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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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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 [...,...].

Network Comparison Type	Value Type	Gene	green	Rank	red	description	network_comparison	Interaction Map	Filtered

Results: HTML CSV LaTeX

Showing element 1 to 50 of 2158 in total

Network Comparison Type  : Subtracted
Value Type  : Measured
green  : 0

Rank	red	description	network_comparison	Interaction Map	Filtered
88	364	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	High confidence	0
170				Low confidence
200	286	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	286
201		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
206	154	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	154	High confidence
207		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
316	82	ero1-like. [refseq;acc:nm_014584]	82
338	60	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60
386	35	dok-like protein. [refseq;acc:nm_024872]	35
429	18	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	18
494	0	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	0
495		histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
496		mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
497		histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
498		translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
499		homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
500		rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
501		h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
502		brca1 associated protein. [refseq;acc:nm_006768]
648	37	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	37	Low confidence
649		carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
777	13	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	13
822	2.31962	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	2.31962
837	0	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]	0
838		gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
839		cobw-like protein. [refseq;acc:nm_018491]
840		translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
841		gamma-glutamyltransferase. [sptrembl;acc:q14390]
842		gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
843		gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
2756		3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]		High confidence	1
2757		nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
2758		nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
2759		retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
2760		t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
2761		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]
2762		developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
2763		ring finger protein 3. [refseq;acc:nm_006315]
2764		ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
2765		histone h2a.e (h2a/e). [swissprot;acc:q99878]
2766		ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767		histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
2768		histone h2a.x (h2a/x). [swissprot;acc:p16104]
2769		histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
2770		nipsnap1 protein. [swissprot;acc:q9bpw8]
2771		t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
2772		uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
2773		bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
2774		dc12 protein. [refseq;acc:nm_020187]
2775		jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]

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.