MK5 Microarray Data

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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1080 to 1129 of 3228 in total

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

Rank	description	red	green	network_comparison
1080	secretory carrier-associated membrane protein 2. [swissprot;acc:o15127]	6439.3	7031.73	1.092
1081	secretory carrier-associated membrane protein 3. [swissprot;acc:o14828]
1082	secretory carrier-associated membrane protein 1. [swissprot;acc:o15126]	6439.35	7031.8
1083	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	6213.51	6785.04	1.09198
1084	phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674]	6437.49	7029.22	1.09192
1085	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057]	6520.28	7119.28	1.09187
1086	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272]
1087	junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923]	5732.73	6256.63	1.09139
1088	tax interaction protein 1. [refseq;acc:nm_014604]
1089	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]	6390.28	6973.08	1.0912
1090	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167]	5651.07	6164.55	1.09086
1091	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	5791.05	6316.61	1.09075
1092	hskin17 protein. [refseq;acc:nm_012311]
1093	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]
1094	polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310]
1095	polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]
1096	kinesin protein. [refseq;acc:nm_032559]	5356.23	5842.15	1.09072
1097	homolog of yeast maf1. [refseq;acc:nm_032272]	6133.83	6690.18	1.0907
1098	tumor differentially expressed protein 2. [refseq;acc:nm_178865]
1099	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]
1100	tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]
1101	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
1102	phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9]	5462.88	5958.12	1.09066
1103	ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	5358.18	5843.73	1.09062
1104	kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139]	5359.72	5844.97	1.09054
1105	synaptotagmin xii (sytxii). [swissprot;acc:q8iv01]	5460.49	5954.62	1.09049
1106	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [swissprot;acc:q9uj68]	5489.99	5986.63	1.09046
1107	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617]
1108	rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690]	4846.16	5283.08	1.09016
1109	rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	6545.19	7132.89	1.08979
1110	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]	5947.53	6481.56
1111	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456]	6540.61	7127.41	1.08972
1112	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	5910.54	6440.58	1.08968
1113	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). [swissprot;acc:p18669]
1114	phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259]
1115	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707]	5795.13	6314.19	1.08957
1116	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	5322.16	5798.38	1.08948
1117	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]
1118	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235]
1119	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141]
1120	heat shock factor binding protein 1. [swissprot;acc:o75506]	5915.42	6443.77	1.08932
1121	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	4338.49	4725.86	1.08929
1122	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	7937.72	8646.38	1.08928
1123	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424]	5857.48	6380.4	1.08927
1124	transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725]	6288.27	6846.97	1.08885
1125	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	6287.07	6845.28	1.08879
1126	importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131]	5792.08	6305.67	1.08867
1127	yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470]	5790.65	6303.92	1.08864
1128	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448]		6303.94
1129	voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722]		6303.92

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.