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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3530 to 3579 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
883 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
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Squared 18178.2 21081.9 1.15974
syntaxin 7. [swissprot;acc:o15400] Ranked 217.181 209.012 1.03908
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Measured 5350.87 5896.82 1.10203
891 lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] 5385.04 5933.65 1.10188
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Rooted 56.7818 60.2369 1.06085
rw1 protein (fragment). [swissprot;acc:q92545] Squared 18178.2 21081.9 1.15974
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Ranked 212.028 204.055 1.03907
892 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Rooted 56.7817 60.2369 1.06085
cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Measured 6784.67 7475.48 1.10182
di-ras2. [refseq;acc:nm_017594] Ranked 212.028 204.055 1.03907
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Squared 26312 30514.1 1.1597
893 e-1 enzyme. [refseq;acc:nm_021204] Measured 6603.09 7274.72 1.10171
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Rooted 56.781 60.2344 1.06082
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Ranked 227.585 219.037 1.03903
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Squared 26312 30514.1 1.1597
894 parafibromin. [refseq;acc:nm_024529] Measured 4331.17 4771.22 1.1016
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Ranked 217.491 209.323 1.03902
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Squared 20322.5 23567.1 1.15966
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Rooted 56.2142 59.6282 1.06073
895 exocyst complex component sec8. [swissprot;acc:q96a65] 63.2983 67.1422
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Measured 10247.8 11289 1.1016
leucyl-trna synthetase. [refseq;acc:nm_020117] Squared 21830.4 25308.2 1.15931

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/