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

Results: HTML CSV LaTeX

Showing element 2714 to 2763 of 12912 in total

Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence

Rank	Value Type	description	red	green	network_comparison
679	Ranked	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	132.413	125.389	1.05602
	Squared	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	22337.3	26234.1	1.17445
	Rooted	putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231]	61.5558	66.1861	1.07522
680	Measured	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	6503.03	7282.5	1.11986
	Ranked	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	132.413	125.389	1.05602
	Squared	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]	22336.8	26233.5	1.17445
	Rooted	t54 protein. [swissprot;acc:q92917]	61.5558	66.1861	1.07522
681	Measured	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	7170.83	8029.64	1.11976
	Ranked	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	132.413	125.389	1.05602
	Squared	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]	22335.8	26232.2	1.17445
	Rooted	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	80.2562	86.277	1.07502
682	Measured	syntaxin 12. [refseq;acc:nm_177424]	5552.92	6217.59	1.1197
	Ranked	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	132.413	125.389	1.05602
	Squared	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]	22335.8	26232.2	1.17445
	Rooted	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	86.5959	93.0684	1.07474
683	Measured	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]	7139.5	7994.06	1.11969
	Ranked	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	132.413	125.389	1.05602
	Squared	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	22328.1	26222.3	1.17441
	Rooted	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]	72.8809	78.3254	1.0747
684	Measured	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	4359.82	4880.99	1.11954
	Ranked	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	132.413	125.389	1.05602
	Squared	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]	22328.2	26222.4	1.17441
	Rooted	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	72.9862	78.4342	1.07464
685	Measured	metaxin 1. [swissprot;acc:q13505]	9327.58	10442.2	1.1195
	Ranked	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	132.413	125.389	1.05602
	Squared	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	42363.8	36083.8	1.17404
	Rooted	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]	57.4644	61.7491	1.07456
686	Measured	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	6920.69	7747.63	1.11949
	Ranked	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	132.413	125.389	1.05602
	Squared	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]	28982.3	34012.8	1.17357
	Rooted	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	86.4264	92.8635	1.07448
687	Measured	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	6920.71	7747.65	1.11949
	Ranked	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	132.413	125.389	1.05602
	Squared	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	24633.6	28893.6	1.17293
	Rooted	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	57.6308	61.9165	1.07436
688	Measured	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	6920.67	7747.6	1.11949
	Ranked	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	237.554	250.823	1.05586
	Squared	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526]	22245.5	26087.5	1.17271
	Rooted	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	60.7997	65.3199	1.07435
689	Measured	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	6920.69	7747.63	1.11949
	Ranked	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	135.379	128.225	1.05579
	Squared	dendritic cell protein. [refseq;acc:nm_006360]	33104	38818.5	1.17262
	Rooted	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	100.684	108.135	1.074
690	Measured	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	6920.69	7747.63	1.11949
	Ranked	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	220.593	208.987	1.05553
	Squared	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	33104	38818.5	1.17262
	Rooted	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	86.1101	92.4812	1.07399
691	Measured	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	6920.69	7747.63	1.11949
	Ranked	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	217.602	206.195	1.05532
	Squared	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]	33104	38818.5	1.17262

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.