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 475 to 524 of 3730 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
238	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	0	2198.47	1933.94	1.13678	
238	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	1	27642.5	22440.4	1.23182	
239	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	1	7711.38	6265.8	1.23071	
239	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	0	382.142	434.366	1.13666	
240	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	1	7711.36	6265.79	1.23071	
240	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	0	1475.83	1676.18	1.13575	
241	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	0	1225.47	1079.01	1.13574	
241	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	1	7711.31	6265.76	1.23071	
242	max protein. [source:swissprot;acc:p25912]	1	4640.26	5704.87	1.22943	
242	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	0	729.216	642.343	1.13524	
243	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	1	4246.95	5208.98	1.22652	
243	keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	0	1225.09	1079.36	1.13502	
244	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	0	1225.09	1079.36	1.13502	
244	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	1	4250.14	5211.25	1.22614	
245	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	1	4251.65	5212.33	1.22595	
245	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	0	1225.09	1079.36	1.13502	
246	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	1	4252.66	5213.05	1.22583	
246	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	0	1225.09	1079.36	1.13502	
247	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	0	1225.09	1079.36	1.13502	
247	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	1	6416.68	7865.15	1.22574	
248	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	0	1225.09	1079.37	1.135	
248	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	1	6417.18	7859.6	1.22477	
249	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	0	1225.08	1079.37	1.135	
249	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	1	6417.18	7859.59	1.22477	
250	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	0	1225.08	1079.37	1.135	
250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	1	6417.18	7859.6	1.22477	
251	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	0	1225.08	1079.38	1.13498	
251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	1	6417.18	7859.6	1.22477	
252	crk-like protein. [source:swissprot;acc:p46109]	1	6417.18	7859.6	1.22477	
252	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	0	1225.08	1079.38	1.13498	
253	espin. [source:refseq;acc:nm_031475]	0	1225.07	1079.38	1.13498	
253	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	1	6417.18	7859.59	1.22477	
254	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	0	1318.22	1495.66	1.13461	
254	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	1	6417.18	7859.6	1.22477	
255	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	0	1317.84	1495.22	1.1346	
255	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	1	6417.18	7859.6	1.22477	
256	grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [source:swissprot;acc:o75791]	1	6417.19	7859.51	1.22476	
256	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	0	1224.65	1079.77	1.13418	
257	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	1	6417.31	7858.12	1.22452	
257	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [source:swissprot;acc:p12532]	0	861.401	759.896	1.13358	
258	40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	0	1183.16	1337.54	1.13048	
258	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	1	6417.33	7857.93	1.22449	
259	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	0	1295.49	1463.51	1.1297	
259	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	1	6417.81	7852.52	1.22355	
260	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	1	4244.95	5193.42	1.22343	
260	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	0	1949.36	2202	1.1296	
261	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	0	1295.81	1463.55	1.12945	
261	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	1	4247.36	5192.61	1.22255	
262	adenylyl cyclase-associated protein 2 (cap 2). [source:swissprot;acc:p40123]	0	764.479	676.971	1.12926	
262	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	1	24896.4	20431.7	1.21852	

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/