Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 29840 in total

Value Type

: Measured
Interaction Map

: High confidence

Rank	Network Comparison Type	red	description	Filtered	green	network_comparison
13	Subtracted	1363	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	0	47	1316
13	Subtracted	21591.5	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	1	27904.5	6313
14	Divided	130.512	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	0	6.50325	20.0687
	Divided	398.5	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	1	1281.5	3.21581
	Subtracted	10817.1	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	0	12125.1	1308
	Subtracted	21591.5	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	1	27904.5	6313
15	Divided	10	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	0	156	15.6
	Divided	2671	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	1	871	3.06659
	Subtracted	7981.68	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	0	6685.11	1296.57
	Subtracted	21591.5	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	1	27904.5	6313
16	Divided	1	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	0	15	15
	Divided	2671	protein x 0004. [refseq;acc:nm_016301]	1	871	3.06659
	Subtracted	8852.4	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	0	7572.88	1279.52
	Subtracted	24260.3	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	1	18172.1	6088.2
17	Divided	460	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	1	1365	2.96739
	Divided	859	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	0	58	14.8103
	Subtracted	11223	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	0	12473	1250
	Subtracted	24255.7	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	1	18168.9	6086.8
18	Divided	305.45	60s ribosomal protein l37a. [swissprot;acc:p12751]	0	26.1599	11.6763
	Divided	677.5	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	1	1865.5	2.75351
	Subtracted	15411.3	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	0	14167	1244.3
	Subtracted	24255.7	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	1	18168.9	6086.8
19	Divided	305.45	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	0	26.1599	11.6763
	Divided	677.5	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	1	1865.5	2.75351
	Subtracted	1593	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	0	2804	1211
	Subtracted	24250	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	1	18164.9	6085.1
20	Divided	82	ero1-like. [refseq;acc:nm_014584]	0	0.00001	8200000
	Divided	677.5	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	1	1865.5	2.75351
	Subtracted	8763	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	0	7608	1155
	Subtracted	23421.5	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	1	17580.4	5841.1
21	Divided	118.878	syntaxin 10 (syn10). [swissprot;acc:o60499]	0	17.6611	6.73106
	Divided	677.5	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	1	1865.5	2.75351
	Subtracted	6804.88	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	0	5690.63	1114.25
	Subtracted	23693.7	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	1	18263	5430.7
22	Divided	60	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	0	0.00001	6000000
	Divided	677.5	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	1	1865.5	2.75351
	Subtracted	23693.7	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	1	18263	5430.7
	Subtracted	31122	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	0	30022.4	1099.6
23	Divided	0.00001	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0	59	5900000
	Divided	699.76	gbp protein isoform a. [refseq;acc:nm_017870]	1	1894.39	2.7072
	Subtracted	6596.23	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	0	5540.2	1056.03
	Subtracted	23693.7	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	1	18263	5430.7
24	Divided	30	ptd016 protein. [refseq;acc:nm_016125]	0	158	5.26667
	Divided	950.561	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	1	2108.52	2.21818
	Subtracted	3233.86	fos-related antigen 2. [swissprot;acc:p15408]	0	2208.1	1025.76
	Subtracted	23693.7	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	1	18263	5430.7
25	Divided	148	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	0	773	5.22297
	Divided	1833.01	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	1	892.67	2.0534
	Subtracted	459.5	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236]	0	1377	917.5
	Subtracted	23693.7	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	1	18263	5430.7

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.

- http://analysis.yellowcouch.org/