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.


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 4458 to 4507 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
2229	surfeit locus protein 5. [source:swissprot;acc:q15528]	Divided	3650.8	3484.94	1.04759	
2230	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [source:swissprot;acc:p40818]	Subtracted	5783.73	6048.91	265.18	
2230	zinc finger protein 291. [source:swissprot;acc:q9by12]	Divided	3650.8	3484.94	1.04759	
2231	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	Divided	3650.8	3484.94	1.04759	
2231	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [source:refseq;acc:nm_005156]	Subtracted	5783.73	6048.91	265.18	
2232	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	Subtracted	5783.73	6048.91	265.18	
2232	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Divided	3650.8	3484.94	1.04759	
2233	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Divided	3614.08	3450.07	1.04754	
2233	adaptor-associated kinase 1. [source:refseq;acc:nm_014911]	Subtracted	5783.73	6048.91	265.18	
2234	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [source:swissprot;acc:p54259]	Subtracted	5783.7	6048.88	265.18	
2234	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Divided	3614.07	3450.07	1.04754	
2235	40s ribosomal protein s3. [source:swissprot;acc:p23396]	Divided	3674.29	3508.13	1.04736	
2235	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Subtracted	5783.73	6048.91	265.18	
2236	rho-gtpase activating protein 10. [source:refseq;acc:nm_020824]	Subtracted	5783.73	6048.91	265.18	
2236	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [source:swissprot;acc:p05023]	Divided	5902.27	6181.21	1.04726	
2237	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [source:swissprot;acc:o60911]	Divided	5902.26	6181.21	1.04726	
2237	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	Subtracted	5783.76	6048.94	265.18	
2238	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [source:swissprot;acc:p07711]	Divided	5902.27	6181.21	1.04726	
2238	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	Subtracted	5783.7	6048.88	265.18	
2239	2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [source:swissprot;acc:p21953]	Subtracted	5783.76	6048.94	265.18	
2239	sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [source:swissprot;acc:p13637]	Divided	5902.27	6181.21	1.04726	
2240	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [source:refseq;acc:nm_013316]	Subtracted	5783.76	6048.94	265.18	
2240	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Divided	5902.27	6181.21	1.04726	
2241	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	Subtracted	5783.75	6048.93	265.18	
2241	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Divided	3670.45	3504.91	1.04723	
2242	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Divided	3670.45	3504.91	1.04723	
2242	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	Subtracted	5783.71	6048.89	265.18	
2243	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]	Divided	5776.96	6049.61	1.0472	
2243	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	Subtracted	5783.76	6048.94	265.18	
2244	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [source:swissprot;acc:p49915]	Divided	5776.96	6049.61	1.0472	
2244	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [source:swissprot;acc:p26599]	Subtracted	5783.76	6048.94	265.18	
2245	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	Subtracted	5783.73	6048.91	265.18	
2245	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [source:swissprot;acc:p20839]	Divided	5776.96	6049.61	1.0472	
2246	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [source:sptrembl;acc:q9ugb5]	Divided	6209.77	6501.99	1.04706	
2246	eyes absent homolog 3. [source:swissprot;acc:q99504]	Subtracted	5779.66	6044.78	265.12	
2247	eyes absent homolog 4. [source:swissprot;acc:o95677]	Subtracted	5784.9	6049.99	265.09	
2247	rna-binding protein with multiple splicing (rbp-ms). [source:swissprot;acc:q93062]	Divided	5819.36	6092.93	1.04701	
2248	eyes absent homolog 2. [source:swissprot;acc:o00167]	Subtracted	5786.15	6050.71	264.56	
2248	signal recognition particle 54 kda protein (srp54). [source:swissprot;acc:p13624]	Divided	5833.01	6106.48	1.04688	
2249	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [source:swissprot;acc:p11766]	Divided	6834.03	7153.66	1.04677	
2249	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [source:refseq;acc:nm_022572]	Subtracted	6711.27	6974.49	263.22	
2250	esterase d (ec 3.1.1.1). [source:swissprot;acc:p10768]	Divided	6834.03	7153.66	1.04677	
2250	yl-1 protein (transcription factor-like 1). [source:swissprot;acc:q15906]	Subtracted	6707.29	6970.07	262.78	
2251	hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [source:swissprot;acc:q16775]	Subtracted	6707.29	6970.07	262.78	
2251	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [source:swissprot;acc:o15270]	Divided	6196.65	6486.12	1.04671	
2252	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	Divided	5840.54	6113.01	1.04665	
2252	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [source:refseq;acc:nm_015920]	Subtracted	4806.38	5067	260.62	
2253	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Subtracted	4806.33	5066.92	260.59	
2253	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	Divided	3629.21	3467.48	1.04664	
2254	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [source:swissprot;acc:p19652]	Divided	7383.13	7727.39	1.04663	

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/