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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1558 to 1607 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
Interaction Map
red
green
network_comparison
390 ATG4B Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] High confidence 56.7841 75.447 18.6629
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 162.755 155.476 7.279
MRPL13 Divided 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] High confidence 241.828 263.62 1.09011
391 no value Subtracted rna binding protein. [refseq;acc:nm_032509] Low confidence 206.88 199.607 7.273
HTRA2 Divided 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] 200.046 192.943 1.03681
RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] High confidence 241.828 263.62 1.09011
TXNL4A Subtracted spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 225.719 207.072 18.647
392 LEPR leptin receptor gene-related protein (ob-r gene related protein) (ob- rgrp). [swissprot;acc:o15243] Low confidence 206.88 199.607 7.273
NUBP1 Divided nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 200.894 193.766 1.03679
POLR3C Subtracted polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] High confidence 239.092 257.705 18.613
RPL13A Divided 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 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
LEPROTL1 Subtracted leptin receptor overlapping transcript-like 1 (my047 protein). [swissprot;acc:o95214] 206.88 199.607 7.273
POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] High confidence 238.921 257.327 18.406
TXNL4A Divided spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] 225.719 207.072 1.09005
394 CLTC Subtracted clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] 207.889 226.226 18.337
CRNKL1 Divided crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Low confidence 204.815 197.606 1.03648
Subtracted 7.209
DPP9 Divided 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
JPH4 Subtracted 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 7.195
PDCL phosducin-like protein (phlp). [swissprot;acc:q13371] High confidence 207.908 226.218 18.31
396 no value Divided 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
RPA1 Subtracted 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 18.31
SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Low confidence 201.176 193.984 7.192
397 CCT3 Divided 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
OXA1L Subtracted cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 211.182 203.991 7.191
RPA2 replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] High confidence 207.908 226.218 18.31
398 GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Low confidence 207.797 214.954 7.157
ITGB1BP3 Divided muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] High confidence 218.818 238.358 1.0893
PDC Subtracted phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] 207.908 226.218 18.31
YME1L1 Divided yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Low confidence 205.997 213.496 1.0364
399 no value Subtracted 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 7.154
CLTC Divided 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
RAD52 Subtracted dna repair protein rad52 homolog. [swissprot;acc:p43351] High confidence 207.908 226.218 18.31
400 CLTCL1 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 207.931 226.209 18.278
NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Low confidence 200.894 193.766 7.128
PDCL Divided 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
HTRA1 Subtracted serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 200.057 192.938 7.119
MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] High confidence 254.434 236.224 18.21
RPA1 Divided 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] 207.908 226.218 1.08807
402 CACNG5 Subtracted voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Low confidence 210.292 203.181 7.111
NDC80 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] High confidence 231.802 249.983 18.181
RPA2 Divided replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] 207.908 226.218 1.08807

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/