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 1002 to 1051 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1002	"FUMARATE HYDRATASE, MITOCHONDRIAL PRECURSOR (EC 4.2.1.2) (FUMARASE). [Source:SWISSPROT;Acc:P07954]"	0.131317	0.51515	0.25491022	FH	
1003	HUNTINGTIN INTERACTING PROTEIN E; HUNTINGTIN INTERACTOR PROTEIN E. [Source:RefSeq;Acc:NM_007076]	0.0281805	0.110551	0.254909499		
1004	PROBABLE SERINE/THREONINE-PROTEIN KINASE KIAA0537 (EC 2.7.1.-). [Source:SWISSPROT;Acc:O60285]	0.139695	0.54802	0.25490858	NUAK1	
1005	DEOXYHYPUSINE SYNTHASE (EC 2.5.1.46) (DHS). [Source:SWISSPROT;Acc:P49366]	0.138205	0.542366	0.254818702	DHPS	
1006	ORPHAN NUCLEAR RECEPTOR TR2. [Source:SWISSPROT;Acc:P13056]	0.211877	0.831867	0.254700571	NR2C1	
1007	ORPHAN NUCLEAR RECEPTOR NR2E1 (NUCLEAR RECEPTOR TLX) (TAILLESS HOMOLOG) (TLL) (HTLL). [Source:SWISSPROT;Acc:Q9Y466]	0.280845	1.10266	0.254697731	NR2E1	
1008	TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN; ETS1-ASSOCIATED PROTEIN 2. [Source:RefSeq;Acc:NM_016614]	0.228495	0.897587	0.254565853	TTRAP	
1009		0.0413585	0.162467	0.254565543	C20orf72	
1010	PUTATATIVE 28 KDA PROTEIN. [Source:RefSeq;Acc:NM_020143]	0.222495	0.87407	0.254550551	PNO1	
1011	SORTING NEXIN 5. [Source:SWISSPROT;Acc:Q9Y5X3]	0.317621	1.24807	0.254489732	SNX5	
1012	BETA-CATENIN (PRO2286). [Source:SWISSPROT;Acc:P35222]	0.126011	0.495862	0.25412514	CTNNB1	
1013	TRANSCRIPTION INITIATION FACTOR TFIID 28 KDA SUBUNIT (TAFII-28) (TAFII28) (TFIID SUBUNIT P30-BETA). [Source:SWISSPROT;Acc:Q15544]	0.343318	1.35164	0.254001065	TAF11	
1014	HIV-1 REV BINDING PROTEIN-LIKE; REV/REX ACTIVATION DOMAIN BINDING PROTEIN-RELATED. [Source:RefSeq;Acc:NM_006076]	0.0736761	0.290228	0.253855934	HRBL	
1015	INTERSECTIN 2 (SH3 DOMAIN-CONTAINING PROTEIN 1B) (SH3P18) (SH3P18-LIKE WASP ASSOCIATED PROTEIN). [Source:SWISSPROT;Acc:Q9NZM3]	0.079717	0.314025	0.253855585		
1016	PRAM-1 PROTEIN; PML-RARA TARGET GENE ENCODING AN ADAPTOR MOLECULE-1. [Source:RefSeq;Acc:NM_032152]	0.2316	0.91233	0.253855513	PRAM1	
1017	NUCLEOPORIN-LIKE PROTEIN RIP (HIV-1 REV-BINDING PROTEIN) (REV INTERACTING PROTEIN) (REV/REX ACTIVATION DOMAIN-BINDING PROTEIN). [Source:SWISSPROT;Acc:P52594]	0.0957789	0.377297	0.253855451	HRB	
1018	CGTHBA PROTEIN (-14 GENE PROTEIN). [Source:SWISSPROT;Acc:Q12980]	0.0593831	0.233925	0.253855296	C16orf35	
1019	INTERSECTIN 1 (SH3 DOMAIN-CONTAINING PROTEIN 1A) (SH3P17). [Source:SWISSPROT;Acc:Q15811]	0.0927584	0.365399	0.253855101		
1020	HIV TAT SPECIFIC FACTOR 1; COFACTOR REQUIRED FOR TAT ACTIVATION OF HIV-1 TRANSCRIPTION. [Source:RefSeq;Acc:NM_014500]	0.0333753	0.131474	0.253854755	HTATSF1	
1021	"FTSJ HOMOLOG 3; LIKELY ORTHOLOG OF MOUSE ECTOPLACENTAL CONE, INVASIVE TROPHOBLAST GIANT CELLS, EXTRAEMBRYONIC ECTODERM AND CHORION SEQUENCE 3. [Source:RefSeq;Acc:NM_017647]"	0.280943	1.10792	0.253576973	FTSJ3	
1022		0.178897	0.705791	0.25347022	TBC1D10B	
1023	SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 4 (TRPC4) (TRP-RELATED PROTEIN 4) (HTRP-4) (HTRP4). [Source:SWISSPROT;Acc:Q9UBN4]	0.185352	0.731277	0.253463462	TRPC4	
1024	UBIQUITIN-LIKE PROTEIN SMT3B (SENTRIN 2) (HSMT3). [Source:SWISSPROT;Acc:P55855]	0.0979873	0.386626	0.253442086		
1025	ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [Source:RefSeq;Acc:NM_052957]	0.0649343	0.256212	0.25343973	ACRC	
1026	SHORT TRANSIENT RECEPTOR POTENTIAL CHANNEL 5 (TRPC5) (HTRP-5) (HTRP5). [Source:SWISSPROT;Acc:Q9UL62]	0.2166	0.854644	0.253438859	TRPC5	
1027	EBP50-PDZ INTERACTOR OF 64 KDA (EPI64 PROTEIN). [Source:SWISSPROT;Acc:Q9BXI6]	0.2166	0.854644	0.253438859	TBC1D10A	
