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 3732 to 3781 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
1866	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144]	Subtracted	5369.43	5738.73	369.3
1867	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Divided	6076.66	6463.12	1.0636
	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]	Subtracted	5369.43	5738.73	369.3
1868	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]	Divided	6076.66	6463.12	1.0636
	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	Subtracted	5739.49	6108.72	369.23
1869	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]
	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]	Divided	6076.66	6463.12	1.0636
1870	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]	Subtracted	5739.49	6108.72	369.23
	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	Divided	6076.66	6463.13	1.0636
1871	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991]	Subtracted	6682.05	7051.02	368.97
	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	Divided	6076.66	6463.12	1.0636
1872	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]	Subtracted	6682.05	7051.02	368.97
	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]	Divided	6076.66	6463.12	1.0636
1873	40s ribosomal protein s11. [swissprot;acc:p04643]		3618.46	3402.09
	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]	Subtracted	6682.05	7051.02	368.97
1874	heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900]		5746.06	6113.79	367.73
	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	Divided	6076.66	6463.12	1.0636
1875	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Subtracted	5106.13	5472.96	366.83
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Divided	6076.66	6463.14	1.0636
1876	dna polymerase delta p38 subunit. [refseq;acc:nm_015584]	Subtracted	5106.13	5472.96	366.83
	espin. [refseq;acc:nm_031475]	Divided	6076.66	6463.12	1.0636
1877	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	Subtracted	5497.73	5132.35	365.38
	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]	Divided	6076.66	6463.12	1.0636
1878	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1]	Subtracted	5501.3	5866.02	364.72
	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]	Divided	6076.66	6463.12	1.0636
1879	lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]
	nucleoporin like 1. [refseq;acc:nm_014089]	Subtracted	6174.74	6538.73	363.99
1880	d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917]	Divided	6076.66	6463.12	1.0636
	rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320]	Subtracted	6174.74	6538.73	363.99
1881	cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Divided	6076.68	6462.56	1.0635
1882	eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042]	Subtracted	5423.67	5787.46	363.79
	eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091]	Divided	5490.24	5838.67	1.06346
1883	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]		5826	6195.48	1.06342
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	Subtracted	5949.31	6313.1	363.79
1884	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]	Divided	5826	6195.48	1.06342
	potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122]	Subtracted	5633.44	5997	363.56
1885	solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7]
	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]	Divided	5826	6195.48	1.06342
1886	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991]	Subtracted	5633.44	5997	363.56
	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]	Divided	5826	6195.48	1.06342
1887	adp-ribosylation factor 4. [swissprot;acc:p18085]	Subtracted	5633.44	5997	363.56
	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	Divided	5438.6	5783.11	1.06335
1888	bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]
	fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]	Subtracted	5633.44	5997	363.56
1889	shc transforming protein. [swissprot;acc:p29353]
	testis-specific bromodomain protein. [refseq;acc:nm_001726]	Divided	5438.68	5783.2	1.06335
1890	nag14 protein. [refseq;acc:nm_022143]		5438.6	5783.11
	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]	Subtracted	5633.44	5997	363.56
1891	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	Divided	5438.18	5782.62	1.06334

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.