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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Gene Rank description measured expected final Hugo

Results: HTML CSV LaTeX

Showing element 1852 to 1901 of 3206 in total

Rank	description	measured	expected	final	Hugo	
1852	PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [Source:SWISSPROT;Acc:Q8TCT7]	0.0331615	0.142049	0.233451133		
1853		0.0331615	0.142049	0.233451133		
1854		0.0274494	0.117581	0.233450983		
1855	PRESENILIN-LIKE PROTEIN 2 (EC 3.4.99.-) (SPPL2A PROTEIN). [Source:SWISSPROT;Acc:Q8TCT8]	0.0275157	0.117865	0.233450982		
1856	GTP-BINDING NUCLEAR PROTEIN RAN (TC4) (RAN GTPASE) (ANDROGEN RECEPTOR- ASSOCIATED PROTEIN 24). [Source:SWISSPROT;Acc:P17080]	0.46892	2.00865	0.233450327	RANP1	
1857		0.0252313	0.108089	0.233430784	FCF1	
1858	DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB7). [Source:SWISSPROT;Acc:P52433]	0.222313	0.952373	0.233430599	POLR2G	
1859		0.111248	0.476584	0.233427895	GTPBP8	
1860		0.107268	0.459557	0.233416094	POLR3GL	
1861	POLYMERASE (RNA) III (DNA DIRECTED) (32KD). [Source:RefSeq;Acc:NM_006467]	0.130061	0.557208	0.233415529	POLR3G	
1862	ALANYL-TRNA SYNTHETASE (EC 6.1.1.7) (ALANINE--TRNA LIGASE) (ALARS). [Source:SWISSPROT;Acc:P49588]	0.321507	1.37786	0.23333793	AARS	
1863		0.031449	0.134819	0.233268308	DOLK	
1864	THYMIDYLATE KINASE (EC 2.7.4.9) (DTMP KINASE). [Source:SWISSPROT;Acc:P23919]	0.51096	2.19044	0.233268202	DTYMK	
1865	DYNACTIN 4. [Source:RefSeq;Acc:NM_032486]	0.0462274	0.198227	0.233204357	DCTN5	
1866	DIPHOSPHOMEVALONATE DECARBOXYLASE (EC 4.1.1.33) (MEVALONATE PYROPHOSPHATE DECARBOXYLASE) (MEVALONATE (DIPHOSPHO)DECARBOXYLASE). [Source:SWISSPROT;Acc:P53602]	0.0688073	0.295201	0.23308627	MVD	
1867	NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE [CARBOXYLATING] (EC 2.4.2.19) (QUINOLINATE PHOSPHORIBOSYLTRANSFERASE [DECARBOXYLATING]) (QAPRTASE) (QPRTASE). [Source:SWISSPROT;Acc:Q15274]	0.133589	0.573452	0.232955853	QPRT	
1868	DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 4 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 4) (FMO 4) (DIMETHYLANILINE OXIDASE 4). [Source:SWISSPROT;Acc:P31512]	0.0525547	0.225696	0.232856143	FMO4	
1869	DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 1 (EC 1.14.13.8) (FETAL HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 1) (FMO 1) (DIMETHYLANILINE OXIDASE 1). [Source:SWISSPROT;Acc:Q01740]	0.0533745	0.229226	0.232846623	FMO1	
1870	"CREATINE KINASE, B CHAIN (EC 2.7.3.2) (B-CK). [Source:SWISSPROT;Acc:P12277]"	0.235164	1.00998	0.232840254	CKB	
1871	DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 2 (EC 1.14.13.8) (PULMONARY FLAVIN-CONTAINING MONOOXYGENASE 2) (FMO 2) (DIMETHYLANILINE OXIDASE 2) (FMO 1B1). [Source:SWISSPROT;Acc:Q99518]	0.0540721	0.232231	0.232837563	FMO2	
1872	26S PROTEASE REGULATORY SUBUNIT 4 (P26S4). [Source:SWISSPROT;Acc:Q03527]	0.825694	3.54636	0.23282859	PSMC1	
1873	DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 3 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 3) (FMO 3) (DIMETHYLANILINE OXIDASE 3) (FMO FORM 2) (FMO II). [Source:SWISSPROT;Acc:P31513]	0.0571767	0.245601	0.232803205	FMO3	
1874	CELLULAR MODULATOR OF IMMUNE RECOGNITION. [Source:RefSeq;Acc:NM_145021]	0.0341996	0.146922	0.232773853	MARCH8	
1875	GOLGI COMPLEX ASSOCIATED PROTEIN 1; GOLGI RESIDENT PROTEIN GCP60; PERIPHERIAL BENZODIAZEPINE RECEPTOR ASSOCIATED PROTEIN; GOLGI PHOSPHOPROTEIN 1; PBR ASSOCIATED PROTEIN; PKA (RIALPHA)-ASSOCIATED PROTEIN. [Source:RefSeq;Acc:NM_022735]	0.154668	0.664457	0.232773528	ACBD3	
