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 636 to 685 of 3730 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    
Rank	description	Filtered	red	green	network_comparison	
318	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [source:swissprot;acc:q9nyl9]	0	8918.54	9465.32	1.06131	
319	60s ribosomal protein l19. [source:swissprot;acc:p14118]	1	240.73	264.729	1.09969	
319	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [source:swissprot;acc:q9y5x1]	0	8918.54	9465.32	1.06131	
320	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	0	11627.8	10958.2	1.0611	
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [source:swissprot;acc:p12830]	1	241.892	265.96	1.0995	
321	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	0	11634.4	10989.9	1.05864	
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [source:sptrembl;acc:q9br02]	1	241.892	265.959	1.09949	
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [source:refseq;acc:nm_021233]	1	86.7483	78.8995	1.09948	
322	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	0	11634.4	10989.9	1.05864	
323	60s ribosomal protein l23a. [source:swissprot;acc:p29316]	1	241.884	265.945	1.09947	
323	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [source:swissprot;acc:p15154]	0	17387.1	16427.3	1.05843	
324	40s ribosomal protein s23. [source:swissprot;acc:p39028]	1	243.944	268.195	1.09941	
324	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [source:swissprot;acc:o14658]	0	17387.1	16427.3	1.05843	
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [source:swissprot;acc:o15235]	1	243.944	268.195	1.09941	
325	mstp028 protein. [source:refseq;acc:nm_031954]	0	7965.66	7528.21	1.05811	
326	60s ribosomal protein l5. [source:swissprot;acc:p46777]	1	241.899	265.924	1.09932	
326	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	0	11948.4	11295.6	1.05779	
327	3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	9897.29	10466.5	1.05751	
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	1	243.817	267.962	1.09903	
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [source:swissprot;acc:q9gzr7]	1	258.437	235.183	1.09888	
328	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [source:swissprot;acc:q96t37]	0	10897	11520	1.05717	
329	neurogenic differentiation factor 2 (neurod2). [source:swissprot;acc:q15784]	1	312	284	1.09859	
329	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	0	15977.3	15115.5	1.05701	
330	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [source:swissprot;acc:q12873]	1	312	284	1.09859	
330	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm_032152]	0	12320.2	13018.5	1.05668	
331	40s ribosomal protein s3a. [source:swissprot;acc:p49241]	0	10405.1	10992.4	1.05644	
331	doc-1 related protein (doc-1r). [source:swissprot;acc:o75956]	1	312	284	1.09859	
332	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [source:swissprot;acc:p13533]	0	8125.5	7697.5	1.0556	
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	1	312	284	1.09859	
333	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [source:swissprot;acc:q9y623]	0	8125.5	7697.5	1.0556	
333	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	1	312	284	1.09859	
334	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [source:swissprot;acc:q9ukx2]	0	8125.5	7697.5	1.0556	
334	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	1	312	284	1.09859	
335	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	1	312	284	1.09859	
335	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	0	8125.5	7697.5	1.0556	
336	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	1	312	284	1.09859	
336	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	0	8125.5	7697.5	1.0556	
337	60s ribosomal protein l12. [source:swissprot;acc:p30050]	1	243.583	267.527	1.0983	
337	glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [source:swissprot;acc:q06210]	0	12953.2	12273.2	1.05541	
338	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	1	243.583	267.528	1.0983	
338	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [source:swissprot;acc:p46597]	0	11149.7	10571.4	1.0547	
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	1	243.583	267.527	1.0983	
339	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [source:swissprot;acc:q13888]	0	10344.1	10903.3	1.05406	
340	guanine nucleotide-binding protein g(q), alpha subunit. [source:swissprot;acc:p50148]	0	11372.3	10792.3	1.05374	
340	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	1	235.383	258.476	1.09811	
341	60s ribosomal protein l9. [source:swissprot;acc:p32969]	1	240.243	263.798	1.09805	
341	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	0	8702.94	9169.98	1.05366	
342	40s ribosomal protein s20. [source:swissprot;acc:p17075]	1	243.5	267.21	1.09737	
342	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	0	10074	10609	1.05311	
343	casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	0	8356.31	8788.62	1.05173	

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/