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 1663 to 1712 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
832	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	Divided	4489.72	4965.35	1.10594	
832	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	Subtracted	5929.48	6531.48	602	
833	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [source:refseq;acc:nm_139279]	Subtracted	5929.55	6531.52	601.97	
833	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	Divided	4489.72	4965.35	1.10594	
834	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	Divided	5623.18	6218.77	1.10592	
834	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	Subtracted	5929.55	6531.52	601.97	
835	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	Divided	5623.18	6218.77	1.10592	
835	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	Subtracted	5929.61	6531.55	601.94	
836	atp-dependent rna helicase rok1; atp-dependent rna helicase. [source:refseq;acc:nm_007010]	Divided	4049	4477.43	1.10581	
836	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [source:swissprot;acc:q16781]	Subtracted	6229.69	6829.58	599.89	
837	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	Divided	4063.64	4492.98	1.10565	
837	kinesin family member c3. [source:refseq;acc:nm_005550]	Subtracted	5995.49	6595.35	599.86	
838	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [source:swissprot;acc:p57057]	Subtracted	6520.28	7119.28	599	
838	pbk1 protein. [source:sptrembl;acc:o76021]	Divided	4064.23	4493.36	1.10559	
839	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	Divided	7093.86	7842.67	1.10556	
839	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	Subtracted	6520.28	7119.28	599	
840	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	Subtracted	10300	9701.33	598.67	
840	poly (adp-ribose) glycohydrolase. [source:refseq;acc:nm_003631]	Divided	5786.67	6395.78	1.10526	
841	conserved oligomeric golgi complex component 7. [source:swissprot;acc:p83436]	Subtracted	10300	9701.33	598.67	
841	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Divided	5786.67	6395.78	1.10526	
842	atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	Subtracted	5623.18	6218.77	595.59	
842	loh1cr12. [source:refseq;acc:nm_058169]	Divided	5195.48	5741.63	1.10512	
843	28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [source:swissprot;acc:q9nvs2]	Subtracted	5623.18	6218.77	595.59	
843	unr protein. [source:swissprot;acc:o75534]	Divided	5195.48	5741.63	1.10512	
844	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Subtracted	3641.89	4236.95	595.06	
844	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	Divided	6276.97	6934.8	1.1048	
845	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]	Divided	6276.97	6934.8	1.1048	
845	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	Subtracted	5797.88	6391.75	593.87	
846	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [source:swissprot;acc:p50747]	Divided	5607.43	6194.98	1.10478	
846	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Subtracted	5797.88	6391.75	593.87	
847	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [source:swissprot;acc:o43639]	Divided	6776.85	7485.55	1.10458	
847	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	Subtracted	5797.88	6391.75	593.87	
848	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [source:swissprot;acc:q92903]	Subtracted	6441.56	7034.86	593.3	
848	wd-repeat protein bing4. [source:swissprot;acc:o15213]	Divided	4066.56	4491.65	1.10453	
849	dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [source:swissprot;acc:q16531]	Divided	6194.15	6839.37	1.10417	
849	solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [source:swissprot;acc:q9ukg4]	Subtracted	6439.63	7032.19	592.56	
850	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [source:swissprot;acc:p05166]	Divided	6194.15	6839.37	1.10417	
850	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [source:swissprot;acc:q8wwt9]	Subtracted	6439.66	7032.22	592.56	
851	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	Divided	4307.12	4755.03	1.10399	
851	solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [source:swissprot;acc:q9bzw2]	Subtracted	6439.63	7032.19	592.56	
852	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	Divided	4307.12	4755.03	1.10399	
852	solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [source:swissprot;acc:q13183]	Subtracted	6439.66	7032.22	592.56	
853	apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	Divided	4078.45	4502.32	1.10393	
853	secretory carrier-associated membrane protein 1. [source:swissprot;acc:o15126]	Subtracted	6439.35	7031.8	592.45	
854	secretory carrier-associated membrane protein 2. [source:swissprot;acc:o15127]	Subtracted	6439.3	7031.73	592.43	
854	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	Divided	6562.98	7242.37	1.10352	
855	ero1-like. [source:refseq;acc:nm_014584]	Divided	6562.98	7242.37	1.10352	
855	secretory carrier-associated membrane protein 3. [source:swissprot;acc:o14828]	Subtracted	6439.3	7031.73	592.43	
856	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	Subtracted	5734.15	6326.41	592.26	
856	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849]	Divided	5210.58	5749.33	1.1034	

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/