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 101 to 150 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
101	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	2353.63	3225.65	1.3705	
102	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	2353.63	3225.65	1.3705	
103	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	2353.63	3225.65	1.3705	
104	musashi 2 isoform a. [source:refseq;acc:nm_138962]	4241.57	5810.79	1.36996	
105	musashi 1. [source:refseq;acc:nm_002442]	4241.57	5810.79	1.36996	
106	nuclear protein ukp68. [source:refseq;acc:nm_024824]	4241.57	5810.79	1.36996	
107	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	4266.04	5843.51	1.36977	
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]	4366.44	5899.76	1.35116	
109	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	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]	4366.44	5899.76	1.35116	
111	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	4366.44	5899.76	1.35116	
112	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	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]	4366.44	5899.76	1.35116	
114	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	4300.47	5807.72	1.35048	
115	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	21185	28492	1.34491	
116	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	21185	28492	1.34491	
117	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	21185	28492	1.34491	
118	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	21185	28492	1.34491	
119	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	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]	5136.78	6895.98	1.34247	
121	transcription factor jun-b. [source:swissprot;acc:p17275]	5579.18	7488.4	1.3422	
122	high-mobility group 20a. [source:refseq;acc:nm_018200]	5140.14	6893.53	1.34112	
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	24260.3	18172.1	1.33503	
124	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	24255.7	18168.9	1.33501	
125	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	24255.7	18168.9	1.33501	
126	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	24250	18164.9	1.33499	
127	transcription factor jun-d. [source:swissprot;acc:p17535]	5638.2	7523.39	1.33436	
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	4355.61	5810.82	1.3341	
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	4358.13	5811.49	1.33348	
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [source:refseq;acc:nm_138457]	2234.68	2978.53	1.33287	
131	forkhead box protein p1 (hspc215). [source:swissprot;acc:q9h334]	2234.73	2978.57	1.33285	
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [source:swissprot;acc:q9bzs1]	2236.61	2980.35	1.33253	
133	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	23421.5	17580.4	1.33225	
134	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	21785.2	16426.1	1.32626	
135	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	21785.2	16426.1	1.32626	
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]	3620.77	4763.34	1.31556	
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]	3620.77	4763.34	1.31556	
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	2755.15	2094.3	1.31555	
139	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	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]	2760.28	2100.27	1.31425	
141	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	4405.4	5782.08	1.3125	
142	metalloprotease 1; metalloprotease 1 (pitrilysin family). [source:refseq;acc:nm_014889]	9276.47	7090.37	1.30832	
143	beta-1,4 mannosyltransferase. [source:refseq;acc:nm_019109]	9275.1	7089.65	1.30826	
144	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	3349.9	4362.61	1.30231	
145	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	16771.5	12889.1	1.30122	
146	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	11068	8508.5	1.30082	
147	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	11068	8508.5	1.30082	
148	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	11068	8508.5	1.30082	
149	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	11068	8508.5	1.30082	
150	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	11068	8508.5	1.30082	

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/