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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green 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
Hugo
Network Comparison Type
red
green
network_comparison
238 metastasis-associated protein mta1. [swissprot;acc:q13330] MTA1 Subtracted 252.512 228.356 24.156
rd protein. [swissprot;acc:p18615] no value Divided 227.357 254.15 1.11785
239 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] POLR2A Subtracted 243.817 267.962 24.145
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] GSTO1 Divided 227.357 254.15 1.11785
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] AIG1
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] RBBP4 Subtracted 252.39 228.297 24.093
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] ATP5F1 Divided 227.357 254.15 1.11785
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] CDH1 Subtracted 241.892 265.96 24.068
242 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] no value 265.959 24.067
j domain containing protein 1. [swissprot;acc:q9ukb3] DNAJC12 Divided 227.357 254.15 1.11785
243 60s ribosomal protein l23a. [swissprot;acc:p29316] no value Subtracted 241.884 265.945 24.061
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] SNX13 Divided 227.357 254.15 1.11785
244 60s ribosomal protein l5. [swissprot;acc:p46777] RPL5 Subtracted 241.899 265.924 24.025
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] GSTO2 Divided 227.357 254.15 1.11785
245 60s ribosomal protein l19. [swissprot;acc:p14118] RPL19 Subtracted 240.73 264.729 23.999
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Divided 226.109 202.333 1.11751
246 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] no value Subtracted 243.583 267.528 23.945
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Divided 237.312 212.363 1.11748
247 60s ribosomal protein l12. [swissprot;acc:p30050] no value Subtracted 243.583 267.527 23.944
rna-binding protein. [refseq;acc:nm_019027] Divided 237.302 212.41 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 243.583 267.527 23.944
249 ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Divided 237.302 212.41 1.11719
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Subtracted 226.109 202.333 23.776
250 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Divided 237.302 212.41 1.11719
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] PLDN Subtracted 210.693 186.95 23.743
251 40s ribosomal protein s20. [swissprot;acc:p17075] RPS20 243.5 267.21 23.71
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Divided 186.172 166.661 1.11707
252 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 237.292 212.457 1.11689
mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Subtracted 228 204.333 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] NFYB Subtracted 251.679 228.037 23.642
254 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 227.999 204.357
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Divided 200.691 179.88 1.11569
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Subtracted 227.999 204.366 23.633
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Divided 200.691 179.88 1.11569
256 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Subtracted 227.999 204.37 23.629
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 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] DDOST 200.691 179.88
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] CMPK Subtracted 242.14 265.697 23.557
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] AK3
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Divided 227.999 204.366 1.11564
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] no value Subtracted 242.14 265.696 23.556
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Divided 227.999 204.37 1.11562
260 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] HS3ST6 219.421 196.978 1.11394
surfeit locus protein 5. [swissprot;acc:q15528] MED22 Subtracted 242.14 265.696 23.556
261 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 Divided 219.421 196.978 1.11394
zinc finger protein 291. [swissprot;acc:q9by12] SCAPER Subtracted 242.14 265.696 23.556
262 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1 Divided 219.421 196.978 1.11394
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] PEX1 Subtracted 242.14 265.696 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
- 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/