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 2152 to 2201 of 3206 in total

Rank	description	measured	expected	final	Hugo	
2152	PP1201 PROTEIN. [Source:RefSeq;Acc:NM_022152]	0.0628846	0.276631	0.22732304	TMBIM1	
2153	STEROL REGULATORY ELEMENT BINDING PROTEIN-1 (SREBP-1) (STEROL REGULATORY ELEMENT-BINDING TRANSCRIPTION FACTOR 1). [Source:SWISSPROT;Acc:P36956]	0.0687827	0.302577	0.227322962	SREBF1	
2154	Z-PROTEIN (PROTEIN CGI-119) (S1R PROTEIN). [Source:SWISSPROT;Acc:Q9HC24]	0.0343914	0.151289	0.227322542	TMBIM4	
2155	LEUCYL-TRNA SYNTHETASE. [Source:RefSeq;Acc:NM_020117]	0.159792	0.703125	0.227259733	LARS	
2156	"PROBABLE LEUCYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.4) (LEUCINE--TRNA LIGASE) (LEURS). [Source:SWISSPROT;Acc:Q15031]"	0.159922	0.7037	0.227258775	LARS2	
2157		0.0141571	0.0622988	0.227245148	BPIL2	
2158	MICROSOMAL SIGNAL PEPTIDASE 25 KDA SUBUNIT (EC 3.4.-.-) (SPASE 25 KDA SUBUNIT) (SPC25). [Source:SWISSPROT;Acc:Q15005]	0.0254509	0.111998	0.227244237	SPCS2	
2159	BACTERICIDAL PERMEABILITY-INCREASING PROTEIN PRECURSOR (BPI) (CAP 57). [Source:SWISSPROT;Acc:P17213]	0.0196608	0.0865184	0.227244147	BPI	
2160	LIPOPOLYSACCHARIDE-BINDING PROTEIN PRECURSOR (LBP). [Source:SWISSPROT;Acc:P18428]	0.0157159	0.0691587	0.227244005	LBP	
2161	URIDINE 5'-MONOPHOSPHATE SYNTHASE (UMP SYNTHASE) [INCLUDES: OROTATE PHOSPHORIBOSYLTRANSFERASE (EC 2.4.2.10) (OPRTASE); OROTIDINE 5'- PHOSPHATE DECARBOXYLASE (EC 4.1.1.23) (OMPDECASE)]. [Source:SWISSPROT;Acc:P11172]	0.485259	2.13541	0.227243948	UMPS	
2162	CLEFT LIP AND PALATE ASSOCIATED TRANSMEMBRANE PROTEIN 1. [Source:RefSeq;Acc:NM_001294]	0.0206788	0.0909983	0.227243806	CLPTM1	
2163	PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [Source:SWISSPROT;Acc:P55058]	0.0139025	0.0611788	0.227243751	PLTP	
2164	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 2 (26S PROTEASOME REGULATORY SUBUNIT S2) (26S PROTEASOME SUBUNIT P97) (TUMOR NECROSIS FACTOR TYPE 1 RECEPTOR ASSOCIATED PROTEIN 2) (55.11 PROTEIN). [Source:SWISSPROT;Acc:Q13200]	0.399289	1.75758	0.227181124	PSMD2	
2165		0.299286	1.31793	0.227087933		
2166	60S RIBOSOMAL PROTEIN L7. [Source:SWISSPROT;Acc:P18124]	0.30758	1.35464	0.227056635		
2167	SERINE PALMITOYLTRANSFERASE 1 (EC 2.3.1.50) (LONG CHAIN BASE BIOSYNTHESIS PROTEIN 1) (LCB 1) (SERINE-PALMITOYL-COA TRANSFERASE 1) (SPT 1) (SPT1). [Source:SWISSPROT;Acc:O15269]	0.0595157	0.262124	0.227051701	SPTLC1	
2168	GLYCOGENIN-2 (EC 2.4.1.186) (GN-2) (GN2). [Source:SWISSPROT;Acc:O15488]	0.0525739	0.231578	0.227024588	GYG2	
