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	Rank	Gene	description	expected	final

Results: HTML CSV LaTeX

Showing element 451 to 500 of 3206 in total

measured	Hugo	Rank	description	expected	final
0.0359748	RCOR3	708		0.135679	0.265146412
0.0359807	TBC1D22B	559	TBC1 DOMAIN FAMILY PROTEIN C22ORF4-LIKE (FRAGMENT). [SWISSPROT;Acc:Q9NU19]	0.132771	0.270998185
0.0360136	COX4I1	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]"	0.15771	0.228353307
	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	763	RAB COUPLING PROTEIN; RAB-INTERACTING RECYCLING PROTEIN; RAB EFFECTOR PROTEIN; RAB11-FAMILY INTERACTING PROTEIN 1. [RefSeq;Acc:NM_025151]	0.136657	0.263640355
0.036083	MAP4	1895	MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [SWISSPROT;Acc:P27816]	0.155117	0.232617959
0.036112	B3GNT1	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"	0.141665	0.254911234
0.0361228	COG7	1804	CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 7. [SWISSPROT;Acc:P83436]	0.153963	0.234620006
0.0362497	C20orf118	555	DJ132F21.2 (CONTAINS A NOVEL PROTEIN SIMILAR TO THE L82E FROM DROSOPHILA) (FRAGMENT). [SPTREMBL;Acc:Q9H125]	0.133763	0.270999454
0.0362539	ARHGEF4	2091	RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320]	0.158511	0.228715357
0.0364961	no value	1550	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK). [SWISSPROT;Acc:P56559]	0.150941	0.241790501
0.0365106	RECQL5	2424	ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762]	0.167562	0.217893078
0.0365299	C1orf156	3070		0.353982	0.103197055
0.0365656	DYNLT3	3027	T-COMPLEX ASSOCIATED-TESTIS-EXPRESSED 1-LIKE (PROTEIN 91/23). [SWISSPROT;Acc:P51808]	0.307503	0.11891136
0.0365698	C14orf122	766	PROTEIN C14ORF122 (CGI-112). [SWISSPROT;Acc:Q9Y3B6]	0.138711	0.26364023
0.0366052	PERLD1	970	CAB2. [RefSeq;Acc:NM_033419]	0.143236	0.255558658
0.0366237	SCAMP2	2655	SECRETORY CARRIER-ASSOCIATED MEMBRANE PROTEIN 2. [SWISSPROT;Acc:O15127]	0.174446	0.209942905
0.0366305	TXNDC1	2346	THIOREDOXIN DOMAIN CONTAINING; THIOREDOXIN-RELATED TRANSMEMBRANE PROTEIN; THIOREDOXIN DOMAIN-CONTAINING. [RefSeq;Acc:NM_030755]	0.166118	0.220508915
0.0366317	AURKA	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]	0.148106	0.247334342
	CYLD	1256	"CYLINDROMATOSIS (TURBAN TUMOR SYNDROME); CYLINDROMATOSIS 1, TURBAN TUMOR SYNDROME. [RefSeq;Acc:NM_015247]"
0.0366899	STT3B	2998	SOURCE OF IMMUNODOMINANT MHC-ASSOCIATED PEPTIDES; HOMOLOG OF YEAST STT3 GENE. [RefSeq;Acc:NM_178862]	0.271591	0.135092474
0.036734	PTPRB	2833	PROTEIN-TYROSINE PHOSPHATASE BETA PRECURSOR (EC 3.1.3.48) (R-PTP- BETA). [SWISSPROT;Acc:P23467]	0.190263	0.193069593
0.0367538	no value	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"	0.139602	0.263275598
0.0368025	DPP9	2887	DIPEPTIDYLPEPTIDASE 9; DIPEPTIDYL PEPTIDASE 9; DIPEPTIDYL PEPTIDASE IV-RELATED PROTEIN-2. [RefSeq;Acc:NM_139159]	0.204515	0.179950126
0.0368198	TLX2	870	T-CELL LEUKEMIA HOMEOBOX PROTEIN 2 (HOMEOBOX PROTEIN HOX-11L1) (NEURAL CREST HOMEOBOX PROTEIN). [SWISSPROT;Acc:O43763]	0.14147	0.260265781
0.036822	no value	1495	IMPORTIN 7; RAN-BINDING PROTEIN 7. [RefSeq;Acc:NM_006391]	0.15167	0.242777082
	ARFGEF2	1496	BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 2 (BREFELDIN A-INHIBITED GEP 2). [SWISSPROT;Acc:Q9Y6D5]
0.0368814	no value	554	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN 2 (FOVEA-ASSOCIATED SH3 DOMAIN BINDING PROTEIN). [SWISSPROT;Acc:Q9UJC5]	0.136094	0.270999456
0.0368889	CSDE1	1036	UNR PROTEIN. [SWISSPROT;Acc:O75534]	0.145611	0.25333869
0.0369154	MTR	1107	"5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (EC 2.1.1.13) (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT) (MS). [SWISSPROT;Acc:Q99707]"	0.147123	0.250915221
0.0369504	GPATCH1	788	EVOLUTIONARILY CONSERVED G-PATCH DOMAIN CONTAINING. [RefSeq;Acc:NM_018025]	0.140933	0.262184158
0.0370125	MSI2	164	MUSASHI 2 ISOFORM A. [RefSeq;Acc:NM_138962]	0.107534	0.344193464
0.0370257	TSR2	396		0.132897	0.278604483
0.0370628	SIN3B	2027		0.160934	0.230298135
0.0370737	ZFAND1	1081		0.147075	0.252073432
0.0370824	GALNTL1	564	SIMILAR TO EXPRESSED SEQUENCE AI415388 (FRAGMENT). [SPTREMBL;Acc:Q8N428]	0.136931	0.270810846
0.0371202	ZMYND8	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]	0.141681	0.261998433
0.0371369	no value	2872		0.196598	0.188897649
0.0371738	SH3BGRL	556	SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [SWISSPROT;Acc:O75368]	0.137173	0.270999395
0.0372023	no value	2862	CGI-142; HEPATOMA-DERIVED GROWTH FACTOR 2. [RefSeq;Acc:NM_016073]	0.196899	0.188941031
	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	1666	44050 PROTEIN. [RefSeq;Acc:NM_178832]	0.156155	0.238801191
0.0373117	no value	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]	0.130845	0.28515954
0.0373336	JUP	1074	JUNCTION PLAKOGLOBIN (DESMOPLAKIN III). [SWISSPROT;Acc:P14923]	0.147992	0.25226769
0.0373888	PMP2	288	MYELIN P2 PROTEIN. [SWISSPROT;Acc:P02689]	0.123882	0.301809787
0.0374306	TLX1	873	T-CELL LEUKEMIA HOMEOBOX PROTEIN 1 (HOMEOBOX PROTEIN HOX-11) (TCL-3 PROTO-ONCOGENE). [SWISSPROT;Acc:P31314]	0.143817	0.260265476
0.0374428	CTNNAL1	2875	"CATENIN (CADHERIN-ASSOCIATED PROTEIN), ALPHA-LIKE 1; ALPHA-CATULIN. [RefSeq;Acc:NM_003798]"	0.198705	0.188434111

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