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	Interaction Map	Rank	green	Filtered	description	Network Comparison Type	network_comparison	red

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Showing element 594 to 643 of 3228 in total

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

Rank	green	description	network_comparison	red
594	210.136	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	1.06256	223.282
595	199.849	vav proto-oncogene. [swissprot;acc:p15498]	1.0618	212.2
596	199.908	vav-3 protein. [swissprot;acc:q9ukw4]	1.06175	212.253
597	200.212	vav-2 protein. [swissprot;acc:p52735]	1.0615	212.526
598	234.095	rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	1.06138	248.463
599		rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]
600		rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]
601	218.792	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	1.06069	206.274
602		microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
603	212.945	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	1.0605	225.829
604	230.978	60s ribosomal protein l15. [swissprot;acc:p39030]	1.0602	217.862
605	233.441	histone h2b.c (h2b/c). [swissprot;acc:q99880]	1.0601	247.47
606		histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
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]
608		histone h2b. [refseq;acc:nm_175055]
609		histone h2b.s (h2b/s). [swissprot;acc:p57053]
610		histone h2b.d (h2b/d). [swissprot;acc:q99877]
611		histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
612		testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
613		histone h2b.e (h2b/e). [swissprot;acc:q99879]
614	202.125	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	1.06002	214.257
615	202.132	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	1.05999
616		homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]
617	202.135	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	1.05997
618	202.139	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928]	1.05994	214.256
619		forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
620	202.14	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]
621		gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
622		gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
623		gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]
624	202.139	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]
625	202.14	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]
626		gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
627	202.139	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]
628	202.14	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]
629		gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
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]	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]	1.05979	214.254
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]	1.05958	226.523
635	242.258	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	1.05957	228.639
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]	1.05938	217.67
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]

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.