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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2730 to 2779 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
2730	C1QBP	complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [source:swissprot;acc:q07021]	212.922	212.985	1.0003	
2731	SIRT1	sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [source:refseq;acc:nm_012238]	212.922	212.985	1.0003	
2732	GCN5L2	general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [source:swissprot;acc:q92830]	202.233	202.175	1.00029	
2733	PCAF	p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [source:swissprot;acc:q92831]	202.229	202.172	1.00028	
2734		ischemia/reperfusion inducible protein. [source:refseq;acc:nm_024640]	219.95	220.007	1.00026	
2735	HSP90AA2	heat shock protein hsp 90-alpha (hsp 86). [source:swissprot;acc:p07900]	220.943	220.887	1.00025	
2736		transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [source:swissprot;acc:o15525]	198.278	198.321	1.00022	
2737	MAFF	transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [source:swissprot;acc:q9ulx9]	198.278	198.321	1.00022	
2738		transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [source:swissprot;acc:o60675]	198.278	198.321	1.00022	
2739	CHL1	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [source:refseq;acc:nm_006614]	198.278	198.321	1.00022	
2740		neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [source:swissprot;acc:p32004]	198.278	198.321	1.00022	
2741	TAF9	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [source:swissprot;acc:q16594]	198.278	198.321	1.00022	
2742	NFE2L1	nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [source:swissprot;acc:q14494]	198.278	198.321	1.00022	
2743	NFE2L3	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [source:refseq;acc:nm_004289]	198.278	198.321	1.00022	
2744	TADA3L	transcriptional adaptor 3-like isoform a. [source:refseq;acc:nm_006354]	201.476	201.514	1.00019	
2745	FRG1	frg1 protein (fshd region gene 1 protein). [source:swissprot;acc:q14331]	201.476	201.514	1.00019	
2746	TADA2L	transcriptional adapter 2-like (ada2-like protein) (kl04p). [source:swissprot;acc:o75478]	201.476	201.514	1.00019	
2747	BRD7	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [source:refseq;acc:nm_013263]	201.477	201.514	1.00018	
2748	SGTA	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [source:swissprot;acc:o43765]	189.563	189.531	1.00017	
2749	HGS	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	190.522	190.496	1.00014	
2750	COG7	conserved oligomeric golgi complex component 7. [source:swissprot;acc:p83436]	190.522	190.496	1.00014	
2751	PSMA1	proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [source:swissprot;acc:p25786]	215.338	215.312	1.00012	
2752	TP53RK	p53-related protein kinase (ec 2.7.1.-) (nori-2). [source:swissprot;acc:q96s44]	221.7	221.716	1.00007	
2753	AGXT	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [source:swissprot;acc:p21549]	208.859	208.846	1.00006	
2754	MTHFS	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [source:swissprot;acc:p49914]	210.638	210.642	1.00002	
2755	DHPS	deoxyhypusine synthase (ec 2.5.1.46) (dhs). [source:swissprot;acc:p49366]	212.403	212.401	1.00001	
2756		3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	0.00001	0.00001	1	
2757	NAP1L1	nucleosome assembly protein 1-like 1 (nap-1 related protein). [source:swissprot;acc:p55209]	0.00001	0.00001	1	
2758	NAP1L2	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [source:swissprot;acc:q9ulw6]	0.00001	0.00001	1	
2759	RXRA	retinoic acid receptor rxr-alpha. [source:swissprot;acc:p19793]	0.00001	0.00001	1	
2760	TAL2	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [source:swissprot;acc:q16559]	0.00001	0.00001	1	
2761	GNB1L	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	0.00001	0.00001	1	
2762	DRG1	developmentally regulated gtp-binding protein 1 (drg 1). [source:swissprot;acc:q9y295]	0.00001	0.00001	1	
2763	PCGF3	ring finger protein 3. [source:refseq;acc:nm_006315]	0.00001	0.00001	1	
2764	RAB11B	ras-related protein rab-11b (gtp-binding protein ypt3). [source:swissprot;acc:q15907]	0.00001	0.00001	1	
2765		histone h2a.e (h2a/e). [source:swissprot;acc:q99878]	0.00001	0.00001	1	
2766	SS18L1	ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]	0.00001	0.00001	1	
2767		histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [source:swissprot;acc:p02261]	0.00001	0.00001	1	
2768	HIST2H2AB	histone h2a.x (h2a/x). [source:swissprot;acc:p16104]	0.00001	0.00001	1	
2769	HIST2H2AC	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [source:swissprot;acc:q16777]	0.00001	0.00001	1	
2770	NIPSNAP1	nipsnap1 protein. [source:swissprot;acc:q9bpw8]	0.00001	0.00001	1	
2771	TBX1	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [source:swissprot;acc:o43435]	0.00001	0.00001	1	
2772	NUDT14	uridine diphosphate glucose pyrophosphatase. [source:refseq;acc:nm_177533]	0.00001	0.00001	1	
2773	BMP8A	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]	0.00001	0.00001	1	
2774	C3orf37	dc12 protein. [source:refseq;acc:nm_020187]	0.00001	0.00001	1	
2775	JRKL	jerky protein homolog like (hhmjg). [source:swissprot;acc:q9y4a0]	0.00001	0.00001	1	
2776	BCOR	bcl-6 interacting corepressor isoform 1. [source:refseq;acc:nm_017745]	0.00001	0.00001	1	
2777	RABIF	guanine nucleotide exchange factor mss4 (rab interacting factor). [source:swissprot;acc:p47224]	0.00001	0.00001	1	
2778	MAFA	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [source:sptrembl;acc:q8nhw3]	0.00001	0.00001	1	
2779	CAV3	caveolin-3 (m-caveolin). [source:swissprot;acc:p56539]	0.00001	0.00001	1	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/