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 2458 to 2507 of 3206 in total

Rank	description	measured	expected	final	Hugo	
2458		0.565608	2.60988	0.21671801	OXSM	
2459		0.027214	0.125575	0.21671511	C20orf80	
2460	BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [Source:RefSeq;Acc:NM_013263]	0.26631	1.22885	0.216714815	BRD7	
2461		0.0337015	0.155511	0.216714573	RPAP1	
2462	FRG1 PROTEIN (FSHD REGION GENE 1 PROTEIN). [Source:SWISSPROT;Acc:Q14331]	0.0337015	0.155511	0.216714573	FRG1	
2463	TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [Source:RefSeq;Acc:NM_006354]	0.0337015	0.155511	0.216714573	TADA3L	
2464	TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [Source:SWISSPROT;Acc:O75478]	0.42132	1.94413	0.216713903	TADA2L	
2465		0.210228	0.970087	0.21671046	BRD9	
2466	GALECTIN-4 (LACTOSE-BINDING LECTIN 4) (L-36 LACTOSE BINDING PROTEIN) (L36LBP) (ANTIGEN NY-CO-27). [Source:SWISSPROT;Acc:P56470]	0.384329	1.77366	0.216686964	LGALS4	
2467	RIBONUCLEASE HI LARGE SUBUNIT (EC 3.1.26.-) (RNASE HI LARGE SUBUNIT) (RNASE H(35)) (RIBONUCLEASE H2) (RNASE H2). [Source:SWISSPROT;Acc:O75792]	0.321097	1.48248	0.21659449	RNASEH2A	
2468	45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [Source:SWISSPROT;Acc:Q9BRK5]	0.0737619	0.340556	0.216592572	SDF4	
2469	"SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [Source:SWISSPROT;Acc:Q9NRC6]"	0.0737619	0.340556	0.216592572	SPTBN5	
2470		0.0737619	0.340556	0.216592572	LSM14B	
2471	BAND 4.1-LIKE PROTEIN 3 (4.1B) (DIFFERENTIALLY EXPRESSED IN ADENOCARCINOMA OF THE LUNG PROTEIN 1) (DAL-1). [Source:SWISSPROT;Acc:Q9Y2J2]	0.115589	0.533671	0.216592245	EPB41L3	
2472		0.139984	0.646308	0.216590233	CUEDC2	
2473	PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [Source:SWISSPROT;Acc:P11171]	0.0900531	0.415778	0.216589382	EPB41	
2474	BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [Source:SWISSPROT;Acc:O43491]	0.0915902	0.422875	0.216589299	EPB41L2	
2475	BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [Source:SWISSPROT;Acc:Q9H4G0]	0.0882127	0.407281	0.216589284	EPB41L1	
2476		0.0586202	0.270652	0.21658883	LSM14A	
2477	SIMILAR TO TRNA SYNTHETASE CLASS II. [Source:RefSeq;Acc:NM_152268]	0.205001	0.946559	0.216574984	PARS2	
2478	GALECTIN-9 (HOM-HD-21) (ECALECTIN). [Source:SWISSPROT;Acc:O00182]	0.522708	2.41413	0.216520237	LGALS9	
2479	PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [Source:SWISSPROT;Acc:O94913]	0.251152	1.15996	0.216517811	PCF11	
2480	CHROMODOMAIN Y-LIKE PROTEIN 2. [Source:RefSeq;Acc:NM_152342]	0.549251	2.53881	0.216341908	CDYL2	
2481	TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [Source:SWISSPROT;Acc:Q9Y6F7]	0.659303	3.04797	0.216308888	CDY2B	
2482	TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [Source:SWISSPROT;Acc:Q9Y6F8]	0.663776	3.06866	0.216308095	CDY1B	
2483	"CHROMODOMAIN PROTEIN, Y CHROMOSOME-LIKE ISOFORM A; CDY-LIKE, AUTOSOMAL; TESTIS-SPECIFIC CHROMODOMAIN Y-LIKE PROTEIN. [Source:RefSeq;Acc:NM_004824]"	0.663776	3.06866	0.216308095	CDYL	
2484	HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [Source:SWISSPROT;Acc:Q9Y5R4]	0.343973	1.59051	0.216265852	HEMK1	
