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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 982 to 1031 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	243.312	235.351	1.03383	
983	pbk1 protein. [source:sptrembl;acc:o76021]	243.312	235.353	1.03382	
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	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]	233.402	225.782	1.03375	
986	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	116.771	120.707	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]	218.459	211.338	1.03369	
988	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	218.461	211.343	1.03368	
989	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	218.462	211.345	1.03367	
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	243.297	235.373	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]	203.381	196.76	1.03365	
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	218.468	211.357	1.03364	
993	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	211.071	204.205	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]	116.845	120.772	1.03361	
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	219.656	212.547	1.03345	
996	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	219.656	212.547	1.03345	
997	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	219.656	212.547	1.03345	
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	225.557	218.271	1.03338	
999	vinculin (metavinculin). [source:swissprot;acc:p18206]	215.92	208.95	1.03336	
1000	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	225.167	217.922	1.03325	
1001	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	225.167	217.922	1.03325	
1002	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	225.167	217.922	1.03325	
1003	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	225.167	217.922	1.03325	
1004	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	238.725	231.059	1.03318	
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	225.448	218.232	1.03307	
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	116.524	120.375	1.03305	
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	162.055	156.884	1.03296	
1008	wd-repeat protein bing4. [source:swissprot;acc:o15213]	243.227	235.475	1.03292	
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	229.116	221.823	1.03288	
1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	217.523	210.648	1.03264	
1011	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	217.026	210.189	1.03253	
1012	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	217.021	210.185	1.03252	
1013	protein bap28. [source:swissprot;acc:q9h583]	244.312	236.647	1.03239	
1014	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	243.045	235.422	1.03238	
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	221.73	228.906	1.03236	
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	217.369	210.561	1.03233	
1017	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	217.365	210.558	1.03233	
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	217.361	210.554	1.03233	
1019	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	221.302	214.409	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]	221.28	214.409	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]	221.278	214.409	1.03204	
1022	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	205.632	199.266	1.03195	
1023	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	205.632	199.266	1.03195	
1024	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	205.632	199.266	1.03195	
1025	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	205.632	199.266	1.03195	
1026	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	205.632	199.266	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]	211.908	218.627	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]	211.908	218.627	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]	222.364	215.535	1.03168	
1030	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [source:swissprot;acc:p05166]	222.364	215.535	1.03168	
1031	probable ribosome biogenesis protein nep1 (c2f protein). [source:swissprot;acc:q92979]	242.978	235.518	1.03167	

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/