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 1727 to 1776 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
864 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Divided 240.194 230.957 1.03999
exocyst complex component sec8. [swissprot;acc:q96a65] Subtracted 217.762 209.449 8.313
865 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Divided 211.961 203.814 1.03997
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Subtracted 269.963 278.239 8.276
866 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Divided 221.306 212.806 1.03994
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Subtracted 269.96 278.232 8.272
867 40s ribosomal protein s3a. [swissprot;acc:p49241] Divided 225.689 234.674 1.03981
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Subtracted 269.956 278.223 8.267
868 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Divided 233.298 242.571 1.03975
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Subtracted 269.956 278.223 8.267
869 exocyst complex component sec8. [swissprot;acc:q96a65] Divided 217.762 209.449 1.03969
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Subtracted 269.955 278.221 8.266
870 transcription factor btf3 homolog 3. [swissprot;acc:q13892] Divided 211.908 203.832 1.03962
zinc finger protein 305. [swissprot;acc:o43309] Subtracted 269.954 278.219 8.265
871 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 110.2 114.552 1.03949
zinc finger protein 232. [swissprot;acc:q9uny5] Subtracted 269.954 278.218 8.264
872 heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] Divided 224.413 233.272 1.03948
zinc finger protein 99. [refseq;acc:nm_032164] Subtracted 269.954 278.218 8.264
873 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Divided 224.413 233.272 1.03948
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Subtracted 269.954 278.217 8.263
874 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Divided 212.002 203.954 1.03946
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Subtracted 269.953 278.215 8.262
875 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Divided 212.002 203.954 1.03946
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Subtracted 223.906 215.653 8.253
876 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Divided 212.002 203.954 1.03946
tax interaction protein 1. [refseq;acc:nm_014604] Subtracted 223.906 215.653 8.253
877 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 212.002 203.954 1.03946
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Subtracted 269.896 278.093 8.197
878 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Divided 212.002 203.954 1.03946
syntaxin 7. [swissprot;acc:o15400] Subtracted 217.181 209.012 8.169
879 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Divided 212.002 203.954 1.03946
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Subtracted 217.491 209.323 8.168
880 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Divided 212.002 203.954 1.03946
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Subtracted 217.491 209.323 8.168
881 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Divided 227.604 219.001 1.03928
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Subtracted 211.961 203.814 8.147
882 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 198.781 190.66 8.121
n-myc proto-oncogene protein. [swissprot;acc:p04198] Divided 227.601 219.008 1.03924
883 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 227.596 219.017 1.03917
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Subtracted 198.781 190.66 8.121
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] Divided 227.596 219.017 1.03917
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Subtracted 232.473 224.372 8.101
885 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
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] Divided 227.596 219.017 1.03917
886 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 219.018
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Subtracted 211.908 203.832 8.076
887 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 212.002 203.954 8.048
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 244.155 234.96 1.03913
888 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 212.002 203.954 8.048
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Divided 212.027 204.05 1.03909

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.
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