2485	GLUCOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.9) (GPI) (PHOSPHOGLUCOSE ISOMERASE) (PGI) (PHOSPHOHEXOSE ISOMERASE) (PHI) (NEUROLEUKIN) (NLK) (SPERM ANTIGEN-36) (SA-36). [Source:SWISSPROT;Acc:P06744]	0.13384	0.618915	0.216249404	GPI	
2486	CEREBRAL CELL ADHESION MOLECULE. [Source:RefSeq;Acc:NM_016174]	0.155588	0.719698	0.216185122	CEECAM1	
2487		0.166202	0.768906	0.21615386	GLT25D1	
2488	FIBULIN-2 PRECURSOR. [Source:SWISSPROT;Acc:P98095]	0.195152	0.90295	0.216127139	FBLN2	
2489		0.194172	0.898593	0.216084479		
2490	XPMC2 PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG; XENOPUS PREVENTS MITOTIC CATASTROPHE 2 HOMOLOG. [Source:RefSeq;Acc:NM_020385]	0.172887	0.801332	0.215749527	REXO4	
2491	DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [Source:RefSeq;Acc:NM_024887]	0.238591	1.10654	0.215618956	DHDDS	
2492		0.239571	1.11109	0.215617997		
2493	SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [Source:SWISSPROT;Acc:Q99963]	0.171407	0.795244	0.215540136	SH3GL3	
2494	METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [Source:SWISSPROT;Acc:P56192]	0.0641898	0.297931	0.2154519	MARS	
2495	HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [Source:SWISSPROT;Acc:P19113]	0.0866317	0.402189	0.215400471	HDC	
2496	ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [Source:SWISSPROT;Acc:P55145]	0.0869714	0.403767	0.215399971	ARMET	
2497	SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [Source:SWISSPROT;Acc:Q99962]	0.158519	0.735941	0.215396343	SH3GL2	
2498	"UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [Source:SWISSPROT;Acc:P31930]"	0.167149	0.776201	0.215342418	UQCRC1	
2499	"MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [Source:SWISSPROT;Acc:Q10713]"	0.235517	1.09378	0.215323923	PMPCA	
2500	"MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (BETA-MPP) (P-52). [Source:SWISSPROT;Acc:O75439]"	0.208649	0.969013	0.215321157	PMPCB	
2501	SH3-CONTAINING GRB2-LIKE PROTEIN 1 (SH3 DOMAIN PROTEIN 2B) (EXTRA ELEVEN-NINETEEN LEUKEMIA FUSION GENE) (EEN) (EEN FUSION PARTNER OF MLL). [Source:SWISSPROT;Acc:Q99961]	0.172401	0.800978	0.215238121	SH3GL1	
2502	KERATIN ASSOCIATED PROTEIN 9-4; KERATIN ASSOCIATED PROTEIN 9.4. [Source:RefSeq;Acc:NM_033191]	1.02862	4.7857	0.214936164		
2503	JUNCTIONAL ADHESION MOLECULE 1 PRECURSOR (JAM) (PLATELET ADHESION MOLECULE 1) (PAM-1) (PLATELET F11 RECEPTOR). [Source:SWISSPROT;Acc:Q9Y624]	0.26445	1.23096	0.214832326	F11R	
2504	ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [Source:SWISSPROT;Acc:O14977]	0.174979	0.814661	0.214787501	AZIN1	
2505	ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [Source:SWISSPROT;Acc:Q96A70]	0.177719	0.827431	0.214784073	ADC	
2506	"PLECKSTRIN HOMOLOGY DOMAIN CONTAINING, FAMILY C (WITH FERM DOMAIN) MEMBER 1; MITOGEN INDUCIBLE 2; KINDLIN 2. [Source:RefSeq;Acc:NM_006832]"	0.0405241	0.188688	0.214767765	PLEKHC1	
2507	ALPHA-PARVIN (CALPONIN-LIKE INTEGRIN-LINKED KINASE BINDING PROTEIN) (CH-ILKBP). [Source:SWISSPROT;Acc:Q9NVD7]	0.0405241	0.188688	0.214767765		

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/