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 Rank green Interaction Map network_comparison description

Results: HTML CSV LaTeX

Showing element 1 to 50 of 19268 in total

Filtered

: 0
Value Type

: Ranked

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