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 Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 527 to 576 of 6456 in total 
Value Type	Measured
Filtered	1
Interaction Map	High confidence

Rank	description	Network Comparison Type	red	green	network_comparison	
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	
265	wd-repeat protein wdc146. [source:swissprot;acc:q9c0j8]	Divided	24806.9	20369.9	1.21782	
266	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [source:swissprot;acc:q10570]	Divided	24806.9	20369.9	1.21782	
266	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	Subtracted	11222.2	9948.93	1273.27	
267	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	Subtracted	11222.2	9948.93	1273.27	
267	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Divided	14021.4	11523	1.21682	
268	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	Subtracted	11222.2	9948.93	1273.27	
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Divided	24473.9	20127.8	1.21593	
269	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Subtracted	4808.79	6074.21	1265.42	
269	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Divided	4590.18	5575.52	1.21466	
270	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Divided	23640.2	19479.8	1.21358	
270	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Subtracted	4810.22	6075.04	1264.82	
271	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Divided	2554.89	3093.78	1.21092	
271	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Subtracted	4812.01	6076.09	1264.08	
272	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Divided	3858.52	4669.27	1.21012	
272	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Subtracted	1991.03	3221.38	1230.35	
273	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Divided	3199.4	3870.8	1.20985	
273	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Subtracted	5181.2	6410.58	1229.38	
274	chromosome 3p21.1 gene sequence. [source:refseq;acc:nm_013286]	Divided	3119.98	2579.49	1.20953	
274	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Subtracted	5181.2	6410.58	1229.38	
275	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Subtracted	10264.9	9043.51	1221.39	
275	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [source:swissprot;acc:p49795]	Divided	3119.98	2579.49	1.20953	
276	gbp protein isoform a. [source:refseq;acc:nm_017870]	Subtracted	699.76	1894.39	1194.63	
276	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	Divided	3119.98	2579.49	1.20953	
277	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [source:swissprot;acc:q15388]	Subtracted	8600.02	9792.49	1192.47	
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]	Divided	3119.98	2579.49	1.20953	
278	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [source:swissprot;acc:p40855]	Subtracted	8600.02	9792.49	1192.47	
278	transcription factor lbx1. [source:swissprot;acc:p52954]	Divided	3119.98	2579.49	1.20953	
279	mosaic protein lgn. [source:swissprot;acc:p81274]	Divided	3119.98	2579.49	1.20953	
279	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	Subtracted	4771.21	5961.43	1190.22	
280	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [source:refseq;acc:nm_033256]	Subtracted	677.5	1865.5	1188	
280	regulator of g-protein signaling 17 (rgs17). [source:swissprot;acc:q9ugc6]	Divided	3119.98	2579.49	1.20953	
281	guanine nucleotide-binding protein g(o), alpha subunit 1. [source:swissprot;acc:p09471]	Divided	3119.98	2579.49	1.20953	
281	microfibril-associated glycoprotein 4 precursor. [source:swissprot;acc:p55083]	Subtracted	677.5	1865.5	1188	
282	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [source:refseq;acc:nm_017726]	Subtracted	677.5	1865.5	1188	
282	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Divided	3119.98	2579.49	1.20953	
283	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [source:swissprot;acc:q15485]	Subtracted	677.5	1865.5	1188	
283	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Divided	5221.28	6314.35	1.20935	
284	paxillin. [source:swissprot;acc:p49023]	Divided	5221.28	6314.35	1.20935	
284	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [source:refseq;acc:nm_030949]	Subtracted	677.5	1865.5	1188	
285	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Subtracted	4068.56	5252.6	1184.04	
285	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Divided	23326.5	19296.4	1.20885	
286	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Divided	23316	19288.8	1.20878	
286	rna-binding protein. [source:refseq;acc:nm_019027]	Subtracted	4069.83	5252.17	1182.34	
287	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Subtracted	4069.83	5252.17	1182.34	
287	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Divided	23303.1	19279.5	1.2087	
288	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Divided	23422.4	19380.3	1.20857	
288	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Subtracted	4069.83	5252.17	1182.34	

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/