene family
Src activating and signaling molecule (Srcasm)
CD44 antigen
insulin-like growth factor I receptor
postsynaptic 43kD protein
IFN-gamma induced (Mg11) mRNA
homolog to heterogeneous nuclear ribonucleoprotein L (hnRNP L)
B cells
Absent
plasma cells
Present
Gene
Human BTB and CNC homology 1, basic leucine zipper transcription factor 1
(BACH1)
KRAB-containing zinc-finger protein KRAZ2, mRNA
Son of sevenless homolog 2, (Drosophila)
Protective protein for beta galactosidase
ubiquitin specific protease 3 (USP3)
Similar to centrosome-associated protein 350
cytohesin binding protein (Cbp)
radixin mRNA
autophagy 12-like (S. cerevisiae)
NCU-G1 mRNA for kidney predominant protein
similar to envelope protein (4632419I22Rik)
pre-B cells
Absent
GeneBankTM
Accession No
U05837
plasma cells
Present
Gene
pre-B cells
Present
Proba
bility
0.773
B cells
Absent
B cells
Present
Gene
Hexosaminidase A
Protein
type
TF
TF
STP
ME
CP
CP
CP
CP
CP
plasma cells
Absent
Protein
type
ME
Table VI: Lists of genes with discontinuous expression patterns.
Table shows genes that found to be expressed in more than one B cell developmental
stages. Genes were considered as "Present" (P), "Absent" (A) or "Mixed" (M) with the
same criteria as in Table I. The lists include only the genes that were found to have
Tsapogas et al.
specific expression patterns with a probability higher than 0.7, following Present/Absent
statistical analysis. For every gene, the second highest probability to have another
expression pattern is indicated (Probability 2), as well as the corresponding pattern
(Pattern 2). Abbreviations used: TF: Transcription Factor, STP: Signal Transduction
Protein, MP: Membrane Protein, ME: Metabolic Enzyme, CP: Cytoplasmic Protein.
39
expression
pattern
PAAA
APAA
AAPA
AAAP
PPAA
PPPA
APPP
APPA
APAP
PAAP
PPAP
PAPA
Tsapogas et al.
TF
STP
MP
ME
SP
CP
Ig
total
9
5
3
3
3
2
3
1
2
1
2
34
8
4
2
2
1
4
2
2
1
26
9
4
2
2
3
1
3
1
3
28
6
1
1
5
1
5
1
1
1
1
23
6
1
2
1
1
11
3
3
4
6
1
2
5
24
17
1
18
47
35
9
17
17
18
24
8
3
8
16
1
203
Table VII: Summary of Probabilistic state analysis allows for the identification of 203
genes with stage restricted expression. Table II shows a summary of the genes calculated
to display stage restricted expression patterns based on P/A based probabilistic state
analysis (Bilke et al. Submited). PAAA indicates pro-B cell, APAA pre-B, AAPA B and
AAAP plasma cell restricted genes. Genes with expression at several stages and indicated
in accordance with the same patterns. The lists include only the genes that were found to
have specific expression patterns with a probability higher than 0.7, following
Present/Absent statistical analysis. Abbreviations used: TF: Transcription Factor, STP:
Signal Transduction Protein, MP: Membrane Protein, ME: Metabolic Enzyme, SP:
Secreted Protein, CP: Cytoplasmic Protein, Ig: Immunoglobulin.
40
Tsapogas et al.