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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 694 to 743 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
347 SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Subtracted 231.481 211.131 20.35
348 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Divided 242.14 265.696 1.09728
SLC15A2 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 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 20.308
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Divided 242.14 265.696 1.09728
350 no value 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
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Divided 242.14 265.696 1.09728
351 GTF2H1 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
PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Divided 242.14 265.696 1.09728
352 RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 237.862 217.739 20.123
TXNDC9 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Divided 242.14 265.696 1.09728
353 GIPC1 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 231.73 211.252 1.09694
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Subtracted 94 114 20
354 CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]
STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Divided 234.691 257.442 1.09694
355 STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Subtracted 94 114 20
STX6 syntaxin 6. [swissprot;acc:o43752] Divided 234.673 257.414 1.09691
356 no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796 1.09684
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 94 114 20
357 no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Divided 243.12 266.661 1.09683
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Subtracted 94 114 20
358 RAB37 ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 260.193 19.906
RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 243.12 266.662 1.09683
359 RAB26 ras-related protein rab-26. [swissprot;acc:q9ulw5] Subtracted 240.287 260.193 19.906
RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Divided 239.277 262.434 1.09678
360 POLR2C dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Subtracted 240.287 260.193 19.906
SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Divided 243.072 266.559 1.09663
361 KATNA1 katanin p60 subunit a 1. [refseq;acc:nm_007044] Subtracted 232.431 252.238 19.807
MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 242.83 266.248 1.09644
362 KATNB1 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
SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Divided 231.492 211.136 1.09641
363 SETMAR set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Subtracted 233.539 253.197 19.658
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Divided 231.481 211.131 1.09639
364 CLEC4M cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Subtracted 233.539 253.197 19.658
POLR2B 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 FCER2 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Subtracted 233.539 253.197 19.658
MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Divided 242.744 266.07 1.09609
366 CD209 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Subtracted 233.539 253.197 19.658
RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Divided 242.473 265.756 1.09602
367 DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Subtracted 218.827 238.407 19.58
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Divided 234.146 256.627 1.09601
368 DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Subtracted 218.827 238.407 19.58
PUS1 trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Divided 242.66 265.715 1.09501
369 MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 1.09475
POLR2E dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Subtracted 239.977 259.525 19.548
370 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 218.818 238.358 19.54
NUDT12 nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Divided 242.159 265.104 1.09475
371 RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 186.52 170.42 1.09447
SLC15A1 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Subtracted 186.172 166.661 19.511
372 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided 186.52 170.42 1.09447

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/