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 2663 to 2712 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
666	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Measured	6374.65	7145.59	1.12094	
666	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]	Ranked	229.072	216.576	1.0577	
667	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]	Ranked	229.072	216.576	1.0577	
667	proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [source:swissprot;acc:o43272]	Squared	29224	34362.1	1.17582	
667	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Measured	6374.65	7145.59	1.12094	
667	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [source:swissprot;acc:p47985]	Rooted	51.2483	47.5889	1.0769	
668	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm_002313]	Ranked	229.072	216.576	1.0577	
668	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [source:swissprot;acc:p49748]	Rooted	95.4476	102.785	1.07687	
668	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [source:swissprot;acc:p41252]	Squared	23969.3	28175.3	1.17547	
668	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Measured	6374.65	7145.59	1.12094	
669	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Rooted	79.931	86.0693	1.07679	
669	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Measured	6374.65	7145.59	1.12094	
669	synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]	Ranked	229.072	216.576	1.0577	
669	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Squared	18548.7	21798.2	1.17519	
670	autoantigen ngp-1. [source:swissprot;acc:q13823]	Ranked	250.302	236.817	1.05694	
670	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [source:swissprot;acc:o15160]	Rooted	51.2122	47.5637	1.07671	
670	dok-like protein. [source:refseq;acc:nm_024872]	Squared	28911	33971.3	1.17503	
670	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Measured	6374.65	7145.59	1.12094	
671	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Squared	28911	33971.3	1.17503	
671	nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	Ranked	210.739	199.398	1.05688	
671	proline synthetase co-transcribed bacterial homolog protein. [source:swissprot;acc:o94903]	Rooted	68.6822	73.8955	1.0759	
671	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Measured	6374.65	7145.59	1.12094	
672	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [source:swissprot;acc:q9h9y6]	Rooted	51.4203	47.7936	1.07588	
672	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Squared	28911	33971.3	1.17503	
672	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Ranked	210.739	199.398	1.05688	
672	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Measured	6374.65	7145.59	1.12094	
673	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	Ranked	226.497	214.355	1.05664	
673	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Rooted	132.156	122.835	1.07588	
673	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	Measured	6933.17	7766.54	1.1202	
673	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Squared	28911	33971.3	1.17503	
674	apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	Squared	42467.5	36156.7	1.17454	
674	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Rooted	132.114	122.802	1.07583	
674	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	Ranked	226.497	214.355	1.05664	
674	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Measured	5549.2	6215.42	1.12006	
675	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [source:swissprot;acc:q9bwt3]	Rooted	132.063	122.761	1.07577	
675	single-minded homolog 1. [source:swissprot;acc:p81133]	Ranked	226.497	214.355	1.05664	
675	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Measured	5549.2	6215.42	1.12006	
675	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [source:swissprot;acc:o14874]	Squared	22347.6	26247.3	1.1745	
676	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [source:swissprot;acc:q9ukf6]	Rooted	132.467	123.158	1.07559	
676	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	Squared	22337.3	26234.1	1.17445	
676	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]	Ranked	232.469	245.613	1.05654	
676	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Measured	5549.2	6215.42	1.12006	
677	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	Squared	22335.8	26232.2	1.17445	
677	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [source:swissprot;acc:q9uju2]	Rooted	59.2629	63.7418	1.07558	
677	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Measured	5549.2	6215.42	1.12006	
677	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Ranked	228.944	216.745	1.05628	
678	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	Rooted	56.8369	52.8585	1.07527	
678	sorting nexin 5. [source:swissprot;acc:q9y5x3]	Ranked	208.482	220.175	1.05609	
678	surfeit locus protein 1. [source:swissprot;acc:q15526]	Squared	22335.8	26232.2	1.17445	
678	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Measured	6938.22	7770.65	1.11998	

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/