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 444 to 493 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
2866	STX5	Rooted	syntaxin 5. [swissprot;acc:q13190]
2867	no value	Measured	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
		Ranked
		Squared
		Rooted
2868	SNORA67	Measured	eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765]
		Ranked
		Squared
		Rooted
2869	PRPSAP1	Measured	phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [swissprot;acc:q14558]
		Ranked
		Squared
		Rooted
2870	SH2B2	Measured	adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979]
		Ranked
		Squared
		Rooted
2871	VPS28	Measured	vps28 protein homolog. [swissprot;acc:q9uk41]
		Ranked
		Squared
		Rooted
2872	BTBD14B	Measured	transcriptional repressor nac1. [refseq;acc:nm_052876]
		Ranked
		Squared
		Rooted
2873	ITGB2	Measured	integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107]
		Ranked
		Squared
		Rooted
2874	C21orf2	Measured	protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822]
		Ranked
		Squared
		Rooted
2875	CRYAA	Measured	alpha crystallin a chain. [swissprot;acc:p02489]
		Ranked
		Squared
		Rooted
2876	PDE9A	Measured	high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083]
		Ranked
		Squared
		Rooted
2877	RUNX1	Measured	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]
		Ranked
		Squared
		Rooted
2878	NDUFS2	Measured	nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [swissprot;acc:o75306]
		Ranked
		Squared
		Rooted
2879	no value	Measured	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]

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.