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 475 to 524 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
119 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 1 318.982 259.004 1.23157
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted 0 7739.47 9580.95 1841.48
120 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1 227.199 192.715 34.484
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 269.278 327.709 1.21699
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 5797 4873 1.18962
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Subtracted 11438 13277.1 1839.1
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 1 269.254 327.655 1.2169
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted 0 18241.7 16405 1836.7
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1 227.202 192.823 34.379
zinc finger protein 232. [swissprot;acc:q9uny5] Divided 0 11523.7 13686.9 1.18772
122 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Subtracted 1 199.949 234.187 34.238
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 0 12384.7 10549.4 1835.3
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Divided 1 269.248 327.642 1.21688
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 0 11523 13685.4 1.18766
123 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Subtracted 12335.3 10506.8 1828.5
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 1 269.23 327.601 1.21681
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 227.032 193.056 33.976
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided 0 11522.8 13684.9 1.18764
124 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Subtracted 12328.5 10501 1827.5
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided 1 208.52 171.595 1.21519
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 285.684 252.234 33.45
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided 0 11520.7 13680.4 1.18746
125 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Subtracted 12314.9 10489.3 1825.6
high-mobility group 20a. [refseq;acc:nm_018200] Divided 1 208.588 171.778 1.21429
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0 22038 18578 1.18624
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 1 285.684 252.234 33.45
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided 94 114 1.21277
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Subtracted 0 12314.9 10489.3 1825.6
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 1 285.684 252.234 33.45
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Divided 0 9722.71 11493.8 1.18216
127 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] Subtracted 11732 13530.6 1798.6
cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1 285.684 252.234 33.45
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 94 114 1.21277
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 0 9411.34 11119.7 1.18152
128 60s ribosomal protein l39. [swissprot;acc:p02404] 11564.4 9794.29 1.18073
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 1 94 114 1.21277
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 285.684 252.234 33.45
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 0 9722.71 11493.8 1771.09
129 60s ribosomal protein l39. [swissprot;acc:p02404] 11564.4 9794.29 1770.11
cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1 285.684 252.234 33.45
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Divided 0 14222.5 12058.6 1.17945
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 1 94 114 1.21277
130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 0 14476.2 17069.5 1.17914
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Subtracted 1 242.735 276.059 33.324
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 0 14922.7 13174.5 1748.2
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 1 94 114 1.21277
131 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 0 8375.43 9873.58 1.17887
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Subtracted 1 242.718 276.018 33.3
integral membrane protein cii-3b. [sptrembl;acc:o75609] 0 14951.6 13204.2 1747.4
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Divided 1 294.053 242.562 1.21228

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/