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 Hugo final

Results: HTML CSV LaTeX

Showing element 2458 to 2507 of 3206 in total

Rank	description	measured	expected	Hugo	final	
2458		0.565608	2.60988	OXSM	0.21671801	
2459		0.027214	0.125575	C20orf80	0.21671511	
2460	BROMODOMAIN CONTAINING 7; BROMODOMAIN PROTEIN; BROMODOMAIN-CONTAINING 7. [Source:RefSeq;Acc:NM_013263]	0.26631	1.22885	BRD7	0.216714815	
2461		0.0337015	0.155511	RPAP1	0.216714573	
2462	FRG1 PROTEIN (FSHD REGION GENE 1 PROTEIN). [Source:SWISSPROT;Acc:Q14331]	0.0337015	0.155511	FRG1	0.216714573	
2463	TRANSCRIPTIONAL ADAPTOR 3-LIKE ISOFORM A. [Source:RefSeq;Acc:NM_006354]	0.0337015	0.155511	TADA3L	0.216714573	
2464	TRANSCRIPTIONAL ADAPTER 2-LIKE (ADA2-LIKE PROTEIN) (KL04P). [Source:SWISSPROT;Acc:O75478]	0.42132	1.94413	TADA2L	0.216713903	
2465		0.210228	0.970087	BRD9	0.21671046	
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	LGALS4	0.216686964	
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	RNASEH2A	0.21659449	
2468	45 KDA CALCIUM-BINDING PROTEIN PRECURSOR (CAB45) (STROMAL CELL-DERIVED FACTOR 4) (SDF-4). [Source:SWISSPROT;Acc:Q9BRK5]	0.0737619	0.340556	SDF4	0.216592572	
2469	"SPECTRIN BETA CHAIN, BRAIN 4 (SPECTRIN, NON-ERYTHROID BETA CHAIN 4) (BETA-V SPECTRIN) (BSPECV). [Source:SWISSPROT;Acc:Q9NRC6]"	0.0737619	0.340556	SPTBN5	0.216592572	
2470		0.0737619	0.340556	LSM14B	0.216592572	
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	EPB41L3	0.216592245	
2472		0.139984	0.646308	CUEDC2	0.216590233	
2473	PROTEIN 4.1 (BAND 4.1) (P4.1) (EPB4.1) (4.1R). [Source:SWISSPROT;Acc:P11171]	0.0900531	0.415778	EPB41	0.216589382	
2474	BAND 4.1-LIKE PROTEIN 2 (GENERALLY EXPRESSED PROTEIN 4.1) (4.1G). [Source:SWISSPROT;Acc:O43491]	0.0915902	0.422875	EPB41L2	0.216589299	
2475	BAND 4.1-LIKE PROTEIN 1 (NEURONAL PROTEIN 4.1) (4.1N). [Source:SWISSPROT;Acc:Q9H4G0]	0.0882127	0.407281	EPB41L1	0.216589284	
2476		0.0586202	0.270652	LSM14A	0.21658883	
2477	SIMILAR TO TRNA SYNTHETASE CLASS II. [Source:RefSeq;Acc:NM_152268]	0.205001	0.946559	PARS2	0.216574984	
2478	GALECTIN-9 (HOM-HD-21) (ECALECTIN). [Source:SWISSPROT;Acc:O00182]	0.522708	2.41413	LGALS9	0.216520237	
2479	PRE-MRNA CLEAVAGE COMPLEX II PROTEIN PCF11 (FRAGMENT). [Source:SWISSPROT;Acc:O94913]	0.251152	1.15996	PCF11	0.216517811	
2480	CHROMODOMAIN Y-LIKE PROTEIN 2. [Source:RefSeq;Acc:NM_152342]	0.549251	2.53881	CDYL2	0.216341908	
2481	TESTIS-SPECIFIC CHROMODOMAIN PROTEIN Y PROTEIN 2. [Source:SWISSPROT;Acc:Q9Y6F7]	0.659303	3.04797	CDY2B	0.216308888	
2482	TESTIS-SPECIFIC CHROMODOMAIN Y PROTEIN 1. [Source:SWISSPROT;Acc:Q9Y6F8]	0.663776	3.06866	CDY1B	0.216308095	
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	CDYL	0.216308095	
2484	HEMK PROTEIN HOMOLOG (EC 2.1.1.-) (M.HSAHEMKP). [Source:SWISSPROT;Acc:Q9Y5R4]	0.343973	1.59051	HEMK1	0.216265852	
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	GPI	0.216249404	
2486	CEREBRAL CELL ADHESION MOLECULE. [Source:RefSeq;Acc:NM_016174]	0.155588	0.719698	CEECAM1	0.216185122	
2487		0.166202	0.768906	GLT25D1	0.21615386	
2488	FIBULIN-2 PRECURSOR. [Source:SWISSPROT;Acc:P98095]	0.195152	0.90295	FBLN2	0.216127139	
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	REXO4	0.215749527	
2491	DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [Source:RefSeq;Acc:NM_024887]	0.238591	1.10654	DHDDS	0.215618956	
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	SH3GL3	0.215540136	
2494	METHIONYL-TRNA SYNTHETASE (EC 6.1.1.10) (METHIONINE--TRNA LIGASE) (METRS). [Source:SWISSPROT;Acc:P56192]	0.0641898	0.297931	MARS	0.2154519	
2495	HISTIDINE DECARBOXYLASE (EC 4.1.1.22) (HDC). [Source:SWISSPROT;Acc:P19113]	0.0866317	0.402189	HDC	0.215400471	
2496	ARMET PROTEIN PRECURSOR (ARGININE-RICH PROTEIN). [Source:SWISSPROT;Acc:P55145]	0.0869714	0.403767	ARMET	0.215399971	
2497	SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [Source:SWISSPROT;Acc:Q99962]	0.158519	0.735941	SH3GL2	0.215396343	
2498	"UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL PRECURSOR (EC 1.10.2.2). [Source:SWISSPROT;Acc:P31930]"	0.167149	0.776201	UQCRC1	0.215342418	
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	PMPCA	0.215323923	
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	PMPCB	0.215321157	
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	SH3GL1	0.215238121	
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	F11R	0.214832326	
2504	ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [Source:SWISSPROT;Acc:O14977]	0.174979	0.814661	AZIN1	0.214787501	
2505	ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [Source:SWISSPROT;Acc:Q96A70]	0.177719	0.827431	ADC	0.214784073	
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	PLEKHC1	0.214767765	
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/