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 Value Type Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided 1 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
132 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted 229.406 196.695 32.711
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 0 10883 12622.8 1739.8
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Divided 19048 22389 1.1754
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 350 290 1.2069
133 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 6814 8009 1.17537
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 1 226.887 194.72 32.167
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 17144.8 15405.6 1739.2
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Divided 1 350 290 1.2069
134 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 0 12314.9 10489.3 1.17404
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1 350 290 1.2069
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Subtracted 226.884 194.79 32.094
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 0 12157.6 13890.3 1732.7
135 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 8871.11 10603.2 1732.09
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 10489.3 1.17404
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1 350 290 1.2069
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 231.407 31.808
136 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Divided 0 12335.3 10506.8 1.17403
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 350 290 1.2069
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 231.407 31.808
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 0 12759.4 11028.8 1730.6
137 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Divided 12328.5 10501 1.17403
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Subtracted 1 263.191 231.394 31.797
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 0 16853 15123 1730
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Divided 1 350 290 1.2069
138 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Subtracted 174.667 205.556 30.889
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Divided 0 12384.7 10549.4 1.17397

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/