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	Value Type	description	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 930 to 979 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
2988	MYH10	Ranked	myosin heavy chain, nonmuscle type b (cellular myosin heavy chain, type b) (nonmuscle myosin heavy chain-b) (nmmhc-b). [swissprot;acc:p35580]
		Squared
		Rooted
2989	no value	Measured	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]
		Ranked
		Squared
		Rooted
2990	CDK8	Measured	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]
		Ranked
		Squared
		Rooted
2991	NMUR2	Measured	neuromedin u receptor 2. [refseq;acc:nm_020167]
		Ranked
		Squared
		Rooted
2992	ALDH3B2	Measured	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]
		Ranked
		Squared
		Rooted
2993	VPS4A	Measured	vacuolar protein sorting factor 4a; skd1-homolog; vacuolar sorting protein 4. [refseq;acc:nm_013245]
		Ranked
		Squared
		Rooted
2994	no value	Measured	skeletal muscle and kidney enriched inositol phosphatase isoform 1; 43-kda form skeletal muscle and kidney enriched inositol phosphatase. [refseq;acc:nm_016532]
		Ranked
		Squared
		Rooted
2995	CCT6B	Measured	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]
		Ranked
		Squared
		Rooted
2996	RBM8A	Measured	rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [swissprot;acc:q9y5s9]
		Ranked
		Squared
		Rooted
2997	PSME3	Measured	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]
		Ranked
		Squared
		Rooted
2998	ZFYVE20	Measured	fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340]
		Ranked
		Squared
		Rooted
2999	TAF4	Measured	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]
		Ranked
		Squared
		Rooted
3000	PXDN	Measured	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]
		Ranked
		Squared

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.