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 green red 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
green
red
network_comparison
670 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Measured 7145.59 6374.65 1.12094
671 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Squared 33971.3 28911 1.17503
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Ranked 199.398 210.739 1.05688
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Rooted 73.8955 68.6822 1.0759
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Measured 7145.59 6374.65 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 47.7936 51.4203 1.07588
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Squared 33971.3 28911 1.17503
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Ranked 199.398 210.739 1.05688
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Measured 7145.59 6374.65 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 214.355 226.497 1.05664
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Rooted 122.835 132.156 1.07588
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Measured 7766.54 6933.17 1.1202
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Squared 33971.3 28911 1.17503
674 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 36156.7 42467.5 1.17454
exocyst complex component sec5. [swissprot;acc:q96kp1] Rooted 122.802 132.114 1.07583
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Ranked 214.355 226.497 1.05664
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Measured 6215.42 5549.2 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 122.761 132.063 1.07577
single-minded homolog 1. [swissprot;acc:p81133] Ranked 214.355 226.497 1.05664
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Measured 6215.42 5549.2 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 26247.3 22347.6 1.1745
676 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Rooted 123.158 132.467 1.07559
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Squared 26234.1 22337.3 1.17445
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Ranked 245.613 232.469 1.05654
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Measured 6215.42 5549.2 1.12006
677 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Squared 26232.2 22335.8 1.17445
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Rooted 63.7418 59.2629 1.07558
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Measured 6215.42 5549.2 1.12006
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Ranked 216.745 228.944 1.05628
678 myelin gene expression factor 2. [refseq;acc:nm_016132] Rooted 52.8585 56.8369 1.07527
sorting nexin 5. [swissprot;acc:q9y5x3] Ranked 220.175 208.482 1.05609
surfeit locus protein 1. [swissprot;acc:q15526] Squared 26232.2 22335.8 1.17445
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Measured 7770.65 6938.22 1.11998
679 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 7282.94 6503.1 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 26234.1 22337.3 1.17445
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Ranked 125.389 132.413 1.05602
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Rooted 66.1861 61.5558 1.07522
680 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Measured 7282.5 6503.03 1.11986
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Ranked 125.389 132.413 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 26233.5 22336.8 1.17445
t54 protein. [swissprot;acc:q92917] Rooted 66.1861 61.5558 1.07522
681 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Squared 26232.2 22335.8 1.17445
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Ranked 125.389 132.413 1.05602
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Rooted 86.277 80.2562 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 8029.64 7170.83 1.11976
682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Ranked 125.389 132.413 1.05602
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Squared 26232.2 22335.8 1.17445
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Rooted 93.0684 86.5959 1.07474
syntaxin 12. [refseq;acc:nm_177424] Measured 6217.59 5552.92 1.1197
683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Ranked 125.389 132.413 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/