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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
638	sorting nexin 17. [source:swissprot;acc:q15036]	Ranked	228.639	242.258	1.05957	
638	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Rooted	60.0129	64.7371	1.07872	
639	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817]	Squared	17618.8	20776.8	1.17924	
639	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Rooted	60.0129	64.7371	1.07872	
639	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [source:swissprot;acc:p52594]	Ranked	217.67	230.596	1.05938	
639	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	Measured	7753.59	8728.13	1.12569	
640	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Rooted	60.0129	64.7371	1.07872	
640	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Measured	4811.02	5414.64	1.12547	
640	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	Ranked	217.67	230.596	1.05938	
640	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [source:swissprot;acc:q15274]	Squared	22848.5	26941.5	1.17914	
641	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	Measured	4810.85	5414.21	1.12542	
641	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm_032152]	Ranked	217.67	230.596	1.05938	
641	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Rooted	60.0129	64.7371	1.07872	
641	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Squared	18364.9	21653.8	1.17909	
642	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	Squared	16123.9	19009.7	1.17898	
642	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	Measured	4810.85	5414.23	1.12542	
642	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	Ranked	217.67	230.596	1.05938	
642	ponsin; sh3-domain protein 5 (ponsin). [source:refseq;acc:nm_015385]	Rooted	64.4857	69.5606	1.0787	
643	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	Squared	16126.5	19012.6	1.17897	
643	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	Rooted	87.4586	81.0798	1.07867	
643	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [source:refseq;acc:nm_006076]	Ranked	217.67	230.596	1.05938	
643	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025]	Measured	4810.85	5414.23	1.12542	
644	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	Squared	16156.3	19046	1.17886	
644	cgthba protein (-14 gene protein). [source:swissprot;acc:q12980]	Ranked	217.67	230.596	1.05938	
644	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	Measured	4810.85	5414.22	1.12542	
644	rna polymerase i associated factor 53. [source:refseq;acc:nm_022490]	Rooted	51.1896	47.4617	1.07855	
645	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	Measured	4810.71	5413.89	1.12538	
645	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [source:refseq;acc:nm_014500]	Ranked	217.67	230.596	1.05938	
645	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	Squared	22722.5	26786.5	1.17885	
645	preimplantation protein 3; likely ortholog of preimplantation protein 3. [source:refseq;acc:nm_015387]	Rooted	63.1463	68.1044	1.07852	
646	3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Squared	27898	32866.2	1.17808	
646	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [source:swissprot;acc:q9ubs4]	Rooted	63.1463	68.1044	1.07852	
646	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	Measured	4019.88	4522.61	1.12506	
646	short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm_032547]	Ranked	216.731	229.549	1.05914	
647	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [source:swissprot;acc:p04632]	Rooted	64.5657	69.6237	1.07834	
647	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [source:swissprot;acc:p07858]	Squared	33384.2	39324.9	1.17795	
647	dynein light chain 2. [source:refseq;acc:nm_080677]	Ranked	216.731	229.549	1.05914	
647	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Measured	5167.88	4594.43	1.12481	
648	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	Ranked	218.227	206.078	1.05895	
648	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [source:swissprot;acc:p28749]	Squared	29174	34363.5	1.17788	
648	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	Measured	5248.07	5901.72	1.12455	
648	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [source:swissprot;acc:o14497]	Rooted	64.5685	69.6269	1.07834	
649	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	Ranked	233.725	220.751	1.05877	
649	grancalcin. [source:swissprot;acc:p28676]	Rooted	64.5659	69.624	1.07834	
649	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [source:swissprot;acc:q08999]	Squared	29173.8	34362.7	1.17786	
649	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	Measured	5248.07	5901.72	1.12455	
650	chromodomain y-like protein 2. [source:refseq;acc:nm_152342]	Squared	29016.1	34169.2	1.17759	
650	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	Measured	8362.81	9402.7	1.12435	
650	sorcin (22 kda protein) (cp-22) (v19). [source:swissprot;acc:p30626]	Rooted	64.566	69.6241	1.07834	
650	u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	Ranked	228.986	216.276	1.05877	

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/