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

Results: HTML CSV LaTeX

Showing element 5358 to 5407 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2679	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	Divided	5358.78	5384.44	1.00479
2680	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Subtracted	4591.08	4621.88	30.8
	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	Divided	5358.3	5383.94	1.00479
2681	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	Subtracted	8991.87	9019.99	28.12
	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177]	Divided	5358.31	5383.94	1.00478
2682	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83]		5358.3	5383.93
	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]	Subtracted	4071.9	4099.01	27.11
2683	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153]	Divided	5358.3	5383.93	1.00478
	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	Subtracted	7913.63	7939.94	26.31
2684	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	Divided	5357.73	5383.33	1.00478
	transcription factor relb (i-rel). [swissprot;acc:q01201]	Subtracted	7913.63	7939.94	26.31
2685	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	Divided	3953.53	3972.32	1.00475
	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]	Subtracted	7913.63	7939.94	26.31
2686	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]	Divided	3953.53	3972.32	1.00475
2687	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Subtracted	4336.58	4310.3	26.28
	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	Divided	3953.53	3972.32	1.00475
2688	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Subtracted	4336.62	4310.35	26.27
	oligophrenin 1. [swissprot;acc:o60890]	Divided	3953.53	3972.32	1.00475
2689	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		4113.79	4095.53	1.00446
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	Subtracted	5358.78	5384.44	25.66
2690	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Divided	4113.79	4095.53	1.00446
	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	Subtracted	5358.3	5383.94	25.64
2691	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	Divided	4113.79	4095.53	1.00446
	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177]	Subtracted	5358.31	5383.94	25.63
2692	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83]		5358.3	5383.93
	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	Divided	4113.79	4095.53	1.00446
2693	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]
	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153]	Subtracted	5358.3	5383.93	25.63
2694	60s ribosomal protein l18. [swissprot;acc:q07020]	Divided	4113.79	4095.53	1.00446
	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	Subtracted	5357.73	5383.33	25.6
2695	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	Divided	5176.92	5154.43	1.00436
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Subtracted	4338.79	4313.52	25.27
2696	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]		10198.1	10174.3	23.8
	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	Divided	5176.92	5154.43	1.00436
2697	endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249]	Subtracted			22.49
	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	Divided			1.00436
2698	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	Subtracted			22.49
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Divided	4163.36	4145.95	1.0042
2699	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]		5356.83	5378.19	1.00399
	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	Subtracted	5176.92	5154.43	22.49
2700	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]		5356.83	5378.19	21.36
	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	Divided	5239.33	5260	1.00395
2701	dynein light chain 2. [refseq;acc:nm_080677]
	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	Subtracted			20.67
2702	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540]	Divided	8971.66	9006.92	1.00393
	dynein light chain 2. [refseq;acc:nm_080677]	Subtracted	5239.33	5260	20.67
2703	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Divided	8972.87	9007.71	1.00388
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Subtracted	10143.6	10163.6	20
2704	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	Divided	8980.12	9013.33	1.0037

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.