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 751 to 800 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
751		0.0771387	0.291643	0.264497005	C15orf44	
752	LIPOPOLYSACCHARIDE-RESPONSIVE AND BEIGE-LIKE ANCHOR PROTEIN (CDC4-LIKE PROTEIN) (BEIGE-LIKE PROTEIN). [Source:SWISSPROT;Acc:P50851]	0.0321572	0.121579	0.264496336		
753	LUPUS LA PROTEIN (SJOGREN SYNDROME TYPE B ANTIGEN) (SS-B) (LA RIBONUCLEOPROTEIN) (LA AUTOANTIGEN). [Source:SWISSPROT;Acc:P05455]	0.302351	1.14316	0.264487036	SSB	
754	U4/U6-ASSOCIATED RNA SPLICING FACTOR. [Source:RefSeq;Acc:NM_004698]	0.351386	1.32896	0.264406754	PRPF3	
755		0.0328701	0.124442	0.264139921	CCDC93	
756	BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 (APOPTOSIS INHIBITOR SURVIVIN) (APOPTOSIS INHIBITOR 4). [Source:SWISSPROT;Acc:O15392]	0.168097	0.636394	0.264139825	BIRC5	
757	FAS APOPTOTIC INHIBITORY MOLECULE. [Source:RefSeq;Acc:NM_018147]	0.118199	0.447876	0.2639101	FAIM	
758	43 KDA RECEPTOR-ASSOCIATED PROTEIN OF THE SYNAPSE (RAPSYN) (ACETYLCHOLINE RECEPTOR-ASSOCIATED 43 KDA PROTEIN) (43 KDA POSTSYNAPTIC PROTEIN). [Source:SWISSPROT;Acc:Q13702]	0.552551	2.09375	0.263904955	RAPSN	
759	C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN ISOFORM 2; PUTATIVE PROTEIN TYROSINE PHOSPHATASE; C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN; TENSIN 2. [Source:RefSeq;Acc:NM_015319]	0.260485	0.987283	0.263840257	TENC1	
760	TUMOR ENDOTHELIAL MARKER 6; THYROID SPECIFIC PTB DOMAIN PROTEIN; TENSIN 3. [Source:RefSeq;Acc:NM_022748]	0.283226	1.0738	0.263760477	TNS3	
761	SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1 (DISHEVELLED-1) (DSH HOMOLOG 1). [Source:SWISSPROT;Acc:O14640]	0.217793	0.825859	0.26371693	DVL1	
762	SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2 (DISHEVELLED-2) (DSH HOMOLOG 2). [Source:SWISSPROT;Acc:O14641]	0.223153	0.846393	0.263651755	DVL2	
763	RAB COUPLING PROTEIN; RAB-INTERACTING RECYCLING PROTEIN; RAB EFFECTOR PROTEIN; RAB11-FAMILY INTERACTING PROTEIN 1. [Source:RefSeq;Acc:NM_025151]	0.0360283	0.136657	0.263640355	RAB11FIP1	
764	POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IIA (EC 3.6.1.-). [Source:SWISSPROT;Acc:O75110]	0.0460867	0.174809	0.263640316	ATP9A	
765	GAMMA-SNAP-ASSOCIATED FACTOR 1; RAB11-INTERACTING PROTEIN. [Source:RefSeq;Acc:NM_015470]	0.0460867	0.174809	0.263640316	RAB11FIP5	
766	PROTEIN C14ORF122 (CGI-112). [Source:SWISSPROT;Acc:Q9Y3B6]	0.0365698	0.138711	0.26364023	C14orf122	
767		0.0355674	0.134909	0.263639935	RAB11FIP2	
768	DPY-30-LIKE PROTEIN. [Source:SWISSPROT;Acc:Q9C005]	0.3486	1.32226	0.263639526		
769	NEIGHBOR OF COX4. [Source:SWISSPROT;Acc:O43402]	0.0269837	0.102351	0.263638851	COX4NB	
770	HSP90 CO-CHAPERONE CDC37 (HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT) (P50CDC37). [Source:SWISSPROT;Acc:Q16543]	0.188365	0.715239	0.26335952	CDC37	
771	SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-3 (DISHEVELLED-3) (DSH HOMOLOG 3). [Source:SWISSPROT;Acc:Q92997]	0.256243	0.973151	0.263312682	DVL3	
772	CASEIN KINASE II BETA CHAIN (CK II) (PHOSVITIN) (G5A). [Source:SWISSPROT;Acc:P13862]	0.492676	1.87133	0.263275852		
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"	0.0367538	0.139602	0.263275598		
