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

Results: HTML CSV LaTeX

Showing element 1512 to 1561 of 1892 in total

Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0

Rank	Hugo	description	Value Type
3133	IFT52	ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366]	Rooted
3134	RABGGTA	rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696]	Measured
			Ranked
			Squared
			Rooted
3135	SEC23A	protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]	Measured
			Ranked
			Squared
			Rooted
3136	VRK1	vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384]	Measured
			Ranked
			Squared
			Rooted
3137	CDKL1	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]	Measured
			Ranked
			Squared
			Rooted
3138	C14orf124	hcdi protein. [refseq;acc:nm_020195]	Measured
			Ranked
			Squared
			Rooted
3139	BRD1	bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696]	Measured
			Ranked
			Squared
			Rooted
3140	MYH9	myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [swissprot;acc:p35579]	Measured
			Ranked
			Squared
			Rooted
3141	TTLL1	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]	Measured
			Ranked
			Squared
			Rooted
3142	PACSIN2	protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]	Measured
			Ranked
			Squared
			Rooted
3143	PICK1	prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5]	Measured
			Ranked
			Squared
			Rooted
3144	HMG1L10	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	Measured
			Ranked
			Squared
			Rooted
3145	UPB1	beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1]	Measured
			Ranked
			Squared
			Rooted
3146	DERL3	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]	Measured

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.