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 green red network_comparison
Results: HTML CSV LaTeX Showing element 1162 to 1211 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
660	actin binding lim protein 2. [source:refseq;acc:nm_032432]	216.576	229.072	1.0577	
661	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	216.576	229.072	1.0577	
662	synapsin ii. [source:swissprot;acc:q92777]	216.576	229.072	1.0577	
663	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	216.576	229.072	1.0577	
664	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]	216.576	229.072	1.0577	
665	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm_012259]	216.576	229.072	1.0577	
666	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	216.576	229.072	1.0577	
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	216.576	229.072	1.0577	
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	216.576	229.072	1.0577	
669	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	216.576	229.072	1.0577	
670	autoantigen ngp-1. [source:swissprot;acc:q13823]	236.817	250.302	1.05694	
671	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	199.398	210.739	1.05688	
672	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	199.398	210.739	1.05688	
673	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	214.355	226.497	1.05664	
674	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	214.355	226.497	1.05664	
675	single-minded homolog 1. [source:swissprot;acc:p81133]	214.355	226.497	1.05664	
676	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	245.613	232.469	1.05654	
677	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	216.745	228.944	1.05628	
678	sorting nexin 5. [source:swissprot;acc:q9y5x3]	220.175	208.482	1.05609	
679	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	125.389	132.413	1.05602	
680	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	125.389	132.413	1.05602	
681	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	125.389	132.413	1.05602	
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	125.389	132.413	1.05602	
683	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	125.389	132.413	1.05602	
684	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	125.389	132.413	1.05602	
685	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	125.389	132.413	1.05602	
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	125.389	132.413	1.05602	
687	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	125.389	132.413	1.05602	
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	250.823	237.554	1.05586	
689	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	128.225	135.379	1.05579	
690	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	208.987	220.593	1.05553	
691	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm_005872]	206.195	217.602	1.05532	
692	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [source:refseq;acc:nm_001253]	206.195	217.602	1.05532	
693	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]	234.847	222.554	1.05524	
694	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [source:swissprot;acc:q07864]	229.35	241.907	1.05475	
695	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]	214.405	226.135	1.05471	
696	sr rich protein. [source:refseq;acc:nm_032870]	213.64	225.293	1.05455	
697	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	209.113	220.444	1.05419	
698	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	209.118	220.437	1.05413	
699	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	209.118	220.438	1.05413	
700	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	209.118	220.438	1.05413	
701	disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]	209.118	220.438	1.05413	
702	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	209.118	220.438	1.05413	
703	limkain b1. [source:refseq;acc:nm_019081]	209.118	220.438	1.05413	
704	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	209.118	220.438	1.05413	
705	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	209.118	220.438	1.05413	
706	disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]	209.118	220.438	1.05413	
707	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	209.118	220.438	1.05413	
708	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [source:swissprot;acc:q9p1a6]	209.118	220.438	1.05413	
709	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	209.118	220.438	1.05413	

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/