MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.

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measured	Hugo	Gene	expected	final	Rank	description

Results: HTML CSV LaTeX

Showing element 451 to 500 of 3206 in total

measured	Hugo	expected	final	Rank	description
0.0359748	RCOR3	0.135679	0.265146412	708
0.0359807	TBC1D22B	0.132771	0.270998185	559	TBC1 DOMAIN FAMILY PROTEIN C22ORF4-LIKE (FRAGMENT). [SWISSPROT;Acc:Q9NU19]
0.0360136	COX4I1	0.15771	0.228353307	2101	"CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-1) (CYTOCHROME C OXIDASE POLYPEPTIDE IV). [SWISSPROT;Acc:P13073]"
	COX4I2			2099	"CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 2, MITOCHONDRIAL PRECURSOR (EC 1.9.3.1) (COX IV-2). [SWISSPROT;Acc:Q96KJ9]"
	PPIB			2100	PEPTIDYL-PROLYL CIS-TRANS ISOMERASE B PRECURSOR (EC 5.2.1.8) (PPIASE) (ROTAMASE) (CYCLOPHILIN B) (S-CYCLOPHILIN) (SCYLP) (CYP-S1). [SWISSPROT;Acc:P23284]
0.0360283	RAB11FIP1	0.136657	0.263640355	763	RAB COUPLING PROTEIN; RAB-INTERACTING RECYCLING PROTEIN; RAB EFFECTOR PROTEIN; RAB11-FAMILY INTERACTING PROTEIN 1. [RefSeq;Acc:NM_025151]
0.036083	MAP4	0.155117	0.232617959	1895	MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [SWISSPROT;Acc:P27816]
0.036112	B3GNT1	0.141665	0.254911234	999	"N-ACETYLLACTOSAMINIDE BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.149) (POLY-N-ACETYLLACTOSAMINE EXTENSION ENZYME) (I-BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE) (IGNT) (UDP-GLCNAC:BETAGAL BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE 6). [SWISSP"
0.0361228	COG7	0.153963	0.234620006	1804	CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 7. [SWISSPROT;Acc:P83436]
0.0362497	C20orf118	0.133763	0.270999454	555	DJ132F21.2 (CONTAINS A NOVEL PROTEIN SIMILAR TO THE L82E FROM DROSOPHILA) (FRAGMENT). [SPTREMBL;Acc:Q9H125]
0.0362539	ARHGEF4	0.158511	0.228715357	2091	RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320]
0.0364961	no value	0.150941	0.241790501	1550	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559]
0.0365106	RECQL5	0.167562	0.217893078	2424	ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762]
0.0365299	C1orf156	0.353982	0.103197055	3070
0.0365656	DYNLT3	0.307503	0.11891136	3027	T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808]
0.0365698	C14orf122	0.138711	0.26364023	766	PROTEIN C14ORF122 (CGI-112). [SWISSPROT;Acc:Q9Y3B6]
0.0366052	PERLD1	0.143236	0.255558658	970	CAB2. [RefSeq;Acc:NM_033419]
0.0366237	SCAMP2	0.174446	0.209942905	2655	SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127]
0.0366305	TXNDC1	0.166118	0.220508915	2346	THIOREDOXIN DOMAIN CONTAINING; THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN; THIOREDOXIN DOMAIN-CONTAINING. [RefSeq;Acc:NM_030755]
0.0366317	AURKA	0.148106	0.247334342	1255	SERINE/THREONINE KINASE 6 (EC 2.7.1.37) (SERINE/THREONINE KINASE 15) (AURORA/IPL1-RELATED KINASE 1) (AURORA-RELATED KINASE 1) (HARK1) (AURORA-A) (BREAST-TUMOR-AMPLIFIED KINASE). [SWISSPROT;Acc:O14965]
	CYLD			1256	"CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]"
0.0366899	STT3B	0.271591	0.135092474	2998	SOURCE OF IMMUNODOMINANT MHC-ASSOCIATED PEPTIDES; HOMOLOG OF YEAST STT3 GENE. [RefSeq;Acc:NM_178862]
