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 1925 to 1974 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
963	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [source:swissprot;acc:p50995]	Subtracted	5778.65	6328.56	549.91	
963	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [source:swissprot;acc:p13073]	Divided	11773	10733.2	1.09688	
964	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	Divided	11773	10733.2	1.09688	
964	synapsin iii. [source:swissprot;acc:o14994]	Subtracted	5791.82	6340.86	549.04	
965	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	Subtracted	5791.82	6340.86	549.04	
965	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	Divided	11773.7	10733.8	1.09688	
966	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	Divided	7817.9	8575.12	1.09686	
966	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]	Subtracted	5791.82	6340.86	549.04	
967	actin binding lim protein 2. [source:refseq;acc:nm_032432]	Subtracted	5791.82	6340.86	549.04	
967	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	Divided	7813.35	8569.96	1.09684	
968	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	Subtracted	5791.82	6340.86	549.04	
968	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	Divided	7813.48	8570.11	1.09684	
969	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	Divided	7813.34	8569.95	1.09684	
969	synapsin ii. [source:swissprot;acc:q92777]	Subtracted	5791.82	6340.86	549.04	
970	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	Divided	7813.45	8570.07	1.09684	
970	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	Subtracted	5791.82	6340.86	549.04	
971	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	Divided	7813.36	8569.97	1.09684	
971	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	Subtracted	5791.82	6340.86	549.04	
972	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	Divided	7813.48	8570.11	1.09684	
972	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	Subtracted	5791.82	6340.86	549.04	
973	galectin-9 (hom-hd-21) (ecalectin). [source:swissprot;acc:o00182]	Divided	7810.11	8566.29	1.09682	
973	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Subtracted	5791.82	6340.86	549.04	
974	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Subtracted	5791.82	6340.86	549.04	
974	dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [source:swissprot;acc:q99518]	Divided	5365.06	5884.52	1.09682	
975	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Subtracted	5791.82	6340.86	549.04	
975	dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [source:swissprot;acc:q01740]	Divided	5365.14	5884.43	1.09679	
976	dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [source:swissprot;acc:p31512]	Divided	5365.22	5884.32	1.09675	
976	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Subtracted	5791.82	6340.86	549.04	
977	annexin a7 (annexin vii) (synexin). [source:swissprot;acc:p20073]	Subtracted	5780.34	6329.3	548.96	
977	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [source:swissprot;acc:o00566]	Divided	4115.9	4513.14	1.09651	
978	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	Subtracted	5385.04	5933.65	548.61	
978	vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [source:swissprot;acc:p19065]	Divided	6654.42	7296.51	1.09649	
979	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	Subtracted	3890.53	4439.07	548.54	
979	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [source:swissprot;acc:p23763]	Divided	6654.42	7296.51	1.09649	
980	similar to lim domain only 7 (fragment). [source:sptrembl;acc:q8n6m2]	Subtracted	5887.52	6434.32	546.8	
980	vesicule-associated membrane protein 4 (vamp-4). [source:swissprot;acc:o75379]	Divided	6654.42	7296.51	1.09649	
981	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [source:swissprot;acc:o14735]	Divided	6654.42	7296.51	1.09649	
981	loh1cr12. [source:refseq;acc:nm_058169]	Subtracted	5195.48	5741.63	546.15	
982	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [source:swissprot;acc:q8n6t3]	Divided	6654.42	7296.51	1.09649	
982	unr protein. [source:swissprot;acc:o75534]	Subtracted	5195.48	5741.63	546.15	
983	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [source:swissprot;acc:p48775]	Subtracted	5350.87	5896.82	545.95	
983	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [source:swissprot;acc:q15836]	Divided	6654.42	7296.51	1.09649	
984	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	Subtracted	5568.96	6113.35	544.39	
984	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [source:swissprot;acc:q9y287]	Divided	6362.64	6976.1	1.09642	
985	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	Subtracted	3720.18	4264.46	544.28	
985	integral membrane protein 2c (transmembrane protein bri3) (npd018). [source:swissprot;acc:q9nqx7]	Divided	6362.64	6976.1	1.09642	
986	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]	Subtracted	6436.19	6980.13	543.94	
986	integral membrane protein 2a (e25 protein). [source:swissprot;acc:o43736]	Divided	6362.64	6976.1	1.09642	
987	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [source:swissprot;acc:q13368]	Divided	6660.04	7301.81	1.09636	
987	tubulin-tyrosine ligase. [source:refseq;acc:nm_153712]	Subtracted	5511.2	6054.71	543.51	

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/