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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1012 to 1061 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Network Comparison Type	Value Type	red	green	network_comparison
127	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted	Rooted	153.191	166.771	13.58
	HMG20A	high-mobility group 20a. [refseq;acc:nm_018200]	Divided	Rooted	60.9353	75.094	1.23236
	JUND	transcription factor jun-d. [swissprot;acc:p17535]	Divided	Measured	5638.2	7523.39	1.33436
	MIP	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Subtracted	Squared	71386.9	96032.5	24645.6
	RHOBTB2	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
128	no value	pnas-18. [sptrembl;acc:q9bzu3]	Divided	Squared	87787.3	58155.8	1.50952
	AQP1	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
	LUC7L2	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Divided	Measured	4355.61	5810.82	1.3341
	PSEN1	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Subtracted	Ranked	285.684	252.234	33.45
	STAMBP	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Divided	Ranked	94	114	1.21277
	TARDBP	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Divided	Rooted	48.0515	39.0445	1.23069
	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Subtracted	Measured	11004.2	12944.2	1940
	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]		Rooted	54.6527	67.9743	13.3216
129	CUL1	cullin homolog 1 (cul-1). [swissprot;acc:q13616]		Ranked	285.684	252.234	33.45
	LUC7L	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Divided	Measured	4358.13	5811.49	1.33348
	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Rooted	54.2343	66.7323	1.23044
	PCF11	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]		Squared	178263	118639	1.50257
	PPP1R13B	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Subtracted	Measured	15274.9	13346.9	1928
	SSR4	translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]		Squared	71062.4	95488.9	24426.5
	TIAL1	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]		Rooted	54.6625	67.9477	13.2852
	VPS24	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Divided	Ranked	94	114	1.21277
130	no value	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]		Rooted	55.1026	67.5701	1.22626
	C10orf83	44050 protein. [refseq;acc:nm_178832]		Squared	148058	99628.4	1.4861
	CHMP4A	protein hspc134 (protein cda04). [swissprot;acc:q9by43]		Ranked	94	114	1.21277
	CLSTN1	calsyntenin-1 precursor. [swissprot;acc:o94985]	Subtracted	Squared	71062.4	95488.9	24426.5
	EGFL8	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
	FOXP4	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
	GATAD2A	p66 alpha. [refseq;acc:nm_017660]	Subtracted	Measured	12839	10911.1	1927.9
	RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	Rooted	144.606	157.824	13.218
131	no value	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Divided	Rooted	55.1113	67.5537	1.22577
	no value	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
	EGFL7	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Subtracted	Ranked	242.718	276.018	33.3
	FOXP1	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Divided	Measured	2234.73	2978.57	1.33285
	GATAD2B	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Subtracted	Measured	12839	10911.1	1927.9
	PPP1R8	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	Squared	148058	99628.4	1.4861
	RRAGC	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	Rooted	144.606	157.824	13.218
	SON	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
132	no value	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Subtracted	Measured	12839	10911.1	1927.9
	ATG5	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Divided	Squared	36359.2	24466.8	1.48606
	FOXP3	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]		Measured	2236.61	2980.35	1.33253
	HAT1	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]		Rooted	44.963	55.0576	1.22451
	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Subtracted	Ranked	229.406	196.695	32.711
	PTPRB	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467]		Squared	71062.2	95488.6	24426.4
	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]		Rooted	144.606	157.824	13.218
	TOB2	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided	Ranked	350	290	1.2069
133	no value	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Subtracted	Ranked	226.887	194.72	32.167
	ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]		Rooted	144.606	157.824	13.218
	CDK3	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]		Measured	12798.9	10887.2	1911.7
	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Divided	Measured	23421.5	17580.4	1.33225
	OSR1	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Divided	Rooted	45.4558	55.5995	1.22316

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
- Hugo is the HGNC identifier if it exists
- 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/