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 1808 to 1857 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
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	
913	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Subtracted	3847.31	4409.22	561.91	
913	ww domain binding protein 2 (wbp-2). [source:swissprot;acc:q969t9]	Divided	5768.5	6342.05	1.09943	
914	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [source:swissprot;acc:p07858]	Divided	6513.45	7161	1.09942	
914	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	Subtracted	4997	5557.17	560.17	
915	cytochrome b5 reductase b5r.2. [source:refseq;acc:nm_016229]	Divided	6289.72	6911.96	1.09893	
915	zinc finger protein t86. [source:swissprot;acc:o00488]	Subtracted	4052.77	4612.54	559.77	
916	cytochrome b5 reductase 1 (b5r.1). [source:refseq;acc:nm_016243]	Divided	6289.72	6911.96	1.09893	
916	pescadillo homolog 1. [source:swissprot;acc:o00541]	Subtracted	3751.14	4310.89	559.75	
917	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [source:swissprot;acc:p00387]	Divided	6289.72	6911.96	1.09893	
917	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	Subtracted	5036.92	5596.36	559.44	
918	scratch; scratch 1. [source:refseq;acc:nm_031309]	Divided	7281.6	8001.64	1.09888	
918	transducin-like enhancer protein 2 (esg2). [source:swissprot;acc:q04725]	Subtracted	6288.27	6846.97	558.7	
919	limbic system-associated membrane protein precursor (lsamp). [source:swissprot;acc:q13449]	Divided	5396.36	5929.41	1.09878	
919	transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	Subtracted	6287.07	6845.28	558.21	
920	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [source:sptrembl;acc:q9nq03]	Divided	7273.78	7991.72	1.0987	
920	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	Subtracted	3761.59	4319.69	558.1	
921	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	Subtracted	3831.17	4388.74	557.57	
921	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [source:swissprot;acc:p46199]	Divided	6324.31	6948.5	1.0987	
922	eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [source:swissprot;acc:p56537]	Subtracted	3893.85	4450.98	557.13	
922	tubulin-tyrosine ligase. [source:refseq;acc:nm_153712]	Divided	5511.2	6054.71	1.09862	
923	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	Divided	4057.54	4457.66	1.09861	
923	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	Subtracted	3790.11	4346.98	556.87	
924	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	Subtracted	10243.4	9686.82	556.58	
924	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [source:swissprot;acc:q14982]	Divided	5406.5	5939.42	1.09857	
925	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [source:swissprot;acc:q8taa5]	Subtracted	4134.77	4691.24	556.47	
925	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [source:swissprot;acc:q15118]	Divided	5637.43	6193.07	1.09856	
926	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [source:swissprot;acc:q9hav7]	Subtracted	4134.77	4691.24	556.47	
926	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [source:swissprot;acc:q15119]	Divided	5637.45	6193.08	1.09856	
927	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	Divided	5638.64	6194.22	1.09853	
927	swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [source:refseq;acc:nm_003077]	Subtracted	4134.77	4691.24	556.47	
928	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	Divided	5638.46	6194.04	1.09853	
928	swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [source:refseq;acc:nm_003078]	Subtracted	4134.77	4691.24	556.47	
929	surfeit locus protein 1. [source:swissprot;acc:q15526]	Divided	5638.46	6194.04	1.09853	

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/