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 643 to 692 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
643	HRBL	hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076]	217.67	230.596	1.05938
644	C16orf35	cgthba protein (-14 gene protein). [swissprot;acc:q12980]
645	HTATSF1	hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500]
646	SCOC	short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547]	216.731	229.549	1.05914
647	DYNLL2	dynein light chain 2. [refseq;acc:nm_080677]
648	MARS	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	218.227	206.078	1.05895
649	EIF4E	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	233.725	220.751	1.05877
650	no value	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	228.986	216.276
651	BAIAP3	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	233.725	220.751
652	no value	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886]	248.994	235.255	1.0584
653		dok-like protein. [refseq;acc:nm_024872]	216.504	204.622	1.05807
654	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]
655	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
656	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]
657	SYN3	synapsin iii. [swissprot;acc:o14994]	229.072	216.576	1.0577
658	no value	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
659	HEY1	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3]
660	ABLIM2	actin binding lim protein 2. [refseq;acc:nm_032432]
661	HEYL	hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
662	SYN2	synapsin ii. [swissprot;acc:q92777]
663	MRRF	mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
664	PEX5	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
665	HEY2	hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
666	HES1	transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]
667	ECH1	delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
668	ABLIM1	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
669	SYN1	synapsin i (brain protein 4.1). [swissprot;acc:p17600]
670	GNL2	autoantigen ngp-1. [swissprot;acc:q13823]	250.302	236.817	1.05694
671	NUBP1	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	210.739	199.398	1.05688
672	NUBP2	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
673	CASK	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	226.497	214.355	1.05664
674	HIF3A	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]
675	SIM1	single-minded homolog 1. [swissprot;acc:p81133]
676	POLR2G	dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433]	232.469	245.613	1.05654
677	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	228.944	216.745	1.05628
678	SNX5	sorting nexin 5. [swissprot;acc:q9y5x3]	208.482	220.175	1.05609
679	no value	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	132.413	125.389	1.05602
680	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]
681	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]
682	no value	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
683	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]
684	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
685	HOXA5	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]
686	no value	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
687	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]
688	POLR2D	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	237.554	250.823	1.05586
689	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	135.379	128.225	1.05579
690	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	220.593	208.987	1.05553
691	BCAS2	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	217.602	206.195	1.05532
692	CDC5L	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]

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.