774	TARGET OF MYB1-LIKE 2; TARGET OF MYB1 (CHICKEN) HOMOLOG-LIKE 2. [Source:RefSeq;Acc:NM_144678]	0.179057	0.680239	0.263226601	TOM1L2	
775	TRIPLE FUNCTIONAL DOMAIN PROTEIN (PTPRF INTERACTING PROTEIN). [Source:SWISSPROT;Acc:O75962]	0.0734189	0.278919	0.2632266	TRIO	
776	TARGET OF MYB PROTEIN 1. [Source:SWISSPROT;Acc:O60784]	0.230424	0.875383	0.263226496	TOM1	
777	HUNTINGTIN-ASSOCIATED PROTEIN-INTERACTING PROTEIN (DUO PROTEIN). [Source:SWISSPROT;Acc:O60229]	0.0568574	0.216002	0.263226266		
778	ARP2/3 COMPLEX 34 KDA SUBUNIT (P34-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 2). [Source:SWISSPROT;Acc:O15144]	0.427564	1.62441	0.263211874	ARPC2	
779	TENSIN. [Source:RefSeq;Acc:NM_022648]	0.320357	1.21727	0.263176617	TNS1	
780	RNA-BINDING REGION CONTAINING PROTEIN 2 (HEPATOCELLULAR CARCINOMA PROTEIN 1) (SPLICING FACTOR HCC1). [Source:SWISSPROT;Acc:Q14498]	0.349158	1.32674	0.263169875	RBM39	
781	"NUCLEAR FACTOR, INTERLEUKIN 3 REGULATED. [Source:RefSeq;Acc:NM_005384]"	0.150787	0.573002	0.263152659	NFIL3	
782	SYNTAXIN 12. [Source:RefSeq;Acc:NM_177424]	0.206261	0.78389	0.263124928	STX12	
783	WW DOMAIN BINDING PROTEIN 2 (WBP-2). [Source:SWISSPROT;Acc:Q969T9]	0.0979343	0.372839	0.262671823	WBP2	
784		0.0378601	0.144194	0.26256363		
785	BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN. [Source:SWISSPROT;Acc:P38398]	0.11358	0.432583	0.262562329	BRCA1	
786	SYNTAXIN 7. [Source:SWISSPROT;Acc:O15400]	0.209282	0.797115	0.262549318	STX7	
787	CBF1 INTERACTING COREPRESSOR. [Source:RefSeq;Acc:NM_004882]	0.363013	1.38457	0.262184649		
788	EVOLUTIONARILY CONSERVED G-PATCH DOMAIN CONTAINING. [Source:RefSeq;Acc:NM_018025]	0.0369504	0.140933	0.262184158	GPATCH1	
789	ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [Source:SWISSPROT;Acc:Q15326]	0.0552487	0.210853	0.262024728	ZMYND11	
790	SYNTAXIN 16 (SYN16). [Source:SWISSPROT;Acc:O14662]	0.279039	1.06498	0.262013371	STX16	
791	SYNTAXIN 1A (NEURON-SPECIFIC ANTIGEN HPC-1). [Source:SWISSPROT;Acc:Q16623]	0.147338	0.562331	0.262012943	STX1A	
792		0.0377474	0.144067	0.262012813	TMCC2	
793	"BETA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-BETA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, BETA). [Source:SWISSPROT;Acc:Q9H115]"	0.129493	0.494224	0.262012772	NAPB	
794	INFLAMMATION-RELATED G PROTEIN-COUPLED RECEPTOR EX33. [Source:RefSeq;Acc:NM_020370]	0.0690966	0.263715	0.2620124	GPR84	
795	PALMITOYL-PROTEIN THIOESTERASE 1 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 1). [Source:SWISSPROT;Acc:P50897]	0.0690966	0.263715	0.2620124	PPT1	
796	SIMILAR TO NUCLEAR PROTEIN E3-3 ORF1. [Source:SPTREMBL;Acc:Q9BU61]	0.0690966	0.263715	0.2620124	C3orf60	
797	ADIPOCYTE PLASMA MEMBRANE-ASSOCIATED PROTEIN (BSCV PROTEIN). [Source:SWISSPROT;Acc:Q9HDC9]	0.0870266	0.332147	0.262012302	C20orf3	
798		0.0312832	0.119396	0.262012128	TMCC3	
799	SYNAPTOSOMAL-ASSOCIATED PROTEIN 29 (SNAP-29) (VESICLE-MEMBRANE FUSION PROTEIN SNAP-29) (SOLUBLE 29 KDA NSF ATTACHMENT PROTEIN). [Source:SWISSPROT;Acc:O95721]	0.14026	0.535319	0.262011997	SNAP29	
800	SYNTAXIN 1B. [Source:SWISSPROT;Acc:Q15531]	0.120499	0.459899	0.262011877	STX1B	

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/