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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1613 to 1662 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
404	adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520]	Squared	26819.1	32855.4	1.22507
	dna repair protein rad52 homolog. [swissprot;acc:p43351]	Ranked	207.908	226.218	1.08807
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Measured	5201.41	4479.76	1.16109
	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Rooted	59.6834	65.6741	1.10037
405	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Squared	26822.2	32858.1	1.22503
	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	Rooted	116.576	105.948	1.10031
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Ranked	207.931	226.209	1.0879
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	Measured	5201.41	4479.76	1.16109
406	60s ribosomal protein l12. [swissprot;acc:p30050]	Rooted	49.9858	45.4433	1.09996
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	Squared	18995.7	23245.6	1.22373
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Measured	5201.41	4479.76	1.16109
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Ranked	265.634	244.304	1.08731
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		239.75	260.544	1.08673
	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Rooted	49.9856	45.4431	1.09996
	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	Squared	18995.7	23244.9	1.22369
	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	Measured	6603.41	7664.65	1.16071
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Ranked	255.112	234.804	1.08649
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Rooted	49.9856	45.4432	1.09996
	dok-like protein. [refseq;acc:nm_024872]	Measured	6102.59	7081.46	1.1604
	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	Squared	18995.7	23244.7	1.22368
409	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Measured	6102.59	7081.46	1.1604
	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Rooted	50.4409	45.8795	1.09942
	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Ranked	241.045	261.874	1.08641
	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	Squared	18995.6	23242.8	1.22359
410	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]		19546.1	23881.6	1.22181
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Measured	6102.59	7081.46	1.1604
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Rooted	55.5489	50.535	1.09922
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Ranked	233.376	253.539	1.0864
411	pp3111 protein. [refseq;acc:nm_022156]	Rooted	55.5489	50.535	1.09922
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Squared	17861.2	21821.8	1.22174
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Ranked	233.376	253.539	1.0864
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Measured	6102.59	7081.46	1.1604
412	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]		3594.31	4169.95	1.16015
	syntaxin 18. [swissprot;acc:q9p2w9]	Rooted	55.5489	50.535	1.09922
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Squared	19556	23891.8	1.22171
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Ranked	240.788	261.416	1.08567
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]		240.913	261.45	1.08525
	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	Squared	19568.3	23904.6	1.2216
	rd protein. [swissprot;acc:p18615]	Rooted	55.5489	50.535	1.09922
	vav proto-oncogene. [swissprot;acc:p15498]	Measured	6644.99	7707.8	1.15994
414	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]		6744.05	5815.13	1.15974
	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	Squared	22109.6	26989.4	1.22071
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Rooted	55.5489	50.535	1.09922
	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Ranked	232.431	252.238	1.08522
415	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	Rooted	55.5489	50.535	1.09922
	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Ranked	232.382	252.166	1.08514
	vav-3 protein. [swissprot;acc:q9ukw4]	Measured	6647.43	7706.18	1.15927
	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	Squared	29160.4	35570.2	1.21981
416	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Rooted	55.5489	50.535	1.09922
	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	Ranked	240.6	261.041	1.08496

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
- 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.