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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Gene Rank description measured expected final Hugo

Results: HTML CSV LaTeX

Showing element 1652 to 1701 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1652	AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [Source:RefSeq;Acc:NM_052853]	0.0340138	0.142333	0.238973393	ADCK2	
1653	AARF DOMAIN CONTAINING KINASE 4. [Source:RefSeq;Acc:NM_024876]	0.0274831	0.115005	0.238973088	ADCK4	
1654	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 13 (26S PROTEASOME REGULATORY SUBUNIT S11) (26S PROTEASOME REGULATORY SUBUNIT P40.5). [Source:SWISSPROT;Acc:Q9UNM6]	0.75685	3.16764	0.238931823	PSMD13	
1655	APURINIC/APYRIMIDINIC ENDONUCLEASE 2; APURINIC/APYRIMIDINIC ENDONUCLEASE-LIKE 2; APEX NUCLEASE-LIKE 2. [Source:RefSeq;Acc:NM_014481]	0.0730689	0.305877	0.238883277	APEX2	
1656	COPPER-TRANSPORTING ATPASE 1 (EC 3.6.3.4) (COPPER PUMP 1) (MENKES DISEASE-ASSOCIATED PROTEIN). [Source:SWISSPROT;Acc:Q04656]	0.0806616	0.337708	0.238850131	ATP7A	
1657	CYCLIN M2; ANCIENT CONSERVED DOMAIN PROTEIN 2. [Source:RefSeq;Acc:NM_017649]	0.317455	1.3291	0.238849597	CNNM2	
1658	TRIPARTITE MOTIF PROTEIN 3 (RING FINGER PROTEIN 22) (BRAIN-EXPRESSED RING FINGER PROTEIN). [Source:SWISSPROT;Acc:O75382]	0.271838	1.13816	0.238839882	TRIM3	
1659	TCD37 HOMOLOG; PRUNE. [Source:RefSeq;Acc:NM_021222]	0.118202	0.494902	0.238839205	PRUNE	
1660	CYCLIN M4; ANCIENT CONSERVED DOMAIN PROTEIN 4. [Source:RefSeq;Acc:NM_020184]	0.285611	1.19583	0.238839133	CNNM4	
1661	COPPER-TRANSPORTING ATPASE 2 (EC 3.6.3.4) (COPPER PUMP 2) (WILSON DISEASE-ASSOCIATED PROTEIN). [Source:SWISSPROT;Acc:P35670]	0.0958705	0.401402	0.238839119	ATP7B	
1662		0.0879782	0.368359	0.238838199	PRUNE2	
1663	CYCLIN M1; ANCIENT CONSERVED DOMAIN PROTEIN 1. [Source:RefSeq;Acc:NM_020348]	0.264548	1.10767	0.238832865	CNNM1	
1664	CYCLIN M3; ANCIENT CONSERVED DOMAIN PROTEIN 3. [Source:RefSeq;Acc:NM_017623]	0.258494	1.08234	0.238828834	CNNM3	
1665	"NUCLEAR INHIBITOR OF PROTEIN PHOSPHATASE-1 (NIPP-1) (PROTEIN PHOSPHATASE 1, REGULATORY INHIBITOR SUBUNIT 8) [INCLUDES: ACTIVATOR OF RNA DECAY (EC 3.1.4.-) (ARD-1)]. [Source:SWISSPROT;Acc:Q12972]"	0.179673	0.752395	0.238801427	PPP1R8	
1666	44050 PROTEIN. [Source:RefSeq;Acc:NM_178832]	0.03729	0.156155	0.238801191	C10orf83	
1667	PROTEASOME SUBUNIT ALPHA TYPE 3 (EC 3.4.25.1) (PROTEASOME COMPONENT C8) (MACROPAIN SUBUNIT C8) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C8). [Source:SWISSPROT;Acc:P25788]	0.956289	4.005	0.238773783	PSMA3	
1668	MESODERM INDUCTION EARLY RESPONSE 1. [Source:RefSeq;Acc:NM_020948]	0.0415385	0.173966	0.238773668		
1669		0.0415385	0.173966	0.238773668	DEPDC5	
1670		0.0336981	0.14113	0.238773471	MIER3	
1671		0.0335839	0.140652	0.238773	MIER2	
1672	"SPLICING FACTOR, PROLINE-AND GLUTAMINE-RICH (POLYPYRIMIDINE TRACT- BINDING PROTEIN-ASSOCIATED SPLICING FACTOR) (PTB-ASSOCIATED SPLICING FACTOR) (PSF) (DNA-BINDING P52/P100 COMPLEX, 100 KDA SUBUNIT). [Source:SWISSPROT;Acc:P23246]"	0.263446	1.10501	0.238410512	SFPQ	
1673		0.847098	3.55339	0.238391508	IMP3	
1674	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10 (26S PROTEASOME REGULATORY SUBUNIT P28) (GANKYRIN). [Source:SWISSPROT;Acc:O75832]	0.41158	1.7269	0.238334588	PSMD10	
1675	PARASPECKLE PROTEIN 1. [Source:RefSeq;Acc:NM_018282]	0.203402	0.853581	0.238292558	PSPC1	
1676	"54 KDA NUCLEAR RNA- AND DNA-BINDING PROTEIN (P54(NRB)) (P54NRB) (55 KDA NUCLEAR PROTEIN) (NMT55) (NON-POU DOMAIN-CONTAINING OCTAMER- BINDING PROTEIN) (DNA-BINDING P52/P100 COMPLEX, 52 KDA SUBUNIT). [Source:SWISSPROT;Acc:Q15233]"	0.201833	0.847008	0.238289367	NONO	
