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 1201 to 1250 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
601	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241]	Subtracted	207.26	194.346	12.914
	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	Divided	206.274	218.792	1.06069
602	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769]	Subtracted	207.26	194.346	12.914
603	ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]		207.27	194.368	12.902
	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	Divided	225.829	212.945	1.0605
604	60s ribosomal protein l15. [swissprot;acc:p39030]		217.862	230.978	1.0602
	homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	Subtracted	207.272	194.371	12.901
605	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Divided	247.47	233.441	1.0601
	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	Subtracted	225.829	212.945	12.884
606	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Divided	247.47	233.441	1.0601
	neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401]	Subtracted	207.309	194.452	12.857
607	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Divided	247.47	233.441	1.0601
	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	Subtracted	216.731	229.549	12.818
608	dynein light chain 2. [refseq;acc:nm_080677]
	histone h2b. [refseq;acc:nm_175055]	Divided	247.47	233.441	1.0601
609	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Subtracted	226.523	213.786	12.737
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Divided	247.47	233.441	1.0601
610	histone h2b.d (h2b/d). [swissprot;acc:q99877]
	son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889]	Subtracted	205.74	193.021	12.719
611	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Divided	247.47	233.441	1.0601
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Subtracted	228.986	216.276	12.71
612	son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890]		205.89	193.183	12.707
	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	Divided	247.47	233.441	1.0601
613	histone h2b.e (h2b/e). [swissprot;acc:q99879]
	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	Subtracted	247.769	235.074	12.695
614	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Divided	214.257	202.125	1.06002
	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	Subtracted	232.468	245.048	12.58
615	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]		241.907	229.35	12.557
	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	Divided	214.257	202.132	1.05999
616	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Subtracted	177.698	190.24	12.542
617	carboxypeptidase b precursor. [refseq;acc:nm_020361]			190.239	12.541
	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	Divided	214.257	202.135	1.05997
618	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]		214.256	202.139	1.05994
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Subtracted	177.699	190.24	12.541
619	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Divided	214.256	202.139	1.05994
	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	Subtracted	206.274	218.792	12.518
620	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	Divided	214.256	202.14	1.05994
	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	Subtracted	206.274	218.792	12.518
621	60s acidic ribosomal protein p2. [swissprot;acc:p05387]		231.92	244.435	12.515
	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	Divided	214.256	202.14	1.05994
622	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
	synapsin iii. [swissprot;acc:o14994]	Subtracted	229.072	216.576	12.496
623	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]	Divided	214.256	202.14	1.05994
624	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]	Subtracted	229.072	216.576	12.496
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Divided	214.256	202.139	1.05994
625	actin binding lim protein 2. [refseq;acc:nm_032432]	Subtracted	229.072	216.576	12.496
	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]	Divided	214.256	202.14	1.05994

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.