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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2612 to 2661 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
653 SORBS2 Rooted arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 64.4927 69.539 1.07825
654 no value Measured histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 4088.63 4593.43 1.12346
Squared sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 27174.1 31992.4 1.17731
CASK Rooted peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 59.9021 64.5838 1.07816
DOK2 Ranked docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 216.504 204.622 1.05807
655 no value Measured dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 4088.63 4593.43 1.12346
DOK1 Ranked docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 216.504 204.622 1.05807
HIF3A Rooted hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] 59.9021 64.5838 1.07816
SPRY3 Squared sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 27174.1 31992.4 1.17731
656 APOA1BP Measured apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 6139.04 6893.7 1.12293
FRK Ranked tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 216.504 204.622 1.05807
SIM1 Rooted single-minded homolog 1. [swissprot;acc:p81133] 59.9021 64.5838 1.07816
SPRY1 Squared sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 27174.1 31992.4 1.17731
657 GIPC1 Measured rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 6079.26 6824.47 1.12258
SORBS3 Rooted vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 64.75 69.8065 1.07809
SPRY2 Squared sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 27174.1 31992.4 1.17731
SYN3 Ranked synapsin iii. [swissprot;acc:o14994] 229.072 216.576 1.0577
658 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
EIF3B Rooted eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 52.7523 56.8686 1.07803
PARS2 Squared similar to trna synthetase class ii. [refseq;acc:nm_152268] 22293.8 26242.6 1.17713
SHROOM2 Measured apical-like protein (apxl protein). [swissprot;acc:q13796] 6088.77 6834.87 1.12254
659 HEY1 Ranked hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] 229.072 216.576 1.0577
MRPS9 Rooted 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 51.7081 47.9816 1.07767
OTC Squared ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 24614 28973.4 1.17711
SHROOM3 Measured shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 6089.21 6835.34 1.12253
660 no value u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 5575.18 6254.85 1.12191
ABLIM2 Ranked actin binding lim protein 2. [refseq;acc:nm_032432] 229.072 216.576 1.0577
FIP1L1 Rooted fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 133.216 123.627 1.07756
NDUFB9 Squared nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 33024.9 38867.8 1.17692
661 ALAD delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 22223.1 26152.4 1.17681
HEYL Ranked hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 229.072 216.576 1.0577
NXF5 Rooted nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 68.8243 74.1496 1.07738
SLU7 Measured step ii splicing factor slu7. [refseq;acc:nm_006425] 5575.18 6254.85 1.12191
662 no value Squared ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 23947.4 28163.7 1.17607
NXF3 Rooted nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 68.8237 74.1484 1.07737
PARD6G Measured partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 6374.65 7145.59 1.12094
SYN2 Ranked synapsin ii. [swissprot;acc:q92777] 229.072 216.576 1.0577
663 ACRC Squared acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 23947.7 28163.9 1.17606
MRRF Ranked mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 229.072 216.576 1.0577
NXF1 Rooted nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 68.8197 74.1413 1.07733
TUB Measured tubby protein homolog. [swissprot;acc:p50607] 6374.65 7145.59 1.12094
664 NET1 Rooted neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 51.6042 55.574 1.07693
PEX5 Ranked peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 229.072 216.576 1.0577
PRKCI Measured protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 6374.65 7145.59 1.12094
SUMO3 Squared ubiquitin-like protein smt3a. [swissprot;acc:p55854] 23948 28164.1 1.17605
665 ARHGEF3 Rooted rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] 51.6042 55.574 1.07693
HEY2 Ranked hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] 229.072 216.576 1.0577
LSM6 Squared u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 18960.3 22298 1.17604
NUMB Measured numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] 6374.65 7145.59 1.12094
666 HES1 Ranked transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 229.072 216.576 1.0577

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/