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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3508 to 3557 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
877 star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Rooted 84.6378 89.8201 1.06123
878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Ranked 212.002 203.954 1.03946
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Measured 5797.88 6391.75 1.10243
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Rooted 84.6378 89.8201 1.06123
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared 23242.1 26955.1 1.15975
879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Ranked 212.002 203.954 1.03946
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Squared 23242.1 26955.1 1.15975
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Rooted 84.6378 89.8201 1.06123
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Measured 5797.88 6391.75 1.10243
880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Ranked 212.002 203.954 1.03946
lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Squared 23242.1 26955.1 1.15975
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Rooted 84.6378 89.8201 1.06123
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Measured 5166.04 5694.55 1.1023
881 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 5912.84 6517.69 1.10229
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Ranked 227.604 219.001 1.03928
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] Rooted 84.6378 89.8201 1.06123
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Squared 23242.1 26955.1 1.15975
882 n-myc proto-oncogene protein. [swissprot;acc:p04198] Ranked 227.601 219.008 1.03924
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Rooted 84.6378 89.8201 1.06123
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Squared 23242.1 26955.1 1.15975
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Measured 5912.84 6517.69 1.10229
883 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Ranked 227.596 219.017 1.03917
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Rooted 84.6378 89.8201 1.06123
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Squared 18178.2 21081.9 1.15974
884 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Ranked 227.596 219.017 1.03917
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Squared 18178.2 21081.9 1.15974
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Measured 5167.15 5695.44 1.10224
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Rooted 84.6378 89.8201 1.06123
885 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Squared 18178.2 21081.9 1.15974
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Rooted 60.6175 64.3272 1.0612
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Measured 5168.01 5696.12 1.10219
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Ranked 227.596 219.017 1.03917
886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Squared 18178.2 21081.9 1.15974
tax interaction protein 1. [refseq;acc:nm_014604] Rooted 60.6175 64.3272 1.0612
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Measured 5903.18 6506.32 1.10217
887 60s ribosomal protein l8. [swissprot;acc:p25120] Squared 18178.2 21081.9 1.15974
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Rooted 49.6944 52.7281 1.06105
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Measured 5903.18 6506.32 1.10217
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Ranked 244.155 234.96 1.03913
888 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Rooted 56.7827 60.2401 1.06089
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Squared 18178.2 21081.9 1.15974
lbp-9. [refseq;acc:nm_014553] Measured 5903.18 6506.32 1.10217
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Ranked 212.027 204.05 1.03909
889 alpha-nac protein. [sptrembl;acc:q9h009] 212.028 204.053 1.03908
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Rooted 56.7817 60.2368 1.06085
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Squared 18178.2 21081.9 1.15974
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Measured 5903.18 6506.32 1.10217
890 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Rooted 56.7818 60.2369 1.06085

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/