1028	UBIQUITIN-LIKE PROTEIN SMT3A. [Source:SWISSPROT;Acc:P55854]	0.101711	0.401325	0.253437987	SUMO3	
1029	RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE SMALL CHAIN). [Source:SWISSPROT;Acc:P31350]	0.282811	1.11593	0.253430771	RRM2	
1030	RETINOBLASTOMA-LIKE PROTEIN 2 (130 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB2) (P130) (RBR-2). [Source:SWISSPROT;Acc:Q08999]	0.152107	0.600397	0.253344037	RBL2	
1031	SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-2 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 2) (NA+/K+ ATPASE 2). [Source:SWISSPROT;Acc:P50993]	0.063502	0.250657	0.253342217	ATP1A2	
1032	SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-1 CHAIN PRECURSOR (EC 3.6.3.9) (SODIUM PUMP 1) (NA+/K+ ATPASE 1). [Source:SWISSPROT;Acc:P05023]	0.063502	0.250657	0.253342217	ATP1A1	
1033	CATHEPSIN L PRECURSOR (EC 3.4.22.15) (MAJOR EXCRETED PROTEIN) (MEP). [Source:SWISSPROT;Acc:P07711]	0.184799	0.729445	0.253341924	CTSL1	
1034	SODIUM/POTASSIUM-TRANSPORTING ATPASE ALPHA-3 CHAIN (EC 3.6.3.9) (SODIUM PUMP 3) (NA+/K+ ATPASE 3) (ALPHA(III)). [Source:SWISSPROT;Acc:P13637]	0.0735677	0.290389	0.253341897	ATP1A3	
1035	CATHEPSIN L2 PRECURSOR (EC 3.4.22.43) (CATHEPSIN V) (CATHEPSIN U). [Source:SWISSPROT;Acc:O60911]	0.163807	0.646587	0.253341004	CTSL2	
1036	UNR PROTEIN. [Source:SWISSPROT;Acc:O75534]	0.0368889	0.145611	0.25333869	CSDE1	
1037	LOH1CR12. [Source:RefSeq;Acc:NM_058169]	0.147556	0.582446	0.253338507	LOH12CR1	
1038	RETINOBLASTOMA-LIKE PROTEIN 1 (107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB1) (P107). [Source:SWISSPROT;Acc:P28749]	0.128252	0.506251	0.253336784	RBL1	
1039	HEAT SHOCK PROTEIN HSP 90-BETA (HSP 84) (HSP 90). [Source:SWISSPROT;Acc:P08238]	0.341129	1.34662	0.253322392	HSP90AB1	
1040	"ATP-DEPENDENT DNA HELICASE II, 70 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P70) (KU70) (70 KDA SUBUNIT OF KU ANTIGEN) (THYROID-LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 75 KDA SUBUNIT) (CTCBF) (CTC75). [Source:SWISSPROT;Acc:P12956]"	0.0397033	0.156754	0.253284127		
1041	RAD17 HOMOLOG ISOFORM 1; RAD17-LIKE PROTEIN; CELL CYCLE CHECKPOINT PROTEIN (RAD17); RF-C ACTIVATOR 1 HOMOLOG. [Source:RefSeq;Acc:NM_002873]	0.0746521	0.294737	0.253283775	RAD17	
1042	"ATP-DEPENDENT DNA HELICASE II, 80 KDA SUBUNIT (LUPUS KU AUTOANTIGEN PROTEIN P86) (KU86) (KU80) (86 KDA SUBUNIT OF KU ANTIGEN) (THYROID- LUPUS AUTOANTIGEN) (TLAA) (CTC BOX BINDING FACTOR 85 KDA SUBUNIT) (CTCBF) (CTC85) (NUCLEAR FACTOR IV) (DNA-REPAIR PROTE"	0.114355	0.451492	0.25328245	XRCC5	
1043		0.0327294	0.12923	0.253264722	TMEM87B	
1044		0.343832	1.3576	0.253264585	ASCC1	
1045		0.0425806	0.168127	0.253264496	TMEM87A	
1046	HEAT SHOCK PROTEIN HSP 90-ALPHA (HSP 86). [Source:SWISSPROT;Acc:P07900]	0.310662	1.22676	0.253237797	HSP90AA2	
1047	SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN. [Source:RefSeq;Acc:NM_153825]	0.293391	1.16068	0.252775097	SEPSECS	
1048	ANNEXIN A11 (ANNEXIN XI) (CALCYCLIN-ASSOCIATED ANNEXIN 50) (CAP-50) (56 KDA AUTOANTIGEN). [Source:SWISSPROT;Acc:P50995]	0.114013	0.451047	0.252774101	ANXA11	
1049	CALMEGIN PRECURSOR. [Source:SWISSPROT;Acc:O14967]	0.0356563	0.14106	0.252773997	CLGN	
1050	CALNEXIN PRECURSOR (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN-BINDING PROTEIN P88) (P90) (IP90). [Source:SWISSPROT;Acc:P27824]	0.0429594	0.169952	0.252773724	CANX	
1051	RNA (GUANINE-7-) METHYLTRANSFERASE. [Source:RefSeq;Acc:NM_003799]	0.0429379	0.169867	0.252773641	RNMT	

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/