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	Value Type	Rank	red	description	Interaction Map	green	Filtered	network_comparison

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Showing element 7412 to 7461 of 25824 in total

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

Rank	red	description	green	network_comparison
956	24804.6	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270]	28595.4	1.15283
957	26822.8	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776]	30911.4	1.15243
958	29830.2	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	34375.9	1.15239
959		flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
960		inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]
961		selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]
962		inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]
963	23594.2	transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401]	27188.9	1.15236
964	22271.9	inositol polyphosphate multikinase. [refseq;acc:nm_152230]	25656.8	1.15198
965		afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6]
966		alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5]
967	25580.6	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	29466.1	1.15189
968		mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]
969	19488.7	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	22447.5	1.15182
970	24426.8	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	28125	1.1514
971	27478.1	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19]	31623.7	1.15087
972	21083.8	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	24262	1.15074
973	27404	solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094]	31534	1.15071
974	27403.4	delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062]	31533.3
975		lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739]
976	27403.7	solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330]	31533.7
977	27402.5	very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975]	31532.3
978	27403.4	disrupter of silencing 10. [refseq;acc:nm_020368]	31533.3
979		very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031]	31533.4
980	27403.6	solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254]	31533.6
981	27403.1	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	31533
982	30999.6	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	35666.3	1.15054
983	31010.8	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	35677.6	1.15049
984	59338.5	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	68268.3
985	22569.9	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053]	25956.6	1.15005
986		purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491]
987	20465.9	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5]	23535.3	1.14998
988	18082.5	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	20792.7	1.14988
989	23339.9	kccr13l. [refseq;acc:nm_139179]	26834.1	1.14971
990		dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
991	26705.9	aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868]	30699	1.14952
992	18885.2	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046]	21708.3	1.14949
993	29881.4	peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162]	34348	1.14948
994	18761.8	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	21564.5	1.14938
995	25141.4	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	28896.8	1.14937
996		lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760]
997		lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330]
998		mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]
999		lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]
1000	27225.4	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	31287.9	1.14922
1001	21068.2	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	24205.2	1.1489
1002		splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]
1003	17541.4	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	20148.6	1.14863
1004		exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]
1005		exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]

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.