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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1001 to 1050 of 25824 in total

Filtered

: 1
Interaction Map

: High confidence

Rank	Value Type	description	Network Comparison Type	green	red	network_comparison
126	Measured	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Divided	18164.9	24250	1.33499
	Measured	rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	2394.5	450.5	1944
	Ranked	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Divided	114	94	1.21277
	Ranked	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	252.234	285.684	33.45
	Squared	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	96033.4	71387.4	24646
	Squared	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Divided	124480	189976	1.52616
	Rooted	high-mobility group 20a. [refseq;acc:nm_018200]	Subtracted	75.094	60.9353	14.1587
	Rooted	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	75.1387	60.9342	1.23311
127	Measured	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Subtracted	2394.5	450.5	1944
	Measured	transcription factor jun-d. [swissprot;acc:p17535]	Divided	7523.39	5638.2	1.33436
	Ranked	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Subtracted	252.234	285.684	33.45
	Ranked	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Divided	114	94	1.21277
	Squared	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Divided	58423.3	88432.6	1.51365
	Squared	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Subtracted	96032.5	71386.9	24645.6
	Rooted	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	166.771	153.191	13.58
	Rooted	high-mobility group 20a. [refseq;acc:nm_018200]	Divided	75.094	60.9353	1.23236
128	Measured	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Divided	5810.82	4355.61	1.3341
	Measured	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Subtracted	12944.2	11004.2	1940
	Ranked	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Divided	114	94	1.21277
	Ranked	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Subtracted	252.234	285.684	33.45
	Squared	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Subtracted	95965.1	71346.6	24618.5
	Squared	pnas-18. [sptrembl;acc:q9bzu3]	Divided	58155.8	87787.3	1.50952
	Rooted	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Subtracted	67.9743	54.6527	13.3216
	Rooted	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Divided	39.0445	48.0515	1.23069
129	Measured	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Divided	5811.49	4358.13	1.33348
	Measured	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Subtracted	13346.9	15274.9	1928
	Ranked	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Subtracted	252.234	285.684	33.45
	Ranked	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Divided	114	94	1.21277
	Squared	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Divided	118639	178263	1.50257
	Squared	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Subtracted	95488.9	71062.4	24426.5
	Rooted	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Divided	66.7323	54.2343	1.23044
	Rooted	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Subtracted	67.9477	54.6625	13.2852
130	Measured	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Divided	2978.53	2234.68	1.33287
	Measured	p66 alpha. [refseq;acc:nm_017660]	Subtracted	10911.1	12839	1927.9
	Ranked	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Subtracted	276.059	242.735	33.324
	Ranked	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Divided	114	94	1.21277
	Squared	44050 protein. [refseq;acc:nm_178832]	Divided	99628.4	148058	1.4861
	Squared	calsyntenin-1 precursor. [swissprot;acc:o94985]	Subtracted	95488.9	71062.4	24426.5
	Rooted	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Divided	67.5701	55.1026	1.22626
	Rooted	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	157.824	144.606	13.218
131	Measured	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Divided	2978.57	2234.73	1.33285
	Measured	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Subtracted	10911.1	12839	1927.9
	Ranked	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Subtracted	276.018	242.718	33.3
	Ranked	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	242.562	294.053	1.21228
	Squared	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]	Divided	99628.4	148058	1.4861
	Squared	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	95488.9	71062.4	24426.5
	Rooted	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Divided	67.5537	55.1113	1.22577
	Rooted	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	157.824	144.606	13.218
132	Measured	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Divided	2980.35	2236.61	1.33253
132	Measured	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Subtracted	10911.1	12839	1927.9

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/