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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3977 to 4026 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
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]
survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] Divided 5047.2 5344.68 1.05894
2003 probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Subtracted 5448.35 5777.35 329
2004 splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368]
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Divided 5047.87 5344.95 1.05885
2005 atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396] 6064.92 6421.65 1.05882
scribble. [refseq;acc:nm_015356] Subtracted 5516.89 5844.37 327.48
2006 lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] 5517.24 5844.68 327.44
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Divided 5048.26 5345.1 1.0588
2007 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] 5684.61 6018.72 1.05877
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Subtracted 4980.54 5307.81 327.27
2008 40s ribosomal protein s15a. [swissprot;acc:p39027] Divided 3637.47 3435.61 1.05876
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Subtracted 4980.54 5307.81 327.27
2009 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Divided 4934.48 5223.69 1.05861
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Subtracted 4980.54 5307.81 327.27
2010 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] Divided 5671.62 6003.67 1.05855
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Subtracted 4980.54 5307.81 327.27
2011 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Divided 5391.27 5706.64 1.0585
inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] Subtracted 5204.25 5530.11 325.86
2012 hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Divided 5391.27 5706.64 1.0585
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Subtracted 5204.25 5530.11 325.86
2013 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Divided 5391.27 5706.64 1.0585

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/