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

Results: HTML CSV LaTeX

Showing element 1512 to 1561 of 2060 in total

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

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

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.