Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 1751 to 1800 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
1751	VACUOLAR ATP SYNTHASE SUBUNIT G 2 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 2) (VACUOLAR PROTON PUMP G SUBUNIT 2) (V-ATPASE 13 KDA SUBUNIT 2). [Source:SWISSPROT;Acc:O95670]	0.0861167	0.363797	0.236716356		
1752	SECRETORY PATHWAY COMPONENT SEC31B-1. [Source:RefSeq;Acc:NM_015490]	0.107954	0.456048	0.236716311	SEC31B	
1753	SEC13-RELATED PROTEIN. [Source:SWISSPROT;Acc:P55735]	0.126518	0.534471	0.236716305	SEC13	
1754	VACUOLAR ATP SYNTHASE SUBUNIT G 3 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 3) (VACUOLAR PROTON PUMP G SUBUNIT 3) (V-ATPASE 13 KDA SUBUNIT 3). [Source:SWISSPROT;Acc:Q96LB4]	0.0486762	0.205631	0.236716254	ATP6V1G3	
1755	APOPTOSIS INHIBITOR 5; FIBROBLAST GROWTH FACTOR 2-INTERACTING FACTOR 2; API5-LIKE 1. [Source:RefSeq;Acc:NM_006595]	0.0646874	0.27327	0.236716068	API5	
1756	VACUOLAR ATP SYNTHASE SUBUNIT G 1 (EC 3.6.3.14) (V-ATPASE G SUBUNIT 1) (VACUOLAR PROTON PUMP G SUBUNIT 1) (V-ATPASE 13 KDA SUBUNIT 1) (VACUOLAR ATP SYNTHASE SUBUNIT M16). [Source:SWISSPROT;Acc:O75348]	0.063055	0.266374	0.236716046	ATP6V1G1	
1757		0.420128	1.77482	0.236715836	ATP6V1E2	
1758	"DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 39 ISOFORM 1; NUCLEAR RNA HELICASE, DECD VARIANT OF DEAD BOX FAMILY. [Source:RefSeq;Acc:NM_005804]"	0.0299559	0.126548	0.236715713	DDX39	
1759	"VACUOLAR ATP SYNTHASE SUBUNIT B, KIDNEY ISOFORM (EC 3.6.3.14) (V- ATPASE B1 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 1) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT). [Source:SWISSPROT;Acc:P15313]"	0.299765	1.26636	0.236713889	ATP6V1B1	
1760	VACUOLAR ATP SYNTHASE SUBUNIT F (EC 3.6.3.14) (V-ATPASE F SUBUNIT) (VACUOLAR PROTON PUMP F SUBUNIT) (V-ATPASE 14 KDA SUBUNIT). [Source:SWISSPROT;Acc:Q16864]	0.424679	1.79432	0.236679634	ATP6V1F	
1761	O-SIALOGLYCOPROTEIN ENDOPEPTIDASE. [Source:RefSeq;Acc:NM_017807]	0.346601	1.46589	0.236444072	OSGEP	
1762	RUVB-LIKE 2 (EC 3.6.1.-) (48-KDA TATA BOX-BINDING PROTEIN-INTERACTING PROTEIN) (48-KDA TBP-INTERACTING PROTEIN) (TIP49B) (REPRESSING PONTIN 52) (REPTIN 52) (51 KDA ERYTHROCYTE CYTOSOLIC PROTEIN) (ECP-51) (TIP60-ASSOCIATED PROTEIN 54-BETA) (TAP54-BETA) (CG	0.245894	1.04017	0.236397896	RUVBL2	
1763	"ATPASE, H+ TRANSPORTING, LYSOSOMAL 38KDA, V0 SUBUNIT D ISOFORM 2. [Source:RefSeq;Acc:NM_152565]"	0.33278	1.40872	0.236228633	ATP6V0D2	
1764		0.0607427	0.257167	0.236199435		
1765	GLUTATHIONE S-TRANSFERASE P (EC 2.5.1.18) (GST CLASS-PI) (GSTP1-1). [Source:SWISSPROT;Acc:P09211]	0.208499	0.882968	0.236134265	GSTP1	
