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 1551 to 1600 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
388 HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Divided Low confidence 200.049 192.942 1.03683
MAP1LC3B microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Subtracted High confidence 56.7244 75.3948 18.6704
389 no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 162.755 155.476 7.279
HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Divided 200.049 192.942 1.03683
MAP1LC3A microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Subtracted High confidence 56.7252 75.3954 18.6702
SNRPF small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Divided 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
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 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 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Divided High confidence 241.828 263.62 1.09011
391 no value rna binding protein. [refseq;acc:nm_032509] Subtracted Low confidence 206.88 199.607 7.273
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] Divided 200.046 192.943 1.03681
RPS16 40s ribosomal protein s16. [swissprot;acc:p17008] High confidence 241.828 263.62 1.09011
TXNL4A spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Subtracted 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 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Divided 200.894 193.766 1.03679
POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Subtracted High confidence 239.092 257.705 18.613
RPL13A 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Divided 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 leptin receptor overlapping transcript-like 1 (my047 protein). [swissprot;acc:o95214] Subtracted 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 spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided 225.719 207.072 1.09005
394 CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Subtracted 207.889 226.226 18.337
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided Low confidence 204.815 197.606 1.03648
Subtracted 7.209
DPP9 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Divided 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 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Subtracted 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 putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Divided 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 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] Subtracted 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 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 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 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Subtracted 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 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Divided High confidence 218.818 238.358 1.0893
PDC phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Subtracted 207.908 226.218 18.31
YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Divided Low confidence 205.997 213.496 1.0364
399 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] Subtracted 205.017 197.863 7.154
CLTC clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Divided 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 dna repair protein rad52 homolog. [swissprot;acc:p43351] Subtracted 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 phosducin-like protein (phlp). [swissprot;acc:q13371] Divided 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

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/