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.


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 3608 to 3657 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
902 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Rooted 66.5785 70.6139 1.06061
903 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Ranked 246.354 237.223 1.03849
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Rooted 66.5785 70.6139 1.06061
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Squared 28068.5 32522.9 1.1587
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Measured 4986.58 5492.51 1.10146
904 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Squared 25492.1 29535.4 1.15861
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Ranked 246.354 237.223 1.03849
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Measured 6167.33 6785.98 1.10031
prohibitin. [swissprot;acc:p35232] Rooted 63.4547 67.3003 1.0606
905 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] Squared 27382 31722.9 1.15853
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Ranked 230.768 239.632 1.03841
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Rooted 63.4547 67.3003 1.0606
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Measured 10230.1 11256.2 1.1003
906 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Squared 25498.1 29537.7 1.15843
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Ranked 230.764 239.62 1.03838
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Rooted 61.6325 65.3619 1.06051
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Measured 6165.1 6783.01 1.10023
907 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 11852.9 10773.5 1.10019
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Squared 28767.1 33317.5 1.15818
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Ranked 223.906 215.653 1.03827
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Rooted 53.6328 56.8668 1.0603
908 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Measured 11848.8 10770.3 1.10014
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Rooted 62.6851 66.4615 1.06024
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Squared 28767.1 33317.5 1.15818
tax interaction protein 1. [refseq;acc:nm_014604] Ranked 223.906 215.653 1.03827
909 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Squared 28767.1 33317.5 1.15818
kinesin family member c3. [refseq;acc:nm_005550] Measured 5995.49 6595.35 1.10005
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Rooted 62.6851 66.4615 1.06024
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Ranked 142.077 136.846 1.03823
910 porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Squared 19732.4 22852.4 1.15812
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Rooted 55.9078 59.2557 1.05988
sipl protein. [refseq;acc:nm_018269] Measured 6522.94 7175.18 1.09999
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Ranked 217.168 209.207 1.03805
911 ero1-like. [refseq;acc:nm_014584]
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Measured 4982.81 5480.91 1.09996
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Squared 13688.1 15849.2 1.15788
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Rooted 64.1165 67.9451 1.05971
912 importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Squared 30826.4 35693.3 1.15788
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212] Measured 4982.81 5480.91 1.09996
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Rooted 64.1184 67.9467 1.05971
wd-repeat protein 3. [swissprot;acc:q9unx4] Ranked 243.896 234.96 1.03803
913 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Rooted 82.0749 86.9643 1.05957
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Ranked 210.863 218.878 1.03801
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Squared 30802.6 35663.9 1.15782
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Measured 5768.5 6342.05 1.09943
914 15 kda selenoprotein precursor. [swissprot;acc:o60613] Squared 29772.1 34456.5 1.15734
annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Rooted 61.4687 65.1194 1.05939
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Measured 6513.45 7161 1.09942
pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Ranked 210.863 218.878 1.03801
915 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Measured 6289.72 6911.96 1.09893

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/