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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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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1630 to 1679 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
815 syntaxin 1b. [swissprot;acc:q15531] High confidence 212.386 221.785 1.04425
816 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
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] High confidence 212.386 221.785 1.04425
817 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Low confidence 202.15 197.002 1.02613
818 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] High confidence 168.592 161.452 1.04422
serine hydrolase-like protein (ec 3.1.-.-). [swissprot;acc:q9h4i8] Low confidence 208.488 203.181 1.02612
819 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
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 actin binding lim protein 2. [refseq;acc:nm_032432] Low confidence 208.488 203.181 1.02612
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] High confidence 221.716 231.501 1.04413
821 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
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] High confidence 221.676 231.453 1.0441
822 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Low confidence 208.488 203.181 1.02612
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 ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Low confidence 186.275 181.537 1.0261
transcription factor iib. [refseq;acc:nm_013242] High confidence 206.068 197.471 1.04354
824 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
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] High confidence 206.068 197.471 1.04354
825 early hematopoietic zinc finger. [refseq;acc:nm_015461] Low confidence 204.914 199.706 1.02608
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] High confidence 206.214 197.614 1.04352
826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 1.04335
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Low confidence 201.026 195.916 1.02608
827 loh1cr12. [refseq;acc:nm_058169] High confidence 230.087 220.579 1.0431
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 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
unr protein. [swissprot;acc:o75534] High confidence 230.087 220.579 1.0431
829 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] 135.844 130.259 1.04288
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
830 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 201.067 195.971 1.026
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] High confidence 231.734 222.222 1.0428
831 hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
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 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] High confidence 231.734 222.222 1.0428
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 gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
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 60s ribosomal protein l8. [swissprot;acc:p25120]
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Low confidence 206.26 201.038 1.02598
835 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
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 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] High confidence 231.734 222.222 1.0428
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 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 194.47 189.552 1.02595
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] High confidence 231.734 222.222 1.0428
838 lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Low confidence 194.47 189.552 1.02595
rw1 protein (fragment). [swissprot;acc:q92545] High confidence 231.734 222.222 1.0428
839 lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Low confidence 194.47 189.552 1.02595
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] High confidence 177.776 170.499 1.04268
840 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 198.781 190.66 1.04259

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
- 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/