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 1013 to 1062 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
127	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	Squared	Subtracted	71386.9	96032.5	24645.6	
127	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Ranked	Divided	94	114	1.21277	
127	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	Measured	Subtracted	450.5	2394.5	1944	
127	transcription factor jun-d. [source:swissprot;acc:p17535]	Measured	Divided	5638.2	7523.39	1.33436	
128	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	Squared	Subtracted	71346.6	95965.1	24618.5	
128	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Ranked	Divided	94	114	1.21277	
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Measured	Divided	4355.61	5810.82	1.3341	
128	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Rooted	Subtracted	54.6527	67.9743	13.3216	
128	pnas-18. [source:sptrembl;acc:q9bzu3]	Squared	Divided	87787.3	58155.8	1.50952	
128	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Ranked	Subtracted	285.684	252.234	33.45	
128	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Measured	Subtracted	11004.2	12944.2	1940	
128	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Rooted	Divided	48.0515	39.0445	1.23069	
129	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Ranked	Subtracted	285.684	252.234	33.45	
129	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Rooted	Divided	54.2343	66.7323	1.23044	
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Measured	Divided	4358.13	5811.49	1.33348	
129	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Ranked	Divided	94	114	1.21277	
129	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Rooted	Subtracted	54.6625	67.9477	13.2852	
129	pre-mrna cleavage complex ii protein pcf11 (fragment). [source:swissprot;acc:o94913]	Squared	Divided	178263	118639	1.50257	
129	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [source:refseq;acc:nm_015316]	Measured	Subtracted	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	71062.4	95488.9	24426.5	
130	44050 protein. [source:refseq;acc:nm_178832]	Squared	Divided	148058	99628.4	1.4861	
130	calsyntenin-1 precursor. [source:swissprot;acc:o94985]	Squared	Subtracted	71062.4	95488.9	24426.5	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	Measured	Divided	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	55.1026	67.5701	1.22626	
130	p66 alpha. [source:refseq;acc:nm_017660]	Measured	Subtracted	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	242.735	276.059	33.324	
130	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	Ranked	Divided	94	114	1.21277	
130	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Rooted	Subtracted	144.606	157.824	13.218	
131	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	Ranked	Subtracted	242.718	276.018	33.3	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	Measured	Divided	2234.73	2978.57	1.33285	
131	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Rooted	Divided	55.1113	67.5537	1.22577	
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	148058	99628.4	1.4861	
131	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Rooted	Subtracted	144.606	157.824	13.218	
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	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	71062.4	95488.9	24426.5	
131	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Measured	Subtracted	12839	10911.1	1927.9	
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [source:swissprot;acc:q9h1y0]	Squared	Divided	36359.2	24466.8	1.48606	
132	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Ranked	Subtracted	229.406	196.695	32.711	
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	Measured	Divided	2236.61	2980.35	1.33253	
132	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Rooted	Divided	44.963	55.0576	1.22451	
132	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	Squared	Subtracted	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	144.606	157.824	13.218	
132	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Ranked	Divided	350	290	1.2069	
132	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Measured	Subtracted	12839	10911.1	1927.9	
133	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Rooted	Subtracted	144.606	157.824	13.218	
133	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Measured	Subtracted	12798.9	10887.2	1911.7	
133	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Ranked	Subtracted	226.887	194.72	32.167	
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Measured	Divided	23421.5	17580.4	1.33225	
133	gbp protein isoform a. [source:refseq;acc:nm_017870]	Squared	Divided	1182.25	1726.55	1.46039	
133	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Rooted	Divided	45.4558	55.5995	1.22316	

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/