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.


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 608 to 657 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
608	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	4510.61	5098.74	1.13039	
609	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	3886.62	3438.82	1.13022	
610	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	8430.03	9518.11	1.12907	
611	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [source:swissprot;acc:q13409]	5148.71	5811.74	1.12878	
612	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]	3975.77	4485.05	1.1281	
613	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	3975.77	4485.05	1.1281	
614	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	11222.2	9948.93	1.12798	
615	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	11222.2	9948.93	1.12798	
616	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	11222.2	9948.93	1.12798	
617	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [source:swissprot;acc:o14576]	5162.52	5822.47	1.12783	
618	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	7878.27	8879.08	1.12703	
619	nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	3879.99	4371.24	1.12661	
620	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	6227.87	7012.9	1.12605	
621	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	4115.39	4633.96	1.12601	
622	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm_177478]	6228.42	7013.21	1.126	
623	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	6228.39	7013.19	1.126	
624	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	6228.39	7013.19	1.126	
625	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]	6228.39	7013.19	1.126	
626	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	6228.39	7013.19	1.126	
627	limkain b1. [source:refseq;acc:nm_019081]	6228.39	7013.19	1.126	
628	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	6228.39	7013.19	1.126	
629	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	6228.39	7013.19	1.126	
630	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]	6228.39	7013.19	1.126	
631	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	6228.39	7013.19	1.126	
632	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]	6228.39	7013.19	1.126	
633	ferritin light chain (ferritin l subunit). [source:swissprot;acc:p02792]	6228.39	7013.19	1.126	
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]	6228.39	7013.19	1.126	
635	ferritin heavy polypeptide-like 17. [source:swissprot;acc:q9bxu8]	6228.97	7013.53	1.12595	
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]	5713.41	6432.92	1.12593	
637	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [source:swissprot;acc:o60361]	7756.51	8731.76	1.12573	
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]	7755.69	8730.74	1.12572	
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]	7753.59	8728.13	1.12569	
640	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	4811.02	5414.64	1.12547	
641	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	4810.85	5414.21	1.12542	
642	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	4810.85	5414.23	1.12542	
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]	4810.85	5414.23	1.12542	
644	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	4810.85	5414.22	1.12542	
645	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	4810.71	5413.89	1.12538	
646	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	4019.88	4522.61	1.12506	
647	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	5167.88	4594.43	1.12481	
648	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	5248.07	5901.72	1.12455	
649	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	5248.07	5901.72	1.12455	
650	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	8362.81	9402.7	1.12435	
651	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	5168.43	4597.44	1.1242	
652	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	5168.43	4597.44	1.1242	
653	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	5560.06	6248.27	1.12378	
654	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	4088.63	4593.43	1.12346	
655	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	4088.63	4593.43	1.12346	
656	apolipoprotein a-i binding protein; apoa-i binding protein. [source:refseq;acc:nm_144772]	6139.04	6893.7	1.12293	
657	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	6079.26	6824.47	1.12258	

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/