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 480 to 529 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
240	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm_004635]	Subtracted	9649.61	11053.5	1403.89	
241	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [source:swissprot;acc:q16539]	Subtracted	9649.61	11053.5	1403.89	
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]	Divided	7711.31	6265.76	1.23071	
242	max protein. [source:swissprot;acc:p25912]	Divided	4640.26	5704.87	1.22943	
242	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [source:swissprot;acc:p43681]	Subtracted	9649.61	11053.5	1403.89	
243	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Divided	4246.95	5208.98	1.22652	
243	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [source:swissprot;acc:p32297]	Subtracted	9649.61	11053.5	1403.89	
244	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	Subtracted	9649.61	11053.5	1403.89	
244	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Divided	4250.14	5211.25	1.22614	
245	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Divided	4251.65	5212.33	1.22595	
245	methyltransferase like 2. [source:refseq;acc:nm_018396]	Subtracted	13241.4	11864	1377.4	
246	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Subtracted	13241.4	11864	1377.4	
246	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	Divided	4252.66	5213.05	1.22583	
247	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Subtracted	13241.4	11864	1377.4	
247	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Divided	6416.68	7865.15	1.22574	
248	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Subtracted	13241.4	11864	1377.4	
248	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	Divided	6417.18	7859.6	1.22477	
249	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Subtracted	4405.4	5782.08	1376.68	
249	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	Divided	6417.18	7859.59	1.22477	
250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Divided	6417.18	7859.6	1.22477	
250	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	Subtracted	4578.09	5939.91	1361.82	
251	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Subtracted	4579.34	5940.64	1361.3	
251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	Divided	6417.18	7859.6	1.22477	
252	crk-like protein. [source:swissprot;acc:p46109]	Divided	6417.18	7859.6	1.22477	
252	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	Subtracted	9648.27	10994.9	1346.63	
253	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	Subtracted	9642.22	10986.4	1344.18	
253	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	Divided	6417.18	7859.59	1.22477	
254	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	Subtracted	9634.98	10976.2	1341.22	
254	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	Divided	6417.18	7859.6	1.22477	
255	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Subtracted	4455.95	5774.03	1318.08	
255	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	Divided	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]	Divided	6417.19	7859.51	1.22476	
256	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Subtracted	4456.67	5773.77	1317.1	
257	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	Divided	6417.31	7858.12	1.22452	
257	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Subtracted	4456.93	5773.67	1316.74	
258	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	Divided	6417.33	7857.93	1.22449	
258	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Subtracted	4457.06	5773.63	1316.57	
259	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Divided	6417.81	7852.52	1.22355	
259	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Subtracted	4569.48	5885.79	1316.31	
260	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [source:refseq;acc:nm_019857]	Subtracted	12515.4	11221.1	1294.3	
260	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Divided	4244.95	5193.42	1.22343	
261	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Divided	4247.36	5192.61	1.22255	
261	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Subtracted	4571.89	5864.86	1292.97	
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]	Divided	24896.4	20431.7	1.21852	
262	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Subtracted	4571.89	5864.86	1292.97	
263	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Subtracted	4571.89	5864.86	1292.97	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	Divided	24896.4	20431.7	1.21852	
264	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Divided	4987.58	4094.57	1.2181	
264	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Subtracted	12503.3	11212	1291.3	
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Subtracted	4638.1	5923.4	1285.3	

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/