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

Results: HTML CSV LaTeX

Showing element 3458 to 3507 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
865	Ranked	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	211.961	203.814	1.03997
	Squared	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]	24242.8	28127.6	1.16025
	Rooted	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]	62.7551	66.6474	1.06202
866	Measured	ring finger protein 38. [refseq;acc:nm_022781]	5595.65	6173.23	1.10322
	Ranked	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	221.306	212.806	1.03994
	Squared	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]	24242.8	28127.6	1.16025
	Rooted	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	51.8306	55.0247	1.06163
867	Measured	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]	5595.65	6173.23	1.10322
	Ranked	40s ribosomal protein s3a. [swissprot;acc:p49241]	225.689	234.674	1.03981
	Squared	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]	24242.8	28127.6	1.16025
	Rooted	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	61.668	65.4526	1.06137
868	Measured	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]	5595.65	6173.23	1.10322
	Ranked	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	233.298	242.571	1.03975
	Squared	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	31099.4	36082.4	1.16023
	Rooted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	61.668	65.4526	1.06137
869	Measured	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]	5595.65	6173.23	1.10322
	Ranked	exocyst complex component sec8. [swissprot;acc:q96a65]	217.762	209.449	1.03969
	Squared	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	20273.1	23521.2	1.16022
	Rooted	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	61.668	65.4526	1.06137
870	Measured	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]	5595.65	6173.23	1.10322
	Ranked	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	211.908	203.832	1.03962
	Squared	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	21086.3	24464.1	1.16019
	Rooted	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	84.6378	89.8201	1.06123
871	Measured	protein bap28. [swissprot;acc:q9h583]	3956.25	4364.25	1.10313
	Ranked	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	110.2	114.552	1.03949
	Squared	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	20281	23528.5	1.16013
	Rooted	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	84.6378	89.8201	1.06123
872	Measured	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	6781.05	7480.15	1.1031
	Ranked	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	224.413	233.272	1.03948
	Squared	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	18650.4	21632	1.15987
	Rooted	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	84.6378	89.8201	1.06123
873	Measured	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	4749.52	5237.77	1.1028
	Ranked	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]	224.413	233.272	1.03948
	Squared	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976]	18650.4	21632	1.15987
	Rooted	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	84.6378	89.8201	1.06123
874	Measured	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	9921.43	10941.2	1.10278
	Ranked	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	212.002	203.954	1.03946
	Squared	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590]	18650.4	21632	1.15987
	Rooted	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	84.6378	89.8201	1.06123
875	Measured	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	10263.8	11318.6	1.10277
	Ranked	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	212.002	203.954	1.03946
	Squared	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380]	18650.4	21632	1.15987
	Rooted	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	84.6378	89.8201	1.06123
876	Measured	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	5644.68	6223.23	1.10249
	Ranked	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	212.002	203.954	1.03946
	Squared	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649]	18650.4	21632	1.15987
	Rooted	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	84.6378	89.8201	1.06123
877	Measured	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	5797.88	6391.75	1.10243
	Ranked	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	212.002	203.954	1.03946
	Squared	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	18650.4	21632	1.15987

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.