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 Interaction Map Network Comparison Type Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1875 to 1924 of 14920 in total

Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
235	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Rooted	1	137.446	120.823	1.13758	
235	nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	Squared	1	42411.6	55802.1	1.31573	
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	Ranked	1	227.357	254.15	1.11785	
235	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Measured	1	5181.2	6410.58	1.23728	
235	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [source:swissprot;acc:o14640]	Squared	0	23310.5	31089.6	1.33372	
235	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Rooted	0	26.1597	29.2445	1.11792	
236	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Rooted	1	137.446	120.823	1.13758	
236	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [source:swissprot;acc:p49753]	Measured	0	2715.75	3103.01	1.1426	
236	pnas-18. [source:sptrembl;acc:q9bzu3]	Rooted	0	24.2086	21.6857	1.11634	
236	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [source:swissprot;acc:q9h361]	Squared	0	18175.2	13699.8	1.32668	
236	pp3111 protein. [source:refseq;acc:nm_022156]	Ranked	1	227.357	254.15	1.11785	
236	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Ranked	0	15245.4	16788.5	1.10122	
236	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Measured	1	4723.53	5828.46	1.23392	
236	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]	Squared	1	42411.6	55802.1	1.31573	
237	aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]	Squared	0	5219.15	3979.89	1.31138	
237	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]	Ranked	0	9984	9067	1.10114	
237	dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Rooted	0	21.2911	23.7622	1.11606	
237	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Rooted	1	137.446	120.823	1.13758	
237	p28 ing5. [source:refseq;acc:nm_032329]	Measured	0	2551.23	2243.69	1.13707	
237	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]	Squared	1	42411.6	55802.1	1.31573	
237	syntaxin 18. [source:swissprot;acc:q9p2w9]	Ranked	1	227.357	254.15	1.11785	
237	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Measured	1	4567.04	5631.2	1.23301	
238	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	Measured	0	2198.47	1933.94	1.13678	
238	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Ranked	0	12677.7	13941.7	1.0997	
238	lipocalin-interacting membrane receptor. [source:refseq;acc:nm_018113]	Rooted	0	20.6514	18.5098	1.1157	
238	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Rooted	1	137.446	120.823	1.13758	
238	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]	Squared	1	42411.6	55802.1	1.31573	
238	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Measured	1	27642.5	22440.4	1.23182	
238	rd protein. [source:swissprot;acc:p18615]	Ranked	1	227.357	254.15	1.11785	
238	uncharacterized bone marrow protein bm033. [source:refseq;acc:nm_018452]	Squared	0	5219.15	3979.89	1.31138	
239	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Measured	1	7711.38	6265.8	1.23071	
239	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	Squared	0	43393.5	56658.6	1.30569	
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	Ranked	1	227.357	254.15	1.11785	
239	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	Measured	0	382.142	434.366	1.13666	
239	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Rooted	1	137.446	120.823	1.13758	
239	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm_004635]	Squared	1	42411.6	55802.1	1.31573	
239	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Ranked	0	8907.41	9795.36	1.09969	
239	p28 ing5. [source:refseq;acc:nm_032329]	Rooted	0	32.711	36.4589	1.11458	
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	Ranked	1	227.357	254.15	1.11785	
240	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [source:swissprot;acc:p05106]	Rooted	0	19.303	21.5023	1.11394	
240	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Measured	1	7711.36	6265.79	1.23071	
240	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Rooted	1	137.446	120.823	1.13758	
240	methyltransferase like 2. [source:refseq;acc:nm_018396]	Ranked	0	17946	16326	1.09923	
240	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [source:swissprot;acc:q16539]	Squared	1	42411.6	55802.1	1.31573	
240	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Measured	0	1475.83	1676.18	1.13575	
240	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]	Squared	0	7071.05	5421.2	1.30433	
241	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Squared	0	4734.34	6172.1	1.30369	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	Ranked	1	227.357	254.15	1.11785	
241	fos-related antigen 2. [source:swissprot;acc:p15408]	Rooted	0	44.3292	39.9005	1.11099	
241	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	Measured	0	1225.47	1079.01	1.13574	

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/