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 measured expected Rank description final Hugo
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total 
measured	expected	Rank	description	final	Hugo	
0.000173011	0.7865	3206		0.000219976		
0.000178236	0.81025	3204	ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [Source:RefSeq;Acc:NM_015915]	0.000219977		
0.000571223	2.59675	3205		0.000219976	C1orf166	
0.00386024	0.104721	3199		0.036862138	CHMP2B	
0.0100954	0.273869	3198	PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [Source:RefSeq;Acc:NM_014453]	0.036862149	CHMP2A	
0.0131531	0.0626341	2631	"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [Source:SWISSPROT;Acc:Q15825]"	0.209999026	CHRNA6	
0.0132921	0.0632961	2635	"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [Source:SWISSPROT;Acc:P32297]"	0.20999872	CHRNA3	
0.0139025	0.0611788	2163	PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [Source:SWISSPROT;Acc:P55058]	0.227243751	PLTP	
0.0139875	0.059666	1813	CARBOXYPEPTIDASE B PRECURSOR (EC 3.4.17.2) (PANCREAS-SPECIFIC PROTEIN) (PASP). [Source:SWISSPROT;Acc:P15086]	0.234429994	CPB1	
0.0141571	0.0622988	2157		0.227245148	BPIL2	
0.0142351	0.0677865	2630	"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [Source:SWISSPROT;Acc:Q15822]"	0.209999041	CHRNA2	
0.0142939	0.387764	3192	ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH) LIKE PROTEIN. [Source:RefSeq;Acc:NM_020799]	0.03686237	STAMBPL1	
0.0145774	0.0920202	2932	REGULATOR OF G-PROTEIN SIGNALING 19 (RGS19) (G-ALPHA INTERACTING PROTEIN) (GAIP PROTEIN). [Source:SWISSPROT;Acc:P49795]	0.158415218	RGS19	
0.0147736	0.0932586	2930	REGULATOR OF G-PROTEIN SIGNALING 17 (RGS17). [Source:SWISSPROT;Acc:Q9UGC6]	0.158415417	RGS17	
0.0148857	0.0939662	2929	PUTATIVE RNA-BINDING PROTEIN 15 (RNA BINDING MOTIF PROTEIN 15) (ONE-TWENTY TWO PROTEIN). [Source:SWISSPROT;Acc:Q96T37]	0.158415473	RBM15	
0.015194	0.0959121	2927	TRANSCRIPTION FACTOR LBX1. [Source:SWISSPROT;Acc:P52954]	0.158415883	LBX1	
0.0153184	0.063934	1619	OLIGOPHRENIN 1. [Source:SWISSPROT;Acc:O60890]	0.239597084	OPHN1	
0.0157159	0.0691587	2160	LIPOPOLYSACCHARIDE-BINDING PROTEIN PRECURSOR (LBP). [Source:SWISSPROT;Acc:P18428]	0.227244005	LBP	
0.0163276	0.0681463	1623		0.23959628	ARHGAP10	
0.0164226	0.0707964	1922	CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE B (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE B) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE B) (CT B) (CCT B) (CCT-BETA). [Source:SWISSPROT;Acc:Q9Y5K3]	0.231969422	PCYT1B	
0.0166846	0.0703876	1733	"LIV-1 PROTEIN, ESTROGEN REGULATED. [Source:RefSeq;Acc:NM_012319]"	0.23703891	SLC39A6	
0.0167203	0.0725001	2015	BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [Source:RefSeq;Acc:NM_016567]	0.230624509	BCCIP	
0.016721	0.0728736	2067	RAS-RELATED PROTEIN RAB-26. [Source:SWISSPROT;Acc:Q9ULW5]	0.229452092	RAB26	
0.0167711	0.0715398	1809	CARBOXYPEPTIDASE A5. [Source:RefSeq;Acc:NM_080385]	0.234430345	CPA5	
0.0174686	0.14338	3011	LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (LYMPHOCYTE IGE RECEPTOR) (FC-EPSILON-RII) (CD23) (BLAST-2) (IMMUNOGLOBULIN E-BINDING FACTOR). [Source:SWISSPROT;Acc:P06734]	0.121834287	FCER2	
0.0174991	0.0754368	1916	BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 2 (PAPS SYNTHETHASE 2) (PAPSS 2) (SULFURYLASE KINASE 2) (SK2) (SK 2) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT	0.231970338		
