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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 618 to 667 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
618	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	214.256	202.139	1.05994
619	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
620	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]		202.14
621	GABRA2	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
622	GABRA6	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
623	GABRG2	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]
624	no value	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]		202.139
625	GABRA4	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]		202.14
626	GABRE	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
627	JMJD6	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]		202.139
628	GABRA1	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]		202.14
629	GABRA3	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
630	NDUFA6	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]		202.141	1.05993
631	PDXDC1	similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
632	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	214.254	202.166	1.05979
633	AARS	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	234.106	248.104
634	no value	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	226.523	213.786	1.05958
635	RPL37	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	228.639	242.258	1.05957
636	SFRS1	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
637	PPAT	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
638	SNX17	sorting nexin 17. [swissprot;acc:q15036]
639	HRB	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	217.67	230.596	1.05938
640	no value	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
641	PRAM1	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]
642	no value	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
643	HRBL	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]
644	C16orf35	cgthba protein (-14 gene protein). [swissprot;acc:q12980]
645	HTATSF1	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
646	SCOC	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	216.731	229.549	1.05914
647	DYNLL2	dynein light chain 2. [refseq;acc:nm_080677]
648	MARS	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	218.227	206.078	1.05895
649	EIF4E	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	233.725	220.751	1.05877
650	no value	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	228.986	216.276
651	BAIAP3	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	233.725	220.751
652	no value	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	248.994	235.255	1.0584
653		dok-like protein. [refseq;acc:nm_024872]	216.504	204.622	1.05807
654	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]
655	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
656	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]
657	SYN3	synapsin iii. [swissprot;acc:o14994]	229.072	216.576	1.0577
658	no value	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
659	HEY1	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	ABLIM2	actin binding lim protein 2. [refseq;acc:nm_032432]
661	HEYL	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
662	SYN2	synapsin ii. [swissprot;acc:q92777]
663	MRRF	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
664	PEX5	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	HEY2	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
666	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]
667	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]

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
- Hugo is the HGNC identifier if it exists
- 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.