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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1808 to 1857 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	description	Hugo	Network Comparison Type	Interaction Map	red	green	network_comparison
452	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	SNRPD2	Subtracted	Low confidence	201.134	194.302	6.832
453	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	HS3ST6			207.812	200.994	6.818
	ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]	C19orf29	Divided		210.727	203.693	1.03453
	paxillin. [swissprot;acc:p49023]	PXN	Subtracted	High confidence	221.522	205.286	16.236
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	SNRPA1	Divided		224.161	207.972	1.07784
454	40s ribosomal protein s26. [swissprot;acc:p02383]	no value			210.224	226.578	1.07779
	grb2-related adaptor protein. [swissprot;acc:q13588]	GRAP	Subtracted		223.457	207.222	16.235
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	HS3ST3A1		Low confidence	207.812	200.994	6.818
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	CACNG4	Divided		210.252	203.24	1.0345
455	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	no value	Subtracted	High confidence	224.161	207.972	16.189
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	HS3ST3B1		Low confidence	207.812	200.994	6.818
	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]	TIMM22	Divided	High confidence	210.225	226.578	1.07779
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	CACNG2		Low confidence	210.251	203.241	1.03449
456	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]	ATPAF2		High confidence	210.225	226.578	1.07779
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	HS3ST2	Subtracted	Low confidence	207.812	200.994	6.818
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	SNRPA1		High confidence	224.161	207.972	16.189
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	CACNG8	Divided	Low confidence	210.251	203.241	1.03449
457	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	FNBP1	Subtracted	High confidence	210.578	226.764	16.186
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	DCPS		Low confidence	207.812	200.994	6.818
	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]	UQCRB	Divided	High confidence	210.225	226.578	1.07779
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	CACNG3		Low confidence	210.251	203.241	1.03449
458	adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567]	AP1B1			206.948	200.058	1.03444
	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	DDX18	Subtracted	High confidence	251.653	235.506	16.147
	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]	CYP4A22		Low confidence	203.074	196.277	6.797
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	SRP9	Divided	High confidence	235.922	218.925	1.07764
459	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	BAG3			233.529	216.737	1.07748
	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928]	CYP4A11	Subtracted	Low confidence	203.077	196.283	6.794
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	GNG10	Divided		207.797	214.954	1.03444
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	RRP1	Subtracted	High confidence	250.538	234.401	16.137
460	proactivator polypeptide precursor [contains: saposin a (protein a); saposin b (sphingolipid activator protein 1) (sap-1) (cerebroside sulfate activator) (csact) (dispersin) (sulfatide/gm1 activator); saposin c (co-beta-glucosidase) (a1 activator) (glucosylceramidase activator) (sphingolipid activator protein 2) (sap-2); saposin d (protein c) (component c)]. [swissprot;acc:p07602]	no value	Divided	Low confidence	209.188	202.243	1.03434
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	RPS6KC1	Subtracted	High confidence	186.52	170.42	16.1
	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	RBM39		Low confidence	208.29	201.499	6.791
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	SF3A2	Divided	High confidence	223.648	207.62	1.0772
461	huntingtin interacting protein c. [refseq;acc:nm_012272]	PRPF40B		Low confidence	201.429	194.776	1.03416
	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	KLF5		High confidence	223.648	207.62	1.0772
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	no value	Subtracted		186.52	170.42	16.1
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	GTF3A		Low confidence	193.291	186.506	6.785
462	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	POLR2H		High confidence	236.662	252.708	16.046
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	no value		Low confidence	201.424	194.652	6.772
	large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650]	SLC7A5	Divided		201.466	194.819	1.03412
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	MKI67IP		High confidence	254.434	236.224	1.07709
463	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	POLR3F			238.921	257.327	1.07704
	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]	EXOC1	Subtracted	Low confidence	209.111	202.34	6.771
	paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [swissprot;acc:p54821]	PRRX1	Divided		194.41	201.036	1.03408
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]	SF3A2	Subtracted	High confidence	223.648	207.62	16.028
464	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	FNBP1	Divided		210.578	226.764	1.07686
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	no value	Subtracted	Low confidence	201.418	194.664	6.754
	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	KLF5		High confidence	223.648	207.62	16.028
	rna polymerase ii elongation factor ell2. [swissprot;acc:o00472]	ELL2	Divided	Low confidence	198.618	205.369	1.03399
465	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	HS3ST6			207.812	200.994	1.03392

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.