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

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

Results: HTML CSV LaTeX

Showing element 1358 to 1407 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	Value Type	description	Network Comparison Type	red	green	network_comparison
170	PRMT8	Rooted	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Subtracted	55.6161	66.7332	11.1171
	PRPF40B	Ranked	huntingtin interacting protein c. [refseq;acc:nm_012272]		227.971	200.417	27.554
	TIA1		nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Divided	227.199	192.715	1.17894
171	CTPS	Squared	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]		96602.7	69211.2	1.39577
	LASS2	Rooted	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]		61.6639	71.7355	1.16333
	MAGED2	Measured	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]		23693.7	18263	1.29736
	NCBP2L		dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Subtracted	4117.67	5801.04	1683.37
	SNAI2	Squared	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]		69165	52991.7	16173.3
	SNRP70	Rooted	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]		55.6161	66.7332	11.1171
	TIAL1	Ranked	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Divided	227.202	192.823	1.17829
	TRPC4		short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Subtracted	201.478	228.784	27.306
172	no value	Measured	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]		4556.78	2945.26	1611.52
		Rooted	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]		55.6161	66.7332	11.1171
	CSTF2T	Squared	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	Divided	121579	87259.3	1.39331
	CTBP1		c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	Subtracted	69123.3	52967	16156.3
	SF3B1	Rooted	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Divided	56.7592	65.9889	1.16261
	TBC1D10A	Ranked	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Subtracted	201.515	228.752	27.237
	TIPRL		cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Divided	174.667	205.556	1.17685
	TRO	Measured	trophinin. [swissprot;acc:q12816]		23693.7	18263	1.29736
173	no value	Squared	methyltransferase like 2. [refseq;acc:nm_018396]	Subtracted	71576.8	56326.7	15250.1
	BCAR3	Measured	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Divided	4579.34	5940.64	1.29727
	MRPS17	Rooted	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		145.551	168.796	1.1597
	PPP2R2D	Measured	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Subtracted	4556.79	2945.28	1611.51
	PSEN2	Rooted	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]		37.3005	48.4141	11.1136
	SEPT4	Squared	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Divided	82624.3	115061	1.39258
	SNRPD1	Ranked	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]		227.032	193.056	1.17599
	TRPC5		short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Subtracted	201.515	228.752	27.237
174	DGCR14		dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Divided	335	286	1.17133
	DYNLT1	Squared	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Subtracted	71576.8	56326.7	15250.1
	LUC7L2	Ranked	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]		228.1	200.968	27.132
	MXD1	Measured	mad protein (max dimerizer). [swissprot;acc:q05195]	Divided	4455.95	5774.03	1.2958
	PANK1	Rooted	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		145.551	168.796	1.1597
	PPP2R2B	Measured	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	Subtracted	4556.83	2945.38	1611.45
	SKP1A	Rooted	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]		37.3005	48.4141	11.1136
	ZNF547	Squared	sedlin. [swissprot;acc:o14582]	Divided	112820	157033	1.39189
175	no value		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
	COPS3	Ranked	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]		199.949	234.187	1.17123
	FBXW7	Rooted	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	Subtracted	37.3005	48.4141	11.1136
	FZR1	Squared	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]		71576.8	56326.7	15250.1
	LUC7L	Ranked	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]		228.085	201.006	27.079
	MXI1	Measured	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Divided	4456.67	5773.77	1.29553
	PANK2	Rooted	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		145.551	168.796	1.1597
	PPP2R2C	Measured	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Subtracted	4556.99	2945.8	1611.19
176	CUL2	Rooted	cullin homolog 2 (cul-2). [swissprot;acc:q13617]		37.3005	48.4141	11.1136
	EIF5	Ranked	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]		271.016	244.167	26.849
	HPRT1	Measured	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]		10235.2	11830.8	1595.6
	MXD4		max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Divided	4456.93	5773.67	1.29544
	PANK3	Rooted	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		145.551	168.796	1.1597
	PCSK5	Squared	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Subtracted	71576.8	56326.7	15250.1
	POLE4	Ranked	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Divided	275.754	235.908	1.1689

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.