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

Results: HTML CSV LaTeX

Showing element 480 to 529 of 2060 in total

Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0

Rank	description	Hugo	Value Type
2875	alpha crystallin a chain. [swissprot;acc:p02489]	CRYAA	Rooted
2876	high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083]	PDE9A	Measured
			Ranked
			Squared
			Rooted
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]	RUNX1	Measured
			Ranked
			Squared
			Rooted
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]	NDUFS2	Measured
			Ranked
			Squared
			Rooted
2879	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	no value	Measured
			Ranked
			Squared
			Rooted
2880	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]		Measured
			Ranked
			Squared
			Rooted
2881	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]	COLEC12	Measured
			Ranked
			Squared
			Rooted
2882	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989]	XDH	Measured
			Ranked
			Squared
			Rooted
2883	pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [swissprot;acc:q9nve7]	PANK4	Measured
			Ranked
			Squared
			Rooted
2884	peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1]	PDF	Measured
			Ranked
			Squared
			Rooted
2885	carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786]	CPT2	Measured
			Ranked
			Squared
			Rooted
2886	complement component c8 alpha chain precursor. [swissprot;acc:p07357]	C8A	Measured
			Ranked
			Squared
			Rooted
2887	mothers against decapentaplegic homolog interacting protein (madh-interacting protein) (smad anchor for receptor activation) (receptor activation anchor) (hsara) (novel serine protease) (nsp). [swissprot;acc:o95405]	ZFYVE9	Measured
			Ranked
			Squared
			Rooted
2888	eukaryotic initiation factor 4a-ii (eif-4a-ii) (eif4a-ii). [swissprot;acc:q14240]	EIF4A2	Measured

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.