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 red green network_comparison
Results: HTML CSV LaTeX Showing element 2230 to 2279 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
558	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Squared	8426.68	10010.8	1.18799	
558	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [source:swissprot;acc:p49903]	Measured	6167.93	7007.7	1.13615	
558	ubiquitin activating enzyme e1-like protein. [source:refseq;acc:nm_006395]	Ranked	135.087	144.041	1.06628	
559	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Squared	8426.68	10010.8	1.18799	
559	ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]	Rooted	62.7397	67.9651	1.08329	
559	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [source:refseq;acc:nm_001566]	Measured	6167.93	7007.7	1.13615	
559	neural wiskott-aldrich syndrome protein (n-wasp). [source:swissprot;acc:o00401]	Ranked	207.309	194.452	1.06612	
560	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Measured	5480.24	6222.04	1.13536	
560	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [source:swissprot;acc:q16134]	Squared	26334.7	31272.3	1.18749	
560	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	Rooted	51.0687	47.1439	1.08325	
560	son of sevenless protein homolog 1 (sos-1). [source:swissprot;acc:q07889]	Ranked	205.74	193.021	1.06589	
561	cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm_153836]	Rooted	62.7424	67.9648	1.08324	
561	son of sevenless protein homolog 2 (sos-2). [source:swissprot;acc:q07890]	Ranked	205.89	193.183	1.06578	
561	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Measured	5480.24	6222.04	1.13536	
561	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	Squared	18240.1	21659.2	1.18745	
562	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]	Rooted	62.7424	67.9648	1.08324	
562	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:o00757]	Squared	25294.9	30027.4	1.18709	
562	ptb domain adaptor protein ced-6; engulfment adapter protein. [source:refseq;acc:nm_016315]	Ranked	220.744	207.121	1.06577	
562	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Measured	5480.24	6222.04	1.13536	
563	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	Measured	5480.24	6222.04	1.13536	
563	calcyphosine. [source:swissprot;acc:q13938]	Ranked	220.744	207.121	1.06577	
563	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]	Rooted	62.7424	67.9648	1.08324	
563	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [source:swissprot;acc:o43516]	Squared	30408.3	36092.8	1.18694	
564	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [source:swissprot;acc:p27708]	Squared	25396.2	30143.4	1.18693	
564	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [source:swissprot;acc:q9bzj0]	Ranked	220.744	207.121	1.06577	
564	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]	Rooted	62.7424	67.9648	1.08324	
564	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	Measured	5480.24	6222.04	1.13536	
565	fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [source:swissprot;acc:p09467]	Squared	25287.7	30003.7	1.18649	
565	limkain b1. [source:refseq;acc:nm_019081]	Rooted	62.7424	67.9648	1.08324	
565	sedlin. [source:swissprot;acc:o14582]	Ranked	129.219	121.261	1.06563	
565	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [source:swissprot;acc:o43765]	Measured	10434.4	11846.2	1.1353	
566	autoantigen ngp-1. [source:swissprot;acc:q13823]	Measured	3766.14	4274.79	1.13506	
566	putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]	Rooted	62.7424	67.9648	1.08324	
566	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Ranked	129.219	121.261	1.06563	
566	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Squared	34268.1	40650.4	1.18625	
567	bet3 homolog. [source:swissprot;acc:o43617]	Ranked	129.219	121.261	1.06563	
567	cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm_003851]	Rooted	62.7424	67.9648	1.08324	
567	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Measured	10264.9	9043.51	1.13506	
567	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	Squared	34219.8	40585.4	1.18602	
568	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]	Rooted	62.7424	67.9648	1.08324	
568	grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [source:swissprot;acc:q8taa5]	Measured	4134.77	4691.24	1.13458	
568	max protein. [source:swissprot;acc:p25912]	Squared	18764.5	22255	1.18602	
568	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	Ranked	226.3	212.38	1.06554	
569	grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [source:swissprot;acc:q9hav7]	Measured	4134.77	4691.24	1.13458	
569	kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]	Rooted	62.7424	67.9648	1.08324	
569	t-complex associated-testis-expressed 1-like (protein 91/23). [source:swissprot;acc:p51808]	Squared	52623.3	44380.3	1.18574	
569	t54 protein. [source:swissprot;acc:q92917]	Ranked	226.3	212.38	1.06554	
570	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]	Rooted	62.7424	67.9648	1.08324	
570	double-strand break repair protein mre11a (mre11 homolog 1). [source:swissprot;acc:p49959]	Squared	52623.3	44380.3	1.18574	
570	splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	Ranked	229.709	215.631	1.06529	

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/