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 description Gene Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 151 to 200 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
76 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted 24136.4 20446.1 3690.3
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Divided 3058.57 4599.26 1.50373
77 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 24136.4 20446.1 3690.3
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Divided 3093.6 4612.39 1.49095
78 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 7132.71 4800.81 1.48573
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 24136.4 20446.1 3690.3
79 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 4567.51 3074.57 1.48558
80 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 24136.4 20446.1 3690.3
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 5945.32 4133.47 1.43834
81 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 24136.4 20446.1 3690.3
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Divided 5943.56 4136.36 1.43691
82 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted 24136.4 20446.1 3690.3
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 5954.48 4172.91 1.42694
83 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 18098.7 21644.2 3545.5
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided 7033.29 4932.27 1.42597
84 jun dimerization protein. [refseq;acc:nm_130469]
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Subtracted 18090 21632.5 3542.5
85 fos-related antigen 2. [swissprot;acc:p15408] Divided 7037.11 4941.95 1.42395
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Subtracted 17896.5 21370.8 3474.3
86 protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided 7037.32 4942.49 1.42384
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Subtracted 17896.5 21370.8 3474.3
87 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Divided 7038.04 4944.3 1.42347
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Subtracted 17083.8 20287.2 3203.4
88 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 1695.45 2411.93 1.42259
transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] Subtracted 12888.4 16074 3185.6
89 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 1698.12 2414.22 1.4217
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Subtracted 12886.8 16071.6 3184.8
90 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 1698.75 2414.77 1.4215
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Subtracted 12886.8 16071.6 3184.8
91 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 1700.8 2416.53 1.42082
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Subtracted 12886 16070.4 3184.4
92 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 5801.04 4117.67 1.40882
transforming protein n-ras. [swissprot;acc:p01111] Subtracted 12885.6 16069.8 3184.2
93 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 5942.75 4245.52 1.39977
sedlin. [swissprot;acc:o14582] Subtracted 20483.9 17396.9 3087
94 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 5941.88 4247.86 1.39879
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Subtracted 20483.9 17396.9 3087
95 bet3 homolog. [swissprot;acc:o43617]
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 3343.62 2397.19 1.39481
96 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 5694.99 4110.14 1.3856
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 19235.4 16177.9 3057.5
97 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Divided 3897.1 2820.51 1.3817
septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted 19094.4 16067.4 3027
98 brain protein 44. [swissprot;acc:o95563] 19007.1 15999.1 3008
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Divided 3225.65 2353.63 1.3705
99 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]
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted 19007.1 15999.1 3008
100 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] Divided 3225.65 2353.63 1.3705
septin 6. [swissprot;acc:q14141] Subtracted 18957.1 15959.9 2997.2

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/