2169	GLYCOGENIN-1 (EC 2.4.1.186). [Source:SWISSPROT;Acc:P46976]	0.0648248	0.285541	0.22702449	GYG1	
2170	PROTEIN X 0001. [Source:RefSeq;Acc:NM_016302]	0.0586994	0.25856	0.227024288	CRBN	
2171	ADENOSINE KINASE (EC 2.7.1.20) (AK) (ADENOSINE 5'-PHOSPHOTRANSFERASE). [Source:SWISSPROT;Acc:P55263]	0.156968	0.691417	0.227023634	ADK	
2172	"ORNITHINE CARBAMOYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.3.3) (OTCASE) (ORNITHINE TRANSCARBAMYLASE). [Source:SWISSPROT;Acc:P00480]"	0.235631	1.0381	0.22698295	OTC	
2173	NUCLEAR PORE COMPLEX PROTEIN NUP98 (NUCLEOPORIN NUP98) (98 KDA NUCLEOPORIN). [Source:SWISSPROT;Acc:P52948]	0.245551	1.08201	0.226939677	NUP98	
2174	SCY1-LIKE 1; TELOMERASE REGULATION-ASSOCIATED PROTEIN; HT019 PROTEIN; TELOMERASE REGULATION-ASSOCIATED PROTEIN; N-TERMINAL KINASE-LIKE PROTEIN; TERATOMA-ASSOCIATED TYROSINE KINASE; N-TERMINAL KINASE-LIKE. [Source:RefSeq;Acc:NM_020680]	0.0350787	0.154573	0.226939375	SCYL1	
2175	TATA ELEMENT MODULATORY FACTOR (TMF). [Source:SWISSPROT;Acc:P82094]	0.0350787	0.154573	0.226939375	TMF1	
2176	MRNA-ASSOCIATED PROTEIN MRNP 41 (RAE1 PROTEIN HOMOLOG). [Source:SWISSPROT;Acc:P78406]	0.0350787	0.154573	0.226939375	RAE1	
2177	AMMECR1 PROTEIN. [Source:RefSeq;Acc:NM_015365]	0.0350787	0.154573	0.226939375	AMMECR1	
2178	ADENYLOSUCCINATE SYNTHASE-LIKE 1. [Source:RefSeq;Acc:NM_152328]	0.385887	1.7008	0.226885583	ADSSL1	
2179	ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) (IMP--ASPARTATE LIGASE) (ADSS) (AMPSASE). [Source:SWISSPROT;Acc:P30520]	0.334139	1.47327	0.226800926	ADSS	
2180	"GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL PRECURSOR. [Source:SWISSPROT;Acc:P23434]"	0.207889	0.916816	0.22675106		
2181	RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 6 (PAK-INTERACTING EXCHANGE FACTOR ALPHA) (ALPHA-PIX) (COOL-2). [Source:SWISSPROT;Acc:Q15052]	0.257131	1.13453	0.226640988	ARHGEF6	
2182	SERINE/THREONINE-PROTEIN KINASE PAK 2 (EC 2.7.1.-) (P21-ACTIVATED KINASE 2) (PAK-2) (PAK65) (GAMMA-PAK) (S6/H4 KINASE). [Source:SWISSPROT;Acc:Q13177]	0.0463914	0.204773	0.226550375	PAK2	
2183	SERINE/THREONINE-PROTEIN KINASE PAK 3 (EC 2.7.1.-) (P21-ACTIVATED KINASE 3) (PAK-3) (BETA-PAK) (OLIGOPHRENIN-3). [Source:SWISSPROT;Acc:O75914]	0.048732	0.215105	0.226549825	PAK3	
2184	SERINE/THREONINE-PROTEIN KINASE PAK 1 (EC 2.7.1.-) (P21-ACTIVATED KINASE 1) (PAK-1) (P65-PAK) (ALPHA-PAK). [Source:SWISSPROT;Acc:Q13153]	0.0568471	0.250928	0.226547456	PAK1	
2185	CONSERVED OLIGOMERIC GOLGI COMPLEX SUBUNIT 5 (13S GOLGI TRANSPORT COMPLEX 90 KDA SUBUNIT) (GTC-90) (GOLGI TRANSPORT COMPLEX 1). [Source:SWISSPROT;Acc:Q9UP83]	0.0568471	0.250928	0.226547456	COG5	
