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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1325 to 1374 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
663 integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006] Low confidence 206.32 200.601 1.02851
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] High confidence 229.072 216.576 1.0577
664 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Low confidence 201.821 196.233 1.02848
665 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] High confidence 229.072 216.576 1.0577
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Low confidence 204.882 199.214 1.02845
666 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 200.639 195.092 1.02843
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] High confidence 229.072 216.576 1.0577
667 ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] Low confidence 208.62 202.855 1.02842
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] High confidence 229.072 216.576 1.0577
668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
inositol oxygenase (ec 1.13.99.1) (myo-inositol oxygenase) (aldehyde reductase-like 6) (renal-specific oxidoreductase) (kidney-specific protein 32). [swissprot;acc:q9ugb7] Low confidence 212.062 206.202 1.02842
669 cytochrome p450 3a43 (ec 1.14.14.1). [swissprot;acc:q9hb55] 203.712 198.082
synapsin i (brain protein 4.1). [swissprot;acc:p17600] High confidence 229.072 216.576 1.0577
670 autoantigen ngp-1. [swissprot;acc:q13823] 250.302 236.817 1.05694
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Low confidence 204.551 198.901 1.02841
671 integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] 206.277 200.582 1.02839
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] High confidence 210.739 199.398 1.05688
672 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Low confidence 203.727 198.116 1.02832
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] High confidence 210.739 199.398 1.05688
673 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Low confidence 203.604 197.996 1.02832
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] High confidence 226.497 214.355 1.05664
674 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Low confidence 204.81 199.174 1.0283
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] High confidence 226.497 214.355 1.05664
675 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] Low confidence 203.702 198.095 1.0283
single-minded homolog 1. [swissprot;acc:p81133] High confidence 226.497 214.355 1.05664
676 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Low confidence 202.698 197.124 1.02828
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] High confidence 232.469 245.613 1.05654
677 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Low confidence 207.03 201.339 1.02827
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] High confidence 228.944 216.745 1.05628
678 cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Low confidence 203.747 198.152 1.02824
sorting nexin 5. [swissprot;acc:q9y5x3] High confidence 208.482 220.175 1.05609
679 glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] Low confidence 198.424 192.974 1.02824
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 132.413 125.389 1.05602
680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]
putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] Low confidence 196.228 190.844 1.02821
681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] High confidence 132.413 125.389 1.05602
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Low confidence 206.115 200.462 1.0282
682 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 204.263 198.663 1.02819
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] High confidence 132.413 125.389 1.05602
683 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Low confidence 216.618 210.69 1.02814
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] High confidence 132.413 125.389 1.05602
684 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Low confidence 199.669 194.204 1.02814
685 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] High confidence 132.413 125.389 1.05602
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Low confidence 201.719 196.209 1.02808
686 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 132.413 125.389 1.05602
neurogenin 2 (fragment). [swissprot;acc:q9h2a3] Low confidence 216.554 210.642 1.02807
687 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] High confidence 132.413 125.389 1.05602

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/