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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 651 to 700 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
326 40s ribosomal protein s16. [swissprot;acc:p17008] Subtracted 241.828 263.62 21.792
60s ribosomal protein l5. [swissprot;acc:p46777] Divided 241.899 265.924 1.09932
327 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Subtracted 241.83 263.615 21.785
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Divided 243.817 267.962 1.09903
328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 1.09888
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Subtracted 240.801 262.34 21.539
329 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 21.452
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Divided 312 284 1.09859
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted 224.657 203.235 21.422
331 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided 312 284 1.09859
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Subtracted 224.647 203.242 21.405
332 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 224.633 203.251 21.382
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Divided 312 284 1.09859
333 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Subtracted 265.634 244.304 21.33
334 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Divided 312 284 1.09859
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Subtracted 232.473 211.207 21.266
335 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Divided 312 284 1.09859
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Subtracted 223.273 202.423 20.85
336 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Divided 312 284 1.09859
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Subtracted 241.045 261.874 20.829
337 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 243.583 267.527 1.0983
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Subtracted 200.691 179.88 20.811
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 243.583 267.528 1.0983
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Subtracted 200.691 179.88 20.811
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Divided 243.583 267.527 1.0983
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] Subtracted 200.691 179.88 20.811
340 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 239.75 260.544 20.794
myelin gene expression factor 2. [refseq;acc:nm_016132] Divided 235.383 258.476 1.09811
341 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Subtracted 240.788 261.416 20.628
342 40s ribosomal protein s20. [swissprot;acc:p17075] Divided 243.5 267.21 1.09737
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Subtracted 240.913 261.45 20.537
343 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Divided 241.625 265.136 1.0973
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 231.73 211.252 20.478
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Divided 241.625 265.136 1.0973
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Subtracted 240.6 261.041 20.441
345 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 224.445 204.044 20.401
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Divided 242.14 265.697 1.09729
346 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119
apical-like protein (apxl protein). [swissprot;acc:q13796] Subtracted 231.492 211.136 20.356
347 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Divided 242.14 265.697 1.09729
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Subtracted 231.481 211.131 20.35
348 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Divided 242.14 265.696 1.09728
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Subtracted 185.969 165.623 20.346
349 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 20.308
surfeit locus protein 5. [swissprot;acc:q15528] Divided 242.14 265.696 1.09728
350 tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Subtracted 233.376 253.539 20.163
zinc finger protein 291. [swissprot;acc:q9by12] Divided 242.14 265.696 1.09728

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/