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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Value Type Interaction Map description Network Comparison Type Rank Gene Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2462 to 2511 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	781	5874.76	6533.36	1.11211	
sedlin. [source:swissprot;acc:o14582]	350	17396.9	20483.9	1.17745	
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	308	4977.09	5966.44	1.19878	
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	309	4977.8	5966.14	1.19855	
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	311	4981.52	5964.58	1.19734	
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	558	6167.93	7007.7	1.13615	
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [source:swissprot;acc:q99611]	555	6167.93	7007.7	1.13615	
semaphorin 6b precursor (semaphorin z) (sema z). [source:swissprot;acc:q9h3t3]	2832	0.00001	0.00001	1	
semaphorin 6c precursor (semaphorin y) (sema y). [source:swissprot;acc:q9h3t2]	2933	0.00001	0.00001	1	
semaphorin 6d isoform 3 precursor. [source:refseq;acc:nm_153617]	2964	0.00001	0.00001	1	
senescence marker protein-30 (smp-30) (regucalcin) (rc). [source:swissprot;acc:q15493]	2687	3953.53	3972.32	1.00475	
sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [source:swissprot;acc:q96ld8]	2843	0.00001	0.00001	1	
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	931	5638.59	6194.17	1.09853	
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	346	14229.2	16780.7	1.17931	
septin 10 isoform 1. [source:refseq;acc:nm_144710]	327	16067.4	19094.4	1.18839	
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	334	14924.4	17655.2	1.18298	
septin 6. [source:swissprot;acc:q14141]	330	15959.9	18957.1	1.1878	
septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	329	15999.1	19007.1	1.18801	
septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	325	16177.9	19235.4	1.18899	
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [source:refseq;acc:nm_003900]	1362	6322.75	6820.5	1.07872	
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34896]	1157	5418.33	5895.2	1.08801	
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [source:swissprot;acc:p34897]	1199	5449.48	5921.77	1.08667	
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [source:swissprot;acc:o15269]	1935	6167.29	6544.12	1.0611	
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]	2251	6196.65	6486.12	1.04671	
serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	374	5066.93	5925.38	1.16942	
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	371	5067.02	5926.46	1.16961	
serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	2075	3614.91	3423.89	1.05579	
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [source:swissprot;acc:p21549]	1089	6390.28	6973.08	1.0912	
serine/threonine kinase 38 like. [source:refseq;acc:nm_015000]	2897	0.00001	0.00001	1	
serine/threonine kinase 38; serine threonine protein kinase. [source:refseq;acc:nm_007271]	3071	0.00001	0.00001	1	
serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [source:swissprot;acc:o14965]	1792	5839.72	6227.33	1.06637	
serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [source:swissprot;acc:q96gd4]	1789	5839.72	6227.33	1.06637	
serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [source:swissprot;acc:q9uqb9]	1791	5839.72	6227.33	1.06637	
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [source:swissprot;acc:q9upe1]	1262	5894.47	6383.73	1.083	
serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [source:swissprot;acc:q9y6e0]	3115	0.00001	0.00001	1	
serine/threonine protein kinase 25 (ec 2.7.1.37) (sterile 20/oxidant stress-response kinase 1) (ste20/oxidant stress response kinase-1) (sok-1) (ste20-like kinase). [source:swissprot;acc:o00506]	3048	0.00001	0.00001	1	
serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [source:swissprot;acc:q13188]	3111	0.00001	0.00001	1	
serine/threonine protein kinase mask; ste20-like kinase mst4. [source:refseq;acc:nm_016542]	2982	0.00001	0.00001	1	
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	71	4556.78	2945.26	1.54716	
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005]	73	4556.83	2945.38	1.54711	
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4]	74	4556.99	2945.8	1.54694	
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [source:swissprot;acc:q15172]	197	17738.5	13995.7	1.26742	
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	196	17738.5	13995.7	1.26742	
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [source:swissprot;acc:p30153]	77	4612.39	3093.6	1.49095	
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	76	4599.26	3058.57	1.50373	
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	199	4916.8	3888.18	1.26455	
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [source:swissprot;acc:q08209]	1325	5656.79	6112.02	1.08047	
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [source:swissprot;acc:p16299]	1328	5656.81	6111.84	1.08044	
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [source:swissprot;acc:p48454]	1329	5656.82	6111.8	1.08043	
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [source:swissprot;acc:p33172]	1255	5438.66	5893.87	1.0837	

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/