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.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2964 to 3013 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
1482 LSAMP limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] High confidence 224.354 220.15 1.0191
1483 LETMD1 cervical cancer 1 protooncogene protein p40; regulator of tp53. [refseq;acc:nm_015416] Low confidence 204.229 199.931 1.0215
PDHB 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 ALDH1B1 aldehyde dehydrogenase x, mitochondrial precursor (ec 1.2.1.3) (aldh class 2). [swissprot;acc:p30837] Low confidence 205.089 209.494 1.02148
TMEM91 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] High confidence 198.927 202.726 1.0191
1485 ARHGAP1 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
RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] High confidence 207.877 203.989 1.01906
1486 no value huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Low confidence 201.541 197.306 1.02146
HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] High confidence 207.877 203.989 1.01906
1487 CCNH cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Low confidence 201.236 197.009 1.02146
HIVEP1 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 FH fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Low confidence 201.541 197.306 1.02146
HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] High confidence 207.877 203.989 1.01906
1489 ELAVL1 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Low confidence 202.955 198.692 1.02146
MAP3K7 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 BCCIP 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
PTRH2 protein cgi-147. [swissprot;acc:q9y3e5] High confidence 221.961 226.186 1.01903
1491 GPI 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 smc6 protein. [refseq;acc:nm_024624] Low confidence 200.985 196.766 1.02144
1492 MNAT1 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
OPCML 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 GNL2 autoantigen ngp-1. [swissprot;acc:q13823] Low confidence 201.398 197.173 1.02143
PDHA2 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 GORASP1 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
PDHA1 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 CSNK1A1L casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 1.01874
ORC5L origin recognition complex subunit 5. [swissprot;acc:o43913] Low confidence 202.419 206.753 1.02141
1496 CSNK1A1 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] High confidence 229.459 225.237 1.01874
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Low confidence 200.208 196.012 1.02141
1497 LTA4H leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] 197.941 193.791
XPO1 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
1498 no value neurotrimin precursor (hnt). [swissprot;acc:q9p121] 224.022 219.924 1.01863
FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Low confidence 189.066 185.103 1.02141
1499 no value importin 4. [refseq;acc:nm_024658] 201.224 197.007
DCP1A transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] High confidence 224.509 220.411 1.01859
1500 COPS4 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
GPD1 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 KIFC3 kinesin family member c3. [refseq;acc:nm_005550] High confidence 214.727 210.838 1.01845
MAPK7 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 no value uridine kinase-like 1. [swissprot;acc:q9nwz5] High confidence 218.084 214.149 1.01838
HLTF 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] Low confidence 202.287 198.05 1.02139
1503 KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] High confidence 242.181 237.834 1.01828
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Low confidence 200.237 196.045 1.02138
1504 CDC25C 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
EPN2 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Low confidence 192.267 188.242 1.02138
1505 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] High confidence 216.158 212.316 1.0181
QARS glutaminyl-trna synthetase (ec 6.1.1.18) (glutamine--trna ligase) (glnrs). [swissprot;acc:p47897] Low confidence 202.722 198.48 1.02137
1506 C16orf42 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] High confidence 212.103 208.339 1.01807
RAB8B ras-related protein rab-8b. [swissprot;acc:q92930] Low confidence 200.685 196.487 1.02137
1507 ATP6V1B2 vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] 198.931 194.769

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
- Hugo is the HGNC identifier if it exists
- 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/