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 2991 to 3040 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
748	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	Ranked	245.246	233.483	1.05038	
748	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [source:swissprot;acc:o75439]	Rooted	60.4376	64.4898	1.06705	
749	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	Rooted	66.9737	71.4637	1.06704	
749	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [source:refseq;acc:nm_001253]	Squared	23148.8	27021.5	1.1673	
749	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	Measured	4565.34	5085.92	1.11403	
749	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	Ranked	221.968	211.326	1.05036	
750	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	Ranked	222.138	211.503	1.05028	
750	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [source:swissprot;acc:q10713]	Rooted	60.4385	64.49	1.06704	
750	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [source:swissprot;acc:p05976]	Measured	4565.34	5085.92	1.11403	
750	n-acetyltransferase 5 (ec 2.3.1.-). [source:swissprot;acc:q9y6d2]	Squared	21678.4	25303.3	1.16721	
751	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	Rooted	66.9738	71.4638	1.06704	
751	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Squared	20305.9	23689.4	1.16663	
751	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [source:swissprot;acc:p08590]	Measured	4565.34	5085.92	1.11403	
751	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	Ranked	223.463	212.875	1.04974	
752	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	Rooted	66.9736	71.4636	1.06704	
752	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [source:swissprot;acc:o75380]	Measured	4565.34	5085.92	1.11403	
752	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	Ranked	223.463	212.875	1.04974	
752	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Squared	20305.9	23689.4	1.16663	
753	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	Rooted	66.9737	71.4637	1.06704	
753	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [source:swissprot;acc:p50747]	Squared	24183.6	28211.1	1.16654	
753	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Ranked	224.434	235.583	1.04968	
753	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [source:swissprot;acc:p14649]	Measured	4565.34	5085.92	1.11403	
754	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	Rooted	66.9737	71.4637	1.06704	
754	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [source:swissprot;acc:p54687]	Squared	23958.6	27945.1	1.16639	
754	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [source:swissprot;acc:q15005]	Ranked	224.434	235.583	1.04968	
754	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	Measured	4565.34	5085.92	1.11403	
755	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [source:swissprot;acc:q9y478]	Rooted	66.9737	71.4637	1.06704	
755	branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [source:swissprot;acc:o15382]	Squared	23966.4	27952.2	1.16631	
755	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	Measured	4079.81	4545.01	1.11402	
755	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [source:swissprot;acc:p11172]	Ranked	224.434	235.583	1.04968	
756	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [source:swissprot;acc:q9ugj0]	Rooted	66.9737	71.4637	1.06704	
756	cleft lip and palate associated transmembrane protein 1. [source:refseq;acc:nm_001294]	Ranked	224.434	235.583	1.04968	
756	topoisomerase-related function protein 4-2. [source:refseq;acc:nm_022447]	Measured	4725.28	5261.06	1.11339	
756	transducin-like enhancer protein 4. [source:swissprot;acc:q04727]	Squared	31298	36502	1.16627	
757	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [source:swissprot;acc:p17213]	Ranked	224.434	235.583	1.04968	
757	signal recognition particle 68 kda protein (srp68). [source:swissprot;acc:q9uhb9]	Measured	5622.89	6260.02	1.11331	
757	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	Squared	20248.9	23608.3	1.16591	
757	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [source:swissprot;acc:p31930]	Rooted	60.4457	64.4918	1.06694	
758	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [source:swissprot;acc:p56282]	Measured	3760.3	4185.82	1.11316	
758	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887]	Squared	20248.9	23608.3	1.16591	
758	phospholipid transfer protein precursor (lipid transfer protein ii). [source:swissprot;acc:p55058]	Ranked	224.434	235.583	1.04968	
758	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Rooted	96.6463	103.103	1.06681	
759	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	Measured	4254.62	4736.03	1.11315	
759	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Squared	49280.5	42272.7	1.16578	
759	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Rooted	66.9416	71.4055	1.06668	
759	osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	Ranked	231.809	243.289	1.04952	
760	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	Measured	5870.2	6533.39	1.11298	
760	c18b11 homolog (44.9kd). [source:refseq;acc:nm_152260]	Squared	21186.4	24698.3	1.16576	
760	small gtp-binding tumor suppressor 1. [source:refseq;acc:nm_145173]	Rooted	66.9397	71.4023	1.06667	
760	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Ranked	246.055	234.458	1.04946	

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/