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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Value Type	Gene	Rank	green	description	Network Comparison Type	Filtered	Interaction Map	red	network_comparison

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Showing element 630 to 679 of 3228 in total

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

Rank	green	description	red	network_comparison
630	202.141	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	214.256	1.05993
631		similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
632	202.166	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	214.254	1.05979
633	248.104	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	234.106
634	213.786	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	226.523	1.05958
635	242.258	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	228.639	1.05957
636		splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
637		amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
638		sorting nexin 17. [swissprot;acc:q15036]
639	230.596	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	217.67	1.05938
640		intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
641		pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]
642		intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
643		hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]
644		cgthba protein (-14 gene protein). [swissprot;acc:q12980]
645		hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
646	229.549	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	216.731	1.05914
647		dynein light chain 2. [refseq;acc:nm_080677]
648	206.078	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	218.227	1.05895
649	220.751	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	233.725	1.05877
650	216.276	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	228.986
651	220.751	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	233.725
652	235.255	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	248.994	1.0584
653	204.622	dok-like protein. [refseq;acc:nm_024872]	216.504	1.05807
654		docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]
655		docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
656		tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]
657	216.576	synapsin iii. [swissprot;acc:o14994]	229.072	1.0577
658		aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
659		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]
660		actin binding lim protein 2. [refseq;acc:nm_032432]
661		hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
662		synapsin ii. [swissprot;acc:q92777]
663		mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
664		peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
665		hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
666		transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]
667		delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
668		actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
669		synapsin i (brain protein 4.1). [swissprot;acc:p17600]
670	236.817	autoantigen ngp-1. [swissprot;acc:q13823]	250.302	1.05694
671	199.398	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	210.739	1.05688
672		nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
673	214.355	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	226.497	1.05664
674		hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]
675		single-minded homolog 1. [swissprot;acc:p81133]
676	245.613	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	232.469	1.05654
677	216.745	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	228.944	1.05628
678	220.175	sorting nexin 5. [swissprot;acc:q9y5x3]	208.482	1.05609
679	125.389	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	132.413	1.05602

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.