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 401 to 450 of 3206 in total 
Rank	description	measured	expected	final	Hugo	
401	M-PHASE INDUCER PHOSPHATASE 3 (EC 3.1.3.48) (DUAL SPECIFICITY PHOSPHATASE CDC25C). [Source:SWISSPROT;Acc:P30307]	0.590395	2.12136	0.278309669	CDC25C	
402	CENTAURIN GAMMA 1. [Source:SWISSPROT;Acc:Q99490]	0.0439645	0.158002	0.278252807	CENTG1	
403	CENTAURIN GAMMA 2. [Source:SWISSPROT;Acc:Q9UPQ3]	0.0479426	0.172299	0.27825234	CENTG2	
404	GENERAL VESICULAR TRANSPORT FACTOR P115 (TRANSCYTOSIS ASSOCIATED PROTEIN) (TAP) (VESICLE DOCKING PROTEIN). [Source:SWISSPROT;Acc:O60763]	1.73296	6.22802	0.278252157	USO1	
405	CENTAURIN GAMMA 3. [Source:SWISSPROT;Acc:Q96P47]	0.0546138	0.196275	0.278251433	CENTG3	
406		0.0546138	0.196275	0.278251433	MOSC1	
407		0.0546138	0.196275	0.278251433	MOSC2	
408	PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (DEAH BOX PROTEIN 15) (ATP-DEPENDENT RNA HELICASE #46). [Source:SWISSPROT;Acc:O43143]	0.603245	2.16897	0.278125101	DHX15	
409	"BA138E2.1.2 (FORMIN-BINDING PROTEIN 17 (FBP17), ISOFORM 2). [Source:SPTREMBL;Acc:Q96LH6]"	0.404169	1.45394	0.277981897	FNBP1	
410	EYES ABSENT HOMOLOG 3. [Source:SWISSPROT;Acc:Q99504]	2.06651	7.43888	0.27779854	EYA3	
411		0.356784	1.28488	0.277678849		
412	ARGININE/SERINE-RICH SPLICING FACTOR 10 (TRANSFORMER-2-BETA) (HTRA2- BETA) (TRANSFORMER 2 PROTEIN HOMOLOG) (SILICA-INDUCED PROTEIN 41) (RA301). [Source:SWISSPROT;Acc:Q15815]	0.368948	1.32916	0.277579825	SFRS10	
413		0.197804	0.712745	0.27752422	CCDC49	
414	SAL-LIKE PROTEIN 2 (ZINC FINGER PROTEIN SALL2) (HSAL2). [Source:SWISSPROT;Acc:Q9Y467]	0.13272	0.478487	0.277374307	SALL2	
415	SAL-LIKE PROTEIN 4 (ZINC FINGER PROTEIN SALL4). [Source:SWISSPROT;Acc:Q9UJQ4]	0.135171	0.487324	0.277373985	SALL4	
416	CLATHRIN COAT ASSEMBLY PROTEIN AP180 (CLATHRIN COAT ASSOCIATED PROTEIN AP180) (91 KDA SYNAPTOSOMAL-ASSOCIATED PROTEIN). [Source:SWISSPROT;Acc:O60641]	0.212723	0.766919	0.277373491	SNAP91	
417	ATROPHIN-1 (DENTATORUBRAL-PALLIDOLUYSIAN ATROPHY PROTEIN). [Source:SWISSPROT;Acc:P54259]	0.13427	0.484077	0.277373228	ATN1	
418		0.0384193	0.138512	0.277371636	C8orf79	
419	SAL-LIKE PROTEIN 3 (ZINC FINGER PROTEIN SALL3) (HSALL3). [Source:SWISSPROT;Acc:Q9BXA9]	0.148125	0.534032	0.277371019	SALL3	
420	POLYPYRIMIDINE TRACT BINDING PROTEIN 2; NEURAL POLYPYRIMIDINE TRACT BINDING PROTEIN; PTB-LIKE PROTEIN. [Source:RefSeq;Acc:NM_021190]	0.152427	0.549542	0.277370974	PTBP2	
421	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 8 (EC 3.1.2.15) (UBIQUITIN THIOLESTERASE 8) (UBIQUITIN-SPECIFIC PROCESSING PROTEASE 8) (DEUBIQUITINATING ENZYME 8). [Source:SWISSPROT;Acc:P40818]	0.0884444	0.318867	0.277370816	USP8	
422	ROD1 REGULATOR OF DIFFERENTIATION 1; FISSION YEAST DIFFERENTIATION REGULATOR; REGULATOR OF DIFFERENTIATION (IN S. POMBI) 1; REGULATOR OF DIFFERENTIATION (IN S. POMBE) 1. [Source:RefSeq;Acc:NM_005156]	0.153277	0.552607	0.277370717	ROD1	
423	ADAPTOR-ASSOCIATED KINASE 1. [Source:RefSeq;Acc:NM_014911]	0.168547	0.60766	0.277370569	AAK1	
424		0.0397949	0.143472	0.277370497	ARHGAP23	
425	DEAD (ASP-GLU-ALA-ASP) BOX POLYPEPTIDE 47; HQP0256 PROTEIN. [Source:RefSeq;Acc:NM_016355]	0.0884193	0.318777	0.277370387		
426	RHO-GTPASE ACTIVATING PROTEIN 10. [Source:RefSeq;Acc:NM_020824]	0.0500251	0.180355	0.277370187	ARHGAP21	
