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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1301 to 1350 of 6456 in total 
    Value Type	Ranked
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
651	BAIAP3	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Divided	233.725	220.751	1.05877	
651	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	Subtracted	214.256	202.139	12.117	
652		tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Divided	248.994	235.255	1.0584	
652	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	Subtracted	214.256	202.139	12.117	
653		dok-like protein. [source:refseq;acc:nm_024872]	Divided	216.504	204.622	1.05807	
653		interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	Subtracted	214.256	202.139	12.117	
654	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Divided	216.504	204.622	1.05807	
654	JMJD6	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	Subtracted	214.256	202.139	12.117	
655	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Divided	216.504	204.622	1.05807	
655	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	Subtracted	214.256	202.14	12.116	
656	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Divided	216.504	204.622	1.05807	
656	GABRA2	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	Subtracted	214.256	202.14	12.116	
657	GABRA6	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	Subtracted	214.256	202.14	12.116	
657	SYN3	synapsin iii. [source:swissprot;acc:o14994]	Divided	229.072	216.576	1.0577	
658		aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	Divided	229.072	216.576	1.0577	
658	GABRG2	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	Subtracted	214.256	202.14	12.116	
659	GABRA4	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	Subtracted	214.256	202.14	12.116	
659	HEY1	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]	Divided	229.072	216.576	1.0577	
660	ABLIM2	actin binding lim protein 2. [source:refseq;acc:nm_032432]	Divided	229.072	216.576	1.0577	
660	GABRE	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	Subtracted	214.256	202.14	12.116	
661	GABRA1	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	Subtracted	214.256	202.14	12.116	
661	HEYL	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	Divided	229.072	216.576	1.0577	
662	GABRA3	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	Subtracted	214.256	202.14	12.116	
662	SYN2	synapsin ii. [source:swissprot;acc:q92777]	Divided	229.072	216.576	1.0577	
663	MRRF	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	Divided	229.072	216.576	1.0577	
663	NDUFA6	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	Subtracted	214.256	202.141	12.115	
664	PDXDC1	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	Subtracted	214.256	202.141	12.115	
664	PEX5	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]	Divided	229.072	216.576	1.0577	
665	HEY2	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	Divided	229.072	216.576	1.0577	
665	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	Subtracted	214.254	202.166	12.088	
666	EIF3I	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	Subtracted	250.465	238.38	12.085	
666	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Divided	229.072	216.576	1.0577	
667		trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Subtracted	250.465	238.38	12.085	
667	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Divided	229.072	216.576	1.0577	
668	ABLIM1	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Divided	229.072	216.576	1.0577	
668	FTSJ3	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Subtracted	244.495	232.419	12.076	
669		presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [source:swissprot;acc:q8tct8]	Subtracted	232.601	244.534	11.933	
669	SYN1	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Divided	229.072	216.576	1.0577	
670	GNL2	autoantigen ngp-1. [source:swissprot;acc:q13823]	Divided	250.302	236.817	1.05694	
670	RANP1	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [source:swissprot;acc:p17080]	Subtracted	232.601	244.534	11.933	
671		presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Subtracted	232.601	244.534	11.933	
671	NUBP1	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Divided	210.739	199.398	1.05688	
672		dok-like protein. [source:refseq;acc:nm_024872]	Subtracted	216.504	204.622	11.882	
672	NUBP2	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Divided	210.739	199.398	1.05688	
673	CASK	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	Divided	226.497	214.355	1.05664	
673	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Subtracted	216.504	204.622	11.882	
674	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Subtracted	216.504	204.622	11.882	
674	HIF3A	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	Divided	226.497	214.355	1.05664	
675	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Subtracted	216.504	204.622	11.882	
675	SIM1	single-minded homolog 1. [source:swissprot;acc:p81133]	Divided	226.497	214.355	1.05664	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/