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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 475 to 524 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
238 metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted 228.356 252.512 24.156
rd protein. [swissprot;acc:p18615] Divided 254.15 227.357 1.11785
239 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Subtracted 267.962 243.817 24.145
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Divided 254.15 227.357 1.11785
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Subtracted 228.297 252.39 24.093
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Divided 254.15 227.357 1.11785
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Subtracted 265.96 241.892 24.068
242 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 265.959 24.067
j domain containing protein 1. [swissprot;acc:q9ukb3] Divided 254.15 227.357 1.11785
243 60s ribosomal protein l23a. [swissprot;acc:p29316] Subtracted 265.945 241.884 24.061
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Divided 254.15 227.357 1.11785
244 60s ribosomal protein l5. [swissprot;acc:p46777] Subtracted 265.924 241.899 24.025
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Divided 254.15 227.357 1.11785
245 60s ribosomal protein l19. [swissprot;acc:p14118] Subtracted 264.729 240.73 23.999
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Divided 202.333 226.109 1.11751
246 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Subtracted 267.528 243.583 23.945
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Divided 212.363 237.312 1.11748
247 60s ribosomal protein l12. [swissprot;acc:p30050] Subtracted 267.527 243.583 23.944
rna-binding protein. [refseq;acc:nm_019027] Divided 212.41 237.302 1.11719
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 267.527 243.583 23.944
249 ns1-associated protein 1. [refseq;acc:nm_006372] Divided 212.41 237.302 1.11719
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Subtracted 202.333 226.109 23.776
250 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Divided 212.41 237.302 1.11719
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Subtracted 186.95 210.693 23.743
251 40s ribosomal protein s20. [swissprot;acc:p17075] 267.21 243.5 23.71
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided 166.661 186.172 1.11707
252 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 212.457 237.292 1.11689
mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted 204.333 228 23.667
253 Divided 1.11583
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Subtracted 228.037 251.679 23.642
254 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 227.999
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Divided 179.88 200.691 1.11569
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Subtracted 204.366 227.999 23.633
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 179.88 200.691 1.11569
256 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 204.37 227.999 23.629
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided 204.357 1.11569
257 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 179.88 200.691
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Subtracted 265.697 242.14 23.557
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided 204.366 227.999 1.11564
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Subtracted 265.696 242.14 23.556
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 204.37 227.999 1.11562
260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 219.421 1.11394
surfeit locus protein 5. [swissprot;acc:q15528] Subtracted 265.696 242.14 23.556
261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Divided 196.978 219.421 1.11394
zinc finger protein 291. [swissprot;acc:q9by12] Subtracted 265.696 242.14 23.556
262 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Divided 196.978 219.421 1.11394
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Subtracted 265.696 242.14 23.556

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/