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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 780 to 829 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
98	pp3111 protein. [source:refseq;acc:nm_022156]	Squared	0	147.342	66.4852	2.21616	
98	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	Measured	1	2353.63	3225.65	1.3705	
98	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [source:refseq;acc:nm_022445]	Rooted	0	13.2903	17.4395	1.3122	
98	transcription factor lbx1. [source:swissprot;acc:p52954]	Rooted	1	47.6504	36.9304	1.29028	
98	trs85 homolog. [source:swissprot;acc:q9y2l5]	Squared	1	227160	146079	1.55505	
99	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Ranked	1	88.2482	110.265	1.24949	
99	mosaic protein lgn. [source:swissprot;acc:p81274]	Rooted	1	47.6504	36.9304	1.29028	
99	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Ranked	0	12787.8	10454.7	1.22316	
99	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Squared	0	492.157	225.924	2.17842	
99	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	Rooted	0	31.495	24.0263	1.31086	
99	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991]	Measured	1	2353.63	3225.65	1.3705	
99	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [source:swissprot;acc:q9y4p3]	Measured	0	817.81	551.434	1.48306	
99	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Squared	1	226186	145568	1.55382	
100	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [source:swissprot;acc:p12956]	Measured	0	594	402	1.47761	
100	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Squared	1	226186	145568	1.55382	
100	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	Ranked	0	9183.49	11217.7	1.22151	
100	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	Measured	1	2353.63	3225.65	1.3705	
100	glycine receptor alpha-3 chain precursor. [source:swissprot;acc:o75311]	Rooted	0	20.0501	15.3244	1.30838	
100	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Ranked	1	88.2482	110.265	1.24949	
100	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	Squared	0	492.157	225.924	2.17842	
100	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	Rooted	1	47.6504	36.9304	1.29028	
101	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Squared	1	222655	143584	1.5507	
101	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Measured	1	2353.63	3225.65	1.3705	
101	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Ranked	0	14548.5	11915.2	1.221	
101	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	Rooted	1	47.6504	36.9304	1.29028	
101	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	Rooted	0	12.6886	9.74679	1.30182	
101	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Ranked	1	88.2482	110.265	1.24949	
101	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Measured	0	1442	977	1.47595	
101	transcription factor iiia (factor a) (tfiiia). [source:swissprot;acc:q92664]	Squared	0	956.375	441.285	2.16725	
102	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	Ranked	0	12738.7	10437.1	1.22052	
102	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Squared	1	214143	138337	1.54798	
102	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	Ranked	1	88.2482	110.265	1.24949	
102	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	Measured	0	1442	977	1.47595	
102	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Measured	1	2353.63	3225.65	1.3705	
102	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Rooted	1	47.6504	36.9304	1.29028	
102	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [source:refseq;acc:nm_006916]	Squared	0	61.6678	132.922	2.15545	
102	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	Rooted	0	12.0669	15.6768	1.29916	
103	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Measured	1	2353.63	3225.65	1.3705	
103	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Ranked	0	7495.26	9130.38	1.21815	
103	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	Squared	1	407289	263351	1.54656	
103	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Rooted	0	17.1172	22.2036	1.29715	
103	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	Rooted	1	60.8365	77.7233	1.27758	
103	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [source:refseq;acc:nm_022445]	Squared	0	61.6678	132.922	2.15545	
103	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	Measured	0	197.333	290.667	1.47298	
103	trophinin. [source:swissprot;acc:q12816]	Ranked	1	88.2482	110.265	1.24949	
104	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	Squared	1	407289	263351	1.54656	
104	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Rooted	0	13.7413	17.8164	1.29656	
104	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Ranked	1	252.371	202.016	1.24926	
104	jun dimerization protein. [source:refseq;acc:nm_130469]	Rooted	1	60.8365	77.7233	1.27758	
104	metabotropic glutamate receptor 3 precursor (mglur3). [source:swissprot;acc:q14832]	Squared	0	0.70501	1.50296	2.13183	

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/