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 2958 to 3007 of 3206 in total

Rank	description	measured	expected	final	Hugo	
2958	LEUCINE-RICH REPEAT PROTEIN SHOC-2 (RAS-BINDING PROTEIN SUR-8). [Source:SWISSPROT;Acc:Q9UQ13]	0.100774	0.689453	0.146165148	SHOC2	
2959		0.100774	0.689453	0.146165148	FRMPD4	
2960	RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [Source:SWISSPROT;Acc:O15211]	0.0746316	0.510598	0.146165085		
2961	TRANSFORMING PROTEIN P21/H-RAS-1 (C-H-RAS). [Source:SWISSPROT;Acc:P01112]	0.223524	1.52927	0.146163856	HRAS	
2962	TRANSFORMING PROTEIN N-RAS. [Source:SWISSPROT;Acc:P01111]	0.217355	1.48707	0.146163261		
2963	SEPTIN 1 (LARP) (SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR- 24). [Source:SWISSPROT;Acc:Q8WYJ6]	0.0798252	0.547429	0.145818362	SEPT1	
2964	FORKHEAD BOX PROTEIN P3 (ZINC FINGER PROTEIN JM2) (SCURFIN). [Source:SWISSPROT;Acc:Q9BZS1]	0.193703	1.33367	0.145240577	FOXP3	
2965	FORKHEAD BOX PROTEIN P1 (HSPC215). [Source:SWISSPROT;Acc:Q9H334]	0.137759	0.94872	0.145205118	FOXP1	
2966	FORKHEAD BOX P4; FORK HEAD-RELATED PROTEIN LIKE A; WINGED-HELIX REPRESSOR FOXP4. [Source:RefSeq;Acc:NM_138457]	0.136683	0.941317	0.145204007	FOXP4	
2967	RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR (RALGEF) (RALGDS). [Source:SWISSPROT;Acc:Q12967]	0.122631	0.850955	0.144109853	RALGDS	
2968	RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 1 (RALGDS-LIKE 1). [Source:SWISSPROT;Acc:Q9NZL6]	0.106453	0.742944	0.143285362	RGL1	
2969	COATOMER EPSILON SUBUNIT (EPSILON-COAT PROTEIN) (EPSILON-COP). [Source:SWISSPROT;Acc:O14579]	0.148933	1.04237	0.142879208	COPE	
2970		0.104104	0.735452	0.141551046	RIBC2	
2971	TUBULIN-SPECIFIC CHAPERONE C (TUBULIN-FOLDING COFACTOR C) (CFC). [Source:SWISSPROT;Acc:Q15814]	0.0292681	0.208597	0.140309305	TBCC	
2972	DEAD-BOX PROTEIN. [Source:RefSeq;Acc:NM_018665]	0.0292681	0.208597	0.140309305	DDX43	
2973	PUTATIVE ACYL-COA THIOESTER HYDROLASE CGI-16 (EC 3.1.2.-). [Source:SWISSPROT;Acc:Q9Y305]	0.231971	1.65329	0.140308718	ACOT9	
2974	HOMEOBOX PROTEIN HOX-D4 (HOX-4B) (HOX-5.1) (HHO.C13). [Source:SWISSPROT;Acc:P09016]	0.0311395	0.223127	0.139559533	HOXD4	
2975	HOMEOBOX PROTEIN HOX-C5 (HOX-3D) (CP11). [Source:SWISSPROT;Acc:Q00444]	0.0320568	0.2297	0.139559425	HOXC5	
2976	HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [Source:SWISSPROT;Acc:P09017]	0.0311872	0.223469	0.139559402		
2977	RETINAL SHORT-CHAIN DEHYDROGENASE/REDUCTASE 3. [Source:RefSeq;Acc:NM_016246]	0.518329	3.71404	0.139559348	HSD17B14	
2978	HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [Source:SWISSPROT;Acc:P09630]	0.0308655	0.221164	0.139559332		
2979	HOMEOBOX PROTEIN HOX-B5 (HOX-2A) (HHO.C10) (HU-1). [Source:SWISSPROT;Acc:P09067]	0.035571	0.254881	0.139559245	HOXB5	
2980	HOMEOBOX PROTEIN HOX-A5 (HOX-1C). [Source:SWISSPROT;Acc:P20719]	0.0421586	0.302084	0.139559195	HOXA5	
2981		0.0398119	0.285269	0.139559153	MTERFD1	
2982	HOMEOBOX PROTEIN HOX-B4 (HOX-2F) (HOX-2.6). [Source:SWISSPROT;Acc:P17483]	0.0313539	0.224664	0.139559075	HOXB4	
2983	HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [Source:SWISSPROT;Acc:Q00056]	0.0310799	0.222701	0.13955887		