427	GROWTH-ARREST-SPECIFIC PROTEIN 7 (GAS-7). [Source:SWISSPROT;Acc:O60861]	0.139845	0.504182	0.277370077	GAS7	
428	PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN (CLATHRIN ASSEMBLY LYMPHOID MYELOID LEUKEMIA PROTEIN). [Source:SWISSPROT;Acc:Q13492]	0.276961	0.998529	0.27736901	PICALM	
429	SAL-LIKE PROTEIN 1 (ZINC FINGER PROTEIN SALL1) (SPALT-LIKE TRANSCRIPTION FACTOR 1) (HSAL1). [Source:SWISSPROT;Acc:Q9NSC2]	0.176985	0.63809	0.277366829	SALL1	
430	"CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 4; NOT4 (NEGATIVE REGULATOR OF TRANSCRIPTION 4, YEAST) HOMOLOG; CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT. [Source:RefSeq;Acc:NM_013316]"	0.176985	0.63809	0.277366829	CNOT4	
431	ARGININE-GLUTAMIC ACID DIPEPTIDE (RE) REPEATS; ATROPHIN 1-LIKE; ARGININE GLUTAMIC ACID DIPEPTIDE RE REPEATS. [Source:RefSeq;Acc:NM_012102]	0.176985	0.63809	0.277366829	RERE	
432	"2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.2.4.4) (BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 COMPONENT BETA CHAIN) (BCKDH E1-BETA). [Source:SWISSPROT;Acc:P21953]"	0.176985	0.63809	0.277366829	BCKDHB	
433	POLYPYRIMIDINE TRACT-BINDING PROTEIN 1 (PTB) (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN I) (HNRNP I) (57 KDA RNA-BINDING PROTEIN PPTB-1). [Source:SWISSPROT;Acc:P26599]	0.176985	0.63809	0.277366829	PTBP1	
434	MEMBRANE-ASSOCIATED NUCLEIC ACID BINDING PROTEIN. [Source:RefSeq;Acc:NM_018835]	0.176985	0.63809	0.277366829	RC3H2	
435	EYES ABSENT HOMOLOG 4. [Source:SWISSPROT;Acc:O95677]	1.76157	6.35359	0.277255851	EYA4	
436	EYES ABSENT HOMOLOG 1. [Source:SWISSPROT;Acc:Q99502]	1.76022	6.35074	0.2771677	EYA1	
437	EYES ABSENT HOMOLOG 2. [Source:SWISSPROT;Acc:O00167]	1.69676	6.12181	0.277166394	EYA2	
438	TRANSFORMER-2 PROTEIN HOMOLOG (TRA-2 ALPHA). [Source:SWISSPROT;Acc:Q13595]	0.345566	1.24774	0.276953532		
439	AF-6 PROTEIN. [Source:SWISSPROT;Acc:P55196]	0.263953	0.953667	0.276776904	MLLT4	
440	GLUTATHIONE S-TRANSFERASE THETA 2 (EC 2.5.1.18) (GST CLASS-THETA). [Source:SWISSPROT;Acc:P30712]	0.182551	0.659693	0.276721142	GSTT2B	
441	"ATPASE INHIBITOR, MITOCHONDRIAL PRECURSOR. [Source:SWISSPROT;Acc:Q9UII2]"	0.0602832	0.217862	0.276703601	ATPIF1	
442	POLYAMINE OXIDASE ISOFORM 1; POLYAMINE OXIDASE; FLAVIN-CONTAINING SPERMINE OXIDASE; PUTATIVE CYCLIN G1 INTERACTING PROTEIN; FLAVIN CONTAINING AMINE OXIDASE. [Source:RefSeq;Acc:NM_019025]	0.0602832	0.217862	0.276703601	SMOX	
443	PEROXISOMAL N1-ACETYL-SPERMINE/SPERMIDINE OXIDASE. [Source:RefSeq;Acc:NM_152911]	0.0442587	0.15995	0.276703345	PAOX	
444	CYTOCHROME C-TYPE HEME LYASE (EC 4.4.1.17) (CCHL) (HOLOCYTOCHROME C- TYPE SYNTHASE). [Source:SWISSPROT;Acc:P53701]	0.0485005	0.17528	0.27670299	HCCS	
445	GLUTATHIONE S-TRANSFERASE THETA 1 (EC 2.5.1.18) (GST CLASS-THETA) (GLUTATHIONE TRANSFERASE T1-1). [Source:SWISSPROT;Acc:P30711]	0.230886	0.83446	0.276689116	GSTT1	
446		0.260039	0.939933	0.276656953	NPLOC4	
447	REGUCALCIN GENE PROMOTOR REGION RELATED PROTEIN; RGPR-P117. [Source:RefSeq;Acc:NM_033127]	0.109365	0.395349	0.276629004	SEC16B	
448		0.141581	0.511852	0.276605347	SEC16A	
449		0.0621484	0.224949	0.276277734	TSNARE1	
450		0.0374708	0.135742	0.27604426	ISY1	

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/