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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 647 to 696 of 3228 in total

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

Rank	Hugo	description	red	network_comparison	green
647	DYNLL2	dynein light chain 2. [refseq;acc:nm_080677]	216.731	1.05914	229.549
648	MARS	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192]	218.227	1.05895	206.078
649	EIF4E	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	233.725	1.05877	220.751
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	1.0584	235.255
653		dok-like protein. [refseq;acc:nm_024872]	216.504	1.05807	204.622
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	1.0577	216.576
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	1.05694	236.817
671	NUBP1	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	210.739	1.05688	199.398
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	1.05664	214.355
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	1.05654	245.613
677	LSM4	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	228.944	1.05628	216.745
678	SNX5	sorting nexin 5. [swissprot;acc:q9y5x3]	208.482	1.05609	220.175
679	no value	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	132.413	1.05602	125.389
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	1.05586	250.823
689	TCP1	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	135.379	1.05579	128.225
690	SNW1	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	220.593	1.05553	208.987
691	BCAS2	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	217.602	1.05532	206.195
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]
693	NOVA1	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	222.554	1.05524	234.847
694	POLE	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	241.907	1.05475	229.35
695	PPIL4	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	226.135	1.05471	214.405
696	SFRS18	sr rich protein. [refseq;acc:nm_032870]	225.293	1.05455	213.64

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.