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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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 Gene green description network_comparison Interaction Map Rank red Network Comparison Type

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Value Type

: Measured
Filtered

: 0
Network Comparison Type

: Divided

green	description	network_comparison	Interaction Map	Rank	red
0.00001	brca1 associated protein. [refseq;acc:nm_006768]	1	High confidence	502	0.00001
	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	22	37
	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]	3700000		23	37
	cobw-like protein. [refseq;acc:nm_018491]	1		839	0.00001
	dok-like protein. [refseq;acc:nm_024872]	3500000	High confidence	31	35
	ero1-like. [refseq;acc:nm_014584]	8200000	High confidence	20	82
	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	1	Low confidence	838	0.00001
	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	6	13
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	36400000	High confidence	1	364
		36400000	Low confidence	1	364
	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	1	High confidence	496	0.00001
	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	28600000	Low confidence	44	286
	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	28600000	Low confidence	45	286
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	15400000	High confidence	95	154
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	1800000		65	18
	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	1		500	0.00001
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	6000000		22	60
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	231962	Low confidence	7	2.31962
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	15400000	High confidence	96	154
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	1	High confidence	498	0.00001
		1	Low confidence	840	0.00001
5.56738	serpin b12. [swissprot;acc:q96p63]	35.8425	High confidence	11	199.549
5.56738	serpin b12. [swissprot;acc:q96p63]	35.8425	Low confidence	10	199.549
5.71669	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	High confidence	12	199.249
5.71669		34.8539	Low confidence	11	199.249
6.50325	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	20.0687	High confidence	14	130.512
10.6048	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	36.1876	Low confidence	9	383.762
11.5	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	1.21739	High confidence	190	14
11.5		1.21739	Low confidence	176	14
14.3333	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	1.3721	High confidence	121	19.6667
15	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	15	High confidence	16	1
17.5166	jumonji protein. [swissprot;acc:q92833]	1751660	Low confidence	5	0.00001
17.6611	syntaxin 10 (syn10). [swissprot;acc:o60499]	6.73106	High confidence	21	118.878
18	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). [swissprot;acc:o00750]	1800000		64	0.00001
19	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	1.21053		195	23
		1.21053	Low confidence	184	23
	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]	5.21053	Low confidence	18	99
21	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	2.09524	High confidence	50	44
23.6984	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	2.03615	Low confidence	64	48.2534
26.1599	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	11.6763	High confidence	19	305.45
26.1599	60s ribosomal protein l37a. [swissprot;acc:p12751]	11.6763	High confidence	18	305.45

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/