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 3508 to 3557 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
877 STARD13 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 no value mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Measured 5797.88 6391.75 1.10243
LIPF triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Squared 23242.1 26955.1 1.15975
PRKAG3 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Ranked 212.002 203.954 1.03946
STARD8 star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Rooted 84.6378 89.8201 1.06123
879 CHRNA2 neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
LIPM ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Squared 23242.1 26955.1 1.15975
NUP88 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Measured 5797.88 6391.75 1.10243
PRKAB1 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Ranked 212.002 203.954 1.03946
880 LIPA 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
MAPKAPK3 mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Rooted 84.6378 89.8201 1.06123
MTRF1 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Measured 5166.04 5694.55 1.1023
PRKAG2 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
881 no value adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Measured 5912.84 6517.69 1.10229
MAPK14 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
MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Ranked 227.604 219.001 1.03928
SARS2 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 ATP6V0D1 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
CHRNA4 neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Rooted 84.6378 89.8201 1.06123
MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] Ranked 227.601 219.008 1.03924
SARS seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Squared 23242.1 26955.1 1.15975
883 ARL4A adp-ribosylation factor-like protein 4. [swissprot;acc:p40617] Measured 5912.84 6517.69 1.10229
CHRNA3 neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Rooted 84.6378 89.8201 1.06123
GABPA 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
PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Squared 18178.2 21081.9 1.15974
884 no value 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
MPDU1 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
SPHK2 sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Rooted 84.6378 89.8201 1.06123
885 no value cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Squared 18178.2 21081.9 1.15974
JUP junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Rooted 60.6175 64.3272 1.0612
MTRF1L mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Measured 5168.01 5696.12 1.10219
NDUFS8 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 no value tax interaction protein 1. [refseq;acc:nm_014604] Rooted 60.6175 64.3272 1.0612
ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Ranked 227.596 219.018 1.03917
PSIP1 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
UBP1 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Measured 5903.18 6506.32 1.10217
887 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Rooted 49.6944 52.7281 1.06105
RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Squared 18178.2 21081.9 1.15974
TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Ranked 244.155 234.96 1.03913
TFCP2 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Measured 5903.18 6506.32 1.10217
888 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Ranked 212.027 204.05 1.03909
GSTT2B glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Rooted 56.7827 60.2401 1.06089
HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Squared 18178.2 21081.9 1.15974
TFCP2L1 lbp-9. [refseq;acc:nm_014553] Measured 5903.18 6506.32 1.10217
889 no value alpha-nac protein. [sptrembl;acc:q9h009] Ranked 212.028 204.053 1.03908
HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Squared 18178.2 21081.9 1.15974
PAOX peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Rooted 56.7817 60.2368 1.06085
SFRS3 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Measured 5903.18 6506.32 1.10217
890 ATPIF1 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
- 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/