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 2962 to 3011 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1481 sr rich protein. [refseq;acc:nm_032870] Low confidence 204.229 199.931 1.0215
1482 limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] High confidence 224.354 220.15 1.0191
retinoic acid receptor rxr-beta. [swissprot;acc:p28702] Low confidence 203.213 198.936 1.0215
1483 cervical cancer 1 protooncogene protein p40; regulator of tp53. [refseq;acc:nm_015416] 204.229 199.931
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] High confidence 198.927 202.726 1.0191
1484 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]
aldehyde dehydrogenase x, mitochondrial precursor (ec 1.2.1.3) (aldh class 2). [swissprot;acc:p30837] Low confidence 205.089 209.494 1.02148
1485 j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] High confidence 207.877 203.989 1.01906
rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] Low confidence 205.448 201.131 1.02146
1486 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] High confidence 207.877 203.989 1.01906
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Low confidence 201.541 197.306 1.02146
1487 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 201.236 197.009
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] High confidence 207.877 203.989 1.01906
1488 fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Low confidence 201.541 197.306 1.02146
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] High confidence 207.877 203.989 1.01906
1489 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Low confidence 202.955 198.692 1.02146
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] High confidence 213.251 209.264 1.01905
1490 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Low confidence 202.583 198.329 1.02145
protein cgi-147. [swissprot;acc:q9y3e5] High confidence 221.961 226.186 1.01903
1491 glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] 217.704 221.839 1.01899
smc6 protein. [refseq;acc:nm_024624] Low confidence 200.985 196.766 1.02144
1492 cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948] 201.276 197.051
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] High confidence 224.159 220.017 1.01883
1493 autoantigen ngp-1. [swissprot;acc:q13823] Low confidence 201.398 197.173 1.02143
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] High confidence 204.146 207.988 1.01882
1494 golgi reassembly stacking protein 1; golgi peripheral membrane protein p65; golgi reassembly and stacking protein, 65 kda; golgi phosphoprotein 5. [refseq;acc:nm_031899] Low confidence 200.547 196.34 1.02143
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] High confidence 204.133 207.967 1.01878
1495 casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 1.01874
origin recognition complex subunit 5. [swissprot;acc:o43913] Low confidence 202.419 206.753 1.02141
1496 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] High confidence 229.459 225.237 1.01874
vav proto-oncogene. [swissprot;acc:p15498] Low confidence 200.208 196.012 1.02141
1497 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] High confidence 224.476 220.363 1.01866
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Low confidence 197.941 193.791 1.02141
1498 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 189.066 185.103
neurotrimin precursor (hnt). [swissprot;acc:q9p121] High confidence 224.022 219.924 1.01863
1499 importin 4. [refseq;acc:nm_024658] Low confidence 201.224 197.007 1.02141
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] High confidence 224.509 220.411 1.01859
1500 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 213.398 209.52 1.01851
glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Low confidence 200.875 196.667 1.0214
1501 kinesin family member c3. [refseq;acc:nm_005550] High confidence 214.727 210.838 1.01845
mitogen-activated protein kinase 7 (ec 2.7.1.37) (extracellular signal-regulated kinase 5) (erk-5) (erk4) (bmk1 kinase). [swissprot;acc:q13164] Low confidence 200.507 196.307 1.0214
1502 swi/snf-related matrix-associated actin-dependent regulator of chromatin a3; snf2-like 3; helicase-like transcription factor; dna-binding protein/plasminogen activator inhibitor-1 regulator; sucrose nonfermenting-like 3. [refseq;acc:nm_003071] 202.287 198.05 1.02139
uridine kinase-like 1. [swissprot;acc:q9nwz5] High confidence 218.084 214.149 1.01838
1503 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] 242.181 237.834 1.01828
vav-3 protein. [swissprot;acc:q9ukw4] Low confidence 200.237 196.045 1.02138
1504 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] 192.267 188.242
m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] High confidence 259.439 254.797 1.01822
1505 glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Low confidence 202.722 198.48 1.02137
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] High confidence 216.158 212.316 1.0181
1506 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 212.103 208.339 1.01807

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/