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

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Showing element 3658 to 3707 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
229	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Measured	Subtracted	0	1225.08	1079.38	145.7
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Rooted	Divided	1	137.446	120.823	1.13758
	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]	Squared			42411.6	55802.1	1.31573
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Measured			9035	7279.6	1.24114
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Rooted	Subtracted		95.0526	85.3206	9.732
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Ranked	Divided	0	10899.4	9878.1	1.10339
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Measured	Subtracted	1	10434.4	11846.2	1411.8
230	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	Squared			45987	56777.1	10790.1
	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Rooted	Divided	0	35.3509	31.4916	1.12255
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]		Subtracted		22.2195	19.7836	2.4359
	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	Ranked	Divided	1	239.35	267.915	1.11934
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Squared	Subtracted	0	7089.47	7293.03	203.56
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Ranked			15147.2	14091.9	1055.3
	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]	Measured		1	9649.61	11053.5	1403.89
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]		Divided		9035	7279.6	1.24114
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Rooted	Subtracted		95.0526	85.3206	9.732
	necdin. [swissprot;acc:q99608]		Divided		137.446	120.823	1.13758
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Ranked	Subtracted		242.694	267.017	24.323
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Squared	Divided	0	82802.3	111762	1.34975
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]			1	42411.6	55802.1	1.31573
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Measured	Subtracted	0	1225.08	1079.38	145.7
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Ranked	Divided		12364.7	11207.7	1.10323
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Measured			1498.17	1718.6	1.14713
231	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Ranked	Subtracted		12447.6	11392.6	1055
	60s ribosomal protein l9. [swissprot;acc:p32969]	Rooted			26.3707	28.8011	2.4304
	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Measured	Divided		2017.91	1759.22	1.14705
	espin. [refseq;acc:nm_031475]		Subtracted		1225.07	1079.38	145.69
	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	Squared		1	45960.8	56749.6	10788.8
	histone h2b. [refseq;acc:nm_175055]			0	7090.75	7294.29	203.54
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Rooted	Divided		25.0015	28.0435	1.12167
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Ranked		1	239.336	267.881	1.11927
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Rooted			137.446	120.823	1.13758
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Measured			9035	7279.6	1.24114
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Rooted	Subtracted		95.0526	85.3206	9.732
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Ranked			226.411	202.088	24.323
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Squared	Divided	0	1914.2	1419.67	1.34834
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	Measured	Subtracted	1	9649.61	11053.5	1403.89
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Ranked	Divided	0	12364.8	11207.9	1.10322
	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]	Squared		1	42411.6	55802.1	1.31573
232	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]			0	0.108639	0.145878	1.34278
	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Ranked	Subtracted		12448.9	11393.9	1055
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Measured	Divided		1663.73	1906.28	1.14579
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Rooted	Subtracted		15.8745	18.303	2.4285
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Ranked		1	226.401	202.094	24.307
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Squared			41502.9	30836.8	10666.1
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Measured	Divided		9035	7279.6	1.24114
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Rooted		0	15.6205	13.9284	1.12149
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Squared	Subtracted		7090.47	7294.01	203.54
	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Measured			2075.64	2220.68	145.04
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Ranked	Divided		12394.7	11240.2	1.10271

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.