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

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Value Type

: Measured
Filtered

: 0

green	description	network_comparison	Interaction Map	red	Rank	Network Comparison Type
0	brca1 associated protein. [refseq;acc:nm_006768]	0	High confidence	0	502	Subtracted
	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	37	648
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	37		37	649
	cobw-like protein. [refseq;acc:nm_018491]	0		0	839
	dok-like protein. [refseq;acc:nm_024872]	35	High confidence	35	386
	ero1-like. [refseq;acc:nm_014584]	82	High confidence	82	316
	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	0	Low confidence	0	838
	gamma-glutamyltransferase. [sptrembl;acc:q14390]				841
	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]				842
	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]				837
	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]				843
	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]		High confidence		501
	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]				495
	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]				494
	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]				497
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]				499
		13	Low confidence	13	777
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	364	High confidence	364	88
		364	Low confidence	364	170
	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	0	High confidence	0	496
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	286	Low confidence	286	200
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	286	Low confidence	286	201
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	154	High confidence	154	206
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	18		18	429
	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	0		0	500
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	60		60	338
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	2.31962	Low confidence	2.31962	822
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	154	High confidence	154	207
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	0	High confidence	0	498
		0	Low confidence	0	840
0.00001	brca1 associated protein. [refseq;acc:nm_006768]	1	High confidence	0.00001	502	Divided
	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]	3700000	Low confidence	37	22
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	3700000		37	23
	cobw-like protein. [refseq;acc:nm_018491]	1		0.00001	839
	dok-like protein. [refseq;acc:nm_024872]	3500000	High confidence	35	31
	ero1-like. [refseq;acc:nm_014584]	8200000	High confidence	82	20
	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	1	Low confidence	0.00001	838
	gamma-glutamyltransferase. [sptrembl;acc:q14390]				841
	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]				842
	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]				837
	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]				843
	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]		High confidence		501
	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]				495
	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]				494
	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]				497
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]				499
		1300000	Low confidence	13	6
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	High confidence	364	1
		36400000	Low confidence	364	1
	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	1	High confidence	0.00001	496

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.

- http://analysis.yellowcouch.org/