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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 475 to 524 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
238 Divided no value rd protein. [swissprot;acc:p18615] 1.11785 227.357 254.15
Subtracted MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] 24.156 252.512 228.356
239 Divided GSTO1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 1.11785 227.357 254.15
Subtracted POLR2A dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] 24.145 243.817 267.962
240 Divided AIG1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 1.11785 227.357 254.15
Subtracted RBBP4 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] 24.093 252.39 228.297
241 Divided ATP5F1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 1.11785 227.357 254.15
Subtracted CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] 24.068 241.892 265.96
242 Divided DNAJC12 j domain containing protein 1. [swissprot;acc:q9ukb3] 1.11785 227.357 254.15
Subtracted no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 24.067 241.892 265.959
243 Divided SNX13 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 1.11785 227.357 254.15
Subtracted no value 60s ribosomal protein l23a. [swissprot;acc:p29316] 24.061 241.884 265.945
244 Divided GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 1.11785 227.357 254.15
Subtracted RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] 24.025 241.899 265.924
245 Divided SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 1.11751 226.109 202.333
Subtracted RPL19 60s ribosomal protein l19. [swissprot;acc:p14118] 23.999 240.73 264.729
246 Divided EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 1.11748 237.312 212.363
Subtracted no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 23.945 243.583 267.528
247 Divided rna-binding protein. [refseq;acc:nm_019027] 1.11719 237.302 212.41
Subtracted 60s ribosomal protein l12. [swissprot;acc:p30050] 23.944 243.583 267.527
248 Divided apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 1.11719 237.302 212.41
Subtracted dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 23.944 243.583 267.527
249 Divided SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] 1.11719 237.302 212.41
Subtracted SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 23.776 226.109 202.333
250 Divided HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 1.11719 237.302 212.41
Subtracted PLDN pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 23.743 210.693 186.95
251 Divided SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 1.11707 186.172 166.661
Subtracted RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] 23.71 243.5 267.21
252 Divided EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 1.11689 237.292 212.457
Subtracted MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] 23.667 228 204.333
253 Divided 1.11583
Subtracted NFYB 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] 23.642 251.679 228.037
254 Divided STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 1.11569 200.691 179.88
Subtracted MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 23.642 227.999 204.357
255 Divided STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 1.11569 200.691 179.88
Subtracted MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 23.633 227.999 204.366
256 Divided MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 1.11569 204.357
Subtracted RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 23.629 204.37
257 Divided DDOST 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] 1.11569 200.691 179.88
Subtracted CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 23.557 242.14 265.697
258 Divided MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 1.11564 227.999 204.366
Subtracted AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 23.557 242.14 265.697
259 Divided RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 1.11562 227.999 204.37
Subtracted no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 23.556 242.14 265.696
260 Divided HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 1.11394 219.421 196.978
Subtracted MED22 surfeit locus protein 5. [swissprot;acc:q15528] 23.556 242.14 265.696
261 Divided HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 1.11394 219.421 196.978
Subtracted SCAPER zinc finger protein 291. [swissprot;acc:q9by12] 23.556 242.14 265.696
262 Divided HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 1.11394 219.421 196.978
Subtracted PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 23.556 242.14 265.696

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/