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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 4558 to 4607 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	Ranked	Divided	229.709	215.631	1.06529
	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]	Measured		4134.77	4691.24	1.13458
	zinc finger protein t86. [swissprot;acc:o00488]	Rooted	Subtracted	51.0466	56.024	4.9774
571	60s ribosomal protein l32. [swissprot;acc:p02433]			50.519	45.5497	4.9693
	ferritin light chain (ferritin l subunit). [swissprot;acc:p02792]		Divided	62.7424	67.9648	1.08324
	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926]	Ranked		238.529	254.099	1.06528
	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	Squared	Subtracted	31994.3	36720	4725.7
	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415]		Divided	17799.8	21105.3	1.1857
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Measured	Subtracted	3856.29	4624.15	767.86
	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	Ranked		221.807	208.264	13.543
	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]	Measured	Divided	4134.77	4691.24	1.13458
572	cbf1 interacting corepressor. [refseq;acc:nm_004882]	Ranked		227.86	213.945	1.06504
	cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	Squared	Subtracted	31994	36719.6	4725.6
	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	Rooted		50.3803	45.4193	4.961
	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]		Divided	62.7424	67.9648	1.08324
	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]	Ranked	Subtracted	221.807	208.264	13.543
	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902]	Squared	Divided	17799.8	21105.3	1.1857
	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	Measured	Subtracted	5277.4	6042.88	765.48
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]		Divided	4134.77	4691.24	1.13458
573	autoantigen ngp-1. [swissprot;acc:q13823]	Ranked	Subtracted	250.302	236.817	13.485
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Squared		31994	36719.6	4725.6
	evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]	Ranked	Divided	227.86	213.945	1.06504
	fad synthetase. [refseq;acc:nm_025207]	Rooted	Subtracted	50.3803	45.4193	4.961
	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	Measured	Divided	6739.43	7644.55	1.1343
	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	Rooted		62.7427	67.9648	1.08323
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Measured	Subtracted	5281.11	6044.61	763.5
	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]	Squared	Divided	17799.8	21105.3	1.1857
574	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Rooted	Subtracted	50.3803	45.4193	4.961
	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]	Squared		31994	36719.6	4725.6
	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	Ranked		237.554	250.823	13.269
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Rooted	Divided	62.7456	67.9646	1.08318
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Measured	Subtracted	7817.9	8575.12	757.22
	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	Squared	Divided	26570.7	31504.6	1.18569
	homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	Measured		6739.61	7644.58	1.13428
	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	Ranked		221.807	208.264	1.06503
575	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
	homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	Measured		6739.63	7644.59	1.13427
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Rooted		121.695	131.815	1.08316
	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]		Subtracted	50.3803	45.4193	4.961
	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Ranked		223.282	210.136	13.146
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]	Squared		31994	36719.6	4725.6
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Measured		7813.48	8570.11	756.63
	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]	Squared	Divided	26570.7	31504.6	1.18569
576	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	Measured	Subtracted	7813.48	8570.11	756.63
	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]	Squared	Divided	26570.7	31504.6	1.18569
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]	Rooted	Subtracted	50.3803	45.4193	4.961
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	Ranked	Divided	235.18	250.419	1.0648
	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]		Subtracted	232.469	245.613	13.144
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Rooted	Divided	121.695	131.815	1.08316
	homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	Measured		6739.7	7644.6	1.13426

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.