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 29840 in total

Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
118	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Measured	Subtracted	1	9275.1	7089.65	2185.45	
118	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Ranked	Subtracted	0	3845	5699	1854	
118	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Measured	Subtracted	0	324.442	593.094	268.652	
118	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	Rooted	Divided	1	50.3065	62.9788	1.2519	
118	methyltransferase like 2. [source:refseq;acc:nm_018396]	Measured	Divided	0	31	43	1.3871	
118	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	Rooted	Divided	0	9.1258	11.4849	1.25851	
118	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Ranked	Divided	1	284.753	228.934	1.24382	
118	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	Rooted	Subtracted	1	37.2205	52.2064	14.9859	
118	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Ranked	Subtracted	1	274.027	237.79	36.237	
118	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Measured	Divided	1	21185	28492	1.34491	
118	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Squared	Divided	1	210445	136779	1.53858	
118	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	Squared	Divided	0	240.689	124.83	1.92813	
118	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Rooted	Subtracted	0	32.6268	28.4118	4.215	
118	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Squared	Subtracted	1	81888.8	56306.5	25582.3	
119	40s ribosomal protein s29. [source:swissprot;acc:p30054]	Squared	Subtracted	0	5295.67	6326.82	1031.15	
119	60s ribosomal protein l7. [source:swissprot;acc:p18124]	Rooted	Subtracted	0	27.512	31.7228	4.2108	
119	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Measured	Subtracted	1	12998.5	15138.2	2139.7	
119	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Ranked	Subtracted	1	281.582	246.371	35.211	
119	cell division protein kinase 3 (ec 2.7.1.-). [source:swissprot;acc:q00526]	Squared	Subtracted	1	81606.8	56215.8	25391	
119	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	Measured	Divided	0	633.85	460.2	1.37734	
119	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Squared	Divided	1	210335	136716	1.53848	
119	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	Ranked	Divided	0	3609	4302.5	1.19216	
119	methyltransferase like 2. [source:refseq;acc:nm_018396]	Squared	Divided	0	0.227456	0.437633	1.92403	
119	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Measured	Divided	1	21185	28492	1.34491	
119	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	Ranked	Divided	1	318.982	259.004	1.23157	
119	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	Ranked	Subtracted	0	7739.47	9580.95	1841.48	
119	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [source:swissprot;acc:p12931]	Rooted	Divided	0	4.72248	5.90479	1.25036	
119	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Rooted	Subtracted	1	63.6507	48.7127	14.938	
119	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	Rooted	Divided	1	50.3247	62.9892	1.25166	
119	ubiquitin protein ligase. [source:refseq;acc:nm_130466]	Measured	Subtracted	0	620	352.75	267.25	
120	40s ribosomal protein s4, y isoform 2. [source:swissprot;acc:q8td47]	Squared	Subtracted	0	4225.7	5255.44	1029.74	
120	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	Rooted	Divided	0	22.9115	28.547	1.24597	
120	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Squared	Subtracted	1	81592.1	56211.1	25381	
120	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	Rooted	Subtracted	1	40.081	25.1546	14.9264	
120	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	Measured	Divided	1	5136.78	6895.98	1.34247	
120	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Rooted	Divided	1	50.3333	62.9942	1.25154	
120	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Ranked	Subtracted	1	227.199	192.715	34.484	
120	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Squared	Divided	1	210199	136638	1.53836	
120	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Ranked	Divided	1	269.278	327.709	1.21699	
120	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Ranked	Divided	0	5797	4873	1.18962	
120	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Rooted	Subtracted	0	29.5635	33.7491	4.1856	
120	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	Measured	Subtracted	1	4932.27	7033.29	2101.02	
120	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	Measured	Divided	0	494.417	359.631	1.37479	
120	similar to ribosomal protein, large, p0. [source:sptrembl;acc:q96fq9]	Ranked	Subtracted	0	11438	13277.1	1839.1	
120	syntaxin 1a (neuron-specific antigen hpc-1). [source:swissprot;acc:q16623]	Squared	Divided	0	6.45653	12.2937	1.90407	
120	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [source:swissprot;acc:q9y4p3]	Measured	Subtracted	0	817.81	551.434	266.376	
121	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	Measured	Divided	0	19.6667	14.3333	1.3721	
121	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [source:swissprot;acc:p12750]	Squared	Subtracted	0	4224.07	5253.37	1029.3	
121	alpha crystallin a chain. [source:swissprot;acc:p02489]	Squared	Divided	0	1.27019	2.40686	1.89488	
121	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Squared	Subtracted	1	81527.6	56190.6	25337	

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/