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 Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1963 to 2012 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	Divided	243.312	235.351	1.03383	
982	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Subtracted	211.987	204.964	7.023	
983	pbk1 protein. [source:sptrembl;acc:o76021]	Divided	243.312	235.353	1.03382	
983	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Subtracted	211.987	204.964	7.023	
984	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Subtracted	211.987	204.964	7.023	
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Divided	116.71	120.654	1.03379	
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	Divided	233.402	225.782	1.03375	
985	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Subtracted	211.987	204.964	7.023	
986	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Divided	116.771	120.707	1.03371	
986	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Subtracted	211.987	204.964	7.023	
987	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Subtracted	211.987	204.964	7.023	
987	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	Divided	218.459	211.338	1.03369	
988	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Divided	218.461	211.343	1.03368	
988	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Subtracted	236.679	243.679	7	
989	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	Divided	218.462	211.345	1.03367	
989	zinc finger protein 277. [source:swissprot;acc:q9nrm2]	Subtracted	236.679	243.679	7	
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	Divided	243.297	235.373	1.03367	
990	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [source:refseq;acc:nm_012301]	Subtracted	221.682	228.68	6.998	
991	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Divided	203.381	196.76	1.03365	
991	polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [source:swissprot;acc:q01780]	Subtracted	198.494	205.466	6.972	
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Divided	218.468	211.357	1.03364	
992	vinculin (metavinculin). [source:swissprot;acc:p18206]	Subtracted	215.92	208.95	6.97	
993	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [source:swissprot;acc:q14541]	Subtracted	251.863	258.829	6.966	
993	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	Divided	211.071	204.205	1.03362	
994	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [source:swissprot;acc:o95257]	Subtracted	251.863	258.829	6.966	
994	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Divided	116.845	120.772	1.03361	
995	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [source:swissprot;acc:p24522]	Subtracted	251.863	258.829	6.966	
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	Divided	219.656	212.547	1.03345	
996	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [source:swissprot;acc:p41235]	Subtracted	251.863	258.829	6.966	
996	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Divided	219.656	212.547	1.03345	
997	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [source:swissprot;acc:o75293]	Subtracted	251.863	258.829	6.966	
997	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	Divided	219.656	212.547	1.03345	
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	Divided	225.557	218.271	1.03338	
998	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	Subtracted	221.302	214.409	6.893	
999	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [source:swissprot;acc:q14192]	Subtracted	269.608	276.493	6.885	
999	vinculin (metavinculin). [source:swissprot;acc:p18206]	Divided	215.92	208.95	1.03336	
1000	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	Subtracted	217.523	210.648	6.875	
1000	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Divided	225.167	217.922	1.03325	
1001	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [source:swissprot;acc:p40126]	Subtracted	221.28	214.409	6.871	
1001	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Divided	225.167	217.922	1.03325	
1002	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Subtracted	221.278	214.409	6.869	
1002	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Divided	225.167	217.922	1.03325	
1003	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	Subtracted	211.071	204.205	6.866	
1003	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Divided	225.167	217.922	1.03325	
1004	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	Divided	238.725	231.059	1.03318	
1004	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [source:swissprot;acc:q13643]	Subtracted	269.59	276.454	6.864	
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	Divided	225.448	218.232	1.03307	
1005	dyskerin (nucleolar protein nap57) (cbf5 homolog). [source:swissprot;acc:o60832]	Subtracted	231.007	237.864	6.857	
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Divided	116.524	120.375	1.03305	
1006	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Subtracted	217.026	210.189	6.837	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/