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 2708 to 2757 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
677	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Ranked	228.944	216.745	1.05628	
678	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	Rooted	56.8369	52.8585	1.07527	
678	sorting nexin 5. [source:swissprot;acc:q9y5x3]	Ranked	208.482	220.175	1.05609	
678	surfeit locus protein 1. [source:swissprot;acc:q15526]	Squared	22335.8	26232.2	1.17445	
678	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Measured	6938.22	7770.65	1.11998	
679	adenylosuccinate synthase-like 1. [source:refseq;acc:nm_152328]	Measured	6503.1	7282.94	1.11992	
679	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	Squared	22337.3	26234.1	1.17445	
679	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Ranked	132.413	125.389	1.05602	
679	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [source:swissprot;acc:o60231]	Rooted	61.5558	66.1861	1.07522	
680	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [source:swissprot;acc:p30520]	Measured	6503.03	7282.5	1.11986	
680	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Ranked	132.413	125.389	1.05602	
680	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	Squared	22336.8	26233.5	1.17445	
680	t54 protein. [source:swissprot;acc:q92917]	Rooted	61.5558	66.1861	1.07522	
681	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	Squared	22335.8	26232.2	1.17445	
681	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Ranked	132.413	125.389	1.05602	
681	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	Rooted	80.2562	86.277	1.07502	
681	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	Measured	7170.83	8029.64	1.11976	
682	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Ranked	132.413	125.389	1.05602	
682	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [source:swissprot;acc:q12887]	Squared	22335.8	26232.2	1.17445	
682	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Rooted	86.5959	93.0684	1.07474	
682	syntaxin 12. [source:refseq;acc:nm_177424]	Measured	5552.92	6217.59	1.1197	
683	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Ranked	132.413	125.389	1.05602	
683	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	Measured	7139.5	7994.06	1.11969	
683	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	Rooted	72.8809	78.3254	1.0747	
683	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [source:swissprot;acc:q15118]	Squared	22328.1	26222.3	1.17441	
684	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [source:swissprot;acc:p55884]	Measured	4359.82	4880.99	1.11954	
684	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Ranked	132.413	125.389	1.05602	
684	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	Rooted	72.9862	78.4342	1.07464	
684	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [source:swissprot;acc:q15119]	Squared	22328.2	26222.4	1.17441	
685	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	Rooted	57.4644	61.7491	1.07456	
685	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Ranked	132.413	125.389	1.05602	
685	metaxin 1. [source:swissprot;acc:q13505]	Measured	9327.58	10442.2	1.1195	
685	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [source:swissprot;acc:p13693]	Squared	42363.8	36083.8	1.17404	
686	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	Measured	6920.69	7747.63	1.11949	
686	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Rooted	86.4264	92.8635	1.07448	
686	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Ranked	132.413	125.389	1.05602	
686	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [source:swissprot;acc:o75521]	Squared	28982.3	34012.8	1.17357	
687	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	Measured	6920.71	7747.65	1.11949	
687	meiotic recombination protein dmc1/lim15 homolog. [source:swissprot;acc:q14565]	Squared	24633.6	28893.6	1.17293	
687	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	Rooted	57.6308	61.9165	1.07436	
687	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Ranked	132.413	125.389	1.05602	
688	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	Measured	6920.67	7747.6	1.11949	
688	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [source:swissprot;acc:p23526]	Squared	22245.5	26087.5	1.17271	
688	dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Rooted	60.7997	65.3199	1.07435	
688	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]	Ranked	237.554	250.823	1.05586	
689	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	Measured	6920.69	7747.63	1.11949	
689	dendritic cell protein. [source:refseq;acc:nm_006360]	Squared	33104	38818.5	1.17262	
689	hira-interacting protein 5 (cgi-33). [source:swissprot;acc:q9ums0]	Rooted	100.684	108.135	1.074	
689	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Ranked	135.379	128.225	1.05579	
690	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [source:swissprot;acc:q9ugi9]	Measured	6920.69	7747.63	1.11949	

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/