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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 2700 to 2749 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	red	green	network_comparison	
2700	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [source:swissprot;acc:o14521]	188.435	188.31	1.00066	
2701	serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [source:swissprot;acc:o15075]	216.539	216.682	1.00066	
2702	protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [source:swissprot;acc:p23467]	188.435	188.311	1.00066	
2703	thymus-specific serine protease precursor (ec 3.4.-.-). [source:swissprot;acc:q9nqe7]	188.435	188.311	1.00066	
2704	gk001 protein. [source:refseq;acc:nm_020198]	188.435	188.311	1.00066	
2705	calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	188.457	188.334	1.00065	
2706	calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	188.459	188.336	1.00065	
2707	red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [source:swissprot;acc:p24666]	215.096	215.232	1.00063	
2708	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [source:swissprot;acc:p08397]	227.796	227.66	1.0006	
2709	importin 7; ran-binding protein 7. [source:refseq;acc:nm_006391]	220.521	220.395	1.00057	
2710	importin 8; ran-binding protein 8. [source:refseq;acc:nm_006390]	220.521	220.395	1.00057	
2711	brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [source:swissprot;acc:q9y6d5]	220.521	220.395	1.00057	
2712	hsgcn1 (fragment). [source:sptrembl;acc:q99736]	220.521	220.395	1.00057	
2713	brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [source:swissprot;acc:q9y6d6]	220.521	220.395	1.00057	
2714	similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	220.224	220.348	1.00056	
2715	basic proline-rich peptide p-e (ib-9). [source:swissprot;acc:p02811]	216.018	215.903	1.00053	
2716	salivary proline-rich protein po (allele k) [contains: peptide p-d] (fragment). [source:swissprot;acc:p10162]	216.018	215.903	1.00053	
2717	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [source:refseq;acc:nm_014268]	216.521	216.634	1.00052	
2718	histidine-rich membrane protein ke4. [source:swissprot;acc:q92504]	216.52	216.632	1.00052	
2719	microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [source:swissprot;acc:q15691]	216.52	216.632	1.00052	
2720	microtubule-associated protein rp/eb family member 3 (protein eb3). [source:swissprot;acc:q9upy8]	216.52	216.633	1.00052	
2721	bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [source:swissprot;acc:p07814]	221.022	221.116	1.00043	
2722	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [source:swissprot;acc:q9y4p3]	219.308	219.214	1.00043	
2723	lamin b2. [source:swissprot;acc:q03252]	219.323	219.413	1.00041	
2724	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [source:swissprot;acc:p08238]	221.053	220.963	1.00041	
2725	doublecortin (lissencephalin-x) (lis-x) (doublin). [source:swissprot;acc:o43602]	216.496	216.569	1.00034	
2726	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [source:refseq;acc:nm_002873]	221.001	220.927	1.00033	
2727	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [source:swissprot;acc:p12956]	221.001	220.927	1.00033	
2728	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [source:swissprot;acc:p13010]	221.001	220.927	1.00033	
2729	ubiquitin-specific protease otubain 1. [source:refseq;acc:nm_017670]	202.123	202.06	1.00031	
2730	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	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	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	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	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	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	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	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [source:swissprot;acc:q16594]	198.278	198.321	1.00022	
2742	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	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [source:refseq;acc:nm_004289]	198.278	198.321	1.00022	
2744	transcriptional adaptor 3-like isoform a. [source:refseq;acc:nm_006354]	201.476	201.514	1.00019	
2745	frg1 protein (fshd region gene 1 protein). [source:swissprot;acc:q14331]	201.476	201.514	1.00019	
2746	transcriptional adapter 2-like (ada2-like protein) (kl04p). [source:swissprot;acc:o75478]	201.476	201.514	1.00019	
2747	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [source:refseq;acc:nm_013263]	201.477	201.514	1.00018	
2748	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [source:swissprot;acc:o43765]	189.563	189.531	1.00017	
2749	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	

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/