1677		0.461707	1.93809	0.238227843	KCTD17	
1678		0.581959	2.44287	0.238227577	KCTD5	
1679		0.48192	2.02294	0.23822753	KCTD2	
1680	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 12 (26S PROTEASOME REGULATORY SUBUNIT P55). [Source:SWISSPROT;Acc:O00232]	0.563839	2.36701	0.238207274		
1681	DELTA 1-PYRROLINE-5-CARBOXYLATE SYNTHETASE (P5CS) [INCLUDES: GLUTAMATE 5-KINASE (EC 2.7.2.11) (GAMMA-GLUTAMYL KINASE) (GK); GAMMA-GLUTAMYL PHOSPHATE REDUCTASE (GPR) (EC 1.2.1.41) (GLUTAMATE-5-SEMIALDEHYDE DEHYDROGENASE) (GLUTAMYL-GAMMA-SEMIALDEHYDE DEHYDR	0.0224883	0.0944225	0.238166751	ALDH18A1	
1682	NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [Source:RefSeq;Acc:NM_178177]	0.192536	0.808409	0.238166572	NMNAT3	
1683	NUCLEOLAR PROTEIN NOP5 (NUCLEOLAR PROTEIN 5) (NOP58) (HSPC120). [Source:SWISSPROT;Acc:Q9Y2X3]	0.160247	0.672842	0.238164383		
1684	60S RIBOSOMAL PROTEIN L37 (G1.16). [Source:SWISSPROT;Acc:P02403]	0.0238444	0.100146	0.238096379	RPL37	
1685	"SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [Source:SWISSPROT;Acc:Q07955]"	0.0238444	0.100146	0.238096379	SFRS1	
1686	SORTING NEXIN 17. [Source:SWISSPROT;Acc:Q15036]	0.0476887	0.200292	0.23809588	SNX17	
1687	AMIDOPHOSPHORIBOSYLTRANSFERASE PRECURSOR (EC 2.4.2.14) (GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE) (ATASE) (GPAT). [Source:SWISSPROT;Acc:Q06203]	0.214575	0.901215	0.238095238	PPAT	
1688	SERINE/THREONINE-PROTEIN KINASE NEK3 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 3) (HSPK 36). [Source:SWISSPROT;Acc:P51956]	0.0267969	0.112547	0.238095196	NEK3	
1689	"GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, LIVER (EC 1.2.1.12) (GAPDH). [Source:SWISSPROT;Acc:P04406]"	0.414602	1.74133	0.238095019	GAPDH	
1690	SERINE/THREONINE-PROTEIN KINASE NEK1 (EC 2.7.1.37) (NIMA-RELATED PROTEIN KINASE 1) (NY-REN-55 ANTIGEN). [Source:SWISSPROT;Acc:Q96PY6]	0.035086	0.147362	0.238093946	NEK1	
1691	PUTATIVE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE (EC 2.7.1.23) (POLY(P)/ATP NAD KINASE). [Source:SWISSPROT;Acc:O95544]	0.195442	0.821038	0.238042575	NADK	
1692	"ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [Source:SWISSPROT;Acc:P05141]"	0.032514	0.136688	0.237870186	SLC25A5	
1693	"ADP,ATP CARRIER PROTEIN, HEART/SKELETAL MUSCLE ISOFORM T1 (ADP/ATP TRANSLOCASE 1) (ADENINE NUCLEOTIDE TRANSLOCATOR 1) (ANT 1). [Source:SWISSPROT;Acc:P12235]"	0.032514	0.136688	0.237870186	SLC25A4	
1694	DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [Source:SWISSPROT;Acc:Q13561]	0.375423	1.57827	0.237869946	DCTN2	
1695		0.0256535	0.107847	0.237869389	SLC25A31	
1696	"ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [Source:SWISSPROT;Acc:P12236]"	0.0311972	0.131153	0.237868749	SLC25A6	
1697	ASPARAGINE SYNTHETASE [GLUTAMINE-HYDROLYZING] (EC 6.3.5.4) (GLUTAMINE- DEPENDENT ASPARAGINE SYNTHETASE) (TS11 CELL CYCLE CONTROL PROTEIN). [Source:SWISSPROT;Acc:P08243]	0.0326245	0.137154	0.237867652	ASNS	
1698	"VACUOLAR ATP SYNTHASE CATALYTIC SUBUNIT A, UBIQUITOUS ISOFORM (EC 3.6.3.14) (V-ATPASE A SUBUNIT 1) (VACUOLAR PROTON PUMP ALPHA SUBUNIT 1) (V-ATPASE 69 KDA SUBUNIT 1) (ISOFORM VA68). [Source:SWISSPROT;Acc:P38606]"	0.712561	2.99562	0.23786762	ATP6V1A	
1699	HCV NS3-TRANSACTIVATED PROTEIN 1. [Source:RefSeq;Acc:NM_019048]	0.0338955	0.142498	0.237866496	ASNSD1	
1700		0.044904	0.188793	0.237847802		
1701	NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [Source:RefSeq;Acc:NM_016231]	0.210207	0.883788	0.237847764	NLK	

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/