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 Network Comparison Type Interaction Map Value Type green red network_comparison Filtered
Results: HTML CSV LaTeX Showing element 951 to 1000 of 3730 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Value Type  : Ranked
Rank
description
green
red
network_comparison
Filtered
476 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 8329 8403 1.00888 0
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 210.814 226.681 1.07527 1
477 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 234.547 251.926 1.0741
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 15780.2 15920 1.00886 0
478 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 10243.1 10156.4 1.00854
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 212.321 228.051 1.07409 1
479 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 15031.7 15155.8 1.00826 0
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 212.321 228.051 1.07409 1
480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 254.667 237.109 1.07405
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 15031.7 15155.8 1.00826 0
481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 254.667 237.109 1.07405 1
uridine kinase-like 1. [swissprot;acc:q9nwz5] 11462.4 11554.3 1.00802 0
482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 254.667 237.109 1.07405 1
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 6205.67 6156.33 1.00801 0
483 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] 254.667 237.109 1.07405 1
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 12127.5 12223.8 1.00794 0
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 254.667 237.109 1.07405 1
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] 11414.3 11489.7 1.00661 0
485 60s ribosomal protein l18. [swissprot;acc:q07020] 254.667 237.109 1.07405 1
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 12542.3 12461.5 1.00648 0
486 huntingtin interacting protein c. [refseq;acc:nm_012272] 13288.3 13372.4 1.00633
mct-1 protein. [refseq;acc:nm_014060] 243.03 226.313 1.07387 1
487 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 13159.3 13236.8 1.00589 0
488 heat shock factor binding protein 1. [swissprot;acc:o75506] 15127.8 15204.2 1.00505
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] 209.798 225.026 1.07258 1
489 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 8811.09 8854.04 1.00487 0
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 215.627 231.276 1.07257 1
490 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 10338.7 10388.7 1.00484 0
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] 236.015 220.183 1.0719 1
491 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 234.951 251.83 1.07184
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 21880 21970 1.00411 0
492 serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] 235.979 220.171 1.0718 1
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 6829.74 6802.96 1.00394 0
493 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 235.98 220.172 1.0718 1
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 12041.7 11999.1 1.00355 0
494 serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 235.98 220.172 1.0718 1
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 11959.4 11985.5 1.00218 0
495 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 11748.1 11725.2 1.00195
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 235.979 220.171 1.0718 1
496 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 234.134 250.938 1.07177
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] 9411.49 9394 1.00186 0
497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 234.514 251.344 1.07177 1
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 13718.2 13692.7 1.00186 0
498 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 10248.3 10231.8 1.00161
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] 235.95 220.161 1.07172 1
499 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 9069.58 9080.73 1.00123 0
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 248.048 231.496 1.0715 1
500 huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 394 394 1 0
inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 240.673 224.662 1.07127 1

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/