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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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 7262 to 7311 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1816 potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] Measured 5633.44 5997 1.06454
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Ranked 220.462 217.926 1.01164
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Squared 13729.5 15069.8 1.09762
1817 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Ranked 220.462 217.926 1.01164
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] Rooted 62.0498 63.9432 1.03051
solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] Measured 5633.44 5997 1.06454
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Squared 20692.1 22710.4 1.09754
1818 heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991] Measured 5633.44 5997 1.06454
lats homolog 1. [refseq;acc:nm_004690] Rooted 62.0498 63.9432 1.03051
neighbor of cox4. [swissprot;acc:o43402] Ranked 220.462 217.926 1.01164
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Squared 20692.1 22710.4 1.09754
1819 adp-ribosylation factor 4. [swissprot;acc:p18085] Measured 5633.44 5997 1.06454
dead-box protein. [refseq;acc:nm_018665] Squared 20692.1 22710.4 1.09754
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Ranked 220.462 217.926 1.01164
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Rooted 62.0498 63.9432 1.03051
1820 40s ribosomal protein s5. [swissprot;acc:p46782] Squared 13022.7 14290.8 1.09738
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] Measured 5633.44 5997 1.06454
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] Rooted 62.0498 63.9432 1.03051
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Ranked 220.462 217.926 1.01164
1821 dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] Rooted 62.0498 63.9432 1.03051
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Ranked 218.36 215.874 1.01152
shc transforming protein. [swissprot;acc:p29353] Measured 5633.44 5997 1.06454
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Squared 21982.9 24123.2 1.09736
1822 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] Ranked 240.32 243.085 1.01151
lamin b2. [swissprot;acc:q03252] Squared 27353.9 30016.1 1.09732
tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19] Rooted 62.0498 63.9432 1.03051
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] Measured 5633.44 5997 1.06454
1823 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Squared 13145.4 14424.1 1.09727
fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] Ranked 202.386 200.086 1.0115
neuronal shc. [refseq;acc:nm_016848] Measured 5633.44 5997 1.06454
tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7] Rooted 62.0498 63.9432 1.03051
1824 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Squared 13145.4 14424.1 1.09727
adp-ribosylation factor 1. [swissprot;acc:p32889] Measured 5633.44 5997 1.06454
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Ranked 214.722 212.281 1.0115
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Rooted 67.0246 69.0684 1.03049
1825 fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] Ranked 202.386 200.086 1.0115
heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Measured 5633.44 5997 1.06454
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Squared 21994.2 24133.1 1.09725
ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] Rooted 67.8897 69.9589 1.03048
1826 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
adp-ribosylation factor 3. [swissprot;acc:p16587] Measured 5633.44 5997 1.06454
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Ranked 202.393 200.094 1.01149
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Squared 21994.2 24133.1 1.09725
1827 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Ranked 191.39 189.219 1.01147
protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4] Rooted 63.1858 65.1085 1.03043
protein sck (fragment). [swissprot;acc:p98077] Measured 5633.44 5997 1.06454
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Squared 21994.2 24133.1 1.09725
1828 fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] Ranked 202.41 200.115 1.01147
heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] Measured 5633.44 5997 1.06454
nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] Squared 21994.2 24133.1 1.09725

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/