2186	RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [Source:SWISSPROT;Acc:Q14155]	0.214133	0.945656	0.226438578	ARHGEF7	
2187	U3 SNORNP PROTEIN 4 HOMOLOG. [Source:RefSeq;Acc:NM_033416]	0.225682	0.996773	0.226412634	IMP4	
2188		0.19122	0.84475	0.226362829	C12orf65	
2189	DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN PROTEIN A) (SINGLE-STRAND DNA BINDING PROTEIN NF-GMB). [Source:SWISSPROT;Acc:P16989]	0.0613805	0.271164	0.226359325	CSDA	
2190	NUCLEASE SENSITIVE ELEMENT BINDING PROTEIN 1 (Y BOX BINDING PROTEIN-1) (Y-BOX TRANSCRIPTION FACTOR) (YB-1) (CCAAT-BINDING TRANSCRIPTION FACTOR I SUBUNIT A) (CBF-A) (ENHANCER FACTOR I SUBUNIT A) (EFI-A) (DNA-BINDING PROTEIN B) (DBPB). [Source:SWISSPROT;Acc	0.0752905	0.332615	0.226359304	YBX1	
2191	GERM CELL SPECIFIC Y-BOX BINDING PROTEIN; CONTRIN. [Source:RefSeq;Acc:NM_015982]	0.0582372	0.257278	0.226359036	YBX2	
2192	MEVALONATE KINASE (EC 2.7.1.36) (MK). [Source:SWISSPROT;Acc:Q03426]	0.562681	2.48806	0.226152504	MVK	
2193	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE (EC 4.2.99.18) (AP ENDONUCLEASE 1) (APEX NUCLEASE) (APEN) (REF-1 PROTEIN). [Source:SWISSPROT;Acc:P27695]	0.0811054	0.358823	0.226031776	APEX1	
2194	"DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL PRECURSOR (EC 2.3.1.12) (E2) (PDC-E2) (70 KDA MITOCHONDRIAL AUTOANTIGEN OF PRIMARY BILIARY CIRRHOSIS) (PBC) (M2 ANTIGEN COMPLEX 70 KDA SUBUNIT). [Source:SWISSPRO"	0.607431	2.68753	0.226018314	DLAT	
2195	"AXONEMAL DYNEIN LIGHT INTERMEDIATE POLYPEPTIDE 1 (INNER DYNEIN ARM LIGHT CHAIN, AXONEMAL) (HP28). [Source:SWISSPROT;Acc:O14645]"	0.124723	0.551845	0.226010927	DNALI1	
2196	TUMOR SUPPRESSOR P53-BINDING PROTEIN 2 (P53-BINDING PROTEIN 2) (53BP2) (BCL2-BINDING PROTEIN) (BBP). [Source:SWISSPROT;Acc:Q13625]	0.097609	0.431998	0.225947805	TP53BP2	
2197	"PROTEIN PHOSPHATASE 1, REGULATORY (INHIBITOR) SUBUNIT 13B; APOPTOSIS-STIMULATING PROTEIN OF P53, 1. [Source:RefSeq;Acc:NM_015316]"	0.0795635	0.352238	0.225879945	PPP1R13B	
2198	"60S RIBOSOMAL PROTEIN L11, MITOCHONDRIAL PRECURSOR (L11MT) (CGI-113). [Source:SWISSPROT;Acc:Q9Y3B7]"	0.568484	2.51757	0.225806631	MRPL11	
2199	CYTOCHROME B5 REDUCTASE B5R.2. [Source:RefSeq;Acc:NM_016229]	0.112427	0.497956	0.225776976	CYB5R2	
2200	CYTOCHROME B5 REDUCTASE 1 (B5R.1). [Source:RefSeq;Acc:NM_016243]	0.11223	0.497084	0.22577673	CYB5R1	
2201	NADH-CYTOCHROME B5 REDUCTASE (EC 1.6.2.2) (B5R). [Source:SWISSPROT;Acc:P00387]	0.0966308	0.427993	0.22577659	CYB5R3	

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/