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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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 [...,...].
Value Type Rank Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4958 to 5007 of 29840 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1977 rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] Subtracted 6036.68 6379.44 342.76
1978 kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6] 6036.62 6379.38
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Divided 5475.74 5800.97 1.05939
1979 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176] Subtracted 6036.68 6379.44 342.76
1980 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Divided 5830.46 6176.71 1.05939
kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282] Subtracted 6036.68 6379.44 342.76
1981 inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Divided 5475.74 5800.97 1.05939
neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840] Subtracted 6036.68 6379.44 342.76
1982 transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Divided 5475.74 5800.97 1.05939
1983 exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Subtracted 6036.68 6379.44 342.76
myosin vi. [swissprot;acc:q9um54] Divided 5475.74 5800.97 1.05939
1984 kinesin light chain 1 (klc 1). [swissprot;acc:q07866] Subtracted 6036.73 6379.48 342.75
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Divided 5830.03 6176.1 1.05936
1985 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Subtracted 6674.58 7015.93 341.35
scribble. [refseq;acc:nm_015356] Divided 5516.89 5844.37 1.05936
1986 lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] 5517.24 5844.68 1.05935
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Subtracted 6083.39 6423.12 339.73
1987 hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 5444.6 5783.95 339.35
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Divided 5829.74 6175.69 1.05934
1988 protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 3559.49 3360.39 1.05925
seven in absentia homolog 2. [refseq;acc:nm_005067] Subtracted 5399.47 5737.79 338.32
1989 m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Divided 4383.34 4642.93 1.05922
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Subtracted 5396.61 5733.93 337.32
1990 transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Divided 5045.67 5344.06 1.05914
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Subtracted 5096.02 5432.63 336.61
1991 seven in absentia homolog 1. [refseq;acc:nm_003031] 5394.24 5730.73 336.49
solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Divided 5429.27 5749.69 1.05902
1992 solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
ubiquitin. [swissprot;acc:p02248] Subtracted 7484.98 7821.11 336.13
1993 nucleoporin like 1. [refseq;acc:nm_014089] Divided 6174.74 6538.73 1.05895
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Subtracted 5521.07 5856.93 335.86
1994 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 6682.7 7018.29 335.59
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Divided 6174.74 6538.73 1.05895
1995 adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5] Subtracted 5684.61 6018.72 334.11
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Divided 6174.74 6538.73 1.05895
1996 polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Subtracted 6024.47 6356.56 332.09
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Divided 5047.2 5344.68 1.05894
1997 ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Subtracted 6024.47 6356.56 332.09
1998 adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] 5671.62 6003.67 332.05
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Divided 5047.2 5344.68 1.05894
1999 nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Subtracted 6688.64 7020.02 331.38
2000 ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] Divided 5047.2 5344.68 1.05894
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Subtracted 5882.61 6213.34 330.73
2001 dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] Divided 5047.2 5344.68 1.05894
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [refseq;acc:nm_016333] Subtracted 5448.35 5777.35 329
2002 splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081]

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/