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 2530 to 2579 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
633	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	Measured	6228.39	7013.19	1.126	
633	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	Squared	32192.8	37967.2	1.17937	
633	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	Rooted	60.0129	64.7371	1.07872	
634	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Ranked	226.523	213.786	1.05958	
634	disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [source:swissprot;acc:q9y2h0]	Measured	6228.39	7013.19	1.126	
634	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	Squared	32192.8	37967.1	1.17937	
634	synapsin ii. [source:swissprot;acc:q92777]	Rooted	60.0129	64.7371	1.07872	
635	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	Ranked	228.639	242.258	1.05957	
635	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	Measured	6228.97	7013.53	1.12595	
635	homeobox protein hox-c9 (hox-3b). [source:swissprot;acc:p31274]	Squared	32189.9	37963.6	1.17936	
635	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	Rooted	60.0129	64.7371	1.07872	
636	homeobox protein hox-b9 (hox-2e) (hox-2.5). [source:swissprot;acc:p17482]	Squared	32187.7	37961	1.17936	
636	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]	Rooted	60.0129	64.7371	1.07872	
636	proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [source:swissprot;acc:p28066]	Measured	5713.41	6432.92	1.12593	
636	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	Ranked	228.639	242.258	1.05957	
637	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	Ranked	228.639	242.258	1.05957	
637	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	Rooted	60.0129	64.7371	1.07872	
637	homeobox protein hox-a9 (hox-1g). [source:swissprot;acc:p31269]	Squared	32188.2	37961.6	1.17936	
637	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	Measured	7756.51	8731.76	1.12573	
638	homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [source:swissprot;acc:p31260]	Squared	32183.5	37955.7	1.17935	
638	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	Measured	7755.69	8730.74	1.12572	
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	

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/