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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1625 to 1674 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
813 C20orf3 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] High confidence 212.386 221.785 1.04425
SYNJ2 synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] Low confidence 198.561 193.492 1.0262
814 SNAP29 synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] High confidence 212.386 221.785 1.04425
UPF1 regulator of nonsense transcripts 1 (nonsense mrna reducing factor 1) (norf1) (up-frameshift suppressor 1 homolog). [swissprot;acc:q92900] Low confidence 202.069 196.914 1.02618
815 NFYB nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 203.907 198.706 1.02617
STX1B syntaxin 1b. [swissprot;acc:q15531] High confidence 212.386 221.785 1.04425
816 CDC25A m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Low confidence 207.541 202.25 1.02616
MRPL28 melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] High confidence 212.386 221.785 1.04425
817 LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Low confidence 202.15 197.002 1.02613
RFXANK dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] High confidence 212.386 221.785 1.04425
818 RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] 168.592 161.452 1.04422
SERHL2 serine hydrolase-like protein (ec 3.1.-.-). [swissprot;acc:q9h4i8] Low confidence 208.488 203.181 1.02612
819 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
POLR2I dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] High confidence 228.563 238.668 1.04421
820 ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432] Low confidence 208.488 203.181 1.02612
MRPS2 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] High confidence 221.716 231.501 1.04413
821 IMP4 u3 snornp protein 4 homolog. [refseq;acc:nm_033416] 221.676 231.453 1.0441
PEX5 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Low confidence 208.488 203.181 1.02612
822 ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
EIF3B eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] High confidence 243.067 232.805 1.04408
823 C16orf80 transcription factor iib. [refseq;acc:nm_013242] 206.068 197.471 1.04354
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Low confidence 186.275 181.537 1.0261
824 SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] High confidence 206.068 197.471 1.04354
ZNF423 olf-1/ebf associated zinc finger protein; smad- and olf-interacting zinc finger protein. [refseq;acc:nm_015069] Low confidence 204.922 199.711 1.02609
825 no value early hematopoietic zinc finger. [refseq;acc:nm_015461] 204.914 199.706 1.02608
WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] High confidence 206.214 197.614 1.04352
826 CTSB cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Low confidence 201.026 195.916 1.02608
HTATIP 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] High confidence 223.186 213.912 1.04335
827 LOH12CR1 loh1cr12. [refseq;acc:nm_058169] 230.087 220.579 1.0431
SPTLC1 serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Low confidence 207.116 201.851 1.02608
828 COX4I1 cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 204.206 199.02 1.02606
CSDE1 unr protein. [swissprot;acc:o75534] High confidence 230.087 220.579 1.0431
829 PAK3 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Low confidence 202.608 197.472 1.02601
SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] High confidence 135.844 130.259 1.04288
830 FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Low confidence 201.067 195.971 1.026
PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] High confidence 231.734 222.222 1.0428
831 no value hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
TMLHE trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Low confidence 204.064 198.895 1.02599
832 no value cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] High confidence 231.734 222.222 1.0428
GABBR2 gamma-aminobutyric acid type b receptor, subunit 2 precursor (gaba-b receptor 2) (gaba-b-r2) (gb2) (gababr2) (g protein-coupled receptor 51) (gpr 51) (hg20). [swissprot;acc:o75899] Low confidence 204.064 198.895 1.02599
833 ERAL1 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] High confidence 231.734 222.222 1.0428
834 RPL8 60s ribosomal protein l8. [swissprot;acc:p25120]
TYRL tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Low confidence 206.26 201.038 1.02598
835 HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] High confidence 231.734 222.222 1.0428
PAK2 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Low confidence 202.578 197.45 1.02597
836 HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] High confidence 231.734 222.222 1.0428
RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Low confidence 202.357 197.234 1.02597
837 no value dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 194.47 189.552 1.02595
DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] High confidence 231.734 222.222 1.0428

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/