MK5 Microarray Data

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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 1658 to 1707 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
829	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Divided	130.259	135.844	1.04288
830	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]		222.222	231.734	1.0428
	wd-repeat protein 3. [swissprot;acc:q9unx4]	Subtracted	234.96	243.896	8.936
831	60s acidic ribosomal protein p1. [swissprot;acc:p05386]		238.048	229.171	8.877
	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	Divided	222.222	231.734	1.0428
832	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]	Subtracted	238.048	229.171	8.877
833	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Divided	222.222	231.734	1.0428
	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]	Subtracted	238.048	229.171	8.877
834	60s ribosomal protein l8. [swissprot;acc:p25120]	Divided	222.222	231.734	1.0428
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Subtracted	239.632	230.768	8.864
835	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Divided	222.222	231.734	1.0428
	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	Subtracted	233.272	224.413	8.859
836	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Divided	222.222	231.734	1.0428
	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]	Subtracted	233.272	224.413	8.859
837	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Divided	222.222	231.734	1.0428
	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	Subtracted	228.762	237.62	8.858
838	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
	rw1 protein (fragment). [swissprot;acc:q92545]	Divided	222.222	231.734	1.0428
839	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Subtracted	239.62	230.764	8.856
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	Divided	170.499	177.776	1.04268
840	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	Subtracted	245.547	236.741	8.806
	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	Divided	190.66	198.781	1.04259
841	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]
	rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]	Subtracted	245.547	236.741	8.806
842	jm1 protein. [refseq;acc:nm_014008]	Divided	210.806	219.762	1.04248
	map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]	Subtracted	245.547	236.741	8.806
843	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]
	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	Divided	227.796	218.521	1.04244
844	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]		170.82	178.033	1.04223
	meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	Subtracted	245.547	236.741	8.806
845	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3]		241.288	232.512	8.776
	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	Divided	219.399	228.599	1.04193
846	methyltransferase like 2. [refseq;acc:nm_018396]		153.371	147.211	1.04184
	parafibromin. [refseq;acc:nm_024529]	Subtracted	230.991	239.704	8.713
847	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Divided	153.371	147.211	1.04184
	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	Subtracted	219.001	227.604	8.603
848	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Divided	153.371	147.211	1.04184
	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	Subtracted	197.614	206.214	8.6
849	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Divided	153.371	147.211	1.04184
	transcription factor iib. [refseq;acc:nm_013242]	Subtracted	197.471	206.068	8.597
850	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Divided	112.329	107.842	1.04161
	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]	Subtracted	197.471	206.068	8.597
851	n-myc proto-oncogene protein. [swissprot;acc:p04198]		219.008	227.601	8.593
	trs85 homolog. [swissprot;acc:q9y2l5]	Divided	112.329	107.842	1.04161
852	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	Subtracted	219.017	227.596	8.579
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Divided	185.412	193.114	1.04154
853	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]	Subtracted	219.017	227.596	8.579
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Divided	112.772	108.289	1.0414
854	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.