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 230 to 279 of 3730 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence

Rank	description	Filtered	red	green	network_comparison	
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	
126	calcyphosine. [source:swissprot;acc:q13938]	0	472.524	635.875	1.3457	
126	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	1	24250	18164.9	1.33499	
127	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	0	86	64	1.34375	
127	transcription factor jun-d. [source:swissprot;acc:p17535]	1	5638.2	7523.39	1.33436	
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	1	4355.61	5810.82	1.3341	
128	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	0	81.504	60.8613	1.33918	
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	1	4358.13	5811.49	1.33348	
129	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	0	606.485	454.837	1.33341	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	1	2234.68	2978.53	1.33287	
130	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	0	42	56	1.33333	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	1	2234.73	2978.57	1.33285	
131	serpin b11. [source:swissprot;acc:q96p15]	0	42	56	1.33333	
132	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	0	42	56	1.33333	
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	1	2236.61	2980.35	1.33253	
133	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]	0	252	335	1.32937	
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	1	23421.5	17580.4	1.33225	
134	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	1	21785.2	16426.1	1.32626	
134	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [source:refseq;acc:nm_022362]	0	260.986	346.751	1.32862	
135	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	1	21785.2	16426.1	1.32626	
135	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	0	814.485	613.614	1.32736	
136	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	1	3620.77	4763.34	1.31556	
136	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	0	1526.38	1150.51	1.3267	
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	1	3620.77	4763.34	1.31556	
137	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	0	1631.18	1233.41	1.3225	
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	1	2755.15	2094.3	1.31555	
138	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]	0	204.382	154.804	1.32026	
139	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	0	736.737	561.038	1.31317	
139	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	1	2759.61	2099.49	1.31442	
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]	1	2760.28	2100.27	1.31425	

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/