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 Interaction Map Network Comparison Type Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2601 to 2650 of 29840 in total 
    Interaction Map	High confidence
    
Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
163	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	Measured	Subtracted	1	14976.4	13246.6	1729.8	
163	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Measured	Divided	1	23693.7	18263	1.29736	
163	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Measured	Divided	0	7830.62	6193.07	1.26442	
163	p28 ing5. [source:refseq;acc:nm_032329]	Squared	Divided	0	5071.93	3165.6	1.6022	
163	rna polymerase i transcription factor rrn3. [source:refseq;acc:nm_018427]	Measured	Subtracted	0	814.485	613.614	200.871	
163	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Ranked	Divided	0	8409.21	9668.79	1.14979	
163	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Ranked	Subtracted	0	11613	13133.5	1520.5	
163	zinc finger protein 232. [source:swissprot;acc:q9uny5]	Rooted	Divided	0	17.1325	14.7869	1.15863	
164	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Measured	Subtracted	1	4489.19	2765.82	1723.37	
164	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	Measured	Divided	0	1711.55	1354.26	1.26383	
164	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Ranked	Subtracted	1	133	105	28	
164	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Squared	Divided	0	145.887	91.0551	1.60218	
164	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Squared	Subtracted	1	61733.5	45224.1	16509.4	
164	dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Ranked	Divided	0	11971.7	10412.4	1.14975	
164	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Squared	Subtracted	0	14421.3	14982.3	561	
164	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Squared	Divided	1	173408	242989	1.40126	
164	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Ranked	Divided	1	209.299	249.187	1.19058	
164	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Rooted	Divided	1	55.646	65.1534	1.17086	
164	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Measured	Divided	1	23693.7	18263	1.29736	
164	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Rooted	Subtracted	1	54.9787	66.2416	11.2629	
164	neurocalcin delta. [source:swissprot;acc:p29554]	Ranked	Subtracted	0	13973.6	15473.5	1499.9	
164	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Measured	Subtracted	0	1475.83	1676.18	200.35	
164	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Rooted	Subtracted	0	22.1344	25.2414	3.107	
164	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [source:swissprot;acc:p17028]	Rooted	Divided	0	17.1341	14.7892	1.15855	
165	dna mismatch repair protein mlh1 (mutl protein homolog 1). [source:swissprot;acc:p40692]	Ranked	Subtracted	0	8375.43	9873.58	1498.15	
165	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Ranked	Divided	1	209.299	249.187	1.19058	
165	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Measured	Subtracted	1	4489.19	2765.82	1723.37	
165	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Squared	Divided	1	173408	242989	1.40126	
165	integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	Squared	Subtracted	0	15669.3	16209.3	540	
165	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Rooted	Divided	1	55.6486	65.1478	1.1707	
165	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Measured	Divided	1	23693.7	18263	1.29736	
165	mto1 protein homolog (cgi-02). [source:swissprot;acc:q9y2z2]	Measured	Divided	0	1002.2	793.818	1.26251	
165	musashi 1. [source:refseq;acc:nm_002442]	Rooted	Subtracted	1	54.9787	66.2416	11.2629	
165	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	Squared	Divided	0	54383.4	34012.2	1.59894	
165	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Measured	Subtracted	0	293	493	200	
165	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [source:swissprot;acc:p21108]	Ranked	Divided	0	13255.4	15183.2	1.14544	
165	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Rooted	Subtracted	0	26.1597	29.2445	3.0848	
165	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Ranked	Subtracted	1	133	105	28	
165	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Squared	Subtracted	1	59016.1	75486.9	16470.8	
165	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [source:swissprot;acc:q9ul58]	Rooted	Divided	0	17.1346	14.7899	1.15853	
166	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	Squared	Subtracted	1	69201.8	53013.4	16188.4	
166	cysteine endopeptidase aut-like isoform b. [source:refseq;acc:nm_178326]	Measured	Divided	0	5629.62	7099.51	1.2611	
166	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	Ranked	Subtracted	0	14554.5	16027.9	1473.4	
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Ranked	Divided	1	209.299	249.187	1.19058	
166	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Measured	Subtracted	1	4489.19	2765.82	1723.37	
166	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Squared	Divided	1	173408	242989	1.40126	
166	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	Squared	Divided	0	220.039	350.57	1.59322	
166	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Rooted	Divided	1	55.6495	65.1458	1.17064	
166	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Measured	Divided	1	23693.7	18263	1.29736	
166	mesoderm induction early response 1. [source:refseq;acc:nm_020948]	Rooted	Subtracted	0	43.1585	40.0869	3.0716	

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/