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 1051 to 1100 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
132 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured Divided 2236.61 2980.35 1.33253
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Rooted 44.963 55.0576 1.22451
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Squared Subtracted 71062.2 95488.6 24426.4
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Rooted 144.606 157.824 13.218
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked Divided 350 290 1.2069
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured Subtracted 12839 10911.1 1927.9
133 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Rooted 144.606 157.824 13.218
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured 12798.9 10887.2 1911.7
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Ranked 226.887 194.72 32.167
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured Divided 23421.5 17580.4 1.33225
gbp protein isoform a. [refseq;acc:nm_017870] Squared 1182.25 1726.55 1.46039
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted 45.4558 55.5995 1.22316
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Squared Subtracted 71062.2 95488.6 24426.4
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked Divided 350 290 1.2069
134 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Rooted 44.849 54.7964 1.2218
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured Subtracted 12796.8 10886 1910.8
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Divided 21785.2 16426.1 1.32626
gk001 protein. [refseq;acc:nm_020198] Squared Subtracted 71062.2 95488.6 24426.4
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Ranked 226.884 194.79 32.094
p66 alpha. [refseq;acc:nm_017660] Squared Divided 81888.8 56306.5 1.45434
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted Subtracted 54.8203 67.934 13.1137
135 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 54.935 66.6101 1.21253
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Measured 21785.2 16426.1 1.32626
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared Subtracted 71033.4 95440.2 24406.8
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked Divided 350 290 1.2069
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 231.407 31.808
transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 7488.4 1909.22
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared Divided 81888.8 56306.5 1.45434
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Rooted Subtracted 49.2923 62.3969 13.1046
136 adiponectin receptor 2. [refseq;acc:nm_024551] Divided 41.8357 50.6469 1.21061
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared Subtracted 71030.1 95434.8 24404.7
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Measured 12787.6 10880.5 1907.1
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked Divided 350 290 1.2069
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 231.407 31.808
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Measured Divided 3620.77 4763.34 1.31556
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared 81888.8 56306.5 1.45434
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Rooted Subtracted 49.2923 62.3969 13.1046
137 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Measured Divided 3620.77 4763.34 1.31556
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 81606.8 56215.8 1.45167
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked Subtracted 263.191 231.394 31.797
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Measured 12786.6 10879.9 1906.7
musashi 2 isoform a. [refseq;acc:nm_138962] Rooted Divided 54.9787 66.2416 1.20486
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked 350 290 1.2069
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Squared Subtracted 69549 92953.5 23404.5
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Rooted 49.2925 62.397 13.1045
138 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Ranked 174.667 205.556 30.889
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared 70739 93908.8 23169.8
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured Divided 2755.15 2094.3 1.31555
musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 66.2416 1.20486

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/