1766	"DJ850E9.1 (NOVEL C2H2 TYPE ZINC FINGER PROTEIN SIMILAR TO DROSOPHILA SCRATCH (SCRT), SLUG AND XENOPUS SNAIL) (FRAGMENT). [Source:SPTREMBL;Acc:Q9NQ03]"	0.281698	1.1936	0.236007038		
1767	THYROID RECEPTOR INTERACTING PROTEIN 12 (TRIP12). [Source:SWISSPROT;Acc:Q14669]	0.0325717	0.138013	0.236004579	TRIP12	
1768	"DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.61) (E2) (E2K). [Source:SWISSPROT;Acc:P36957]"	0.660595	2.79908	0.23600433	DLSTP	
1769	PEROXISOMAL MEMBRANE PROTEIN 2 (22 KDA PEROXISOMAL MEMBRANE PROTEIN). [Source:SWISSPROT;Acc:Q9NR77]	0.0420153	0.178036	0.235993282	PXMP2	
1770	HEAT SHOCK-RELATED 70 KDA PROTEIN 2 (HEAT SHOCK 70 KDA PROTEIN 2). [Source:SWISSPROT;Acc:P54652]	0.0660691	0.279962	0.235993099	HSPA2	
1771	HEAT SHOCK COGNATE 71 KDA PROTEIN. [Source:SWISSPROT;Acc:P11142]	0.126046	0.534109	0.235993028	HSPA8	
1772	HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [Source:SWISSPROT;Acc:P08107]	0.0654179	0.277203	0.235992756		
1773	"RIBOSOMAL PROTEIN P0-LIKE PROTEIN; 60S ACIDIC RIBOSOMAL PROTEIN PO; RIBOSOMAL PROTEIN, LARGE, P0-LIKE. [Source:RefSeq;Acc:NM_016183]"	0.797221	3.37861	0.235961238	MRTO4	
1774	"DIHYDROLIPOAMIDE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.8.1.4) (GLYCINE CLEAVAGE SYSTEM L PROTEIN). [Source:SWISSPROT;Acc:P09622]"	0.596138	2.52689	0.23591767	DLD	
1775	SCRATCH; SCRATCH 1. [Source:RefSeq;Acc:NM_031309]	0.322861	1.36866	0.235895694		
1776		0.103336	0.438523	0.235645565	WDR70	
1777	CDA11 PROTEIN. [Source:RefSeq;Acc:NM_032026]	0.378654	1.60733	0.235579501	TATDN1	
1778	ARGININOSUCCINATE SYNTHASE (EC 6.3.4.5) (CITRULLINE--ASPARTATE LIGASE). [Source:SWISSPROT;Acc:P00966]	0.161564	0.685844	0.235569605	ASS1	
1779	RETINOL DEHYDROGENASE 8 (ALL-TRANS); PHOTORECEPTOR OUTER SEGMENT ALL-TRANS RETINOL DEHYDROGENASE. [Source:RefSeq;Acc:NM_015725]	0.0319409	0.135713	0.23535623	RDH8	
1780	ADENINE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.7) (APRT). [Source:SWISSPROT;Acc:P07741]	0.273997	1.16418	0.235356216		
1781	ESTRADIOL 17 BETA-DEHYDROGENASE 1 (EC 1.1.1.62) (17-BETA-HSD 1) (PLACENTAL 17-BETA-HYDROXYSTEROID DEHYDROGENASE) (20 ALPHA- HYDROXYSTEROID DEHYDROGENASE) (20-ALPHA-HSD) (E2DH). [Source:SWISSPROT;Acc:P14061]	0.0258082	0.109656	0.235356022	HSD17B1	
1782	17 BETA-HYDROXYSTEROID DEHYDROGENASE. [Source:SPTREMBL;Acc:Q13034]	0.024834	0.105517	0.23535544		
1783	PUTATIVE SIALOGLYCOPROTEASE TYPE 2. [Source:RefSeq;Acc:NM_022353]	0.365106	1.55176	0.235285096	OSGEPL1	
1784	"C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC (C1-THF SYNTHASE) [INCLUDES: METHYLENETETRAHYDROFOLATE DEHYDROGENASE (EC 1.5.1.5); METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE (EC 3.5.4.9); FORMYLTETRAHYDROFOLATE SYNTHETASE (EC 6.3.4.3)]. [Source:SWISSPROT;Acc:P115"	0.156153	0.663781	0.23524777	MTHFD1	
