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 Interaction Map Value Type Network Comparison Type Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 501 to 550 of 7460 in total
Interaction Map  : High confidence
Value Type  : Ranked
Rank
description
Network Comparison Type
Filtered
red
network_comparison
green
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided 1 94 1.21277 114
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 1825.6 10489.3
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 33.45 252.234
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 1.18216 11493.8
127 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] Subtracted 11732 1798.6 13530.6
cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1 285.684 33.45 252.234
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided 94 1.21277 114
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 0 9411.34 1.18152 11119.7
128 60s ribosomal protein l39. [swissprot;acc:p02404] 11564.4 1.18073 9794.29
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 1 94 1.21277 114
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 285.684 33.45 252.234
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 1771.09 11493.8
129 60s ribosomal protein l39. [swissprot;acc:p02404] 11564.4 1770.11 9794.29
cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1 285.684 33.45 252.234
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Divided 0 14222.5 1.17945 12058.6
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 1 94 1.21277 114
130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 0 14476.2 1.17914 17069.5
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Subtracted 1 242.735 33.324 276.059
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 1748.2 13174.5
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 1 94 1.21277 114
131 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 0 8375.43 1.17887 9873.58
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Subtracted 1 242.718 33.3 276.018
integral membrane protein cii-3b. [sptrembl;acc:o75609] 0 14951.6 1747.4 13204.2
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 1.21228 242.562
132 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted 229.406 32.711 196.695
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 0 10883 1739.8 12622.8
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Divided 19048 1.1754 22389
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 350 1.2069 290
133 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 6814 1.17537 8009
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 1 226.887 32.167 194.72
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 17144.8 1739.2 15405.6
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 1 350 1.2069 290
134 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 0 12314.9 1.17404 10489.3
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1 350 1.2069 290
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 226.884 32.094 194.79
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 0 12157.6 1732.7 13890.3
135 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 8871.11 1732.09 10603.2
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Divided 12314.9 1.17404 10489.3
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1 350 1.2069 290
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 31.808 231.407
136 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Divided 0 12335.3 1.17403 10506.8
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 350 1.2069 290
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 31.808 231.407
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 0 12759.4 1730.6 11028.8
137 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Divided 12328.5 1.17403 10501
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Subtracted 1 263.191 31.797 231.394
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 0 16853 1730 15123
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 1 350 1.2069 290
138 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Subtracted 174.667 30.889 205.556
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Divided 0 12384.7 1.17397 10549.4

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/