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

Results: HTML CSV LaTeX

Showing element 458 to 502 of 502 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 0

Rank	Hugo	description	red	green	network_comparison
458	NSUN5B	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	16416.1	16721.6	1.01861
459	TSNAX	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	20875	20495	1.01854
460	no value	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]	20914	20558	1.01732
461		scratch; scratch 1. [refseq;acc:nm_031309]	12164.9	12358.1	1.01588
462		dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	12189.6	12378.3	1.01548
463		dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	5558.06	5473.99	1.01536
464		ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	10076.4	9928.08	1.01494
465		transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	9482.68	9620.66	1.01455
466		aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	1543	1521	1.01446
467		histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	21205	20914	1.01391
468	HIST3H2A	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
469	HIST1H2AA	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
470	H2AFJ	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
471	LGALS4	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	11319.2	11463	1.0127
472	ACOT1	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	7080.27	7165.6	1.01205
473	GPS1	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	816	825	1.01103
474	LMBR1L	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	11290.1	11167.6	1.01097
475	no value	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	18667	18500	1.00903
476		atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	8403	8329	1.00888
477		ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	15920	15780.2	1.00886
478	ACAA1	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	10156.4	10243.1	1.00854
479	ALDH3B2	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	15155.8	15031.7	1.00826
480	C6orf35	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]
481	no value	uridine kinase-like 1. [swissprot;acc:q9nwz5]	11554.3	11462.4	1.00802
482		kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	6156.33	6205.67	1.00801
483		tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	12223.8	12127.5	1.00794
484	SLMO2	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	11489.7	11414.3	1.00661
485	no value	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	12461.5	12542.3	1.00648
486	PRPF40B	huntingtin interacting protein c. [refseq;acc:nm_012272]	13372.4	13288.3	1.00633
487	no value	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	13236.8	13159.3	1.00589
488		heat shock factor binding protein 1. [swissprot;acc:o75506]	15204.2	15127.8	1.00505
489	SHCBP1	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	8854.04	8811.09	1.00487
490	no value	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	10388.7	10338.7	1.00484
491	RWDD1	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	21970	21880	1.00411
492	SMARCD1	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	6802.96	6829.74	1.00394
493	no value	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	11999.1	12041.7	1.00355
494		signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	11985.5	11959.4	1.00218
495		26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	11725.2	11748.1	1.00195
496		vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	9394	9411.49	1.00186
497		sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	13692.7	13718.2
498		adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	10231.8	10248.3	1.00161
499	IMPDH2	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	9080.73	9069.58	1.00123
500	no value	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	394	394	1
501	HGD	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	0.00001
502	BRAP	brca1 associated protein. [refseq;acc:nm_006768]

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
- Hugo is the HGNC identifier if it exists
- 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.