MK5 Microarray Data

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 6262 to 6311 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
3131	protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8]	Subtracted	0	0	0
3132	r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3133	ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3134	rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3135	protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3136	vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3137	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3138	hcdi protein. [refseq;acc:nm_020195]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3139	bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3140	myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [swissprot;acc:p35579]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3141	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3142	protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3143	prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3144	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3145	beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3146	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3147	3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3148	muts protein homolog 5. [swissprot;acc:o43196]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3149	bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3150	cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3151	dna mismatch repair protein msh2. [swissprot;acc:p43246]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3152	histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3153	leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3154	nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [swissprot;acc:q9ukx7]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3155	transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [swissprot;acc:p08112]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3156	tektin 2 (tektin-t) (testicular tektin b1-like protein). [swissprot;acc:q9uif3]	Divided	0.00001	0.00001	1

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.