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 680 to 729 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
340 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
351 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Subtracted 233.376 253.539 20.163
352 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Divided 242.14 265.696 1.09728
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 237.862 217.739 20.123
353 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 94 114 20
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Divided 231.73 211.252 1.09694
354 putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Subtracted 94 114 20
syntaxin 10 (syn10). [swissprot;acc:o60499] Divided 234.691 257.442 1.09694
355 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Subtracted 94 114 20
syntaxin 6. [swissprot;acc:o43752] Divided 234.673 257.414 1.09691
356 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796 1.09684
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 94 114 20
357 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Divided 243.12 266.661 1.09683
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Subtracted 94 114 20
358 ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 260.193 19.906
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 243.12 266.662 1.09683
359 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 239.277 262.434 1.09678
ras-related protein rab-26. [swissprot;acc:q9ulw5] Subtracted 240.287 260.193 19.906
360 dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Divided 243.072 266.559 1.09663
361 katanin p60 subunit a 1. [refseq;acc:nm_007044] Subtracted 232.431 252.238 19.807
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 242.83 266.248 1.09644
362 apical-like protein (apxl protein). [swissprot;acc:q13796] 231.492 211.136 1.09641
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Subtracted 232.382 252.166 19.784
363 set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 233.539 253.197 19.658
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Divided 231.481 211.131 1.09639
364 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Subtracted 233.539 253.197 19.658
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Divided 243.208 266.617 1.09625
365 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 266.07 1.09609

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/