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 1108 to 1157 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
139	g2/mitotic-specific cyclin b2. [source:swissprot;acc:o95067]	Squared	Divided	81592.1	56211.1	1.45153	
139	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Rooted	Divided	54.9787	66.2416	1.20486	
139	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Measured	Divided	2759.61	2099.49	1.31442	
139	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [source:refseq;acc:nm_003473]	Squared	Subtracted	86861.5	65369.7	21491.8	
139	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Rooted	Subtracted	49.3267	62.4167	13.09	
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Ranked	Subtracted	228.306	198.011	30.295	
140	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [source:swissprot;acc:p24941]	Squared	Divided	81527.6	56190.6	1.45091	
140	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Rooted	Divided	55.6161	66.7332	1.19989	
140	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	Measured	Subtracted	2597.5	698.5	1899	
140	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Measured	Divided	2760.28	2100.27	1.31425	
140	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [source:swissprot;acc:p24723]	Squared	Subtracted	86609.4	65234.5	21374.9	
140	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	Ranked	Divided	59	49	1.20408	
140	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Rooted	Subtracted	39.9725	52.9973	13.0248	
141	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	Rooted	Subtracted	105.205	92.2415	12.9635	
141	cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	Ranked	Subtracted	239.991	269.238	29.247	
141	g2/mitotic-specific cyclin b1. [source:swissprot;acc:p14635]	Squared	Divided	81520.8	56188.5	1.45084	
141	hbs1-like. [source:refseq;acc:nm_006620]	Measured	Subtracted	2597.5	698.5	1899	
141	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [source:swissprot;acc:q02156]	Squared	Subtracted	86600.9	65229.9	21371	
141	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	Ranked	Divided	59	49	1.20408	
141	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Rooted	Divided	55.6161	66.7332	1.19989	
141	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Measured	Divided	4405.4	5782.08	1.3125	
142	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [source:swissprot;acc:p06493]	Squared	Divided	81478.9	56175.2	1.45044	
142	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	Measured	Divided	9276.47	7090.37	1.30832	
142	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [source:swissprot;acc:p23284]	Squared	Subtracted	86600.9	65229.9	21371	
142	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Rooted	Divided	55.6161	66.7332	1.19989	
142	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	Rooted	Subtracted	105.205	92.2415	12.9635	
142	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	Ranked	Divided	59	49	1.20408	
142	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Ranked	Subtracted	239.99	269.234	29.244	
142	transcription factor jun-d. [source:swissprot;acc:p17535]	Measured	Subtracted	5638.2	7523.39	1885.19	
143	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	Ranked	Divided	59	49	1.20408	
143	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	Rooted	Subtracted	105.205	92.2415	12.9635	
143	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	Measured	Divided	9275.1	7089.65	1.30826	
143	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	Measured	Subtracted	15427.2	13572.8	1854.4	
143	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Rooted	Divided	55.6161	66.7332	1.19989	
143	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [source:refseq;acc:nm_015316]	Squared	Divided	124319	86848.2	1.43145	
143	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	Ranked	Subtracted	240.133	211.382	28.751	
143	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [source:swissprot;acc:o15294]	Squared	Subtracted	86600.9	65229.9	21371	
144	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Ranked	Subtracted	239.35	267.915	28.565	
144	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]	Squared	Subtracted	86600.9	65229.9	21371	
144	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Ranked	Divided	265.686	319.651	1.20312	
144	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	Rooted	Subtracted	105.205	92.2415	12.9635	
144	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Measured	Subtracted	4133.47	5945.32	1811.85	
144	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Measured	Divided	3349.9	4362.61	1.30231	
144	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [source:swissprot;acc:q13625]	Squared	Divided	123324	86277.9	1.42938	
144	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Rooted	Divided	55.6161	66.7332	1.19989	
145	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [source:swissprot;acc:q96kj9]	Squared	Subtracted	86600.9	65229.9	21371	
145	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Rooted	Divided	55.6161	66.7332	1.19989	
145	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Ranked	Subtracted	239.336	267.881	28.545	
145	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Squared	Divided	310840	442993	1.42515	
145	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Measured	Subtracted	4136.36	5943.56	1807.2	

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/