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 3658 to 3707 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1829	ovarian carcinoma immunoreactive antigen. [source:refseq;acc:nm_017830]	Divided	5633.44	5997	1.06454	
1830	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	Divided	5633.44	5997	1.06454	
1830	prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [source:swissprot;acc:p13674]	Subtracted	6916.14	7295.24	379.1	
1831	homeobox prospero-like protein prox1 (prox 1). [source:swissprot;acc:q92786]	Subtracted	6916.14	7295.24	379.1	
1831	solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [source:swissprot;acc:q9ugh3]	Divided	5633.44	5997	1.06454	
1832	dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [source:swissprot;acc:o14733]	Divided	5633.44	5997	1.06454	
1832	rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [source:refseq;acc:nm_002853]	Subtracted	6916.14	7295.24	379.1	
1833	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [source:swissprot;acc:p49914]	Divided	6175.23	6572.85	1.06439	
1833	prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [source:swissprot;acc:o15460]	Subtracted	6916.14	7295.24	379.1	
1834	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Divided	3593.24	3375.93	1.06437	
1834	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [source:swissprot;acc:p23528]	Subtracted	6230.21	6608.64	378.43	
1835	cofilin, muscle isoform (cofilin 2). [source:swissprot;acc:q9y281]	Subtracted	6230.21	6608.64	378.43	
1835	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [source:swissprot;acc:q15560]	Divided	5019.3	5342.36	1.06436	
1836	destrin (actin-depolymerizing factor) (adf). [source:swissprot;acc:p18282]	Subtracted	6230.21	6608.64	378.43	
1836	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	Divided	5019.3	5342.36	1.06436	
1837	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [source:refseq;acc:nm_002873]	Divided	5739.49	6108.72	1.06433	
1837	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [source:swissprot;acc:q92890]	Subtracted	6230.21	6608.64	378.43	
1838	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [source:swissprot;acc:p12956]	Divided	5739.49	6108.72	1.06433	
1838	c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [source:sptrembl;acc:q9ujk0]	Subtracted	6951.29	7329	377.71	
1839	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [source:swissprot;acc:p13010]	Divided	5739.49	6108.72	1.06433	
1839	serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [source:swissprot;acc:o15269]	Subtracted	6167.29	6544.12	376.83	
1840	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [source:swissprot;acc:o43776]	Subtracted	6847.82	7223.51	375.69	
1840	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	Divided	3591.95	3375.34	1.06417	
1841	fad synthetase. [source:refseq;acc:nm_025207]	Divided	3591.95	3375.34	1.06417	
1841	ring finger protein 20. [source:refseq;acc:nm_019592]	Subtracted	5419.54	5793.94	374.4	
1842	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	Divided	3591.95	3375.34	1.06417	
1842	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [source:refseq;acc:nm_014771]	Subtracted	5419.54	5793.94	374.4	
1843	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	Divided	3591.95	3375.34	1.06417	
1843	spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [source:swissprot;acc:o15020]	Subtracted	5232.14	5605.8	373.66	
1844	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	Divided	3591.95	3375.34	1.06417	
1844	spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [source:swissprot;acc:q01082]	Subtracted	5232.14	5605.8	373.66	
1845	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	Divided	3591.95	3375.34	1.06417	
1845	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [source:swissprot;acc:o95394]	Subtracted	5232.14	5605.8	373.66	
1846	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [source:swissprot;acc:q13126]	Subtracted	5232.99	5606.53	373.54	
1846	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	Divided	3591.95	3375.34	1.06417	
1847	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	Divided	6215.55	6613.46	1.06402	
1847	putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [source:swissprot;acc:q9uet6]	Subtracted	5232.99	5606.53	373.54	
1848	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [source:swissprot;acc:o95749]	Subtracted	4322.65	4696.04	373.39	
1848	heat shock protein hsp 90-alpha (hsp 86). [source:swissprot;acc:p07900]	Divided	5746.06	6113.79	1.064	
1849	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [source:swissprot;acc:p78540]	Divided	6267.93	6668.72	1.06394	
1849	mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [source:swissprot;acc:p34949]	Subtracted	5458.12	5830.76	372.64	
1850	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [source:swissprot;acc:q9ulu4]	Divided	6158.6	6551.94	1.06387	
1850	putative ankyrin-repeat containing protein. [source:refseq;acc:nm_025185]	Subtracted	5458.12	5830.76	372.64	
1851	adenovirus 5 e1a-binding protein (bs69 protein). [source:swissprot;acc:q15326]	Divided	6156.28	6549.03	1.0638	
1851	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	Subtracted	5458.12	5830.76	372.64	
1852	arginase 1 (ec 3.5.3.1) (liver-type arginase). [source:swissprot;acc:p05089]	Divided	6271.17	6670.97	1.06375	
1852	protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [source:swissprot;acc:q9nyq8]	Subtracted	5458.12	5830.76	372.64	
1853	cadherin-related tumor suppressor homolog precursor (fat protein homolog). [source:swissprot;acc:q14517]	Subtracted	5458.12	5830.76	372.64	
1853	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	Divided	6076.65	6463.64	1.06368	
1854	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	Divided	6076.66	6463.14	1.0636	

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/