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.

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

Results: HTML CSV LaTeX

Showing element 1268 to 1317 of 3228 in total

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

red	Rank	green	description	network_comparison
5248.07	649	5901.72	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	1.12455
5254.55	2365	5480.56	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	1.04301
5258.96	2210	5517.06	neurocalcin delta. [swissprot;acc:p29554]	1.04908
5259.1	2209	5517.22	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076]
5259.97	2208	5518.26	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	1.0491
5262.6	2355	5492.58	atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	1.0437
5265.95	2366	5492.28	geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609]	1.04298
	2367		fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727]
	2368		mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485]
	2369		fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]
	2370		fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]
5277.4	487	6042.88	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]	1.14505
5281.11	489	6044.61	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	1.14457
5283.8	1519	5673.81	gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334]	1.07381
	1520		gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335]
5285.03	2189	5033.55	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	1.04996
5285.38	2190	5034.86	phosducin-like protein (phlp). [swissprot;acc:q13371]	1.04976
	2191		replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]
	2192		replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
	2193		phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]
	2194		dna repair protein rad52 homolog. [swissprot;acc:p43351]
5285.79	2197	5036.39	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	1.04952
5291.65	2557	5187.78	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594]	1.02002
	2558		intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]
	2559		pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]
	2560		intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
	2561		hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]
	2562		cgthba protein (-14 gene protein). [swissprot;acc:q12980]
	2563		hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
5291.92	547	6020.19	werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	1.13762
5294.28	2750	5298.42	syntaxin 10 (syn10). [swissprot;acc:o60499]	1.00078
5296.39	2748	5301.11	syntaxin 6. [swissprot;acc:o43752]	1.00089
5309.65	2222	5066.82	sqv-7-like protein (fragment). [sptrembl;acc:o95454]	1.04793
5315.76	1161	5782.63	n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]	1.08783
5317.78	707	5944.25	c18b11 homolog (44.9kd). [refseq;acc:nm_152260]	1.11781
	708		z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]
	709		pp1201 protein. [refseq;acc:nm_022152]
	710		lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]
	711		sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]
	712		sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]
5322.16	1116	5798.38	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561]	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]
5322.74	1151	5793.15	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024]	1.08838
	1152		beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025]
5327.58	2657	5371.47	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	1.00824
5328.73	2127	5616.59	eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	1.05402
	2128		erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]
	2129		bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]

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.