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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 777 to 826 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
389 HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Low confidence 200.049 192.942 1.03683
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] High confidence 227.575 208.756 1.09015
390 no value solute carrier family 35, member e2. [refseq;acc:nm_182838] Low confidence 203.647 211.144 1.03681
MRPL13 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] High confidence 241.828 263.62 1.09011
391 HTRA2 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Low confidence 200.046 192.943 1.03681
RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] High confidence 241.828 263.62 1.09011
392 NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Low confidence 200.894 193.766 1.03679
RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] High confidence 241.83 263.615 1.09008
393 no value small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Low confidence 201.334 194.242 1.03651
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] High confidence 225.719 207.072 1.09005
394 CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Low confidence 204.815 197.606 1.03648
DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] High confidence 218.827 238.407 1.08948
395 no value rna binding protein. [refseq;acc:nm_032509] Low confidence 206.88 199.607 1.03644
DPP8 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] High confidence 218.827 238.407 1.08948
396 no value putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 240.801 262.34 1.08945
LEPR leptin receptor gene-related protein (ob-r gene related protein) (ob- rgrp). [swissprot;acc:o15243] Low confidence 206.88 199.607 1.03644
397 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] High confidence 110.689 101.613 1.08932
LEPROTL1 leptin receptor overlapping transcript-like 1 (my047 protein). [swissprot;acc:o95214] Low confidence 206.88 199.607 1.03644
398 ITGB1BP3 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] High confidence 218.818 238.358 1.0893
YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Low confidence 205.997 213.496 1.0364
399 CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] High confidence 207.889 226.226 1.08821
GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Low confidence 193.291 186.506 1.03638
400 PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] High confidence 207.908 226.218 1.08807
SLC35E1 solute carrier family 35, member e1. [refseq;acc:nm_024881] Low confidence 203.661 211.03 1.03618
401 no value sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 205.017 197.863 1.03616
RPA1 replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] High confidence 207.908 226.218 1.08807
402 RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
TREX2 x-linked protein sts1769. [swissprot;acc:q99871] Low confidence 211.253 203.883 1.03615
403 ATRIP three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166]
PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] High confidence 207.908 226.218 1.08807
404 GRM2 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Low confidence 203.081 196 1.03613
RAD52 dna repair protein rad52 homolog. [swissprot;acc:p43351] High confidence 207.908 226.218 1.08807
405 no value metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Low confidence 203.081 196 1.03613
CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] High confidence 207.931 226.209 1.0879
406 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 265.634 244.304 1.08731
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Low confidence 201.095 194.099 1.03604
407 LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 201.123 194.127
MRPS9 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] High confidence 239.75 260.544 1.08673
408 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 255.112 234.804 1.08649
JPH4 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Low confidence 207.558 200.363 1.03591
409 NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 149.423 144.256 1.03582
POLR1E rna polymerase i associated factor 53. [refseq;acc:nm_022490] High confidence 241.045 261.874 1.08641
410 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] 233.376 253.539 1.0864
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Low confidence 202.074 195.097 1.03576
411 EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 214.628 222.301 1.03575
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] High confidence 233.376 253.539 1.0864
412 SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Low confidence 201.711 194.787 1.03555
UQCRFSL1 ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] High confidence 240.788 261.416 1.08567
413 KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Low confidence 201.711 194.787 1.03555
POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] High confidence 240.913 261.45 1.08525

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/