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

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 2708 to 2757 of 33156 in total

Network Comparison Type  : Divided
Filtered  : 1

Rank	description	Hugo	red	Value Type	Interaction Map	green	network_comparison
339	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	HOXC5	20446.1	Measured	High confidence	24136.4	1.18049
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	HIVEP2	46785.7	Squared		58383.2	1.24789
	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	IDH2	9114.82	Measured	Low confidence	9621.71	1.05561
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	CPB2	77.5797	Rooted	High confidence	70.0179	1.108
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	no value	71.5541		Low confidence	75.2665	1.05188
340	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]	BET1L	201.827	Ranked		194.178	1.03939
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	no value	20446.1	Measured	High confidence	24136.4	1.18049
	myelin gene expression factor 2. [refseq;acc:nm_016132]	MYEF2	235.383	Ranked		258.476	1.09811
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	no value	50915	Squared	Low confidence	47306.4	1.07628
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	PRPF19	58.4926	Rooted	High confidence	64.8047	1.10791
	rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]	RABEP1	71.2599		Low confidence	74.9558	1.05187
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	RRM2B	32117	Squared	High confidence	40054	1.24713
	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	CLEC3B	8940.43	Measured	Low confidence	9437.54	1.0556
341	60s ribosomal protein l9. [swissprot;acc:p32969]	no value	240.243	Ranked	High confidence	263.798	1.09805
	alpha-nac protein. [sptrembl;acc:q9h009]		50910.5	Squared	Low confidence	47302.9	1.07627
	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]	BET1L	72.4676	Rooted		76.2225	1.05181
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	HOXD4	20446.1	Measured	High confidence	24136.4	1.18049
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	KCNIP1	214.027	Ranked	Low confidence	222.415	1.03919
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	SSB	51.9812	Rooted	High confidence	57.5858	1.10782
	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	ARHGEF7	7151	Measured	Low confidence	7548.35	1.05557
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	RRM1	32056.4	Squared	High confidence	39965.8	1.24673
342	40s ribosomal protein s20. [swissprot;acc:p17075]	RPS20	243.5	Ranked		267.21	1.09737
	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	CRNKL1	70.4474	Rooted	Low confidence	74.0813	1.05158
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	HGS	70830.5	Squared	High confidence	56822	1.24653
	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	HOXB5	20446.1	Measured		24136.4	1.18049
	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	EBNA1BP2	49.2715	Rooted		54.5757	1.10765
	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	DIRAS1	50908.3	Squared	Low confidence	47301	1.07626
	tho complex 3. [refseq;acc:nm_032361]	no value	186.383	Ranked		179.374	1.03907
	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294]	OGT	7309.92	Measured		7715.51	1.05548
343	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	no value	50.3169	Rooted	High confidence	45.4333	1.10749
	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	COG7	70830.5	Squared		56822	1.24653
	di-ras2. [refseq;acc:nm_017594]	DIRAS2	50908.1		Low confidence	47300.9	1.07626
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	HOXA5	20446.1	Measured	High confidence	24136.4	1.18049
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	KCNIP4	213.982	Ranked	Low confidence	222.326	1.03899
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	PRMT3	241.625		High confidence	265.136	1.0973
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	ARHGEF6	7155.19	Measured	Low confidence	7551.48	1.05538
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	SNRPD2	71.3123	Rooted		74.9882	1.05155
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	no value	241.625	Ranked	High confidence	265.136	1.0973
	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	CLEC3A	8926.58	Measured	Low confidence	9420	1.05528
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	no value	20446.1		High confidence	24136.4	1.18049
	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	IDH2	37226.9	Squared		46400.1	1.24641
	mitochondrial ribosomal protein l44. [refseq;acc:nm_022915]	MRPL44	216.283	Ranked	Low confidence	208.173	1.03896
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	PPAN-P2RY11	49.4233	Rooted	High confidence	54.7327	1.10743
	transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45]	TM9SF3	49200	Squared	Low confidence	45726.8	1.07596
	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	XPR1	68.8797	Rooted		72.4244	1.05146
345	caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210]	CASP7	49625.1	Squared		46146.2	1.07539
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	KHDRBS2	69.2303	Rooted		72.7851	1.05135
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	KCNIP2	213.976	Ranked		222.312	1.03896
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	DHX15	56.2615	Rooted	High confidence	62.2958	1.10725
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	HSD17B14	20446.1	Measured		24136.4	1.18049

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.