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 201 to 250 of 3730 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
101	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	1	2353.63	3225.65	1.3705	
101	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	0	1442	977	1.47595	
102	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	0	1442	977	1.47595	
102	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	1	2353.63	3225.65	1.3705	
103	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	1	2353.63	3225.65	1.3705	
103	transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [source:swissprot;acc:p51854]	0	197.333	290.667	1.47298	
104	musashi 2 isoform a. [source:refseq;acc:nm_138962]	1	4241.57	5810.79	1.36996	
104	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	0	5106.93	7500.75	1.46874	
105	fos-related antigen 2. [source:swissprot;acc:p15408]	0	3233.86	2208.1	1.46454	
105	musashi 1. [source:refseq;acc:nm_002442]	1	4241.57	5810.79	1.36996	
106	nuclear protein ukp68. [source:refseq;acc:nm_024824]	1	4241.57	5810.79	1.36996	
106	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	0	1251.66	858.525	1.45792	
107	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	1	4266.04	5843.51	1.36977	
107	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	0	326.677	472.605	1.4467	
108	basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	0	292	421	1.44178	
108	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]	1	4366.44	5899.76	1.35116	
109	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	0	100	144	1.44	
109	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	1	4366.44	5899.76	1.35116	
110	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	1	4366.44	5899.76	1.35116	
110	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [source:swissprot;acc:q13813]	0	1833	2637	1.43863	
111	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	1	4366.44	5899.76	1.35116	
111	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	0	2965.5	2063	1.43747	
112	lats homolog 1. [source:refseq;acc:nm_004690]	0	160	112.25	1.42539	
112	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	1	4366.44	5899.76	1.35116	
113	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	1	4366.44	5899.76	1.35116	
113	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [source:swissprot;acc:q9ujc5]	0	160	112.25	1.42539	
114	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	0	671.769	472.945	1.4204	
114	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	1	4300.47	5807.72	1.35048	
115	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	1	21185	28492	1.34491	
115	zinc finger protein-like 1; zinc-finger protein in men1 region. [source:refseq;acc:nm_006782]	0	385	543	1.41039	
116	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	0	668	475	1.40632	
116	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	1	21185	28492	1.34491	
117	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	1	21185	28492	1.34491	
117	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	0	170.5	122	1.39754	
118	methyltransferase like 2. [source:refseq;acc:nm_018396]	0	31	43	1.3871	
118	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	1	21185	28492	1.34491	
119	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source:swissprot;acc:o75454]	0	633.85	460.2	1.37734	
119	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	1	21185	28492	1.34491	
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]	1	5136.78	6895.98	1.34247	
120	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	0	494.417	359.631	1.37479	
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]	0	19.6667	14.3333	1.3721	
121	transcription factor jun-b. [source:swissprot;acc:p17275]	1	5579.18	7488.4	1.3422	
122	high-mobility group 20a. [source:refseq;acc:nm_018200]	1	5140.14	6893.53	1.34112	
122	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [source:refseq;acc:nm_015503]	0	107	78	1.37179	
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	1	24260.3	18172.1	1.33503	
123	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	0	2285.62	1681.3	1.35944	
124	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	1	24255.7	18168.9	1.33501	
124	regulator of chromosome condensation (cell cycle regulatory protein). [source:swissprot;acc:p18754]	0	3248.95	2399.76	1.35386	
125	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	1	24255.7	18168.9	1.33501	
125	probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [source:swissprot;acc:o75185]	0	1095.42	812.166	1.34876	

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/