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 712 to 761 of 12912 in total 
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Value Type	red	green	network_comparison	
178	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Rooted	45.7414	52.932	1.1572	
179	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Ranked	226.884	194.79	1.16476	
179	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Squared	25326.3	18354.1	1.37987	
179	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	Measured	21591.5	27904.5	1.29238	
179	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	Rooted	50.272	43.4634	1.15665	
180	egf-like-domain, multiple 7; neu1 protein. [source:refseq;acc:nm_016215]	Rooted	50.2801	43.4779	1.15645	
180	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Measured	21591.5	27904.5	1.29238	
180	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Squared	25326.2	18354.1	1.37987	
180	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Ranked	256.228	298.438	1.16474	
181	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Ranked	229.818	267.265	1.16294	
181	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	Rooted	57.4432	66.3307	1.15472	
181	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	Measured	4068.56	5252.6	1.29102	
181	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Squared	55630.4	76083.7	1.36766	
182	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Squared	61733.5	45224.1	1.36506	
182	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [source:swissprot;acc:o14929]	Ranked	277.546	240.461	1.15422	
182	rna-binding protein. [source:refseq;acc:nm_019027]	Measured	4069.83	5252.17	1.29051	
182	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [source:swissprot;acc:p50991]	Rooted	57.45	66.332	1.1546	
183	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Ranked	228.306	198.011	1.153	
183	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Squared	79779.8	108084	1.35478	
183	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	Measured	4069.83	5252.17	1.29051	
183	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [source:swissprot;acc:q14511]	Rooted	57.4586	66.3336	1.15446	
184	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Rooted	153.602	133.195	1.15321	
184	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Measured	4069.83	5252.17	1.29051	
184	odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	Ranked	274.027	237.79	1.15239	
184	small glutamine rich protein with tetratricopeptide repeats 2. [source:refseq;acc:nm_019072]	Squared	72886.3	98544.5	1.35203	
185	adiponectin receptor 2. [source:refseq;acc:nm_024551]	Ranked	281.582	246.371	1.14292	
185	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [source:sptrembl;acc:q96qi5]	Squared	41502.9	30836.8	1.34589	
185	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Measured	4069.83	5252.17	1.29051	
185	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	Rooted	153.578	133.176	1.1532	
186	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Measured	4071.1	5251.75	1.29001	
186	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Ranked	226.582	198.444	1.14179	
186	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006042]	Squared	41502.9	30836.8	1.34589	
186	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	Rooted	153.578	133.176	1.1532	
187	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Rooted	153.548	133.153	1.15317	
187	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [source:refseq;acc:nm_006041]	Squared	41502.9	30836.8	1.34589	
187	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Ranked	226.582	198.444	1.14179	
187	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Measured	4569.48	5885.79	1.28807	
188	heparan sulfate d-glucosaminyl  3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [source:refseq;acc:nm_006043]	Squared	41502.9	30836.8	1.34589	
188	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Ranked	226.582	198.444	1.14179	
188	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	Measured	4571.89	5864.86	1.28281	
188	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Rooted	46.0352	53.0192	1.15171	
189	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [source:refseq;acc:nm_014026]	Squared	41502.9	30836.8	1.34589	
189	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Measured	4571.89	5864.86	1.28281	
189	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Ranked	226.582	198.444	1.14179	
189	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Rooted	46.0352	53.0192	1.15171	
190	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	Squared	71389.9	96037.6	1.34525	
190	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	4571.89	5864.86	1.28281	
190	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [source:refseq;acc:nm_007278]	Rooted	149.165	129.699	1.15009	
190	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Ranked	226.582	198.444	1.14179	
191	aquaporin 5. [source:swissprot;acc:p55064]	Squared	71388.5	96035.2	1.34525	

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/