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

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Showing element 51 to 100 of 12912 in total

green  : 0.00001
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
red  : 0.00001
network_comparison  : 1

description	Rank	Value Type
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588]	2788	Squared
		Rooted
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]	3050	Measured
		Ranked
		Squared
		Rooted
adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979]	2870	Measured
		Ranked
		Squared
		Rooted
aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353]	3222	Measured
		Ranked
		Squared
		Rooted
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	2992	Measured
		Ranked
		Squared
		Rooted
aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278]	2960	Measured
		Ranked
		Squared
		Rooted
alpha crystallin a chain. [swissprot;acc:p02489]	2875	Measured
		Ranked
		Squared
		Rooted
alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [swissprot;acc:p02511]	3082	Measured
		Ranked
		Squared
		Rooted
alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [refseq;acc:nm_024083]	2829	Measured
		Ranked
		Squared
		Rooted
amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380]	3191	Measured
		Ranked
		Squared
		Rooted
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	2798	Measured
		Ranked
		Squared
		Rooted
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859]	2893	Measured
		Ranked
		Squared
		Rooted
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964]	2834	Measured
		Ranked
		Squared
		Rooted

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.