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

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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