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 2275 to 2324 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
569	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	Squared	52623.3	44380.3	1.18574	
569	t54 protein. [source:swissprot;acc:q92917]	Ranked	226.3	212.38	1.06554	
570	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]	Rooted	62.7424	67.9648	1.08324	
570	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	Squared	52623.3	44380.3	1.18574	
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Ranked	229.709	215.631	1.06529	
570	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. [source:refseq;acc:nm_003077]	Measured	4134.77	4691.24	1.13458	
571	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	Rooted	62.7424	67.9648	1.08324	
571	malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [source:swissprot;acc:p40926]	Ranked	238.529	254.099	1.06528	
571	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	Squared	17799.8	21105.3	1.1857	
571	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. [source:refseq;acc:nm_003078]	Measured	4134.77	4691.24	1.13458	
572	cbf1 interacting corepressor. [source:refseq;acc:nm_004882]	Ranked	227.86	213.945	1.06504	
572	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	Rooted	62.7424	67.9648	1.08324	
572	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	Squared	17799.8	21105.3	1.1857	
572	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]	Measured	4134.77	4691.24	1.13458	
573	evolutionarily conserved g-patch domain containing. [source:refseq;acc:nm_018025]	Ranked	227.86	213.945	1.06504	
573	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	Measured	6739.43	7644.55	1.1343	
573	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	Rooted	62.7427	67.9648	1.08323	
573	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	Squared	17799.8	21105.3	1.1857	
574	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	Rooted	62.7456	67.9646	1.08318	
574	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	Squared	26570.7	31504.6	1.18569	
574	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	Measured	6739.61	7644.58	1.13428	
574	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source: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). [source:swissprot;acc:q9ubs4]	Ranked	221.807	208.264	1.06503	
575	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	Measured	6739.63	7644.59	1.13427	
575	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Rooted	121.695	131.815	1.08316	
575	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). [source:swissprot;acc:p38606]	Squared	26570.7	31504.6	1.18569	
576	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	Squared	26570.7	31504.6	1.18569	
576	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	Ranked	235.18	250.419	1.0648	
576	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Rooted	121.695	131.815	1.08316	
576	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	Measured	6739.7	7644.6	1.13426	
577	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [source:swissprot;acc:q13510]	Squared	36109.8	42811.6	1.1856	
577	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Ranked	224.606	210.944	1.06477	
577	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	Measured	6739.81	7644.62	1.13425	
577	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Rooted	121.695	131.815	1.08316	
578	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	Measured	6739.81	7644.62	1.13425	
578	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Rooted	121.695	131.815	1.08316	
578	importin alpha-6 subunit (karyopherin alpha-5 subunit). [source:swissprot;acc:o15131]	Squared	23534.9	27890.2	1.18506	
578	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	Ranked	224.606	210.944	1.06477	
579	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	Measured	6739.82	7644.62	1.13425	
579	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Rooted	121.695	131.815	1.08316	
579	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [source:swissprot;acc:o43448]	Squared	23526.4	27879.4	1.18503	
579	zinc finger protein t86. [source:swissprot;acc:o00488]	Ranked	246.805	231.796	1.06475	
580	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	Measured	6739.83	7644.63	1.13425	
580	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Rooted	121.695	131.815	1.08316	
580	yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [source:refseq;acc:nm_020470]	Squared	23526.4	27879.3	1.18502	
580	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [source:refseq;acc:nm_014596]	Ranked	236.751	252.038	1.06457	
581	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	Measured	6739.82	7644.63	1.13425	
581	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Rooted	121.695	131.815	1.08316	
581	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [source:swissprot;acc:o43711]	Ranked	237.28	252.492	1.06411	
581	voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [source:swissprot;acc:q14722]	Squared	23526.4	27879.3	1.18502	

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/