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

Results: HTML CSV LaTeX

Showing element 3101 to 3150 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
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	
783	phosducin (phd) (33 kda phototransducing protein) (meka protein). [source:swissprot;acc:p20941]	Rooted	62.2361	58.3858	1.06595	
783	translin-associated protein x (translin-associated factor x). [source:swissprot;acc:q99598]	Ranked	224.385	235.131	1.04789	
783	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [source:swissprot;acc:p21281]	Measured	5874.78	6533.37	1.1121	
784	dc11 protein. [source:refseq;acc:nm_020186]	Squared	27407.7	31927.7	1.16492	
784	dna repair protein rad52 homolog. [source:swissprot;acc:p43351]	Rooted	62.2361	58.3858	1.06595	
784	polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [source:refseq;acc:nm_005710]	Ranked	224.385	235.131	1.04789	
784	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [source:swissprot;acc:p36543]	Measured	5874.77	6533.36	1.1121	
785	amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [source:refseq;acc:nm_003905]	Squared	27407.7	31927.7	1.16492	
785	clathrin heavy chain 2 (clh-22). [source:swissprot;acc:p53675]	Rooted	62.2332	58.3925	1.06577	
785	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	Measured	4997	5557.17	1.1121	
785	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [source:refseq;acc:nm_005863]	Ranked	244.447	233.508	1.04685	
786	40s ribosomal protein s9. [source:swissprot;acc:p46781]	Rooted	52.0101	48.813	1.0655	
786	5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [source:swissprot;acc:p22557]	Squared	27407.7	31927.7	1.16492	
786	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [source:swissprot;acc:p11498]	Measured	9304.83	10347.3	1.11204	
786	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [source:refseq;acc:nm_019555]	Ranked	244.447	233.508	1.04685	
787	down-regulated in metastasis. [source:refseq;acc:nm_014503]	Ranked	244.447	233.508	1.04685	
787	uba/ubx 33.3 kda protein. [source:swissprot;acc:q04323]	Rooted	64.5489	68.7769	1.0655	
787	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [source:refseq;acc:nm_003968]	Squared	27407.7	31927.7	1.16492	
787	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [source:swissprot;acc:q9y487]	Measured	5890.49	6547.9	1.11161	
788	ero1-like. [source:refseq;acc:nm_014584]	Rooted	64.5489	68.7769	1.0655	
788	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Ranked	138.705	132.538	1.04653	

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/