Table II.

Peptides differentially expressed on EL4 cells versus primary thymocytes

Functional classification	Gene symbol	Gene ID	Function	Sequence	P value	EL4/ Thy
Transcription	Pa2g4 a	18813	Growth regulation	AQFKFTVL	0.02	4.6
	Top2a a	21973	DNA topoisomerase	NSMVLFDHV	0.02	15.6
	Dnmt1 a	13433	DNA methylation	LSLENGTHTL	0.02	8.9
	Pfdn5 a	56612	Protein binding/Folding	SMYVPGKL	0.04	16.6
	Per1 a	18626	Transcription regulator	YTLRNQDTF	0.04	5.0
	Foxp1 a	108655	Transcription factor	QQLQQQHLL	0.01	−4.3
	Bach2 a	12014	Transcription factor	EQLEFIHDI	0.02	−20.2
	Pbrm1	66923	DNA binding	SQVYNDAHI	0.02	−3.5
	Ddx5 a	13207	RNA helicase	NQAINPKLLQL	0.02	−5.7
	Jhdm1d	338523	Histone demethylase	SSIQNGKYTL	0.02	−4.9
Cell differentiation	Ptpn6 a	15170	Key role in hematopoiesis	AQYKFIYV	0.03	3.3
	Mark2	13728	Maintenance of cell polarity	ASIQNGKDSL	0.03	2.7
	Pi3kap1 a	83490	Role in BCR-mediated Pi3K activation	YGLKNLTAL	0.001	−21.8
	Xlr3a/b	22446	Role in lymphocyte development	VAAANREVL	0.02	84.9
	RhoH a	74734	Small GTPase/thymocyte maturation	YSVANHNSFL	0.02	−3.1
Cell cycle	Rcc2	108911	Required in mitosis and cytokinesis	AAYRNLGQNL	0.04	27.0
	Cdkn1b a	12576	Involved in G1 arrest	FGPVNHEEL	0.003	−3.1
Apoptosis	Sgk a	20393	Response to DNA damage stimulus	STLTYSRM	0.02	9.7
	Pdcd10 a	56426	Role in apoptotic pathways	ILQTFKTVA	0.001	−4.3
Signal transduction	Cxcr4 a	12767	Receptor for the chemokine     CXCL12/SDF1	VVFQFQHI	0.003	2.6
	CD97 a	26364	Involved in adhesion and signaling process	KLLSNINSVF	0.03	−4.6
Translation	Eif3s10 a	13669	Translation initiation factor	QSIEFSRL	0.02	3.2
	Eif3s2 a	54709	Translation initiation factor	FGPINSVAF	0.04	5.3
Transport	Tmed9	67511	Intracellular protein transport	VIGNYRTQL	0.02	−6.9
	Copb1	70349	ER to Golgi vesicle-mediated transport	IALRYVAL	0.01	2.9
Cytoskeleton	Tmod1	21916	Cytoskeleton organization	SSIVNKEGL	0.004	10.5
	Mylc2b	67938	Cytoskeleton organization and biogenesis	SLGKNPTDAYL	0.01	4.2
	Mns1	17427	Involved in cell division and motility	KIIEFANI	0.01	−12.4
	Krt5	110308	Strutural constituent of cytoskeleton	AAYMNKVEL	0.04	−106.7
	Krt7	110310	Strutural constituent of cytoskeleton	AAYTNKVEL	0.003	−121.5
Miscellaneous	Igtp a	16145	IFNγ-induced GTPase	IVAENTKTSL	0.001	−15.5
	Nup205	70699	Outer membrane exporter porin	VNNEFEKL	0.005	−4.6
	Dhx15 a	13204	RNA helicase	TLLNVYHAF	0.02	−11.5
	Stk11ip	71728	Serine/Threonine kinase	SALRFLNL	0.01	−3.9
	Pde2a	207728	Catalytic activity	IKNENQEVI	0.02	16.0
	Gtpbp4 a	69237	GTP binding	QILSDFPKL	0.03	2.6
	Narfl	67563	Prelamin recognition	VAYGFRNI	0.01	8.7
	Rmnd5a	68477	Hypothetic role for meiotic nuclear     division	WAVSNREML	0.02	−6.2
Unknown	Specc1	432572		TSLAFESRL	0.01	7.1
	Ccdc41	77048		AQVENVQRI	0.01	−2.8
	2900073G15Rik	67268		SMGKNPTDEYL	0.05	3.8
	D14Ertd436e	218978		SQHVNLDQL	0.04	−2.7
	9230105E10Rik	319236		FISDVEHQL	0.01	−23.2

Gene ID and Gene Symbol description refer to National Center for Biotechnology Information gene entries. Fold change and P values were calculated from biological replicate experiments (n = 3). Functional classification is based upon bibliographic searches.

^aGenes that are involved in neoplastic transformation (see Table S6 [available at http://www.jem.org/cgi/content/full/jem.20071985/DC1] for references).