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 241 to 290 of 3228 in total

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

Rank	description	red	green	network_comparison	
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]	7711.31	6265.76	1.23071	
242	max protein. [source:swissprot;acc:p25912]	4640.26	5704.87	1.22943	
243	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	4246.95	5208.98	1.22652	
244	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	4250.14	5211.25	1.22614	
245	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	4251.65	5212.33	1.22595	
246	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	4252.66	5213.05	1.22583	
247	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	6416.68	7865.15	1.22574	
248	proto-oncogene c-crk (p38) (adapter molecule crk). [source:swissprot;acc:p46108]	6417.18	7859.6	1.22477	
249	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [source:swissprot;acc:p42684]	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]	6417.18	7859.6	1.22477	
251	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [source:swissprot;acc:p08631]	6417.18	7859.6	1.22477	
252	crk-like protein. [source:swissprot;acc:p46109]	6417.18	7859.6	1.22477	
253	proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [source:swissprot;acc:p00519]	6417.18	7859.59	1.22477	
254	proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [source:swissprot;acc:p06241]	6417.18	7859.6	1.22477	
255	proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [source:swissprot;acc:p09769]	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]	6417.19	7859.51	1.22476	
257	ccaat displacement protein (cdp) (cut-like 1). [source:swissprot;acc:p39880]	6417.31	7858.12	1.22452	
258	homeobox protein cux-2 (cut-like 2) (fragment). [source:swissprot;acc:o14529]	6417.33	7857.93	1.22449	
259	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	6417.81	7852.52	1.22355	
260	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	4244.95	5193.42	1.22343	
261	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	4247.36	5192.61	1.22255	
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]	24896.4	20431.7	1.21852	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	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]	4987.58	4094.57	1.2181	
265	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	24806.9	20369.9	1.21782	
266	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	24806.9	20369.9	1.21782	
267	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	14021.4	11523	1.21682	
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	24473.9	20127.8	1.21593	
269	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	4590.18	5575.52	1.21466	
270	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	23640.2	19479.8	1.21358	
271	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	2554.89	3093.78	1.21092	
272	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	3858.52	4669.27	1.21012	
273	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	3199.4	3870.8	1.20985	
274	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	3119.98	2579.49	1.20953	
275	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	3119.98	2579.49	1.20953	
276	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	3119.98	2579.49	1.20953	
277	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [source:swissprot;acc:o76081]	3119.98	2579.49	1.20953	
278	transcription factor lbx1. [source:swissprot;acc:p52954]	3119.98	2579.49	1.20953	
279	mosaic protein lgn. [source:swissprot;acc:p81274]	3119.98	2579.49	1.20953	
280	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	3119.98	2579.49	1.20953	
281	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	3119.98	2579.49	1.20953	
282	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	3119.98	2579.49	1.20953	
283	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	5221.28	6314.35	1.20935	
284	paxillin. [source:swissprot;acc:p49023]	5221.28	6314.35	1.20935	
285	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	23326.5	19296.4	1.20885	
286	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	23316	19288.8	1.20878	
287	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	23303.1	19279.5	1.2087	
288	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	23422.4	19380.3	1.20857	
289	u6 snrna-associated sm-like protein lsm6 (sm protein f). [source:swissprot;acc:q9y4y8]	4682.88	5646.19	1.20571	
290	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	4991.48	6014.08	1.20487	

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/