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 5708 to 5757 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2854	transcriptional coactivator tubedown-100 isoform 1; putative n-acetyltransferase; gastric cancer antigen ga19. [refseq;acc:nm_057175]	Subtracted	0	0	0
2855	15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2856	high mobility group protein 2 (hmg-2). [swissprot;acc:p26583]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2857	protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2858	tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2859	homeobox protein nkx-6.1. [swissprot;acc:p78426]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2860	importin 9. [refseq;acc:nm_018085]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2861	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2862	syndecan-3 (synd3). [swissprot;acc:o75056]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2863	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2864	mago nashi protein homolog. [swissprot;acc:p50606]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2865	t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2866	syntaxin 5. [swissprot;acc:q13190]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2867	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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2868	eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2869	phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [swissprot;acc:q14558]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2870	adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2871	vps28 protein homolog. [swissprot;acc:q9uk41]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2872	transcriptional repressor nac1. [refseq;acc:nm_052876]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2873	integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2874	protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2875	alpha crystallin a chain. [swissprot;acc:p02489]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2876	high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2877	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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2878	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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2879	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	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.