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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2951 to 3000 of 3206 in total
Rank
description
measured
expected
final
Hugo
2951 CYCLIN G2. [SWISSPROT;Acc:Q16589] 0.149439 1.01194 0.147675752 CCNG2
2952 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, ALPHA ISOFORM (PP2A, B SUBUNIT, B' ALPHA ISOFORM) (PP2A, B SUBUNIT, B56 ALPHA ISOFORM) (PP2A, B SUBUNIT, PR61 ALPHA ISOFORM) (PP2A, B SUBUNIT, R5 ALPHA ISOFORM). [SWISSPROT;Acc:Q15" 0.057253 0.387696 0.147674982 PPP2R5A
2953 "SERINE/THREONINE PROTEIN PHOSPHATASE 2A, 56 KDA REGULATORY SUBUNIT, EPSILON ISOFORM (PP2A, B SUBUNIT, B' EPSILON ISOFORM) (PP2A, B SUBUNIT, B56 EPSILON ISOFORM) (PP2A, B SUBUNIT, PR61 EPSILON ISOFORM) (PP2A, B SUBUNIT, R5 EPSILON ISOFORM). [SWISSPR" 0.0735334 0.497941 0.147674925 PPP2R5E
2954 CYCLIN G1 (CYCLIN G). [SWISSPROT;Acc:P51959] 0.134987 0.914083 0.147674774 CCNG1
2955 RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (RAF-1) (C-RAF). [SWISSPROT;Acc:P04049] 0.219758 1.48848 0.147639202 RAF1
2956 A-RAF PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE (EC 2.7.1.-) (A-RAF-1) (PROTO-ONCOGENE PKS). [SWISSPROT;Acc:P10398] 0.218717 1.48145 0.147637112 ARAF
2957 TRANSFORMING PROTEIN P21A (K-RAS 2A) (KI-RAS) (C-K-RAS). [SWISSPROT;Acc:P01116] 0.274014 1.87466 0.146167305 KRAS
2958 LEUCINE-RICH REPEAT PROTEIN SHOC-2 (RAS-BINDING PROTEIN SUR-8). [SWISSPROT;Acc:Q9UQ13] 0.100774 0.689453 0.146165148 SHOC2
2959 FRMPD4
2960 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2 (RALGDS-LIKE FACTOR) (RAS-ASSOCIATED PROTEIN RAB2L). [SWISSPROT;Acc:O15211] 0.0746316 0.510598 0.146165085 no value
2961 TRANSFORMING PROTEIN P21/H-RAS-1 (C-H-RAS). [SWISSPROT;Acc:P01112] 0.223524 1.52927 0.146163856 HRAS
2962 TRANSFORMING PROTEIN N-RAS. [SWISSPROT;Acc:P01111] 0.217355 1.48707 0.146163261 no value
2963 SEPTIN 1 (LARP) (SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR- 24). [SWISSPROT;Acc:Q8WYJ6] 0.0798252 0.547429 0.145818362 SEPT1
2964 FORKHEAD BOX PROTEIN P3 (ZINC FINGER PROTEIN JM2) (SCURFIN). [SWISSPROT;Acc:Q9BZS1] 0.193703 1.33367 0.145240577 FOXP3
2965 FORKHEAD BOX PROTEIN P1 (HSPC215). [SWISSPROT;Acc:Q9H334] 0.137759 0.94872 0.145205118 FOXP1
2966 FORKHEAD BOX P4; FORK HEAD-RELATED PROTEIN LIKE A; WINGED-HELIX REPRESSOR FOXP4. [RefSeq;Acc:NM_138457] 0.136683 0.941317 0.145204007 FOXP4
2967 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR (RALGEF) (RALGDS). [SWISSPROT;Acc:Q12967] 0.122631 0.850955 0.144109853 RALGDS
2968 RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 1 (RALGDS-LIKE 1). [SWISSPROT;Acc:Q9NZL6] 0.106453 0.742944 0.143285362 RGL1
2969 COATOMER EPSILON SUBUNIT (EPSILON-COAT PROTEIN) (EPSILON-COP). [SWISSPROT;Acc:O14579] 0.148933 1.04237 0.142879208 COPE
2970 0.104104 0.735452 0.141551046 RIBC2
2971 TUBULIN-SPECIFIC CHAPERONE C (TUBULIN-FOLDING COFACTOR C) (CFC). [SWISSPROT;Acc:Q15814] 0.0292681 0.208597 0.140309305 TBCC
2972 DEAD-BOX PROTEIN. [RefSeq;Acc:NM_018665] DDX43
2973 PUTATIVE ACYL-COA THIOESTER HYDROLASE CGI-16 (EC 3.1.2.-). [SWISSPROT;Acc:Q9Y305] 0.231971 1.65329 0.140308718 ACOT9
2974 HOMEOBOX PROTEIN HOX-D4 (HOX-4B) (HOX-5.1) (HHO.C13). [SWISSPROT;Acc:P09016] 0.0311395 0.223127 0.139559533 HOXD4
