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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1751 to 1800 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
438	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [source:swissprot;acc:p41227]	Ranked	233.723	216.674	1.07869	
438	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [source:swissprot;acc:o14497]	Measured	6252.58	7192.88	1.15039	
439	40s ribosomal protein s9. [source:swissprot;acc:p46781]	Ranked	238.986	257.784	1.07866	
439	cell division cycle protein 23; anaphase-promoting complex subunit 8. [source:refseq;acc:nm_004661]	Squared	51616.7	42588.9	1.21198	
439	dok-like protein. [source:refseq;acc:nm_024872]	Rooted	63.2134	69.352	1.09711	
439	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	Measured	6252.58	7192.88	1.15039	
440	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	Measured	6251.91	7192.08	1.15038	
440	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [source:swissprot;acc:p11388]	Squared	26348.4	31925.8	1.21168	
440	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Rooted	63.2134	69.352	1.09711	
440	highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101]	Ranked	231.802	249.983	1.07843	
441	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [source:swissprot;acc:q02880]	Squared	26348.7	31924.3	1.21161	
441	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Rooted	63.2134	69.352	1.09711	
441	grancalcin. [source:swissprot;acc:p28676]	Measured	6251.96	7192.13	1.15038	
441	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Ranked	223.457	207.222	1.07835	
442	centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [source:refseq;acc:nm_018451]	Squared	51286.6	42334.5	1.21146	
442	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Ranked	223.802	207.55	1.0783	
442	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Measured	6251.99	7192.17	1.15038	
442	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Rooted	63.2134	69.352	1.09711	
443	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Rooted	50.1766	45.7369	1.09707	
443	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	Measured	6252.27	7192.51	1.15038	
443	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	Ranked	223.79	207.539	1.0783	
443	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [source:swissprot;acc:p46199]	Squared	26472.8	32067.7	1.21135	
444	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	Rooted	50.1636	45.7275	1.09701	
444	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Ranked	223.801	207.549	1.0783	
444	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	Measured	3758.67	4322.87	1.15011	
444	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [source:swissprot;acc:p51965]	Squared	58831	48584.2	1.21091	
445	ad24 protein. [source:refseq;acc:nm_022451]	Measured	3753.71	4315.95	1.14978	
445	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Ranked	223.801	207.549	1.0783	
445	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	Rooted	50.1635	45.7274	1.09701	
445	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	Squared	58831	48584.2	1.21091	
446	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	Rooted	54.9019	60.2111	1.0967	
446	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354]	Ranked	224.049	207.785	1.07827	
446	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	Measured	3766.03	4329.37	1.14958	
446	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Squared	29335.6	35515.5	1.21066	
447	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Rooted	54.9019	60.2111	1.0967	
447	pescadillo homolog 1. [source:swissprot;acc:o00541]	Measured	3751.14	4310.89	1.14922	
447	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955]	Ranked	224.049	207.785	1.07827	
447	sipl protein. [source:refseq;acc:nm_018269]	Squared	30155.1	36495	1.21024	
448	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	Squared	20350.3	16816.1	1.21017	
448	microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2]	Ranked	228.468	246.338	1.07822	
448	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Measured	6259.3	7190.91	1.14884	
448	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	Rooted	50.1671	45.7563	1.0964	
449	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [source:swissprot;acc:q03001]	Ranked	228.463	246.33	1.07821	
449	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [source:swissprot;acc:p17655]	Squared	20348.5	16817.2	1.20998	
449	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Rooted	50.162	45.7659	1.09606	
449	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	Measured	3761.59	4319.69	1.14837	
450	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [source:swissprot;acc:o00763]	Squared	31646.1	38288.7	1.2099	
450	l-myc-1 proto-oncogene protein. [source:swissprot;acc:p12524]	Measured	4889.21	5610.52	1.14753	
450	signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458]	Ranked	235.94	218.837	1.07815	
450	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	Rooted	50.4595	46.0411	1.09597	

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/