1876	SARCOGLYCAN ZETA; ZETA-SARCOGLYCAN. [Source:RefSeq;Acc:NM_139167]	0.0628075	0.269823	0.232772966	SGCZ	
1877	GAMMA-SARCOGLYCAN (GAMMA-SG) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [Source:SWISSPROT;Acc:Q13326]	0.0566858	0.243524	0.232772951	SGCG	
1878	DELTA-SARCOGLYCAN (SG-DELTA) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [Source:SWISSPROT;Acc:Q92629]	0.0630725	0.270962	0.232772492	SGCD	
1879	VACUOLAR ATP SYNTHASE 21 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14) (HATPL). [Source:SWISSPROT;Acc:Q99437]	0.465943	2.00171	0.23277248	ATP6V0B	
1880	VACUOLAR ATP SYNTHASE 16 KDA PROTEOLIPID SUBUNIT (EC 3.6.3.14). [Source:SWISSPROT;Acc:P27449]	0.556589	2.39113	0.232772371	ATP6V0C	
1881		0.0285481	0.122644	0.232772088	MARCH1	
1882	"CREATINE KINASE, UBIQUITOUS MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (U- MTCK) (MIA-CK) (ACIDIC-TYPE MITOCHONDRIAL CREATINE KINASE). [Source:SWISSPROT;Acc:P12532]"	0.199469	0.856983	0.232757243		
1883	"CREATINE KINASE, SARCOMERIC MITOCHONDRIAL PRECURSOR (EC 2.7.3.2) (S- MTCK) (MIB-CK) (BASIC-TYPE MITOCHONDRIAL CREATINE KINASE). [Source:SWISSPROT;Acc:P17540]"	0.197547	0.848743	0.232752435	CKMT2	
1884	PUTATIVE DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 6 (EC 1.14.13.8) (FLAVIN-CONTAINING MONOOXYGENASE 6) (FMO 6) (DIMETHYLANILINE OXIDASE 6). [Source:SWISSPROT;Acc:O60774]	0.0627928	0.269788	0.232748677	FMO6P	
1885	DIMETHYLANILINE MONOOXYGENASE [N-OXIDE FORMING] 5 (EC 1.14.13.8) (HEPATIC FLAVIN-CONTAINING MONOOXYGENASE 5) (FMO 5) (DIMETHYLANILINE OXIDASE 5). [Source:SWISSPROT;Acc:P49326]	0.0627928	0.269788	0.232748677	FMO5	
1886	J DOMAIN PROTEIN C21ORF55. [Source:SWISSPROT;Acc:Q9NX36]	0.107843	0.463351	0.232745802	C21orf55	
1887	PEPTIDYL PROLYL ISOMERASE H; CYCLOPHILIN H. [Source:RefSeq;Acc:NM_006347]	0.039427	0.1694	0.232744982	PPIH	
1888	PRP18 PRE-MRNA PROCESSING FACTOR 18 HOMOLOG. [Source:RefSeq;Acc:NM_003675]	0.184055	0.790803	0.232744438	PRPF18	
1889	DIHYDROFOLATE REDUCTASE (EC 1.5.1.3). [Source:SWISSPROT;Acc:P00374]	0.241532	1.03785	0.232723419		
1890	STROMAL CELL-DERIVED FACTOR 2-LIKE PROTEIN 1 PRECURSOR (SDF2 LIKE PROTEIN 1) (PWP1-INTERACTING PROTEIN 8). [Source:SWISSPROT;Acc:Q9HCN8]	0.0221128	0.0950179	0.232722466	SDF2L1	
1891	STROMAL CELL-DERIVED FACTOR 2 PRECURSOR (SDF-2). [Source:SWISSPROT;Acc:Q99470]	0.0275634	0.118439	0.23272233	SDF2	
1892	THYMIDYLATE SYNTHASE (EC 2.1.1.45) (TS) (TSASE). [Source:SWISSPROT;Acc:P04818]	0.0275634	0.118439	0.23272233	TYMS	
1893	60S RIBOSOMAL PROTEIN L3-LIKE. [Source:SWISSPROT;Acc:Q92901]	1.34083	5.76236	0.232687649	RPL3L	
1894	"CREATINE KINASE, M CHAIN (EC 2.7.3.2) (M-CK). [Source:SWISSPROT;Acc:P06732]"	0.219925	0.945419	0.232621726	CKM	
1895	MICROTUBULE-ASSOCIATED PROTEIN 4 (MAP 4). [Source:SWISSPROT;Acc:P27816]	0.036083	0.155117	0.232617959	MAP4	
1896	VAM6/VPS39-LIKE PROTEIN (HVAM6P). [Source:SWISSPROT;Acc:Q96JC1]	0.403209	1.73336	0.232616998	VPS39	
1897	40S RIBOSOMAL PROTEIN S13. [Source:SWISSPROT;Acc:Q02546]	0.3472	1.49288	0.232570602	RPS13	
1898	"TRANSLATION INITIATION FACTOR IF-2, MITOCHONDRIAL PRECURSOR (IF-2MT) (IF-2(MT)). [Source:SWISSPROT;Acc:P46199]"	0.416108	1.78993	0.232471661	MTIF2	
1899	60S RIBOSOMAL PROTEIN L17 (L23). [Source:SWISSPROT;Acc:P18621]	0.63284	2.72242	0.232454948		
1900	ENDOTHELIAL-DERIVED GENE 1. [Source:RefSeq;Acc:NM_025205]	0.0600275	0.258242	0.232446697	MED28	
1901	RRP5 PROTEIN HOMOLOG (PROGRAMMED CELL DEATH PROTEIN 11). [Source:SWISSPROT;Acc:Q14690]	0.132484	0.570026	0.232417469	PDCD11	

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/