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 Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2912 to 2961 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
728	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [source:swissprot;acc:p21281]	Squared	25911.8	30282.2	1.16866	
729	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	Rooted	62.5069	66.8603	1.06965	
729	huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm_007076]	Ranked	208.874	219.708	1.05187	
729	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [source:swissprot;acc:p38606]	Measured	6000.23	6696.89	1.11611	
729	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [source:swissprot;acc:p15313]	Squared	25910.8	30280.9	1.16866	
730	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	Measured	6000.23	6696.89	1.11611	
730	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Squared	24644.9	28800.7	1.16863	
730	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	Rooted	62.5729	66.9286	1.06961	
730	mitochondrial import inner membrane translocase subunit tim10. [source:swissprot;acc:q9y5j8]	Ranked	208.874	219.708	1.05187	
731	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Rooted	98.2298	91.8648	1.06929	
731	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [source:swissprot;acc:p07954]	Ranked	208.874	219.708	1.05187	
731	methyltransferase like 2. [source:refseq;acc:nm_018396]	Measured	13241.4	11864	1.1161	
731	vinculin (metavinculin). [source:swissprot;acc:p18206]	Squared	27463	32090.3	1.16849	
732	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Measured	13241.4	11864	1.1161	
732	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	Rooted	51.8444	48.4963	1.06904	
732	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	Ranked	124.434	118.318	1.05169	
732	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	Squared	26029.8	30414.4	1.16845	
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Ranked	164	155.961	1.05154	
733	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Measured	13241.4	11864	1.1161	
733	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	Rooted	52.0099	55.5904	1.06884	
733	vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [source:swissprot;acc:q13488]	Squared	26029.1	30413.6	1.16845	
734	loh1cr12. [source:refseq;acc:nm_058169]	Rooted	57.805	61.7803	1.06877	
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	Ranked	232.601	244.534	1.0513	
734	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Measured	13241.4	11864	1.1161	
734	vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [source:swissprot;acc:q93050]	Squared	26032.5	30417.7	1.16845	
735	atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [source:refseq;acc:nm_020632]	Squared	26030.5	30415.2	1.16844	
735	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	Ranked	232.601	244.534	1.0513	
735	unr protein. [source:swissprot;acc:o75534]	Rooted	57.805	61.7803	1.06877	
735	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [source:swissprot;acc:p27449]	Measured	5768.32	6434.78	1.11554	
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Ranked	232.601	244.534	1.0513	
736	putative sialoglycoprotease type 2. [source:refseq;acc:nm_022353]	Squared	22017.1	25721.9	1.16827	
736	sarcoglycan zeta; zeta-sarcoglycan. [source:refseq;acc:nm_139167]	Measured	5768.32	6434.78	1.11554	
736	wd-repeat protein 3. [source:swissprot;acc:q9unx4]	Rooted	51.5438	55.0853	1.06871	
737	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [source:refseq;acc:nm_022735]	Measured	5768.32	6434.78	1.11554	
737	pnas-18. [source:sptrembl;acc:q9bzu3]	Rooted	97.8205	91.5467	1.06853	
737	septin 10 isoform 1. [source:refseq;acc:nm_144710]	Ranked	125.526	119.402	1.05129	
737	transducin-like enhancer protein 2 (esg2). [source:swissprot;acc:q04725]	Squared	31479.4	36770.8	1.16809	
738	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	Measured	5768.32	6434.78	1.11554	
738	syntaxin 7. [source:swissprot;acc:o15400]	Rooted	61.5022	65.7076	1.06838	
738	transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	Squared	31467.1	36752.2	1.16796	
738	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	Ranked	222.825	211.966	1.05123	
739	cellular modulator of immune recognition. [source:refseq;acc:nm_145021]	Measured	5768.32	6434.78	1.11554	
739	exocyst complex component sec10 (hsec10). [source:swissprot;acc:o00471]	Rooted	65.3677	69.828	1.06823	
739	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	Ranked	223.58	235.027	1.0512	
739	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [source:swissprot;acc:o75792]	Squared	25727.7	30046.7	1.16787	
740	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [source:swissprot;acc:p31939]	Ranked	223.58	235.027	1.0512	
740	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	Rooted	53.1114	56.7251	1.06804	
740	o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	Squared	22075.1	25775.1	1.16761	
740	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	Measured	5768.32	6434.78	1.11554	
741	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	Rooted	53.1114	56.7251	1.06804	

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/