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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 980 to 1029 of 29840 in total 
Interaction Map	High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison	
62	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [source:swissprot;acc:p34820]	Rooted	Subtracted	0	15.0883	21.8314	6.7431	
62	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	Measured	Divided	0	210.767	384.407	1.82385	
62	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [source:swissprot;acc:p04720]	Squared	Divided	0	21.2079	6.15501	3.44563	
62	glycine receptor alpha-3 chain precursor. [source:swissprot;acc:o75311]	Ranked	Divided	0	9418.7	12695.6	1.34791	
62	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Measured	Divided	1	4489.19	2765.82	1.6231	
62	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [source:swissprot;acc:p50151]	Ranked	Divided	1	266.865	336.181	1.25974	
62	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Rooted	Subtracted	1	137.446	120.823	16.623	
62	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Squared	Divided	1	219048	129762	1.68808	
62	pnas-18. [source:sptrembl;acc:q9bzu3]	Squared	Subtracted	0	14643.9	11814.6	2829.3	
62	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Rooted	Divided	1	43.4519	31.7522	1.36847	
62	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	Ranked	Subtracted	1	269.23	327.601	58.371	
62	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Measured	Subtracted	0	1442	977	465	
62	ribosome biogenesis regulatory protein homolog. [source:swissprot;acc:q15050]	Squared	Subtracted	1	189976	124480	65496	
63	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Rooted	Divided	0	18.1049	12.6095	1.43581	
63	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [source:swissprot;acc:q9y3k8]	Ranked	Divided	1	266.865	336.178	1.25973	
63	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Rooted	Divided	1	43.4554	31.7576	1.36835	
63	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Rooted	Subtracted	1	137.446	120.823	16.623	
63	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Squared	Divided	1	219048	129762	1.68808	
63	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Measured	Divided	1	4489.19	2765.82	1.6231	
63	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Ranked	Subtracted	1	260.532	204.309	56.223	
63	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	Ranked	Divided	0	8519.83	11453	1.34428	
63	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	Measured	Subtracted	0	1442	977	465	
63	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	Squared	Divided	0	1.24091	0.365145	3.3984	
63	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Rooted	Subtracted	0	37.9737	31.257	6.7167	
63	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Squared	Subtracted	0	99229.9	96418.4	2811.5	
63	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [source:swissprot;acc:p08129]	Squared	Subtracted	1	189976	124480	65496	
63	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Measured	Subtracted	1	6475.5	10307.5	3832	
63	spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	Measured	Divided	0	31.1429	56.278	1.80709	
63	spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	Ranked	Subtracted	0	18662.8	15627	3035.8	
64	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Rooted	Divided	1	63.8686	47.2654	1.35128	
64	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Measured	Subtracted	1	6475.5	10307.5	3832	
64	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Ranked	Subtracted	1	260.532	204.309	56.223	
64	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [source:swissprot;acc:p33551]	Squared	Subtracted	0	14470.6	11676.7	2793.9	
64	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Squared	Subtracted	1	144940	81169.7	63770.3	
64	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Measured	Divided	1	4489.19	2765.82	1.6231	
64	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [source:swissprot;acc:p50152]	Ranked	Divided	1	266.868	336.159	1.25965	
64	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [source:swissprot;acc:q16543]	Ranked	Subtracted	0	8152.55	11134.8	2982.25	
64	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [source:swissprot;acc:p52292]	Measured	Subtracted	0	607	1068	461	
64	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Squared	Divided	1	219048	129762	1.68808	
64	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Rooted	Subtracted	1	137.446	120.823	16.623	
64	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Rooted	Divided	0	15.7225	22.5496	1.43422	
64	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	Measured	Divided	0	0.00001	18	1800000	
64	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	Rooted	Subtracted	0	37.9737	31.257	6.7167	
64	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [source:refseq;acc:nm_032517]	Ranked	Divided	0	15264	20387	1.33563	
64	tyrosinase-related gene segment, exon 5 (fragment). [source:sptrembl;acc:q15677]	Squared	Divided	0	50.8715	15.2519	3.33542	
65	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [source:swissprot;acc:p17643]	Squared	Divided	0	50.642	15.1833	3.33538	
65	60s ribosomal protein l21. [source:swissprot;acc:p46778]	Rooted	Divided	0	20.5734	29.2291	1.42072	
65	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [source:refseq;acc:nm_001326]	Measured	Subtracted	1	22515.5	18702.6	3812.9	
65	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [source:refseq;acc:nm_015409]	Ranked	Divided	0	7853.67	10406.3	1.32502	
65	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Rooted	Divided	1	63.8686	47.2654	1.35128	

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/