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 1552 to 1601 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
1552	TRANSLATION INITIATION FACTOR EIF-2B BETA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR) (S20I15) (S20III15). [Source:SWISSPROT;Acc:P49770]	0.415409	1.71958	0.24157585	EIF2B2	
1553	BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (EC 2.1.2.3) (AICAR TRANSFORMYLASE); IMP CYCLOHYDROLASE (EC 3.5.4.10) (INOSINICASE) (IMP SYNTHETASE) (ATIC)]. [Source:SWISSPROT;Acc:P31939]	0.100408	0.416	0.241365385	ATIC	
1554	PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE (EC 6.3.5.3) (FGAM SYNTHASE) (FGAMS) (FORMYLGLYCINAMIDE RIBOTIDE AMIDOTRANSFERASE) (FGARAT) (FORMYLGLYCINAMIDE RIBOTIDE SYNTHETASE). [Source:SWISSPROT;Acc:O15067]	0.100408	0.416	0.241365385	PFAS	
1555	MULTIFUNCTIONAL PROTEIN ADE2 [INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLE- SUCCINOCARBOXAMIDE SYNTHASE (EC 6.3.2.6) (SAICAR SYNTHETASE); PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE (EC 4.1.1.21) (AIR CARBOXYLASE) (AIRC)]. [Source:SWISSPROT;Acc:P22234]	0.200816	0.832	0.241365385	PAICS	
1556		0.184977	0.766628	0.241286517		
1557		0.0753661	0.312352	0.241285793		
1558	GC-RICH SEQUENCE DNA-BINDING FACTOR HOMOLOG. [Source:SWISSPROT;Acc:Q9Y5B6]	0.037683	0.156176	0.241285473	C21orf66	
1559	TOLL-LIKE RECEPTOR 2 PRECURSOR (TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4). [Source:SWISSPROT;Acc:O60603]	0.037683	0.156176	0.241285473	TLR2	
1560	"THIOREDOXIN INTERACTING PROTEIN; UPREGULATED BY 1,25-DIHYDROXYVITAMIN D-3. [Source:RefSeq;Acc:NM_006472]"	0.0419848	0.174068	0.241197693	TXNIP	
1561		0.0442559	0.183485	0.241196283	ARRDC4	
1562		0.0467541	0.193844	0.241194466	ARRDC3	
1563	U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN MPP10 (M PHASE PHOSPHOPROTEIN 10). [Source:SWISSPROT;Acc:O00566]	0.63619	2.6381	0.241154619	MPHOSPH10	
1564	GCN5-LIKE PROTEIN 1 (RT14 PROTEIN). [Source:SWISSPROT;Acc:P78537]	0.223546	0.927081	0.241128877	BLOC1S1	
1565	PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [Source:SWISSPROT;Acc:P46087]	0.714168	2.96197	0.241112503	NOL1	
1566	ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1. [Source:SWISSPROT;Acc:P40616]	0.0394801	0.163824	0.240990941	ARL1	
1567	NEFA-INTERACTING NUCLEAR PROTEIN NIP30. [Source:RefSeq;Acc:NM_024946]	0.0394801	0.163824	0.240990941		
1568	MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S22 (S22MT) (MRP-S22) (GK002). [Source:SWISSPROT;Acc:P82650]	0.070166	0.291157	0.240990256	MRPS22	
1569	PROTEASOME SUBUNIT BETA TYPE 2 (EC 3.4.25.1) (PROTEASOME COMPONENT C7-I) (MACROPAIN SUBUNIT C7-I) (MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C7-I). [Source:SWISSPROT;Acc:P49721]	0.966048	4.00866	0.240990256	PSMB2	
1570	LIM HOMEOBOX TRANSCRIPTION FACTOR 1 BETA (LIM/HOMEOBOX PROTEIN LMX1B) (LIM-HOMEOBOX PROTEIN 1.2) (LMX-1.2). [Source:SWISSPROT;Acc:O60663]	0.0789602	0.327649	0.240990206	LMX1B	
1571	LIM HOMEOBOX TRANSCRIPTION FACTOR 1 ALPHA (LIM/HOMEOBOX PROTEIN LMX1A) (LIM-HOMEOBOX PROTEIN 1.1) (LMX-1.1). [Source:SWISSPROT;Acc:Q8TE12]	0.0789602	0.327649	0.240990206	LMX1A	
1572	MITOCHONDRIAL PRECURSOR PROTEINS IMPORT RECEPTOR (TRANSLOCASE OF OUTER MEMBRANE TOM70). [Source:SWISSPROT;Acc:O94826]	0.11844	0.491473	0.240989841	TOMM70A	
1573	BULLOUS PEMPHIGOID ANTIGEN 1 ISOFORMS 1/2/3/4/5/8 (230 KDA BULLOUS PEMPHIGOID ANTIGEN) (BPA) (HEMIDESMOSOMAL PLAQUE PROTEIN) (DYSTONIA MUSCULORUM PROTEIN) (FRAGMENT). [Source:SWISSPROT;Acc:Q03001]	0.0777867	0.322851	0.240936841	DST	
