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 1333 to 1382 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Divided	229.072	216.576	1.0577	
667	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Subtracted	250.465	238.38	12.085	
668	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	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	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Divided	229.072	216.576	1.0577	
670	autoantigen ngp-1. [source:swissprot;acc:q13823]	Divided	250.302	236.817	1.05694	
670	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	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Divided	210.739	199.398	1.05688	
671	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [source:swissprot;acc:q8tct7]	Subtracted	232.601	244.534	11.933	
672	dok-like protein. [source:refseq;acc:nm_024872]	Subtracted	216.504	204.622	11.882	
672	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Divided	210.739	199.398	1.05688	
673	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Subtracted	216.504	204.622	11.882	
673	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	
674	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Subtracted	216.504	204.622	11.882	
674	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	Divided	226.497	214.355	1.05664	
675	single-minded homolog 1. [source:swissprot;acc:p81133]	Divided	226.497	214.355	1.05664	
675	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	
676	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	Divided	232.469	245.613	1.05654	
676	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [source:refseq;acc:nm_016183]	Subtracted	245.84	257.636	11.796	
677	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	Subtracted	245.246	233.483	11.763	
677	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Divided	228.944	216.745	1.05628	
678	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [source:refseq;acc:nm_139126]	Subtracted	226.135	214.405	11.73	
678	sorting nexin 5. [source:swissprot;acc:q9y5x3]	Divided	208.482	220.175	1.05609	
679	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Divided	132.413	125.389	1.05602	
679	sorting nexin 5. [source:swissprot;acc:q9y5x3]	Subtracted	208.482	220.175	11.693	
680	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Divided	132.413	125.389	1.05602	
680	sr rich protein. [source:refseq;acc:nm_032870]	Subtracted	225.293	213.64	11.653	
681	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Divided	132.413	125.389	1.05602	
681	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Subtracted	220.593	208.987	11.606	
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Divided	132.413	125.389	1.05602	
682	upf0202 protein kiaa1709. [source:swissprot;acc:q9h0a0]	Subtracted	246.055	234.458	11.597	
683	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Divided	132.413	125.389	1.05602	
683	osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	Subtracted	231.809	243.289	11.48	
684	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Divided	132.413	125.389	1.05602	
684	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [source:swissprot;acc:o15067]	Subtracted	223.58	235.027	11.447	
685	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [source:swissprot;acc:p31939]	Subtracted	223.58	235.027	11.447	
685	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Divided	132.413	125.389	1.05602	
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Divided	132.413	125.389	1.05602	
686	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [source:swissprot;acc:p22234]	Subtracted	223.58	235.027	11.447	
687	dendritic cell protein. [source:refseq;acc:nm_006360]	Subtracted	223.121	211.685	11.436	
687	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Divided	132.413	125.389	1.05602	
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	Divided	237.554	250.823	1.05586	
688	potential carboxypeptidase-like protein x2 precursor. [source:swissprot;acc:q8n436]	Subtracted	223.121	211.685	11.436	
689	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	Subtracted	223.121	211.685	11.436	
689	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Divided	135.379	128.225	1.05579	
690	cpz gene product. [source:refseq;acc:nm_003652]	Subtracted	223.121	211.685	11.436	
690	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Divided	220.593	208.987	1.05553	
691	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm_005872]	Divided	217.602	206.195	1.05532	
691	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	Subtracted	223.121	211.685	11.436	

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/