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.

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

Results: HTML CSV LaTeX

Showing element 1001 to 1050 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	description	Value Type	Network Comparison 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]	Squared	Subtracted	71387.4	96033.4	24646
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked	Divided	94	114	1.21277
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured	Divided	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]	Ranked	Subtracted	285.684	252.234	33.45
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	Subtracted	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]	Rooted	Divided	60.9342	75.1387	1.23311
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	Subtracted	450.5	2394.5	1944
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared	Divided	189976	124480	1.52616
127	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Ranked	Subtracted	285.684	252.234	33.45
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared	Divided	88432.6	58423.3	1.51365
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Rooted	Subtracted	153.191	166.771	13.58
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	Divided	60.9353	75.094	1.23236
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Squared	Subtracted	71386.9	96032.5	24645.6
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked	Divided	94	114	1.21277
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	Subtracted	450.5	2394.5	1944
	transcription factor jun-d. [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). [swissprot;acc:p29972]	Squared	Subtracted	71346.6	95965.1	24618.5
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	Divided	94	114	1.21277
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured	Divided	4355.61	5810.82	1.3341
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Rooted	Subtracted	54.6527	67.9743	13.3216
	pnas-18. [sptrembl;acc:q9bzu3]	Squared	Divided	87787.3	58155.8	1.50952
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Ranked	Subtracted	285.684	252.234	33.45
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Measured	Subtracted	11004.2	12944.2	1940
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	Divided	48.0515	39.0445	1.23069
129	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Ranked	Subtracted	285.684	252.234	33.45
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted	Divided	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]	Rooted	Subtracted	54.6625	67.9477	13.2852
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared	Divided	178263	118639	1.50257
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Measured	Subtracted	15274.9	13346.9	1928
	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Squared	Subtracted	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]	Measured	Divided	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]	Rooted	Divided	55.1026	67.5701	1.22626
	p66 alpha. [refseq;acc:nm_017660]	Measured	Subtracted	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]	Ranked	Subtracted	242.735	276.059	33.324
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked	Divided	94	114	1.21277
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Rooted	Subtracted	144.606	157.824	13.218
131	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Ranked	Subtracted	242.718	276.018	33.3
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Measured	Divided	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]	Rooted	Subtracted	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]	Ranked	Divided	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]	Squared	Subtracted	71062.4	95488.9	24426.5
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Measured	Subtracted	12839	10911.1	1927.9
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Squared	Divided	36359.2	24466.8	1.48606
132	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Ranked	Subtracted	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/