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

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Showing element 1 to 32 of 32 in total

Rank  : 46

description	green	Filtered	Value Type	network_comparison	red	Interaction Map	Network Comparison Type
60s ribosomal protein l37a. [swissprot;acc:p12751]	18499.2	0	Ranked	1.42943	12941.7	High confidence	Divided
apg3p; pc3-96 protein. [refseq;acc:nm_022488]	73157.5	1	Squared	1.77148	129597
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	67.6572		Rooted	7.9751	75.6323	Low confidence	Subtracted
beta-tubulin 4q. [sptrembl;acc:q8wz78]	35675.5	0	Squared	5005.7	40681.2
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	20431.7	1	Measured	4464.7	24896.4	High confidence
deltex 2. [refseq;acc:nm_020892]	43.9629		Rooted	1.5909	27.634		Divided
ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760]	67	0	Measured	2.79167	24	Low confidence
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	24837.5		Squared	5357.5	30195	High confidence	Subtracted
fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	161.068	1	Ranked	1.27053	204.642		Divided
fos39347_1. [sptrembl;acc:o75863]	9.07489	0	Rooted	5.67971	14.7546	Low confidence	Subtracted
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]	9264.5		Ranked	4054	5210.5	High confidence
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	7.48331		Rooted	1.67439	12.53		Divided
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	33.2721			8.102	25.1701		Subtracted
jun dimerization protein. [refseq;acc:nm_130469]	75.4064	1		1.13252	66.5831	Low confidence	Divided
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	120.823			16.623	137.446	High confidence	Subtracted
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	5.80679	0		1.69589	9.84765	Low confidence	Divided
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	17020.5		Ranked	3195	13825.5		Subtracted
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	61881.5	1	Squared	20466.3	82347.8
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]				1.33073			Divided
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	98.4675	0		5.87971	16.747
neuralized-like. [refseq;acc:nm_004210]	266.948	1	Ranked	65.378	332.326	High confidence	Subtracted
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1390.33		Measured	1.78438	779.167		Divided
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	136779		Squared	73666	210445		Subtracted
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	217.217		Ranked	25.525	242.742	Low confidence
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]				1.11751			Divided
putative dynein light chain protein dj8b22.1. [swissprot;acc:q9y3p0]	4196.79	0	Measured	411.04	4607.83		Subtracted
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	12942.3	1		1326.3	11616
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	2436.4	0		587.45	3023.85	High confidence
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	13210.4		Ranked	1.31424	17361.7	Low confidence	Divided
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	83.274		Squared	5.60534	14.8562	High confidence
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	438.035		Measured	2.16674	202.163
transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867]	9645.34	1		1.16027	8313.02	Low confidence

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.