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 2700 to 2749 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2700	short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm_032547]	5239.33	5260	1.00395	
2701	dynein light chain 2. [source:refseq;acc:nm_080677]	5239.33	5260	1.00395	
2702	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [source:swissprot;acc:p17540]	8971.66	9006.92	1.00393	
2703	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	8972.87	9007.71	1.00388	
2704	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [source:swissprot;acc:p06732]	8980.12	9013.33	1.0037	
2705	protein cgi-27 (c21orf19-like protein). [source:swissprot;acc:q9y316]	4137.61	4152.72	1.00365	
2706	peptidyl prolyl isomerase h; cyclophilin h. [source:refseq;acc:nm_006347]	8979.61	9012.31	1.00364	
2707	prp18 pre-mrna processing factor 18 homolog. [source:refseq;acc:nm_003675]	8979.61	9012.31	1.00364	
2708	j domain protein c21orf55. [source:swissprot;acc:q9nx36]	8979.78	9012.42	1.00363	
2709	testis-specific protein tex28. [source:swissprot;acc:o15482]	5603.24	5583.64	1.00351	
2710	similar to nuclear protein e3-3 orf1. [source:sptrembl;acc:q9bu61]	5603.24	5583.64	1.00351	
2711	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [source:swissprot;acc:o43505]	5332.98	5351.72	1.00351	
2712	a kindred of iglon. [source:refseq;acc:nm_173808]	5603.24	5583.64	1.00351	
2713	ankyrin-repeat family a protein 2 (rfxank-like 2). [source:swissprot;acc:q9h9e1]	5603.24	5583.64	1.00351	
2714	inflammation-related g protein-coupled receptor ex33. [source:refseq;acc:nm_020370]	5603.24	5583.64	1.00351	
2715	huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm_007076]	5332.98	5351.72	1.00351	
2716	mitochondrial import inner membrane translocase subunit tim10. [source:swissprot;acc:q9y5j8]	5332.98	5351.72	1.00351	
2717	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [source:swissprot;acc:p50897]	5603.24	5583.64	1.00351	
2718	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [source:swissprot;acc:q9h115]	5603.24	5583.64	1.00351	
2719	syntaxin 16 (syn16). [source:swissprot;acc:o14662]	5603.24	5583.64	1.00351	
2720	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [source:swissprot;acc:o14653]	5603.24	5583.64	1.00351	
2721	syntaxin 1a (neuron-specific antigen hpc-1). [source:swissprot;acc:q16623]	5603.24	5583.64	1.00351	
2722	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [source:swissprot;acc:p54920]	5603.24	5583.64	1.00351	
2723	adipocyte plasma membrane-associated protein (bscv protein). [source:swissprot;acc:q9hdc9]	5603.24	5583.64	1.00351	
2724	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [source:swissprot;acc:o95721]	5603.24	5583.64	1.00351	
2725	syntaxin 1b. [source:swissprot;acc:q15531]	5603.24	5583.64	1.00351	
2726	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [source:swissprot;acc:p07954]	5332.98	5351.72	1.00351	
2727	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [source:swissprot;acc:q13084]	5603.24	5583.64	1.00351	
2728	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [source:swissprot;acc:o14593]	5603.24	5583.64	1.00351	
2729	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [source:swissprot;acc:o60285]	5333	5351.61	1.00349	
2730	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	5214.9	5197.18	1.00341	
2731	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [source:swissprot;acc:q04206]	7913.63	7939.94	1.00332	
2732	transcription factor relb (i-rel). [source:swissprot;acc:q01201]	7913.63	7939.94	1.00332	
2733	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [source:swissprot;acc:p25963]	7913.63	7939.94	1.00332	
2734	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [source:swissprot;acc:p36551]	7913.63	7939.94	1.00332	
2735	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [source:swissprot;acc:p12277]	8991.87	9019.99	1.00313	
2736	inhibitor of growth family, member 1; inhibitor of growth 1. [source:refseq;acc:nm_005537]	4887.59	4902.08	1.00296	
2737	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	4486.83	4499.52	1.00283	
2738	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [source:swissprot;acc:p32780]	4486.83	4499.52	1.00283	
2739	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [source:refseq;acc:nm_001564]	4877.74	4890.64	1.00264	
2740	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434]	4200.59	4210.94	1.00246	
2741	sorting nexin 5. [source:swissprot;acc:q9y5x3]	5339.67	5327.2	1.00234	
2742	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	10198.1	10174.3	1.00234	
2743	60s acidic ribosomal protein p2. [source:swissprot;acc:p05387]	4824.49	4813.92	1.0022	
2744	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	10143.6	10163.6	1.00197	
2745	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [source:swissprot;acc:o75382]	7746.61	7757.23	1.00137	
2746	hpaii tiny  fragments locus 9c. [source:refseq;acc:nm_022727]	4188.5	4194.22	1.00137	
2747	putatative 28 kda protein. [source:refseq;acc:nm_020143]	4708.68	4702.58	1.0013	
2748	syntaxin 6. [source:swissprot;acc:o43752]	5296.39	5301.11	1.00089	
2749	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [source:swissprot;acc:q15911]	7776.91	7783.48	1.00084	

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/