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