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

Results: HTML CSV LaTeX

Showing element 2608 to 2657 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1304	glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [source:swissprot;acc:p00390]	Divided	207.387	212.275	1.02357	
1305	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [source:swissprot;acc:q14206]	Subtracted	218.509	213.649	4.86	
1305	serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [source:swissprot;acc:q08209]	Divided	218.439	213.436	1.02344	
1306	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [source:swissprot;acc:p53805]	Subtracted	218.508	213.648	4.86	
1306	serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [source:swissprot;acc:p48454]	Divided	218.441	213.441	1.02343	
1307	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	Subtracted	218.509	213.649	4.86	
1307	serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [source:swissprot;acc:p16299]	Divided	218.44	213.44	1.02343	
1308	p protein (melanocyte-specific transporter protein). [source:swissprot;acc:q04671]	Divided	218.44	213.439	1.02343	
1308	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Subtracted	217.133	212.289	4.844	
1309	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027]	Subtracted	216.772	221.594	4.822	
1309	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Divided	226.439	221.26	1.02341	
1310	phd finger protein 9. [source:refseq;acc:nm_018062]	Subtracted	216.772	221.594	4.822	
1310	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	Divided	226.439	221.26	1.02341	
1311	small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	Subtracted	216.772	221.594	4.822	
1311	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	Divided	226.439	221.26	1.02341	
1312	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	Subtracted	215.162	210.412	4.75	
1312	rad50 homolog isoform 1. [source:refseq;acc:nm_005732]	Divided	199.739	204.407	1.02337	
1313	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	Subtracted	215.162	210.412	4.75	
1313	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	Divided	222.573	227.75	1.02326	
1314	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	Divided	222.573	227.751	1.02326	
1314	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	Subtracted	215.162	210.412	4.75	
1315	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	Divided	222.574	227.752	1.02326	
1315	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	Subtracted	218.569	213.832	4.737	
1316	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	Divided	222.569	227.739	1.02323	
1316	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	Subtracted	218.572	213.841	4.731	
1317	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	Divided	206.773	202.105	1.0231	
1317	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	Subtracted	218.574	213.847	4.727	
1318	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	Subtracted	218.591	213.899	4.692	
1318	signal transducer and activator of transcription 5a. [source:swissprot;acc:p42229]	Divided	222.546	227.673	1.02304	
1319	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	Subtracted	206.773	202.105	4.668	
1319	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	Divided	159.75	156.153	1.02304	
1320	rad50 homolog isoform 1. [source:refseq;acc:nm_005732]	Subtracted	199.739	204.407	4.668	
1320	signal transducer and activator of transcription 5b. [source:swissprot;acc:p51692]	Divided	222.544	227.667	1.02302	
1321	m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [source:swissprot;acc:p30307]	Subtracted	259.439	254.797	4.642	
1321	probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [source:swissprot;acc:q9unq2]	Divided	226.347	221.259	1.023	
1322	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	Divided	159.86	156.275	1.02294	
1322	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [source:swissprot;acc:o15524]	Subtracted	216.542	211.908	4.634	
1323	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	Divided	205.225	200.625	1.02293	
1323	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	Subtracted	216.542	211.908	4.634	
1324	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	Subtracted	216.542	211.908	4.634	
1324	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Divided	159.993	156.421	1.02284	
1325	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	Subtracted	216.542	211.908	4.634	
1325	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [source:refseq;acc:nm_020135]	Divided	217.133	212.289	1.02282	
1326	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4w2]	Divided	218.509	213.648	1.02275	
1326	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	Subtracted	214.987	210.359	4.628	
1327	eyes absent homolog 3. [source:swissprot;acc:q99504]	Subtracted	218.537	213.91	4.627	
1327	zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [source:swissprot;acc:q8n9l1]	Divided	218.509	213.648	1.02275	
1328	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [source:swissprot;acc:q14206]	Divided	218.509	213.649	1.02275	
1328	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	Subtracted	214.971	210.354	4.617	
1329	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	Subtracted	205.225	200.625	4.6	

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/