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

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Showing element 5980 to 6029 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2990	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Subtracted	0	0	0
2991	neuromedin u receptor 2. [refseq;acc:nm_020167]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2992	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2993	vacuolar protein sorting factor 4a; skd1-homolog; vacuolar sorting protein 4. [refseq;acc:nm_013245]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2994	skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2995	t-complex protein 1, zeta-2 subunit (tcp-1-zeta-2) (cct-zeta-2) (tcp- 1-zeta-like) (cct-zeta-like) (testis-specific tcp20) (testis-specific protein tsa303). [swissprot;acc:q92526]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2996	rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [swissprot;acc:q9y5s9]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2997	proteasome activator complex subunit 3 (proteasome activator 28-gamma subunit) (pa28gamma) (pa28g) (activator of multicatalytic protease subunit 3) (11s regulator complex gamma subunit) (reg-gamma) (ki nuclear autoantigen). [swissprot;acc:q12920]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2998	fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2999	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3000	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3001	ubiquitin-like protein nedd8. [swissprot;acc:q15843]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3002	cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3003	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3004	small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [swissprot;acc:p14648]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3006	dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3007	glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3008	nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3009	cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3010	uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3011	dna replication licensing factor mcm8 (minichromosome maintenance 8). [swissprot;acc:q9uja3]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3012	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3013	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3014	mitochondrial deoxynucleotide carrier (mitochondrial uncoupling protein 1). [swissprot;acc:q9hc21]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3015	pericentrin 1; frount; nucleoporin nup75. [refseq;acc:nm_024844]	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.