MK5 Microarray Data

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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

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.