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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2063 to 2112 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
258	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Rooted	Subtracted	132.063	122.761	9.302	
258	thrombospondin 3 precursor. [source:swissprot;acc:p49746]	Rooted	Divided	51.6132	45.8422	1.12589	
259	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	Ranked	Subtracted	242.14	265.696	23.556	
259	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [source:swissprot;acc:q9y5p4]	Squared	Divided	76360.8	58841.7	1.29773	
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Ranked	Divided	227.999	204.37	1.11562	
259	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Measured	Divided	6417.81	7852.52	1.22355	
259	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Squared	Subtracted	33514.4	42370.8	8856.4	
259	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Rooted	Subtracted	107.961	117.197	9.236	
259	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Measured	Subtracted	4569.48	5885.79	1316.31	
259	tuftelin-interacting protein 11 (hspc006). [source:swissprot;acc:q9ubb9]	Rooted	Divided	58.2964	65.5926	1.12516	
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Ranked	Divided	219.421	196.978	1.11394	
260	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [source:refseq;acc:nm_019857]	Measured	Subtracted	12515.4	11221.1	1294.3	
260	huntingtin interacting protein 1 related (hip1-related) (hip 12). [source:swissprot;acc:o75146]	Squared	Divided	76296.4	58801.6	1.29752	
260	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Rooted	Divided	59.0951	66.4332	1.12417	
260	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	Squared	Subtracted	35793	44595.3	8802.3	
260	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Measured	Divided	4244.95	5193.42	1.22343	
260	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Rooted	Subtracted	56.7592	65.9889	9.2297	
260	surfeit locus protein 5. [source:swissprot;acc:q15528]	Ranked	Subtracted	242.14	265.696	23.556	
261	carboxypeptidase a5. [source:refseq;acc:nm_080385]	Squared	Subtracted	53174	44377.4	8796.6	
261	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Rooted	Subtracted	52.7582	61.9123	9.1541	
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Ranked	Divided	219.421	196.978	1.11394	
261	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	Squared	Divided	48127.9	62245.6	1.29334	
261	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Rooted	Divided	62.3337	70.0738	1.12417	
261	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Measured	Divided	4247.36	5192.61	1.22255	
261	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Measured	Subtracted	4571.89	5864.86	1292.97	
261	zinc finger protein 291. [source:swissprot;acc:q9by12]	Ranked	Subtracted	242.14	265.696	23.556	
262	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	Squared	Subtracted	53174	44377.4	8796.6	
262	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [source:refseq;acc:nm_006693]	Measured	Divided	24896.4	20431.7	1.21852	
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Ranked	Divided	219.421	196.978	1.11394	
262	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Squared	Divided	26157.6	20236.2	1.29261	
262	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Measured	Subtracted	4571.89	5864.86	1292.97	
262	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	Ranked	Subtracted	242.14	265.696	23.556	
262	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	Rooted	Divided	59.4073	66.7002	1.12276	
262	rna-binding protein. [source:refseq;acc:nm_019027]	Rooted	Subtracted	52.7642	61.9019	9.1377	
263	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Squared	Divided	26157.6	20236.2	1.29261	
263	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Rooted	Subtracted	52.7642	61.9019	9.1377	
263	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	Measured	Subtracted	4571.89	5864.86	1292.97	
263	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Ranked	Divided	219.421	196.978	1.11394	
263	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	Squared	Subtracted	53174	44377.4	8796.6	
263	paxillin. [source:swissprot;acc:p49023]	Rooted	Divided	59.4073	66.7002	1.12276	
263	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Ranked	Subtracted	242.14	265.696	23.556	
263	trs85 homolog. [source:swissprot;acc:q9y2l5]	Measured	Divided	24896.4	20431.7	1.21852	
264	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Ranked	Subtracted	243.24	266.796	23.556	
264	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Squared	Divided	26157.6	20236.2	1.29261	
264	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	Squared	Subtracted	53174	44377.4	8796.6	
264	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Measured	Divided	4987.58	4094.57	1.2181	
264	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Measured	Subtracted	12503.3	11212	1291.3	
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Ranked	Divided	219.421	196.978	1.11394	
264	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Rooted	Subtracted	52.7642	61.9019	9.1377	
264	wiskott-aldrich syndrome protein (wasp). [source:swissprot;acc:p42768]	Rooted	Divided	66.1122	74.1438	1.12148	

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/