Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

Results: HTML CSV LaTeX

Showing element 2512 to 2561 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
628	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Rooted	59.6661	64.3692	1.07882	
629	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	Measured	6228.39	7013.19	1.126	
629	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	Ranked	214.256	202.14	1.05994	
629	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	Squared	32192.5	37966.8	1.17937	
629	synapsin iii. [source:swissprot;acc:o14994]	Rooted	60.0129	64.7371	1.07872	
630	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	Rooted	60.0129	64.7371	1.07872	
630	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	Measured	6228.39	7013.19	1.126	
630	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	Squared	32192.8	37967.1	1.17937	
630	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	Ranked	214.256	202.141	1.05993	
631	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	Squared	32192.8	37967.1	1.17937	
631	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). [source:swissprot;acc:q9y5j3]	Rooted	60.0129	64.7371	1.07872	
631	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	Measured	6228.39	7013.19	1.126	
631	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	Ranked	214.256	202.141	1.05993	
632	actin binding lim protein 2. [source:refseq;acc:nm_032432]	Rooted	60.0129	64.7371	1.07872	
632	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	Measured	6228.39	7013.19	1.126	
632	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	Ranked	214.254	202.166	1.05979	
632	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	Squared	32192.5	37966.8	1.17937	
633	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	Ranked	234.106	248.104	1.05979	
633	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	Measured	6228.39	7013.19	1.126	
633	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	Squared	32192.8	37967.2	1.17937	
633	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	Rooted	60.0129	64.7371	1.07872	
634	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Ranked	226.523	213.786	1.05958	
634	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	Measured	6228.39	7013.19	1.126	
634	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	Squared	32192.8	37967.1	1.17937	
634	synapsin ii. [source:swissprot;acc:q92777]	Rooted	60.0129	64.7371	1.07872	
635	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	Ranked	228.639	242.258	1.05957	
635	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	Measured	6228.97	7013.53	1.12595	
635	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	Squared	32189.9	37963.6	1.17936	
635	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	Rooted	60.0129	64.7371	1.07872	
636	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	Squared	32187.7	37961	1.17936	
636	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	Rooted	60.0129	64.7371	1.07872	
636	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	Measured	5713.41	6432.92	1.12593	
636	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	Ranked	228.639	242.258	1.05957	
637	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	Ranked	228.639	242.258	1.05957	
637	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	Rooted	60.0129	64.7371	1.07872	
637	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	Squared	32188.2	37961.6	1.17936	
637	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Measured	7756.51	8731.76	1.12573	
638	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	Squared	32183.5	37955.7	1.17935	
638	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Measured	7755.69	8730.74	1.12572	
638	sorting nexin 17. [source:swissprot;acc:q15036]	Ranked	228.639	242.258	1.05957	
638	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Rooted	60.0129	64.7371	1.07872	
639	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	Squared	17618.8	20776.8	1.17924	
639	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Rooted	60.0129	64.7371	1.07872	
639	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [source:swissprot;acc:p52594]	Ranked	217.67	230.596	1.05938	
639	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Measured	7753.59	8728.13	1.12569	
640	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Rooted	60.0129	64.7371	1.07872	
640	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Measured	4811.02	5414.64	1.12547	
640	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	Ranked	217.67	230.596	1.05938	
640	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [source:swissprot;acc:q15274]	Squared	22848.5	26941.5	1.17914	
641	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	Measured	4810.85	5414.21	1.12542	

Legend:
- Rank is the rank after comparing the two networks
- 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.

- http://analysis.yellowcouch.org/