0.036734	PTPRB	0.190263	0.193069593	2833	PROTEIN-TYROSINE PHOSPHATASE BETA PRECURSOR (EC 3.1.3.48) (R-PTP- BETA). [SWISSPROT;Acc:P23467]
0.0367538	no value	0.139602	0.263275598	773	"SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION"
0.0368025	DPP9	0.204515	0.179950126	2887	DIPEPTIDYLPEPTIDASE 9; DIPEPTIDYL PEPTIDASE 9; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN-2. [RefSeq;Acc:NM_139159]
0.0368198	TLX2	0.14147	0.260265781	870	T-CELL LEUKEMIA HOMEOBOX PROTEIN 2 (HOMEOBOX PROTEIN HOX-11L1) (NEURAL CREST HOMEOBOX PROTEIN). [SWISSPROT;Acc:O43763]
0.036822	no value	0.15167	0.242777082	1495	IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391]
	ARFGEF2			1496	BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 (BREFELDIN A-INHIBITED GEP 2). [SWISSPROT;Acc:Q9Y6D5]
0.0368814	no value	0.136094	0.270999456	554	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5]
0.0368889	CSDE1	0.145611	0.25333869	1036	UNR PROTEIN. [SWISSPROT;Acc:O75534]
0.0369154	MTR	0.147123	0.250915221	1107	"5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (EC 2.1.1.13) (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT) (MS). [SWISSPROT;Acc:Q99707]"
0.0369504	GPATCH1	0.140933	0.262184158	788	EVOLUTIONARILY CONSERVED G-PATCH DOMAIN CONTAINING. [RefSeq;Acc:NM_018025]
0.0370125	MSI2	0.107534	0.344193464	164	MUSASHI 2 ISOFORM A. [RefSeq;Acc:NM_138962]
0.0370257	TSR2	0.132897	0.278604483	396
0.0370628	SIN3B	0.160934	0.230298135	2027
0.0370737	ZFAND1	0.147075	0.252073432	1081
0.0370824	GALNTL1	0.136931	0.270810846	564	SIMILAR TO EXPRESSED SEQUENCE AI415388 (FRAGMENT). [SPTREMBL;Acc:Q8N428]
0.0371202	ZMYND8	0.141681	0.261998433	809	PROTEIN KINASE C BINDING PROTEIN 1 (RACK7) (CUTANEOUS T-CELL LYMPHOMA ASSOCIATED ANTIGEN SE14-3) (CTCL TUMOR ANTIGEN SE14-3) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q9ULU4]
0.0371369	no value	0.196598	0.188897649	2872
0.0371738	SH3BGRL	0.137173	0.270999395	556	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [SWISSPROT;Acc:O75368]
0.0372023	no value	0.196899	0.188941031	2862	CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073]
	ORAI3			2863
	PARK2			2864	"PARKINSON DISEASE (AUTOSOMAL RECESSIVE, JUVENILE) 2, PARKIN ISOFORM 1; PARKIN. [RefSeq;Acc:NM_004562]"
	TMEM131			2861	RW1 PROTEIN (FRAGMENT). [SWISSPROT;Acc:Q92545]
0.03729	C10orf83	0.156155	0.238801191	1666	44050 PROTEIN. [RefSeq;Acc:NM_178832]
0.0373117	no value	0.130845	0.28515954	333	GA BINDING PROTEIN BETA-2 CHAIN (GABP-BETA-2 SUBUNIT) (TRANSCRIPTION FACTOR E4TF1-47) (GAPBP-2) (NUCLEAR RESPIRATORY FACTOR-2 SUBUNIT GAMMA). [SWISSPROT;Acc:Q06545]
0.0373336	JUP	0.147992	0.25226769	1074	JUNCTION PLAKOGLOBIN (DESMOPLAKIN III). [SWISSPROT;Acc:P14923]
0.0373888	PMP2	0.123882	0.301809787	288	MYELIN P2 PROTEIN. [SWISSPROT;Acc:P02689]
0.0374306	TLX1	0.143817	0.260265476	873	T-CELL LEUKEMIA HOMEOBOX PROTEIN 1 (HOMEOBOX PROTEIN HOX-11) (TCL-3 PROTO-ONCOGENE). [SWISSPROT;Acc:P31314]
0.0374428	CTNNAL1	0.198705	0.188434111	2875	"CATENIN (CADHERIN-ASSOCIATED PROTEIN), ALPHA-LIKE 1; ALPHA-CATULIN. [RefSeq;Acc:NM_003798]"

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots