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

Results: HTML CSV LaTeX

Showing element 3001 to 3050 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

red	Rank	green	description	network_comparison
9276.47	142	7090.37	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	1.30832
9304.83	786	10347.3	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	1.11204
9327.58	685	10442.2	metaxin 1. [swissprot;acc:q13505]	1.1195
9596.59	1747	10241.9	cerebral cell adhesion molecule. [refseq;acc:nm_016174]	1.06724
9634.98	522	10976.2	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	1.1392
9642.22	520	10986.4	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	1.13941
9648.27	519	10994.9	glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807]	1.13957
9649.61	471	11053.5	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	1.14549
	472		sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]
	473		udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]
	474		rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]
	475		map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]
	476		neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]
	477		nitrogen fixation cluster-like. [refseq;acc:nm_014301]
	478		star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]
	479		star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]
	480		neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
	481		mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]
	482		mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]
	483		neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]
	484		neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]
	485		sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]
9720.64	1718	9099.1	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621]	1.06831
9895.77	1638	9248.18	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	1.07002
9899.73	1634	9251.16	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	1.07011
	1635		b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]
	1636		zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]
9899.79	1633	9251.2	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]
9903.22	1630	9253.79	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	1.07018
9921.43	874	10941.2	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	1.10278
9946.21	1931	9367.66	ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1]	1.06176
10067.9	504	11511	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	1.14334
10075.5	1500	9377.75	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	1.0744
	1501		coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678]
	1502		coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3]
	1503		coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444]
	1504		peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
	1505		coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
10143.6	2744	10163.6	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	1.00197
10178.5	2070	9638.08	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	1.05607
10198.1	2742	10174.3	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	1.00234
10230.1	905	11256.2	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	1.1003
10231.8	1370	9487.34	t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808]	1.07847
	1371		double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]
10235.2	420	11830.8	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	1.15589
10241.3	2029	9685.21	paraspeckle protein 1. [refseq;acc:nm_018282]	1.05742
10243.4	2028	9686.82	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233]	1.05746
10246.1	902	11285.8	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	1.10147
10247.8	895	11289	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	1.1016
10263.8	875	11318.6	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	1.10277

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.