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 2230 to 2279 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
279 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Rooted Divided 66.0989 74.0609 1.12046
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Measured Subtracted 4771.21 5961.43 1190.22
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked 242.66 265.715 23.055
280 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Squared 30566.4 38866.5 8300.1
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Rooted Divided 57.9068 64.8562 1.12001
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 42.0577 50.424 8.3663
metastasis-associated protein mta1. [swissprot;acc:q13330] Ranked Divided 252.512 228.356 1.10578
musashi 1. [refseq;acc:nm_002442] Squared 15569.5 19953.6 1.28158
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured Subtracted 677.5 1865.5 1188
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Divided 3119.98 2579.49 1.20953
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked Subtracted 267.208 244.168 23.04
281 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 22.945
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 241.808 267.335 1.10557
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Rooted Subtracted 42.0684 50.4323 8.3639
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Measured Divided 3119.98 2579.49 1.20953
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Subtracted 677.5 1865.5 1188
nuclear protein ukp68. [refseq;acc:nm_024824] Squared Divided 15569.5 19953.6 1.28158
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Subtracted 52623.3 44380.3 8243
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Rooted Divided 57.9068 64.8562 1.12001
282 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Ranked 252.39 228.297 1.10553
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Squared Subtracted 52623.3 44380.3 8243
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked 242.159 265.104 22.945
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 677.5 1865.5 1188
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Divided 3119.98 2579.49 1.20953
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Rooted 57.9819 64.9302 1.11984
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Squared 59704 76460.4 1.28066
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Rooted Subtracted 108.671 100.365 8.306
283 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Ranked 242.37 265.255 22.885
60s ribosomal protein l11. [swissprot;acc:p39026] Divided 241.828 267.346 1.10552
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Squared Subtracted 36933 44953.6 8020.6
deltex 2. [refseq;acc:nm_020892] Divided 6627.24 8484.19 1.2802
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Measured Subtracted 677.5 1865.5 1188
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Rooted Divided 57.9819 64.9302 1.11984
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Subtracted 108.659 100.356 8.303
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Measured Divided 5221.28 6314.35 1.20935
284 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 1.28012
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Ranked 224.657 203.235 1.10541
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Rooted 51.8647 46.3161 1.1198
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Ranked Subtracted 242.686 265.516 22.83
paxillin. [swissprot;acc:p49023] Measured Divided 5221.28 6314.35 1.20935
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 677.5 1865.5 1188
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Rooted 108.659 100.356 8.303
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Squared 36735.7 44689.6 7953.9
285 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Rooted Divided 48.4278 54.2262 1.11973
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared 6680.89 8549.44 1.27969
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked Subtracted 242.691 265.481 22.79
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Measured 4068.56 5252.6 1184.04
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Divided 23326.5 19296.4 1.20885
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared Subtracted 32117 40054 7937
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked Divided 224.647 203.242 1.10532

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/