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 2130 to 2179 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
134 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared Divided 0 11625.2 6483.52 1.79304
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Rooted Subtracted 23.9003 19.8655 4.0348
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Ranked Divided 12314.9 10489.3 1.17404
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1 350 290 1.2069
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Rooted 0 10 12 1.2
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 1 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
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Measured Divided 0 260.986 346.751 1.32862
p66 alpha. [refseq;acc:nm_017660] Squared 1 81888.8 56306.5 1.45434
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Ranked Subtracted 0 12157.6 13890.3 1732.7
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted 1 54.8203 67.934 13.1137
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Measured 0 3036.29 2784.08 252.21
135 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted Divided 1 54.935 66.6101 1.21253
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Measured Subtracted 0 728.65 476.619 252.031
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Divided 1 21785.2 16426.1 1.32626
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Ranked Subtracted 0 8871.11 10603.2 1732.09
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared 1 71033.4 95440.2 24406.8
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Ranked Divided 0 12314.9 10489.3 1.17404
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1 350 290 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
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Rooted 0 26.8649 22.8761 3.9888
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Measured Divided 814.485 613.614 1.32736
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Squared 21101.4 11769.5 1.79289
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Rooted 42.8135 51.3517 1.19943
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Squared Subtracted 1592.06 2488.07 896.01
transcription factor jun-b. [swissprot;acc:p17275] Measured 1 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 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Squared 0 6747.71 5878.56 869.15
adiponectin receptor 2. [refseq;acc:nm_024551] Rooted Divided 1 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
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Ranked Divided 0 12335.3 10506.8 1.17403
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 350 290 1.2069
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Rooted 0 23.9877 20.1222 1.1921
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Ranked Subtracted 1 263.215 231.407 31.808
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Measured 0 903.767 1152.06 248.293
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] Divided 1 3620.77 4763.34 1.31556
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Ranked Subtracted 0 12759.4 11028.8 1730.6
Rooted 14.7363 18.7165 3.9802
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared Divided 978.105 1746.18 1.78527
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Measured 1526.38 1150.51 1.3267
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared 1 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
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Ranked 0 12328.5 10501 1.17403

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/