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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3080 to 3129 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
770	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	Measured	5874.74	6533.34	1.11211	
771	40s ribosomal protein s19. [source:swissprot;acc:p39019]	Rooted	55.6817	59.3786	1.06639	
771	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	Measured	5874.74	6533.34	1.11211	
771	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [source:swissprot;acc:p25685]	Ranked	210.946	221.225	1.04873	
771	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [source:refseq;acc:nm_018292]	Squared	24418	28453.7	1.16528	
772	60s ribosomal protein l31. [source:swissprot;acc:p12947]	Rooted	55.6817	59.3786	1.06639	
772	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [source:swissprot;acc:p46055]	Ranked	210.946	221.225	1.04873	
772	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [source:swissprot;acc:o00519]	Squared	24418	28453.7	1.16528	
772	sec13-related protein. [source:swissprot;acc:p55735]	Measured	5874.76	6533.36	1.11211	
773	coactosin-like protein. [source:swissprot;acc:q14019]	Squared	24418	28453.7	1.16528	
773	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	Rooted	127.967	120.003	1.06637	
773	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [source:refseq;acc:nm_022553]	Ranked	210.946	221.225	1.04873	
773	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [source:swissprot;acc:q96lb4]	Measured	5874.74	6533.34	1.11211	
774	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Rooted	65.3248	69.648	1.06618	
774	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [source:refseq;acc:nm_139279]	Ranked	225.996	215.535	1.04854	
774	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [source:swissprot;acc:p13051]	Squared	24418	28453.7	1.16528	
774	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Measured	5874.76	6533.36	1.11211	
775	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	Rooted	62.2385	58.38	1.06609	
775	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	Ranked	226.003	215.541	1.04854	
775	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	Squared	24418	28453.7	1.16528	
775	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [source:swissprot;acc:o75348]	Measured	5874.74	6533.33	1.11211	
776	40s ribosomal protein s13. [source:swissprot;acc:q02546]	Squared	21976	25607.9	1.16527	
776	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	Ranked	225.996	215.535	1.04854	
776	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	Measured	5874.76	6533.36	1.11211	
776	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Rooted	59.6869	63.6262	1.066	
777	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [source:refseq;acc:nm_005804]	Measured	5874.74	6533.34	1.11211	
777	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	Ranked	225.989	215.53	1.04853	
777	importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [source:swissprot;acc:o00505]	Squared	33908.1	39510.9	1.16523	
777	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Rooted	59.6869	63.6262	1.066	
778	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [source:swissprot;acc:q13257]	Squared	32174	37487.2	1.16514	
778	sorting nexin 6 (traf4-associated factor 2). [source:swissprot;acc:q9unh7]	Ranked	209.191	219.332	1.04848	
778	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Rooted	59.6869	63.6262	1.066	
778	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [source:swissprot;acc:p15313]	Measured	5874.63	6533.23	1.11211	
779	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [source:swissprot;acc:p32321]	Ranked	230.516	241.641	1.04826	
779	ganglioside-induced differentiation-associated protein 1. [source:refseq;acc:nm_018972]	Measured	5874.76	6533.36	1.11211	
779	probable cation-transporting atpase 1 (ec 3.6.1.-). [source:swissprot;acc:q9nq11]	Squared	32174	37487.2	1.16514	
779	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Rooted	59.6869	63.6262	1.066	
780	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [source:swissprot;acc:p41584]	Ranked	232.762	243.933	1.04799	
780	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	Rooted	62.2361	58.3858	1.06595	
780	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [source:swissprot;acc:p20226]	Squared	32174	37487.2	1.16514	
780	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [source:swissprot;acc:q9y5k8]	Measured	5874.76	6533.36	1.11211	
781	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [source:swissprot;acc:p27694]	Rooted	62.2361	58.3858	1.06595	
781	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [source:refseq;acc:nm_016183]	Ranked	245.84	257.636	1.04798	
781	secretory pathway component sec31b-1. [source:refseq;acc:nm_015490]	Measured	5874.76	6533.36	1.11211	
781	target of egr1, member 1 (nuclear); target of egr1, member 1. [source:refseq;acc:nm_025077]	Squared	33900.6	39498	1.16511	
782	importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [source:swissprot;acc:o00629]	Squared	33893.6	39486.1	1.165	
782	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [source:swissprot;acc:p15927]	Rooted	62.2361	58.3858	1.06595	
782	translin. [source:swissprot;acc:q15631]	Ranked	224.385	235.131	1.04789	
782	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [source:swissprot;acc:q9ui12]	Measured	5874.74	6533.33	1.11211	
783	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [source:refseq;acc:nm_023934]	Squared	27407.7	31927.7	1.16492	

Legend:
- Rank is the rank after comparing the two networks
- 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/