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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2680 to 2729 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
670 tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Divided Low confidence 204.551 198.901 1.02841
671 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] Subtracted 203.702 198.095 5.607
integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] Divided 206.277 200.582 1.02839
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] High confidence 210.739 199.398 1.05688
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Subtracted 232.601 244.534 11.933
672 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Low confidence 204.263 198.663 5.6
cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Divided 203.727 198.116 1.02832
dok-like protein. [refseq;acc:nm_024872] Subtracted High confidence 216.504 204.622 11.882
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided 210.739 199.398 1.05688
673 cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Subtracted Low confidence 203.747 198.152 5.595
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Divided 203.604 197.996 1.02832
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Subtracted High confidence 216.504 204.622 11.882
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Divided 226.497 214.355 1.05664
674 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Subtracted Low confidence 205.207 199.613 5.594
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] High confidence 216.504 204.622 11.882
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Divided 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
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Subtracted 201.821 196.233 5.588
single-minded homolog 1. [swissprot;acc:p81133] Divided High confidence 226.497 214.355 1.05664
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Subtracted 216.504 204.622 11.882
676 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Divided 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
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Subtracted Low confidence 198.493 192.907 5.586
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] High confidence 245.84 257.636 11.796
677 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Low confidence 202.698 197.124 5.574
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] High confidence 245.246 233.483 11.763
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Divided 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 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] Subtracted Low confidence 205.169 199.601 5.568
cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Divided 203.747 198.152 1.02824
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Subtracted High confidence 226.135 214.405 11.73
sorting nexin 5. [swissprot;acc:q9y5x3] Divided 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
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Subtracted Low confidence 211.36 205.793 5.567
sorting nexin 5. [swissprot;acc:q9y5x3] High confidence 208.482 220.175 11.693
680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided 132.413 125.389 1.05602
putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] Low confidence 196.228 190.844 1.02821
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Subtracted 211.36 205.793 5.567
sr rich protein. [refseq;acc:nm_032870] High confidence 225.293 213.64 11.653
681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided 132.413 125.389 1.05602
interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458] Subtracted Low confidence 204.538 198.974 5.564
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] High confidence 220.593 208.987 11.606
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Divided 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
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Subtracted Low confidence 200.62 195.059 5.561
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] High confidence 246.055 234.458 11.597
683 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided Low confidence 216.618 210.69 1.02814

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/