1574	"MICROTUBULE-ACTIN CROSSLINKING FACTOR 1, ISOFORM 4. [Source:SWISSPROT;Acc:Q96PK2]"	0.0946162	0.392702	0.240936384	MACF1	
1575	"ACTIN, CYTOPLASMIC 2 (GAMMA-ACTIN). [Source:SWISSPROT;Acc:P02571]"	0.228182	0.947072	0.240934163	ACTG1	
1576	RIBOKINASE (EC 2.7.1.15). [Source:SWISSPROT;Acc:Q9H477]	0.102962	0.427411	0.240896935	RBKS	
1577	SERPIN B12. [Source:SWISSPROT;Acc:Q96P63]	0.0598165	0.248312	0.240892506	SERPINB12	
1578	UPF0183 PROTEIN. [Source:SWISSPROT;Acc:Q9BSU1]	0.0385664	0.160098	0.240892453	C16orf70	
1579	OXYSTEROLS RECEPTOR LXR-ALPHA (LIVER X RECEPTOR ALPHA) (NUCLEAR ORPHAN RECEPTOR LXR-ALPHA). [Source:SWISSPROT;Acc:Q13133]	0.110811	0.460002	0.240892431	NR1H3	
1580	SQUAMOUS CELL CARCINOMA ANTIGEN 1 (SCCA-1) (PROTEIN T4-A). [Source:SWISSPROT;Acc:P29508]	0.0820308	0.340529	0.240892259	SERPINB4	
1581	MEGSIN (TP55) (SERPIN B7). [Source:SWISSPROT;Acc:O75635]	0.056548	0.234744	0.240892206	SERPINB7	
1582	OXYSTEROLS RECEPTOR LXR-BETA (LIVER X RECEPTOR BETA) (NUCLEAR ORPHAN RECEPTOR LXR-BETA) (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) (NUCLEAR RECEPTOR NER). [Source:SWISSPROT;Acc:P55055]	0.0824164	0.34213	0.240892059	NR1H2	
1583	TRANSLATION INITIATION FACTOR EIF-2B ALPHA SUBUNIT (EIF-2B GDP-GTP EXCHANGE FACTOR). [Source:SWISSPROT;Acc:Q14232]	0.692768	2.87585	0.240891562	EIF2B1	
1584	HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [Source:SWISSPROT;Acc:Q9UIV8]	0.0653411	0.271247	0.240891512		
1585	ANTITHROMBIN-III PRECURSOR (ATIII) (PRO0309). [Source:SWISSPROT;Acc:P01008]	0.0555356	0.230542	0.240891464	SERPINC1	
1586	EUKARYOTIC TRANSLATION INITIATION FACTOR 5A (EIF-5A) (EIF-4D) (REV- BINDING FACTOR). [Source:SWISSPROT;Acc:P10159]	0.376553	1.56403	0.24075817	EIF5AP1	
1587		0.0612982	0.25461	0.240753309	CHAC1	
1588	EIF-5A2 PROTEIN. [Source:RefSeq;Acc:NM_020390]	0.326192	1.35491	0.240748094	EIF5A2	
1589	HIV-1 REV BINDING PROTEIN 2; REV INTERACTING PROTEIN. [Source:RefSeq;Acc:NM_007043]	0.501293	2.08327	0.240627955	KRR1	
1590	EVOLUTIONARILY CONSERVED SIGNALING INTERMEDIATE IN TOLL PATHWAY; ECSIT. [Source:RefSeq;Acc:NM_016581]	0.28028	1.16562	0.240455723	ECSIT	
1591	BYSTIN. [Source:SWISSPROT;Acc:Q13895]	0.784986	3.26689	0.240285409	BYSL	
1592	LAMIN A/C (70 KDA LAMIN). [Source:SWISSPROT;Acc:P02545]	0.175549	0.730667	0.240258558	LMNA	
1593	CENTAURIN BETA 5 (CNT-B5). [Source:SWISSPROT;Acc:Q96P50]	0.0606318	0.252363	0.240256297	CENTB5	
1594	CENTAURIN BETA 1 (CNT-B1). [Source:SWISSPROT;Acc:Q15027]	0.058923	0.245251	0.240255901	CENTB1	
1595	CENTAURIN BETA 2 (CNT-B2). [Source:SWISSPROT;Acc:Q15057]	0.0726324	0.302313	0.240255629	CENTB2	
1596	LAMIN B1. [Source:SWISSPROT;Acc:P20700]	0.210907	0.877854	0.240252935	LMNB1	
1597	PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT (EIF-3) (FRAGMENT). [Source:SWISSPROT;Acc:O75153]	0.275535	1.14705	0.240211848	KIAA0664	
1598	SERINE/THREONINE PROTEIN PHOSPHATASE 4 (EC 3.1.3.16) (PP4) (PROTEIN PHOSPHATASE X) (PP-X). [Source:SWISSPROT;Acc:P33172]	0.161804	0.67395	0.240083092	PPP4C	
1599	IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANSDUCTION MOLECULE ALPHA 4) (ALPHA 4 PROTEIN). [Source:SWISSPROT;Acc:P78318]	0.0337232	0.140465	0.240082583	IGBP1	
1600	TRANSLIN. [Source:SWISSPROT;Acc:Q15631]	0.218752	0.911432	0.240009128		
1601	TRANSLIN-ASSOCIATED PROTEIN X (TRANSLIN-ASSOCIATED FACTOR X). [Source:SWISSPROT;Acc:Q99598]	0.0312503	0.130205	0.240008448	TSNAX	

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/