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 1151 to 1200 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
576	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	Subtracted	7813.48	8570.11	756.63
	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	Divided	6739.7	7644.6	1.13426
577	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2]	Subtracted	7813.45	8570.07	756.62
	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	Divided	6739.81	7644.62	1.13425
578	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171]	Subtracted	7813.35	8569.96	756.61
579	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]		7813.34	8569.95
	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	Divided	6739.82	7644.62	1.13425
580	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491]	Subtracted	7813.36	8569.97	756.61
	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	Divided	6739.83	7644.63	1.13425
581	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	Subtracted	7810.11	8566.29	756.18
	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]	Divided	6739.82	7644.63	1.13425
582	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]			7644.62
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Subtracted	6834.54	7590.49	755.95
583	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Divided	6739.81	7644.62	1.13425
584	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]		6739.82	7644.63
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	Subtracted	6834.54	7590.49	755.95
585	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]	Divided	6739.82	7644.63	1.13425
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Subtracted	6834.54	7590.49	755.95
586	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]		6139.04	6893.7	754.66
	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	Divided	6739.81	7644.62	1.13425
587	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	Subtracted	6772.75	7526.2	753.45
	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]	Divided	6739.83	7644.63	1.13425
588	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349]	Subtracted	6691.93	7445.09	753.16
589	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	Divided	6739.85	7644.63	1.13424
	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851]	Subtracted	6691.21	7444.22	753.01
590	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]	Divided	6739.85	7644.63	1.13424
	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350]	Subtracted	6690.44	7443.29	752.85
591	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	Divided	6740.5	7644.76	1.13415
	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	Subtracted	5390.78	6142.07	751.29
592	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]		7093.86	7842.67	748.81
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Divided	3946.32	4475.47	1.13409
593	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9]	Subtracted	6770.78	7517.97	747.19
594	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	3946.32	4475.47	1.13409
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Subtracted	6089.21	6835.34	746.13
595	apical-like protein (apxl protein). [swissprot;acc:q13796]		6088.77	6834.87	746.1
	histone h2b. [refseq;acc:nm_175055]	Divided	3946.32	4475.47	1.13409
596	histone h2b.s (h2b/s). [swissprot;acc:p57053]
	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Subtracted	4533.74	5279.4	745.66
597	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Divided	3946.32	4475.47	1.13409
598	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	Subtracted	4533.74	5279.4	745.66
	histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]	Divided	3946.32	4475.47	1.13409
599	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Subtracted	4533.74	5279.4	745.66
	testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]	Divided	3946.32	4475.47	1.13409
600	60s ribosomal protein l8. [swissprot;acc:p25120]	Subtracted	4533.74	5279.4	745.66
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Divided	3946.32	4475.47	1.13409

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.