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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 980 to 1029 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
980	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	134.713	130.289	1.03396	
981	exocyst complex component sec6. [source:swissprot;acc:o60645]	200.398	207.186	1.03387	
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	235.351	243.312	1.03383	
983	pbk1 protein. [source:sptrembl;acc:o76021]	235.353	243.312	1.03382	
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	120.654	116.71	1.03379	
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	225.782	233.402	1.03375	
986	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	120.707	116.771	1.03371	
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]	211.338	218.459	1.03369	
988	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	211.343	218.461	1.03368	
989	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	211.345	218.462	1.03367	
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	235.373	243.297	1.03367	
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]	196.76	203.381	1.03365	
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	211.357	218.468	1.03364	
993	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	204.205	211.071	1.03362	
994	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	120.772	116.845	1.03361	
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	212.547	219.656	1.03345	
996	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	212.547	219.656	1.03345	
997	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	212.547	219.656	1.03345	
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	218.271	225.557	1.03338	
999	vinculin (metavinculin). [source:swissprot;acc:p18206]	208.95	215.92	1.03336	
1000	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	217.922	225.167	1.03325	
1001	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	217.922	225.167	1.03325	
1002	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	217.922	225.167	1.03325	
1003	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	217.922	225.167	1.03325	
1004	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	231.059	238.725	1.03318	
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	218.232	225.448	1.03307	
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	120.375	116.524	1.03305	
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	156.884	162.055	1.03296	
1008	wd-repeat protein bing4. [source:swissprot;acc:o15213]	235.475	243.227	1.03292	
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	221.823	229.116	1.03288	
1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	210.648	217.523	1.03264	
1011	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	210.189	217.026	1.03253	
1012	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	210.185	217.021	1.03252	
1013	protein bap28. [source:swissprot;acc:q9h583]	236.647	244.312	1.03239	
1014	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	235.422	243.045	1.03238	
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	228.906	221.73	1.03236	
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	210.561	217.369	1.03233	
1017	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	210.558	217.365	1.03233	
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	210.554	217.361	1.03233	
1019	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	214.409	221.302	1.03215	
1020	dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [source:swissprot;acc:p40126]	214.409	221.28	1.03205	
1021	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]	214.409	221.278	1.03204	
1022	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	199.266	205.632	1.03195	
1023	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	199.266	205.632	1.03195	
1024	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	199.266	205.632	1.03195	
1025	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	199.266	205.632	1.03195	
1026	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	199.266	205.632	1.03195	
1027	succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [source:swissprot;acc:p53597]	218.627	211.908	1.03171	
1028	succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [source:swissprot;acc:q9p2r7]	218.627	211.908	1.03171	
1029	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [source:swissprot;acc:q16531]	215.535	222.364	1.03168	

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/