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 2680 to 2729 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
670 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Measured 6374.65 7145.59 1.12094
671 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Squared 28911 33971.3 1.17503
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Ranked 210.739 199.398 1.05688
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Rooted 68.6822 73.8955 1.0759
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Measured 6374.65 7145.59 1.12094
672 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Rooted 51.4203 47.7936 1.07588
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Squared 28911 33971.3 1.17503
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Ranked 210.739 199.398 1.05688
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Measured 6374.65 7145.59 1.12094
673 peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Ranked 226.497 214.355 1.05664
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Rooted 132.156 122.835 1.07588
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Measured 6933.17 7766.54 1.1202
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Squared 28911 33971.3 1.17503
674 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 42467.5 36156.7 1.17454
exocyst complex component sec5. [swissprot;acc:q96kp1] Rooted 132.114 122.802 1.07583
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Ranked 226.497 214.355 1.05664
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Measured 5549.2 6215.42 1.12006
675 poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Rooted 132.063 122.761 1.07577
single-minded homolog 1. [swissprot;acc:p81133] Ranked 226.497 214.355 1.05664
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Measured 5549.2 6215.42 1.12006
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Squared 22347.6 26247.3 1.1745
676 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Rooted 132.467 123.158 1.07559
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Squared 22337.3 26234.1 1.17445
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Ranked 232.469 245.613 1.05654
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Measured 5549.2 6215.42 1.12006
677 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Squared 22335.8 26232.2 1.17445
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Rooted 59.2629 63.7418 1.07558
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Measured 5549.2 6215.42 1.12006
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Ranked 228.944 216.745 1.05628
678 myelin gene expression factor 2. [refseq;acc:nm_016132] Rooted 56.8369 52.8585 1.07527
sorting nexin 5. [swissprot;acc:q9y5x3] Ranked 208.482 220.175 1.05609
surfeit locus protein 1. [swissprot;acc:q15526] Squared 22335.8 26232.2 1.17445
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Measured 6938.22 7770.65 1.11998
679 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 6503.1 7282.94 1.11992
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Squared 22337.3 26234.1 1.17445
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked 132.413 125.389 1.05602
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Rooted 61.5558 66.1861 1.07522
680 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Measured 6503.03 7282.5 1.11986
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Ranked 132.413 125.389 1.05602
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Squared 22336.8 26233.5 1.17445
t54 protein. [swissprot;acc:q92917] Rooted 61.5558 66.1861 1.07522
681 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Squared 22335.8 26232.2 1.17445
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Ranked 132.413 125.389 1.05602
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Rooted 80.2562 86.277 1.07502
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Measured 7170.83 8029.64 1.11976
682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Ranked 132.413 125.389 1.05602
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Squared 22335.8 26232.2 1.17445
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Rooted 86.5959 93.0684 1.07474
syntaxin 12. [refseq;acc:nm_177424] Measured 5552.92 6217.59 1.1197
683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Ranked 132.413 125.389 1.05602

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/