0.0175982	0.0742417	1727	"GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [Source:SWISSPROT;Acc:Q05329]"	0.237039292	GAD2	
0.0179282	0.486357	3195	ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM. [Source:RefSeq;Acc:NM_006463]	0.036862223	STAMBP	
0.0184372	0.333333	3175		0.055311655	NIPA2	
0.0184372	0.333333	3176		0.055311655	C6orf130	
0.0184372	0.333333	3177	PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [Source:RefSeq;Acc:NM_016172]	0.055311655	UBAC1	
0.0186658	0.0888852	2632	"NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [Source:SWISSPROT;Acc:P43681]"	0.209998965	CHRNA4	
0.018683	0.117937	2933	REGULATOR OF G-PROTEIN SIGNALING 20 (RGS20) (REGULATOR OF GZ- SELECTIVE PROTEIN SIGNALING 1) (GZ-SELECTIVE GTPASE-ACTIVATING PROTEIN) (G(Z)GAP). [Source:SWISSPROT;Acc:O76081]	0.158415086	RGS20	
0.018683	0.117937	2934	RAP1 GTPASE-ACTIVATING PROTEIN 1 (RAP1GAP). [Source:SWISSPROT;Acc:P47736]	0.158415086	RAP1GAP	
0.018683	0.117937	2935	CHROMOSOME 3P21.1 GENE SEQUENCE. [Source:RefSeq;Acc:NM_013286]	0.158415086	RBM15B	
0.0187206	0.0807026	1917	NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [Source:SWISSPROT;Acc:P16435]	0.231970222	POR	
0.0187206	0.0807026	1918	BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 1 (PAPS SYNTHETHASE 1) (PAPSS 1) (SULFURYLASE KINASE 1) (SK1) (SK 1) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT	0.231970222	PAPSS1	
0.0187206	0.0807026	1919	CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE A (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE A) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE A) (CT A) (CCT A) (CCT-ALPHA). [Source:SWISSPROT;Acc:P49585]	0.231970222	PCYT1A	
0.018755	0.0901743	2695	T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [Source:SWISSPROT;Acc:O95947]	0.207986089	TBX6	
0.0189378	0.0901805	2633	STAR-RELATED LIPID TRANSFER PROTEIN 8 (STARD8) (START DOMAIN- CONTAINING PROTEIN 8). [Source:SWISSPROT;Acc:Q92502]	0.209998836	STARD8	
0.0189917	0.0821011	1950		0.231320896	ESF1	
0.0190828	0.0826631	1992	HYALURONAN SYNTHASE 1 (EC 2.4.1.212) (HYALURONATE SYNTHASE 1) (HYALURONIC ACID SYNTHASE 1) (HA SYNTHASE 1) (HUHAS1). [Source:SWISSPROT;Acc:Q92839]	0.230850283	HAS1	
0.0191226	0.174179	3040	PANTOTHENATE KINASE 3 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 3) (HPANK3). [Source:SWISSPROT;Acc:Q9H999]	0.109787058	PANK3	
0.0193287	0.0871461	2320	MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [Source:SWISSPROT;Acc:P36952]	0.2217965		
0.0193888	0.176603	3037	"PANTOTHENATE KINASE 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 2) (HPANK2). [Source:SWISSPROT;Acc:Q9BZ23]"	0.109787489	PANK2	
0.0194204	0.0875599	2326	SERPIN B11. [Source:SWISSPROT;Acc:Q96P15]	0.221795594		
0.0194686	0.0842001	1961	ZINC FINGER PROTEIN 291. [Source:SWISSPROT;Acc:Q9BY12]	0.231218253	SCAPER	
0.0194686	0.0842002	1963		0.231217978	MED11	
0.0194686	0.0842002	1964	PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [Source:SWISSPROT;Acc:O43933]	0.231217978	PEX1	
0.0196287	0.0946679	2712	DELTA(14)-STEROL REDUCTASE (EC 1.3.1.70) (C-14 STEROL REDUCTASE) (STEROL C14-REDUCTASE) (DELTA14-SR) (TRANSMEMBRANE 7 SUPERFAMILY MEMBER 2) (ANOTHER NEW GENE 1) (PUTATIVE STEROL REDUCTASE SR-1). [Source:SWISSPROT;Acc:O76062]	0.207342721	TM7SF2	

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/