2975 HOMEOBOX PROTEIN HOX-C5 (HOX-3D) (CP11). [SWISSPROT;Acc:Q00444] 0.0320568 0.2297 0.139559425 HOXC5
2976 HOMEOBOX PROTEIN HOX-C4 (HOX-3E) (CP19). [SWISSPROT;Acc:P09017] 0.0311872 0.223469 0.139559402 no value
2977 RETINAL SHORT-CHAIN DEHYDROGENASE/REDUCTASE 3. [RefSeq;Acc:NM_016246] 0.518329 3.71404 0.139559348 HSD17B14
2978 HOMEOBOX PROTEIN HOX-C6 (HOX-3C) (HHO.C8) (CP25). [SWISSPROT;Acc:P09630] 0.0308655 0.221164 0.139559332 no value
2979 HOMEOBOX PROTEIN HOX-B5 (HOX-2A) (HHO.C10) (HU-1). [SWISSPROT;Acc:P09067] 0.035571 0.254881 0.139559245 HOXB5
2980 HOMEOBOX PROTEIN HOX-A5 (HOX-1C). [SWISSPROT;Acc:P20719] 0.0421586 0.302084 0.139559195 HOXA5
2981 0.0398119 0.285269 0.139559153 MTERFD1
2982 HOMEOBOX PROTEIN HOX-B4 (HOX-2F) (HOX-2.6). [SWISSPROT;Acc:P17483] 0.0313539 0.224664 0.139559075 HOXB4
2983 HOMEOBOX PROTEIN HOX-A4 (HOX-1D) (HOX-1.4). [SWISSPROT;Acc:Q00056] 0.0310799 0.222701 0.13955887 no value
2984 SPERMATOGENESIS ASSOCIATED 6. [RefSeq;Acc:NM_019073] 0.107787 0.77996 0.138195548 SPATA6
2985 "BETA-ARRESTIN 1 (ARRESTIN, BETA 1). [SWISSPROT;Acc:P49407]" 0.282189 2.04196 0.138195165 ARRB1
2986 AMP DEAMINASE 2 (EC 3.5.4.6) (AMP DEAMINASE ISOFORM L). [SWISSPROT;Acc:Q01433] 0.138195 1 0.138195 AMPD2
2987 C9orf68
2988 "BETA-ARRESTIN 2 (ARRESTIN, BETA 2). [SWISSPROT;Acc:P32121]" 0.240182 1.738 0.138194476 ARRB2
2989 SEPTIN 4 (PEANUT-LIKE PROTEIN 2) (BRAIN PROTEIN H5) (CELL DIVISION CONTROL-RELATED PROTEIN 2) (HCDCREL-2) (BRADEION BETA) (CE5B3 BETA) (CEREBRAL PROTEIN-7) (HUCEP-7). [SWISSPROT;Acc:O43236] 0.16041 1.17491 0.136529607 SEPT4
2990 0.0210454 0.155504 0.135336712 HS3ST4
2991 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 2; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [RefSeq;Acc:NM_006043] 0.0207502 0.153323 0.135336512 HS3ST2
2992 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3A1; HEPARIN-GLUCOSAMINE 3-O-SULFOTRANSFERASE. [RefSeq;Acc:NM_006042] 0.026835 0.198284 0.135336184 HS3ST3A1
2993 MRNA DECAPPING ENZYME; HISTIDINE TRIAD PROTEIN MEMBER 5; HEAT SHOCK-LIKE PROTEIN 1. [RefSeq;Acc:NM_014026] 0.279017 2.06166 0.135336088 DCPS
2994 HEPARAN SULFATE D-GLUCOSAMINYL 3-O-SULFOTRANSFERASE 3B1. [RefSeq;Acc:NM_006041] 0.0225884 0.166906 0.135336057 HS3ST3B1
2995 C439A6.1 (NOVEL PROTEIN SIMILAR TO HEPARAN SULFATE (GLUCOSAMINE) 3-O- SULFOTRANSFERASES) (FRAGMENT). [SPTREMBL;Acc:Q96QI5] 0.0210051 0.155207 0.135336035 HS3ST6
2996 RING FINGER PROTEIN 25 (EC 6.3.2.-). [SWISSPROT;Acc:Q96BH1] 0.22015 1.62938 0.135112742 RNF25
2997 OLIGOSACCHARYL TRANSFERASE STT3 SUBUNIT HOMOLOG (B5) (INTEGRAL MEMBRANE PROTEIN 1) (TMC). [SWISSPROT;Acc:P46977] 0.0284601 0.210671 0.135092633 STT3A
2998 SOURCE OF IMMUNODOMINANT MHC-ASSOCIATED PEPTIDES; HOMOLOG OF YEAST STT3 GENE. [RefSeq;Acc:NM_178862] 0.0366899 0.271591 0.135092474 STT3B
2999 DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE--PROTEIN GLYCOSYLTRANSFERASE 48 KDA SUBUNIT PRECURSOR (EC 2.4.1.119) (OLIGOSACCHARYL TRANSFERASE 48 KDA SUBUNIT) (DDOST 48 KDA SUBUNIT). [SWISSPROT;Acc:P39656] 0.0217044 0.160664 0.135091869 DDOST
3000 APG3P; PC3-96 PROTEIN. [RefSeq;Acc:NM_022488] 0.206188 1.59883 0.128961803 ATG3

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
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/