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 2058 to 2107 of 29840 in total

Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
129	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	Measured	Subtracted	0	1143.55	1397.66	254.11	
129	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	Rooted	Divided	0	27.8028	22.9122	1.21345	
129	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Squared	Divided	1	178263	118639	1.50257	
129	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Measured	Divided	0	606.485	454.837	1.33341	
129	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [source:refseq;acc:nm_015316]	Measured	Subtracted	1	15274.9	13346.9	1928	
129	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [source:swissprot;acc:p51571]	Squared	Subtracted	1	71062.4	95488.9	24426.5	
129	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:o75310]	Rooted	Subtracted	0	32.4121	28.377	4.0351	
130	44050 protein. [source:refseq;acc:nm_178832]	Squared	Divided	1	148058	99628.4	1.4861	
130	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Squared	Subtracted	0	3686.65	4639.46	952.81	
130	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	Squared	Subtracted	1	71062.4	95488.9	24426.5	
130	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	Measured	Subtracted	0	3053.31	2799.81	253.5	
130	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Squared	Divided	0	21165.1	38499.2	1.81899	
130	enigma protein; lim domain protein. [source:refseq;acc:nm_005451]	Ranked	Divided	0	14476.2	17069.5	1.17914	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Measured	Divided	1	2234.68	2978.53	1.33287	
130	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Rooted	Divided	1	55.1026	67.5701	1.22626	
130	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	Measured	Divided	0	42	56	1.33333	
130	p66 alpha. [source:refseq;acc:nm_017660]	Measured	Subtracted	1	12839	10911.1	1927.9	
130	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	Ranked	Subtracted	1	242.735	276.059	33.324	
130	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Ranked	Subtracted	0	14922.7	13174.5	1748.2	
130	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Ranked	Divided	1	94	114	1.21277	
130	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Rooted	Subtracted	1	144.606	157.824	13.218	
130	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Rooted	Divided	0	12.7347	10.4997	1.21286	
130	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [source:swissprot;acc:p06133]	Rooted	Subtracted	0	32.4121	28.377	4.0351	
131	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Squared	Subtracted	0	101.05	1034.13	933.08	
131	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [source:swissprot;acc:p35268]	Rooted	Divided	0	19.3128	16.0484	1.20341	
131	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	Ranked	Divided	0	8375.43	9873.58	1.17887	
131	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	Ranked	Subtracted	1	242.718	276.018	33.3	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Measured	Divided	1	2234.73	2978.57	1.33285	
131	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [source:swissprot;acc:q07075]	Rooted	Subtracted	0	32.4121	28.377	4.0351	
131	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Rooted	Divided	1	55.1113	67.5537	1.22577	
131	integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	Ranked	Subtracted	0	14951.6	13204.2	1747.4	
131	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	Squared	Divided	1	148058	99628.4	1.4861	
131	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [source:swissprot;acc:p18031]	Measured	Subtracted	0	4912.01	4658.69	253.32	
131	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Rooted	Subtracted	1	144.606	157.824	13.218	
131	serpin b11. [source:swissprot;acc:q96p15]	Measured	Divided	0	42	56	1.33333	
131	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	Ranked	Divided	1	294.053	242.562	1.21228	
131	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	Squared	Subtracted	1	71062.4	95488.9	24426.5	
131	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Measured	Subtracted	1	12839	10911.1	1927.9	
131	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Squared	Divided	0	451.156	817.981	1.81308	
132	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [source:swissprot;acc:o15143]	Squared	Subtracted	0	5671.94	6590.82	918.88	
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	Squared	Divided	1	36359.2	24466.8	1.48606	
132	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	Rooted	Divided	0	23.9003	19.8655	1.20311	
132	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Measured	Divided	0	42	56	1.33333	
132	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Ranked	Subtracted	1	229.406	196.695	32.711	
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Measured	Divided	1	2236.61	2980.35	1.33253	
132	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Rooted	Divided	1	44.963	55.0576	1.22451	
132	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Squared	Divided	0	1.75053	0.969467	1.80566	
132	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Ranked	Subtracted	0	10883	12622.8	1739.8	
132	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Squared	Subtracted	1	71062.2	95488.6	24426.4	
132	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Rooted	Subtracted	1	144.606	157.824	13.218	

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/