1785	S-ADENOSYLMETHIONINE SYNTHETASE GAMMA FORM (EC 2.5.1.6) (METHIONINE ADENOSYLTRANSFERASE) (ADOMET SYNTHETASE) (MAT-II). [Source:SWISSPROT;Acc:P31153]	0.51691	2.19829	0.23514186	MAT2A	
1786	"ARGINASE II, MITOCHONDRIAL PRECURSOR (EC 3.5.3.1) (NON-HEPATIC ARGINASE) (KIDNEY-TYPE ARGINASE). [Source:SWISSPROT;Acc:P78540]"	0.18522	0.787708	0.235137894	ARG2	
1787	PREFOLDIN SUBUNIT 3 (VON HIPPEL-LINDAU BINDING PROTEIN 1) (VHL BINDING PROTEIN-1) (VBP-1) (HIBBJ46). [Source:SWISSPROT;Acc:Q15765]	0.0305539	0.129981	0.235064356	VBP1	
1788	UXT PROTEIN (UBIQUITOUSLY EXPRESSED TRANSCRIPT PROTEIN) (HSPC024). [Source:SWISSPROT;Acc:Q9UBK9]	0.0305539	0.129981	0.235064356	UXT	
1789	PREFOLDIN SUBUNIT 2 (HSPC231). [Source:SWISSPROT;Acc:Q9UHV9]	0.15115	0.643016	0.235064135	PFDN2	
1790	ARGINASE 1 (EC 3.5.3.1) (LIVER-TYPE ARGINASE). [Source:SWISSPROT;Acc:P05089]	0.222245	0.945747	0.234994137	ARG1	
1791	DNA-DIRECTED RNA POLYMERASES III 12.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RNA POLYMERASE III C11 SUBUNIT) (HSC11P) (HRPC11) (MY010 PROTEIN). [Source:SWISSPROT;Acc:Q9Y2Y1]	0.163024	0.693873	0.234947894	POLR3K	
1792	DIMERIC DIHYDRODIOL DEHYDROGENASE; 3-DEOXYGLUCOSONE REDUCTASE. [Source:RefSeq;Acc:NM_014475]	0.0986496	0.419992	0.234884474	DHDH	
1793	"HEXAPRENYLDIHYDROXYBENZOATE METHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.1.114) (DIHYDROXYHEXAPRENYLBENZOATE METHYLTRANSFERASE) (3,4- DIHYDROXY-5-HEXAPRENYLBENZOATE METHYLTRANSFERASE) (DHHB METHYLTRANSFERASE) (DHHB-MT) (DHHB-MTASE). [Source:SWISSPRO"	0.0303966	0.129436	0.234838839	COQ3	
1794	GUANINE DEAMINASE (EC 3.5.4.3) (GUANASE) (GUANINE AMINASE) (GUANINE AMINOHYDROLASE) (GAH) (P51-NEDASIN). [Source:SWISSPROT;Acc:Q9Y2T3]	0.234676	0.999309	0.234838273	GDA	
1795	"ATP SYNTHASE COUPLING FACTOR B, MITOCHONDRIAL PRECURSOR. [Source:SWISSPROT;Acc:Q99766]"	0.0303657	0.129305	0.234837787	ATP5S	
1796	PROGRAMMED CELL DEATH PROTEIN 5 (TFAR19 PROTEIN) (TF-1 CELL APOPTOSIS RELATED GENE-19 PROTEIN). [Source:SWISSPROT;Acc:O14737]	0.218499	0.930463	0.234828252	PDCD5	
1797	DNA TOPOISOMERASE III ALPHA (EC 5.99.1.2). [Source:SWISSPROT;Acc:Q13472]	0.09162	0.390211	0.234796046	TOP3A	
1798	"FOLYLPOLYGLUTAMATE SYNTHASE, MITOCHONDRIAL PRECURSOR (EC 6.3.2.17) (FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE) (FPGS). [Source:SWISSPROT;Acc:Q05932]"	0.107427	0.457652	0.234735126	FPGS	
1799		0.0461397	0.196587	0.234703719	FAM57B	
1800		0.0580492	0.247338	0.234695841		

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/