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 1775 to 1824 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
888	lbp-9. [source:refseq;acc:nm_014553]	Divided	5903.18	6506.32	1.10217	
888	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [source:swissprot;acc:o00459]	Subtracted	5595.65	6173.23	577.58	
889	s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [source:swissprot;acc:p31153]	Subtracted	6123.15	6700.05	576.9	
889	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [source:swissprot;acc:p23152]	Divided	5903.18	6506.32	1.10217	
890	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390]	Subtracted	3594.31	4169.95	575.64	
890	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [source:swissprot;acc:p48775]	Divided	5350.87	5896.82	1.10203	
891	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	Divided	5385.04	5933.65	1.10188	
891	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Subtracted	3804.09	4379.37	575.28	
892	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	Divided	6784.67	7475.48	1.10182	
892	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [source:swissprot;acc:q13257]	Subtracted	6599.84	7174.29	574.45	
893	e-1 enzyme. [source:refseq;acc:nm_021204]	Divided	6603.09	7274.72	1.10171	
893	probable cation-transporting atpase 1 (ec 3.6.1.-). [source:swissprot;acc:q9nq11]	Subtracted	6599.84	7174.29	574.45	
894	parafibromin. [source:refseq;acc:nm_024529]	Divided	4331.17	4771.22	1.1016	
894	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [source:swissprot;acc:p20226]	Subtracted	6599.84	7174.29	574.45	
895	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	Divided	10247.8	11289	1.1016	
895	ww domain binding protein 2 (wbp-2). [source:swissprot;acc:q969t9]	Subtracted	5768.5	6342.05	573.55	
896	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Subtracted	5167.88	4594.43	573.45	
896	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	Divided	5208.27	5737.17	1.10155	
897	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	Subtracted	6201.54	6774.35	572.81	
897	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	Divided	5929.48	6531.48	1.10153	
898	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [source:refseq;acc:nm_139279]	Divided	5929.55	6531.52	1.10152	
898	nucleobindin 1 precursor (calnuc). [source:swissprot;acc:q02818]	Subtracted	5859.25	6432.03	572.78	
899	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	Divided	5929.55	6531.52	1.10152	
899	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	Subtracted	5859.25	6432.03	572.78	
900	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	Divided	4713.58	4279.17	1.10152	
900	nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	Subtracted	5859.25	6432.03	572.78	
901	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	Subtracted	6080.91	6653.52	572.61	
901	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	Divided	5929.61	6531.55	1.10151	
902	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	Divided	10246.1	11285.8	1.10147	
902	saccharomyces cerevisiae nip7p homolog. [source:refseq;acc:nm_016101]	Subtracted	3729.02	4301.58	572.56	
903	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:p09467]	Subtracted	6077.65	6649.22	571.57	
903	red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [source:swissprot;acc:p24666]	Divided	4986.58	5492.51	1.10146	
904	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	Subtracted	6213.51	6785.04	571.53	
904	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [source:swissprot;acc:o00410]	Divided	6167.33	6785.98	1.10031	
905	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Subtracted	5168.43	4597.44	570.99	
905	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	Divided	10230.1	11256.2	1.1003	
906	ran-gtp binding protein (fragment). [source:sptrembl;acc:o60518]	Divided	6165.1	6783.01	1.10023	
906	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Subtracted	5168.43	4597.44	570.99	
907	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	Divided	11852.9	10773.5	1.10019	
907	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	Subtracted	3779.92	4348.48	568.56	
908	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	Divided	11848.8	10770.3	1.10014	
908	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	Subtracted	3721.19	4288.17	566.98	
909	kinesin family member c3. [source:refseq;acc:nm_005550]	Divided	5995.49	6595.35	1.10005	
909	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	Subtracted	3758.67	4322.87	564.2	
910	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	Subtracted	3766.03	4329.37	563.34	
910	sipl protein. [source:refseq;acc:nm_018269]	Divided	6522.94	7175.18	1.09999	
911	ad24 protein. [source:refseq;acc:nm_022451]	Subtracted	3753.71	4315.95	562.24	
911	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [source:swissprot;acc:q99471]	Divided	4982.81	5480.91	1.09996	
912	prefoldin subunit 6 (protein ke2). [source:swissprot;acc:o15212]	Divided	4982.81	5480.91	1.09996	
912	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Subtracted	3847.31	4409.22	561.91	

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/