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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 19268 in total

Filtered

: 0
Value Type

: Ranked

red	Network Comparison Type	green	Rank	network_comparison	Interaction Map	description
0	Subtracted	0	501	0	High confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
			502		High confidence	brca1 associated protein. [refseq;acc:nm_006768]
			837		Low confidence	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
			838			gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
			839			cobw-like protein. [refseq;acc:nm_018491]
			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]
0.00001	Divided	0.00001	501	1	High confidence	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
			502		High confidence	brca1 associated protein. [refseq;acc:nm_006768]
			837		Low confidence	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
			838			gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
			839			cobw-like protein. [refseq;acc:nm_018491]
			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]
394		394	500		High confidence	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
			840		Low confidence
	Subtracted		500	0	High confidence
	Subtracted		840	0	Low confidence
772	Divided	754	433	1.02387	High confidence	trinucleotide repeat containing 15. [refseq;acc:nm_015575]
772	Subtracted	754	495	18		trinucleotide repeat containing 15. [refseq;acc:nm_015575]
775	Divided	696	209	1.11351		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]
775	Subtracted	696	478	79
816	Divided	825	473	1.01103		cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]
816	Subtracted	825	499	9
930	Divided	953	432	1.02473		fibrillin 3. [refseq;acc:nm_032447]
930	Subtracted	953	492	23		fibrillin 3. [refseq;acc:nm_032447]
1091	Divided	1021	307	1.06856		ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]
1091	Subtracted	1021	483	70
1251	Divided	1373	243	1.09752		polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]
1251	Subtracted	1373	469	122
1256	Divided	1294	622	1.03025	Low confidence	caspr5 protein isoform 1. [refseq;acc:nm_130773]
	Divided		623	1.03025		contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
	Subtracted		810	38		caspr5 protein isoform 1. [refseq;acc:nm_130773]
	Subtracted		812	38		contactin associated protein-like 3 precursor (cell recognition molecule caspr3). [swissprot;acc:q9bz76]
1543	Divided	1521	466	1.01446	High confidence	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
	Divided		730	1.01446	Low confidence
	Subtracted		494	22	High confidence
	Subtracted		820	22	Low confidence
2584	Divided	2772	450	1.07276		hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433]
2584	Subtracted	2772	704	188
2671.33	Divided	2668.83	832	1.00094		vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]
2671.33	Subtracted	2668.83	835	2.5
2939	Divided	2876	448	1.02191	High confidence	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]
	Divided		674	1.02191	Low confidence
	Subtracted		484	63	High confidence
	Subtracted		796	63	Low confidence
3032	Divided	3141	602	1.03595		erythropoietin 4 immediate early response; uncharacterized hypothalamus protein ht010. [refseq;acc:nm_018471]
3032	Subtracted	3141	757	109

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/