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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Filtered Value Type Gene Network Comparison Type green red network_comparison Interaction Map Rank description
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
green
red
network_comparison
Interaction Map
Rank
description
958.726 1011.83 1.05539 Low confidence 524 keratin associated protein 1.5. [refseq;acc:nm_031957]
525 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
958.728 522 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]
526 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]
958.732 1.05538 527 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]
958.745 1.05537 531 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]
532 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
958.748 1011.84 1.05538 528 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]
958.749 529 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
958.753 1.05537 530 similar to peptidylprolyl isomerase a (cyclophilin a); cyclophilin-lc; cyclophilin homolog overexpressed in liver cancer; chromosome 1 amplified sequence 2. [refseq;acc:nm_178230]
959.463 1012.08 1.05484 536 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]
961.098 958.429 1.00278 High confidence 484 scribble. [refseq;acc:nm_015356]
965.202 749.494 1.2878 Low confidence 144 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]
969.022 966.085 1.00304 810 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]
971.37 976.734 1.00552 794 dystrophin. [swissprot;acc:p11532]
975 624 1.5625 90 rna transcribed from l1 repetitive element (shr4) (fragment). [sptrembl;acc:q9y443]
91 putative p150. [sptrembl;acc:o00370]
92 lamin-like protein in hindiii repetitive element derived dna, 3' end (fragment). [sptrembl;acc:q14755]
93 line-1 reverse transcriptase (fragment). [sptrembl;acc:o00172]
975.647 870.93 1.12024 High confidence 277 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
Low confidence 367
977 1442 1.47595 High confidence 101 putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]
102 phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]
988.882 1048.65 1.06044 369 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]
989.438 1049.21 1.06041 370 dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]
991.072 1100.34 1.11025 Low confidence 391 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]
992.083 572 1.73441 High confidence 72 60s ribosomal protein l21. [swissprot;acc:p46778]
994.275 1018.78 1.02465 Low confidence 662 spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]
1005.42 916.527 1.09699 411 mitochondrial ribosomal protein l38. [refseq;acc:nm_032478]
1006.57 1012.19 1.00558 792 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]
1010.2 952.812 1.06023 498 solute carrier family 4, sodium bicarbonate cotransporter, member 8. [refseq;acc:nm_004858]
1011.49 1024.55 1.01291 745 tera protein. [refseq;acc:nm_021238]
1011.67 1392.08 1.37602 112 transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
1015.49 1020.35 1.00479 798 scratch; scratch 1. [refseq;acc:nm_031309]
1020.78 876.587 1.16449 315 dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]
1020.84 1.16456 314 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]
1023.76 1249.24 1.22025 High confidence 189 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]
1026.18 1230.54 1.19915 199 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]
1035.81 1073.94 1.03681 Low confidence 599 60s ribosomal protein l15. [swissprot;acc:p39030]
1036.1 1148.04 1.10804 393 dynamin-like 120 kda protein, mitochondrial precursor (optic atrophy 1 gene protein). [swissprot;acc:o60313]
1049.11 768.061 1.36592 114 calponin h2, smooth muscle (neutral calponin). [swissprot;acc:q99439]
1060 1113.5 1.05047 558 histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
559 histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
560 histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
561 h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
1061.23 1108.92 1.04494 576 solute carrier family 12 (potassium/chloride transporters), member 9; cation-chloride cotransporter-interacting protein. [refseq;acc:nm_020246]
1063.6 1287.7 1.2107 183 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]
1066.67 1104.74 1.03569 602 alpha 2 globin. [refseq;acc:nm_000517]
1067.65 1105.65 1.03559 604 hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096]
1068 607 1.75947 High confidence 70 importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]

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/