2984	SPERMATOGENESIS ASSOCIATED 6. [Source:RefSeq;Acc:NM_019073]	0.107787	0.77996	0.138195548	SPATA6	
2985	"BETA-ARRESTIN 1 (ARRESTIN, BETA 1). [Source:SWISSPROT;Acc:P49407]"	0.282189	2.04196	0.138195165	ARRB1	
2986	AMP DEAMINASE 2 (EC 3.5.4.6) (AMP DEAMINASE ISOFORM L). [Source:SWISSPROT;Acc:Q01433]	0.138195	1	0.138195	AMPD2	
2987		0.138195	1	0.138195	C9orf68	
2988	"BETA-ARRESTIN 2 (ARRESTIN, BETA 2). [Source:SWISSPROT;Acc:P32121]"	0.240182	1.738	0.138194476	ARRB2	
2989	SEPTIN 4 (PEANUT-LIKE PROTEIN 2) (BRAIN PROTEIN H5) (CELL DIVISION CONTROL-RELATED PROTEIN 2) (HCDCREL-2) (BRADEION BETA) (CE5B3 BETA) (CEREBRAL PROTEIN-7) (HUCEP-7). [Source:SWISSPROT;Acc:O43236]	0.16041	1.17491	0.136529607	SEPT4	
2990		0.0210454	0.155504	0.135336712	HS3ST4	
2991	HEPARAN SULFATE D-GLUCOSAMINYL  3-O-SULFOTRANSFERASE 2; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [Source:RefSeq;Acc:NM_006043]	0.0207502	0.153323	0.135336512	HS3ST2	
2992	HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3A1; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [Source:RefSeq;Acc:NM_006042]	0.026835	0.198284	0.135336184	HS3ST3A1	
2993	MRNA DECAPPING ENZYME; HISTIDINE TRIAD PROTEIN MEMBER 5; HEAT SHOCK-LIKE PROTEIN 1. [Source:RefSeq;Acc:NM_014026]	0.279017	2.06166	0.135336088	DCPS	
2994	HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3B1. [Source:RefSeq;Acc:NM_006041]	0.0225884	0.166906	0.135336057	HS3ST3B1	
2995	C439A6.1 (NOVEL PROTEIN SIMILAR TO HEPARAN SULFATE (GLUCOSAMINE) 3-O- SULFOTRANSFERASES) (FRAGMENT). [Source:SPTREMBL;Acc:Q96QI5]	0.0210051	0.155207	0.135336035	HS3ST6	
2996	RING FINGER PROTEIN 25 (EC 6.3.2.-). [Source:SWISSPROT;Acc:Q96BH1]	0.22015	1.62938	0.135112742	RNF25	
2997	OLIGOSACCHARYL TRANSFERASE STT3 SUBUNIT HOMOLOG (B5) (INTEGRAL MEMBRANE PROTEIN 1) (TMC). [Source:SWISSPROT;Acc:P46977]	0.0284601	0.210671	0.135092633	STT3A	
2998	SOURCE OF IMMUNODOMINANT MHC-ASSOCIATED PEPTIDES; HOMOLOG OF YEAST STT3 GENE. [Source:RefSeq;Acc:NM_178862]	0.0366899	0.271591	0.135092474	STT3B	
2999	DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE--PROTEIN GLYCOSYLTRANSFERASE 48 KDA SUBUNIT PRECURSOR (EC 2.4.1.119) (OLIGOSACCHARYL TRANSFERASE 48 KDA SUBUNIT) (DDOST 48 KDA SUBUNIT). [Source:SWISSPROT;Acc:P39656]	0.0217044	0.160664	0.135091869	DDOST	
3000	APG3P; PC3-96 PROTEIN. [Source:RefSeq;Acc:NM_022488]	0.206188	1.59883	0.128961803	ATG3	
3001	GABA-A RECEPTOR-ASSOCIATED PROTEIN. [Source:SPTREMBL;Acc:Q9BY60]	0.0506272	0.392576	0.128961526		
3002		0.170944	1.33704	0.12785257	C1orf164	
3003	"GLYCOGEN [STARCH] SYNTHASE, LIVER (EC 2.4.1.11). [Source:SWISSPROT;Acc:P54840]"	0.129726	1.02722	0.126288429	GYS2	
3004	ENDO-BETA-N-ACETYLGLUCOSAMINIDASE. [Source:RefSeq;Acc:NM_022759]	0.0444453	0.352603	0.126049126		
3005	"GLYCOGEN [STARCH] SYNTHASE, MUSCLE (EC 2.4.1.11). [Source:SWISSPROT;Acc:P13807]"	0.158067	1.25601	0.12584852	GYS1	
3006	COATOMER ALPHA SUBUNIT (ALPHA-COAT PROTEIN) (ALPHA-COP) (HEPCOP) (HEP-COP) [CONTAINS: XENIN (XENOPSIN-RELATED PEPTIDE); PROXENIN]. [Source:SWISSPROT;Acc:P53621]	0.329852	2.63087	0.125377537	COPA	
3007		0.136179	1.08705	0.125273906	SEPT11	

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/