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

Results: HTML CSV LaTeX

Showing element 980 to 1029 of 2060 in total

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

Rank	description	Hugo	Value Type
3000	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]	PXDN	Rooted
3001	ubiquitin-like protein nedd8. [swissprot;acc:q15843]	NEDD8	Measured
			Ranked
			Squared
			Rooted
3002	cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563]	CCNT1	Measured
			Ranked
			Squared
			Rooted
3003	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]	LRRC6	Measured
			Ranked
			Squared
			Rooted
3004	small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [swissprot;acc:p14648]	SNRPN	Measured
			Ranked
			Squared
			Rooted
3005	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	NDUFA5	Measured
			Ranked
			Squared
			Rooted
3006	dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5]	DGCR8	Measured
			Ranked
			Squared
			Rooted
3007	glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530]	YEATS4	Measured
			Ranked
			Squared
			Rooted
3008	nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]	NUP214	Measured
			Ranked
			Squared
			Rooted
3009	cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854]	COX6B1	Measured
			Ranked
			Squared
			Rooted
3010	uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132]	UROD	Measured
			Ranked
			Squared
			Rooted
3011	dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3]	MCM8	Measured
			Ranked
			Squared
			Rooted
3012	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	SNRPB	Measured
			Ranked
			Squared
			Rooted
3013	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	CENPB	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.