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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 3808 to 3857 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
476	vav proto-oncogene. [swissprot;acc:p15498]	Squared	1	31223.8	37614.3	1.20467
477	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Squared	0	18353.1	18218.3	1.0074
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Measured		426	429	1.00704
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Rooted		55.5596	55.0873	1.00857
	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]	Rooted	1	62.574	68.4128	1.09331
	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Measured		9649.61	11053.5	1.14549
	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]	Ranked		251.926	234.547	1.0741
	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	Ranked	0	15920	15780.2	1.00886
	vav-3 protein. [swissprot;acc:q9ukw4]	Squared	1	31248.8	37623.4	1.204
478	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]	Ranked	0	10156.4	10243.1	1.00854
	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	Rooted	0	6.24948	6.30196	1.0084
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Rooted	1	50.6084	55.2961	1.09263
	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	Squared	0	13069.7	13161.9	1.00705
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Squared	1	16318.4	19645.8	1.2039
	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Measured	1	9649.61	11053.5	1.14549
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	Measured	0	705.758	701.071	1.00669
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	Ranked	1	228.051	212.321	1.07409
479	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Measured	0	1318.37	1310.67	1.00587
	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Ranked		15155.8	15031.7	1.00826
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Rooted		18.6755	18.8095	1.00718
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Rooted	1	50.6084	55.2961	1.09263
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Squared	0	1891.31	1904.05	1.00674
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	Ranked	1	228.051	212.321	1.07409
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Measured		9649.61	11053.5	1.14549
	translation initiation factor if-2. [swissprot;acc:o60841]	Squared		24031.6	28929.7	1.20382
480	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	Rooted	0	131.742	130.866	1.00669
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Rooted	1	50.6084	55.2961	1.09263
	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	Measured		9649.61	11053.5	1.14549
	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	Ranked		237.109	254.667	1.07405
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Measured	0	6428	6396.8	1.00488
	phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903]	Squared	1	26874.6	32347.4	1.20364
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Squared	0	17185.8	17080.7	1.00615
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Ranked	0	15155.8	15031.7	1.00826
481	histone h2b. [refseq;acc:nm_175055]	Rooted	1	50.6084	55.2961	1.09263
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Rooted	0	197.901	198.708	1.00408
	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	Measured	0	565.785	563.113	1.00475
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Measured	1	9649.61	11053.5	1.14549
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Ranked	1	237.109	254.667	1.07405
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Squared	0	291799	293192	1.00477
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Squared	1	16335.9	19660.7	1.20353
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Ranked	0	11554.3	11462.4	1.00802
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	Ranked	1	237.109	254.667	1.07405
	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	Squared	0	312371	313764	1.00446
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Rooted	1	50.6084	55.2961	1.09263
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Ranked	0	6156.33	6205.67	1.00801
	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Rooted	0	46.0965	45.9175	1.0039
	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]	Measured	1	9649.61	11053.5	1.14549
	solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9]	Squared	1	26867.3	32335.2	1.20352
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Measured	0	793.778	796.85	1.00387
483	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Rooted	0	22.576	22.4903	1.00381

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/