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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 618 to 667 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
618	GABRG3	gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q99928]	214.256	202.139	1.05994	
619	FOXG1	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [source:swissprot;acc:q14488]	214.256	202.139	1.05994	
620	GABRG1	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q8n1c3]	214.256	202.14	1.05994	
621	GABRA2	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p47869]	214.256	202.14	1.05994	
622	GABRA6	gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [source:swissprot;acc:q16445]	214.256	202.14	1.05994	
623	GABRG2	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	214.256	202.14	1.05994	
624		interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	214.256	202.139	1.05994	
625	GABRA4	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	214.256	202.14	1.05994	
626	GABRE	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	214.256	202.14	1.05994	
627	JMJD6	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	214.256	202.139	1.05994	
628	GABRA1	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	214.256	202.14	1.05994	
629	GABRA3	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	214.256	202.14	1.05994	
630	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]	214.256	202.141	1.05993	
631	PDXDC1	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	214.256	202.141	1.05993	
632	HOXD9	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	214.254	202.166	1.05979	
633	AARS	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [source:swissprot;acc:p49588]	234.106	248.104	1.05979	
634		dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	226.523	213.786	1.05958	
635	RPL37	60s ribosomal protein l37 (g1.16). [source:swissprot;acc:p02403]	228.639	242.258	1.05957	
636	SFRS1	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	228.639	242.258	1.05957	
637	PPAT	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [source:swissprot;acc:q06203]	228.639	242.258	1.05957	
638	SNX17	sorting nexin 17. [source:swissprot;acc:q15036]	228.639	242.258	1.05957	
639	HRB	nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [source:swissprot;acc:p52594]	217.67	230.596	1.05938	
640		intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [source:swissprot;acc:q15811]	217.67	230.596	1.05938	
641	PRAM1	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [source:refseq;acc:nm_032152]	217.67	230.596	1.05938	
642		intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	217.67	230.596	1.05938	
643	HRBL	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [source:refseq;acc:nm_006076]	217.67	230.596	1.05938	
644	C16orf35	cgthba protein (-14 gene protein). [source:swissprot;acc:q12980]	217.67	230.596	1.05938	
645	HTATSF1	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [source:refseq;acc:nm_014500]	217.67	230.596	1.05938	
646	SCOC	short coiled-coil protein; short coiled coil protein. [source:refseq;acc:nm_032547]	216.731	229.549	1.05914	
647	DYNLL2	dynein light chain 2. [source:refseq;acc:nm_080677]	216.731	229.549	1.05914	
648	MARS	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	218.227	206.078	1.05895	
649	EIF4E	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	233.725	220.751	1.05877	
650		u6 snrna-associated sm-like protein lsm7. [source:swissprot;acc:q9uk45]	228.986	216.276	1.05877	
651	BAIAP3	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	233.725	220.751	1.05877	
652		tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	248.994	235.255	1.0584	
653		dok-like protein. [source:refseq;acc:nm_024872]	216.504	204.622	1.05807	
654	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	216.504	204.622	1.05807	
655	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	216.504	204.622	1.05807	
656	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	216.504	204.622	1.05807	
657	SYN3	synapsin iii. [source:swissprot;acc:o14994]	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]	229.072	216.576	1.0577	
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]	229.072	216.576	1.0577	
660	ABLIM2	actin binding lim protein 2. [source:refseq;acc:nm_032432]	229.072	216.576	1.0577	
661	HEYL	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	229.072	216.576	1.0577	
662	SYN2	synapsin ii. [source:swissprot;acc:q92777]	229.072	216.576	1.0577	
663	MRRF	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	229.072	216.576	1.0577	
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]	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]	229.072	216.576	1.0577	
666	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	229.072	216.576	1.0577	
667	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	229.072	216.576	1.0577	

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/