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.

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 3632 to 3681 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
908	tax interaction protein 1. [refseq;acc:nm_014604]	Ranked	223.906	215.653	1.03827
909	atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]	Squared	28767.1	33317.5	1.15818
	kinesin family member c3. [refseq;acc:nm_005550]	Measured	5995.49	6595.35	1.10005
	propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166]	Rooted	62.6851	66.4615	1.06024
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Ranked	142.077	136.846	1.03823
910	porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	Squared	19732.4	22852.4	1.15812
	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	Rooted	55.9078	59.2557	1.05988
	sipl protein. [refseq;acc:nm_018269]	Measured	6522.94	7175.18	1.09999
	uba/ubx 33.3 kda protein. [swissprot;acc:q04323]	Ranked	217.168	209.207	1.03805
911	ero1-like. [refseq;acc:nm_014584]
	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	Measured	4982.81	5480.91	1.09996
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Squared	13688.1	15849.2	1.15788
	retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999]	Rooted	64.1165	67.9451	1.05971
912	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	Squared	30826.4	35693.3	1.15788
	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]	Measured	4982.81	5480.91	1.09996
	retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749]	Rooted	64.1184	67.9467	1.05971
	wd-repeat protein 3. [swissprot;acc:q9unx4]	Ranked	243.896	234.96	1.03803
913	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Rooted	82.0749	86.9643	1.05957
	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	Ranked	210.863	218.878	1.03801
	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]	Squared	30802.6	35663.9	1.15782
	ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	Measured	5768.5	6342.05	1.09943
914	15 kda selenoprotein precursor. [swissprot;acc:o60613]	Squared	29772.1	34456.5	1.15734
	annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995]	Rooted	61.4687	65.1194	1.05939
	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	Measured	6513.45	7161	1.09942
	pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399]	Ranked	210.863	218.878	1.03801
915	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	Measured	6289.72	6911.96	1.09893
	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Rooted	55.2209	52.1262	1.05937
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	Squared	19364.5	22408.8	1.15721
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Ranked	146.036	140.692	1.03798
916	annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]	Rooted	61.4775	65.1209	1.05926
	cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]	Measured	6289.72	6911.96	1.09893
	fibulin-1 precursor. [swissprot;acc:p23142]	Squared	44407.1	51387.4	1.15719
	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3]	Ranked	232.512	241.288	1.03774
917	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Squared	23294.5	26946.3	1.15677
	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]	Measured	6289.72	6911.96	1.09893
	parafibromin. [refseq;acc:nm_024529]	Ranked	239.704	230.991	1.03772
	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	Rooted	82.3879	87.2663	1.05921
918	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]		62.3496	66.0388	1.05917
	metastasis-associated protein mta1. [swissprot;acc:q13330]	Squared	23321.7	26976.4	1.15671
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Ranked	212.952	205.292	1.03731
	scratch; scratch 1. [refseq;acc:nm_031309]	Measured	7281.6	8001.64	1.09888
919	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Squared	23346.9	27004.3	1.15665
	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Measured	5396.36	5929.41	1.09878
	midasin (midas-containing protein). [swissprot;acc:q9nu22]	Ranked	237.218	228.698	1.03725
	p66 alpha. [refseq;acc:nm_017660]	Rooted	93.8375	88.6044	1.05906
920	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	Ranked	236.741	245.547	1.0372
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Measured	7273.78	7991.72	1.0987
	protein cgi-147. [swissprot;acc:q9y3e5]	Squared	36787.9	31806.3	1.15662
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Rooted	93.8375	88.6044	1.05906
921	14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	Squared	25739.7	29768.2	1.15651

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.