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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Gene Network Comparison Type Rank description Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 975 to 1024 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	network_comparison	green	
975	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	211.987	1.03426	204.964	
976	t-cell activation wd repeat protein. [source:refseq;acc:nm_139281]	243.34	1.03407	235.322	
977	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [source:swissprot;acc:q99471]	228.953	1.03402	221.421	
978	prefoldin subunit 6 (protein ke2). [source:swissprot;acc:o15212]	228.953	1.03402	221.421	
979	gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	202.027	1.03399	195.386	
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]	130.289	1.03396	134.713	
981	exocyst complex component sec6. [source:swissprot;acc:o60645]	207.186	1.03387	200.398	
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	243.312	1.03383	235.351	
983	pbk1 protein. [source:sptrembl;acc:o76021]	243.312	1.03382	235.353	
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	116.71	1.03379	120.654	
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	233.402	1.03375	225.782	
986	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	116.771	1.03371	120.707	
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	1.03369	211.338	
988	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	218.461	1.03368	211.343	
989	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	218.462	1.03367	211.345	
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	243.297	1.03367	235.373	
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	1.03365	196.76	
992	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	218.468	1.03364	211.357	
993	pinin, desmosome associated protein; pinin. [source:refseq;acc:nm_002687]	211.071	1.03362	204.205	
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	1.03361	120.772	
995	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	219.656	1.03345	212.547	
996	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	219.656	1.03345	212.547	
997	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	219.656	1.03345	212.547	
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	225.557	1.03338	218.271	
999	vinculin (metavinculin). [source:swissprot;acc:p18206]	215.92	1.03336	208.95	
1000	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	225.167	1.03325	217.922	
1001	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	225.167	1.03325	217.922	
1002	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	225.167	1.03325	217.922	
1003	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	225.167	1.03325	217.922	
1004	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm_014633]	238.725	1.03318	231.059	
1005	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	225.448	1.03307	218.232	
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	116.524	1.03305	120.375	
1007	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	162.055	1.03296	156.884	
1008	wd-repeat protein bing4. [source:swissprot;acc:o15213]	243.227	1.03292	235.475	
1009	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	229.116	1.03288	221.823	
1010	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	217.523	1.03264	210.648	
1011	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	217.026	1.03253	210.189	
1012	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	217.021	1.03252	210.185	
1013	protein bap28. [source:swissprot;acc:q9h583]	244.312	1.03239	236.647	
1014	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	243.045	1.03238	235.422	
1015	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	221.73	1.03236	228.906	
1016	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	217.369	1.03233	210.561	
1017	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	217.365	1.03233	210.558	
1018	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	217.361	1.03233	210.554	
1019	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	221.302	1.03215	214.409	
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	1.03205	214.409	
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	1.03204	214.409	
1022	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	205.632	1.03195	199.266	
1023	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	205.632	1.03195	199.266	
1024	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	205.632	1.03195	199.266	

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/