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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 925 to 974 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
463 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 0 5558.06 5473.99 1.01536
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 1 238.921 257.327 1.07704
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 210.578 226.764 1.07686
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 0 10076.4 9928.08 1.01494
465 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 1 248.152 267.226 1.07686
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 0 9482.68 9620.66 1.01455
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 1 248.152 267.226 1.07686
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 0 1543 1521 1.01446
467 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 1 248.152 267.226 1.07686
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] 0 21205 20914 1.01391
468 histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 1 248.152 267.226 1.07686
469 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745] 0 21205 20914 1.01391
470 h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 1 248.152 267.226 1.07686
471 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 0 11319.2 11463 1.0127
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 1 248.152 267.226 1.07686
472 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 0 7080.27 7165.6 1.01205
thymic stromal co-transporter. [refseq;acc:nm_033051] 1 248.152 267.226 1.07686
473 cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] 0 816 825 1.01103
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 1 225.661 209.651 1.07637
474 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] 0 11290.1 11167.6 1.01097
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 1 226.789 210.818 1.07576
475 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 0 18667 18500 1.00903
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 1 226.727 210.816 1.07547
476 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 0 8403 8329 1.00888
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 1 226.681 210.814 1.07527
477 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] 251.926 234.547 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] 0 15920 15780.2 1.00886
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] 10156.4 10243.1 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] 1 228.051 212.321 1.07409
479 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 0 15155.8 15031.7 1.00826
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 1 228.051 212.321 1.07409
480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] 237.109 254.667 1.07405
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 0 15155.8 15031.7 1.00826
481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] 1 237.109 254.667 1.07405
uridine kinase-like 1. [swissprot;acc:q9nwz5] 0 11554.3 11462.4 1.00802
482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 1 237.109 254.667 1.07405
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 0 6156.33 6205.67 1.00801
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] 1 237.109 254.667 1.07405
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 0 12223.8 12127.5 1.00794
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] 1 237.109 254.667 1.07405
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] 0 11489.7 11414.3 1.00661
485 60s ribosomal protein l18. [swissprot;acc:q07020] 1 237.109 254.667 1.07405
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 0 12461.5 12542.3 1.00648
486 huntingtin interacting protein c. [refseq;acc:nm_012272] 13372.4 13288.3 1.00633
mct-1 protein. [refseq;acc:nm_014060] 1 226.313 243.03 1.07387
487 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 0 13236.8 13159.3 1.00589

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/