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.


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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 Interaction Map Value Type Filtered Network Comparison Type red green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 14920 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
description
Value Type
Filtered
red
green
network_comparison
13 dok-like protein. [refseq;acc:nm_024872] Squared 0 0.289941 0.00001 28994.1
Rooted 5.91608 591608
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Ranked 5210.5 9264.5 1.77804
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 288.754 212.554 1.3585
14 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Squared 0 1.73869 19295.9 11098
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Measured 130.512 6.50325 20.0687
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Ranked 1 56.6768 75.3531 1.32952
dystrophin. [swissprot;acc:p11532] 0 10232.5 18054.8 1.76446
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Rooted 0.00001 4.24264 424264
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Measured 1 398.5 1281.5 3.21581
Squared 37.5863 388.696 10.3414
Rooted 19.9625 35.798 1.79326
15 gbp protein isoform a. [refseq;acc:nm_017870] 23.9771 42.4773 1.77158
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Squared 0 1.73869 19295.9 11098
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked 1 56.7244 75.3948 1.32914
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Rooted 0 4.24264 0.00001 424264
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Measured 10 156 15.6
Ranked 19403 11267 1.72211
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Measured 1 2671 871 3.06659
Squared 1688.58 179.56 9.40399
16 cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Ranked 0 12170.7 20670.6 1.69839
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 1 56.7252 75.3954 1.32913
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Squared 0 0.00001 0.0766864 7668.64
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] Measured 1 15 15
protein x 0004. [refseq;acc:nm_016301] 1 2671 871 3.06659
Squared 1688.58 179.56 9.40399
serpin b12. [swissprot;acc:q96p63] Rooted 0 10.2928 1.18697 8.67149
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 51.6817 29.5127 1.75117
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Ranked 56.7841 75.447 1.32866
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured 460 1365 2.96739
Squared 50.0828 441 8.80542
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Ranked 0 11543 6812 1.69451
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Rooted 10.3085 1.2188 8.45791
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Measured 859 58 14.8103
protein x 0004. [refseq;acc:nm_016301] Rooted 1 51.6817 29.5127 1.75117
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Squared 0 0.0766864 0.00001 7668.64
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 1 185.678 245.247 1.32082
60s ribosomal protein l37a. [swissprot;acc:p12751] Measured 0 305.45 26.1599 11.6763
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Squared 439.709 0.52284 841.001
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Rooted 9.20014 60.0707 6.52932
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1 21.4476 36.9459 1.72261
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked 0 22286 13216 1.68629
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured 1 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
19 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Measured 0 305.45 26.1599 11.6763
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked 1 185.678 245.247 1.32082
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 0 22286 13216 1.68629
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Rooted 9.20014 60.0707 6.52932
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 1 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176

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/