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 Value Type description Network Comparison Type Interaction Map Filtered green red 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
green
red
network_comparison
340 myelin gene expression factor 2. [refseq;acc:nm_016132] Divided 258.476 235.383 1.09811
341 60s ribosomal protein l9. [swissprot;acc:p32969] 263.798 240.243 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 261.416 240.788 20.628
342 40s ribosomal protein s20. [swissprot;acc:p17075] Divided 267.21 243.5 1.09737
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Subtracted 261.45 240.913 20.537
343 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Divided 265.136 241.625 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 211.252 231.73 20.478
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Divided 265.136 241.625 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 261.041 240.6 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] 204.044 224.445 20.401
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Divided 265.697 242.14 1.09729
346 40s ribosomal protein s3. [swissprot;acc:p23396] 265.119 241.612
apical-like protein (apxl protein). [swissprot;acc:q13796] Subtracted 211.136 231.492 20.356
347 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Divided 265.697 242.14 1.09729
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Subtracted 211.131 231.481 20.35
348 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Divided 265.696 242.14 1.09728
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Subtracted 165.623 185.969 20.346
349 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 234.804 255.112 20.308
surfeit locus protein 5. [swissprot;acc:q15528] Divided 265.696 242.14 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 253.539 233.376 20.163
zinc finger protein 291. [swissprot;acc:q9by12] Divided 265.696 242.14 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 253.539 233.376 20.163
352 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Divided 265.696 242.14 1.09728
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 217.739 237.862 20.123
353 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 114 94 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 211.252 231.73 1.09694
354 putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Subtracted 114 94 20
syntaxin 10 (syn10). [swissprot;acc:o60499] Divided 257.442 234.691 1.09694
355 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Subtracted 114 94 20
syntaxin 6. [swissprot;acc:o43752] Divided 257.414 234.673 1.09691
356 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 266.796 243.24 1.09684
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 114 94 20
357 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Divided 266.661 243.12 1.09683
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Subtracted 114 94 20
358 ras-related protein rab-37. [swissprot;acc:q96ax2] 260.193 240.287 19.906
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 266.662 243.12 1.09683
359 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 262.434 239.277 1.09678
ras-related protein rab-26. [swissprot;acc:q9ulw5] Subtracted 260.193 240.287 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 266.559 243.072 1.09663
361 katanin p60 subunit a 1. [refseq;acc:nm_007044] Subtracted 252.238 232.431 19.807
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 266.248 242.83 1.09644
362 apical-like protein (apxl protein). [swissprot;acc:q13796] 211.136 231.492 1.09641
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Subtracted 252.166 232.382 19.784
363 set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] 253.197 233.539 19.658
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Divided 211.131 231.481 1.09639
364 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Subtracted 253.197 233.539 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 266.617 243.208 1.09625
365 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 266.07 242.744 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/