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

Results: HTML CSV LaTeX

Showing element 1001 to 1050 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	description	Network Comparison Type	Value Type	red	green	network_comparison
126	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Subtracted	Squared	71387.4	96033.4	24646
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Divided	Ranked	94	114	1.21277
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Divided	Measured	24250	18164.9	1.33499
	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. [refseq;acc:nm_018315]	Subtracted	Ranked	285.684	252.234	33.45
	high-mobility group 20a. [refseq;acc:nm_018200]	Subtracted	Rooted	60.9353	75.094	14.1587
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	Divided	Rooted	60.9342	75.1387	1.23311
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	Measured	450.5	2394.5	1944
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Divided	Squared	189976	124480	1.52616
127	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Subtracted	Ranked	285.684	252.234	33.45
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Divided	Squared	88432.6	58423.3	1.51365
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	Rooted	153.191	166.771	13.58
	high-mobility group 20a. [refseq;acc:nm_018200]	Divided	Rooted	60.9353	75.094	1.23236
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Subtracted	Squared	71386.9	96032.5	24645.6
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Divided	Ranked	94	114	1.21277
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted	Measured	450.5	2394.5	1944
	transcription factor jun-d. [swissprot;acc:p17535]	Divided	Measured	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). [swissprot;acc:p29972]	Subtracted	Squared	71346.6	95965.1	24618.5
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Divided	Ranked	94	114	1.21277
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Divided	Measured	4355.61	5810.82	1.3341
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Subtracted	Rooted	54.6527	67.9743	13.3216
	pnas-18. [sptrembl;acc:q9bzu3]	Divided	Squared	87787.3	58155.8	1.50952
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Subtracted	Ranked	285.684	252.234	33.45
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Subtracted	Measured	11004.2	12944.2	1940
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Divided	Rooted	48.0515	39.0445	1.23069
129	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Subtracted	Ranked	285.684	252.234	33.45
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Divided	Rooted	54.2343	66.7323	1.23044
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]		Measured	4358.13	5811.49	1.33348
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]		Ranked	94	114	1.21277
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Subtracted	Rooted	54.6625	67.9477	13.2852
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Divided	Squared	178263	118639	1.50257
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Subtracted	Measured	15274.9	13346.9	1928
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Subtracted	Squared	71062.4	95488.9	24426.5
130	44050 protein. [refseq;acc:nm_178832]	Divided		148058	99628.4	1.4861
	calsyntenin-1 precursor. [swissprot;acc:o94985]	Subtracted		71062.4	95488.9	24426.5
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Divided	Measured	2234.68	2978.53	1.33287
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Divided	Rooted	55.1026	67.5701	1.22626
	p66 alpha. [refseq;acc:nm_017660]	Subtracted	Measured	12839	10911.1	1927.9
	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Subtracted	Ranked	242.735	276.059	33.324
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Divided	Ranked	94	114	1.21277
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	Rooted	144.606	157.824	13.218
131	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Subtracted	Ranked	242.718	276.018	33.3
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Divided	Measured	2234.73	2978.57	1.33285
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]		Rooted	55.1113	67.5537	1.22577
	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)]. [swissprot;acc:q12972]		Squared	148058	99628.4	1.4861
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	Rooted	144.606	157.824	13.218
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Divided	Ranked	294.053	242.562	1.21228
	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). [swissprot;acc:o14521]	Subtracted	Squared	71062.4	95488.9	24426.5
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Subtracted	Measured	12839	10911.1	1927.9
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Divided	Squared	36359.2	24466.8	1.48606
132	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Subtracted	Ranked	229.406	196.695	32.711

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/