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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description Rank Gene measured final expected Hugo
Results: HTML CSV LaTeX Showing element 1958 to 2007 of 3206 in total
description
Rank
measured
final
expected
Hugo
KETOHEXOKINASE (EC 2.7.1.3) (HEPATIC FRUCTOKINASE). [SWISSPROT;Acc:P50053] 830 0.0303497 0.26109964 0.116238 KHK
KH-TYPE SPLICING REGULATORY PROTEIN (FUSE BINDING PROTEIN 2); KH-TYPE SPLICING REGULATORY PROTEIN (FUSE-BINDING PROTEIN 2). [RefSeq;Acc:NM_003685] 833 0.418445 0.260980067 1.60336 KHSRP
KIDNEY AND LIVER PROLINE OXIDASE 1. [RefSeq;Acc:NM_021232] 2573 0.0574606 0.2133417 0.269336 PRODH2
KINESIN FAMILY MEMBER C3. [RefSeq;Acc:NM_005550] 674 0.0861152 0.26627912 0.323402 KIFC3
KINESIN HEAVY CHAIN (UBIQUITOUS KINESIN HEAVY CHAIN) (UKHC). [SWISSPROT;Acc:P33176] 894 0.131086 0.259876768 0.504416 KIF5B
KINESIN HEAVY CHAIN ISOFORM 5C (KINESIN HEAVY CHAIN NEURON-SPECIFIC 2). [SWISSPROT;Acc:O60282] 886 0.152626 0.25987829 0.587298 KIF5C
KINESIN LIGHT CHAIN 1 (KLC 1). [SWISSPROT;Acc:Q07866] 895 0.684483 0.259876304 2.63388 KLC1
KINESIN LIGHT CHAIN 2 (KLC 2). [SWISSPROT;Acc:Q9H0B6] 887 0.527178 0.259877943 2.02856 KLC2
KINESIN PROTEIN. [RefSeq;Acc:NM_032559] 227 0.331603 0.316859526 1.04653 KIF2B
KINESIN-LIKE PROTEIN KIF13A (KINESIN-LIKE PROTEIN RBKIN). [SWISSPROT;Acc:Q9H1H9] 854 0.0796144 0.260534523 0.305581 KIF13A
KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8] 852 0.0651843 0.260535025 0.250194 no value
KINESIN-LIKE PROTEIN KIF2 (KINESIN-2) (HK2). [SWISSPROT;Acc:O00139] 229 0.425718 0.31608185 1.34686 KIF2A
KINESIN-LIKE PROTEIN KIF23 (MITOTIC KINESIN-LIKE PROTEIN-1) (KINESIN- LIKE PROTEIN 5). [SWISSPROT;Acc:Q02241] 1258 0.310673 0.247333392 1.25609 KIF23
KINESIN-LIKE PROTEIN KIF3B (MICROTUBULE PLUS END-DIRECTED KINESIN MOTOR 3B) (HH0048). [SWISSPROT;Acc:O15066] 1525 0.105382 0.242324319 0.43488 KIF3B
KINESIN-LIKE PROTEIN KIF3C. [SWISSPROT;Acc:O14782] 1529 0.0849863 0.242295334 0.350755 KIF3C
KININOGEN PRECURSOR (ALPHA-2-THIOL PROTEINASE INHIBITOR) [CONTAINS: BRADYKININ]. [SWISSPROT;Acc:P01042] 52 0.586469 0.411156135 1.42639 KNG1
KRUEPPEL-LIKE FACTOR 5 (INTESTINAL-ENRICHED KRUEPPEL-LIKE FACTOR) (COLON KRUEPPEL-LIKE FACTOR) (TRANSCRIPTION FACTOR BTEB2) (BASIC TRANSCRIPTION ELEMENT BINDING PROTEIN 2) (BTE-BINDING PROTEIN 2) (GC BOX BINDING PROTEIN 2). [SWISSPROT;Acc:Q13887] 299 0.0416551 0.3003988 0.138666 KLF5
KRUPPEL-RELATED ZINC FINGER PROTEIN HCKROX. [RefSeq;Acc:NM_015872] 2805 0.0949294 0.19771027 0.480144 ZBTB7B
KV CHANNEL INTERACTING PROTEIN 1; VESICLE APC-BINDING PROTEIN; A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 1. [RefSeq;Acc:NM_014592] 1204 0.287166 0.248344749 1.15632 KCNIP1
KV CHANNEL INTERACTING PROTEIN 2 ISOFORM 4; A-TYPE POTASSIUM CHANNEL MODULATORY PROTEIN 2; CARDIAC VOLTAGE GATED POTASSIUM CHANNEL MODULATORY SUBUNIT. [RefSeq;Acc:NM_173193] 1199 0.244748 0.248355362 0.985475 KCNIP2
KYNURENINASE (EC 3.7.1.3) (L-KYNURENINE HYDROLASE). [SWISSPROT;Acc:Q16719] 2614 0.397319 0.211324157 1.88014 KYNU
KYNURENINE 3-MONOOXYGENASE (KYNURENINE 3-HYDROXYLASE). [RefSeq;Acc:NM_003679] 2397 0.132423 0.219254268 0.60397 KMO
L-MYC-1 PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P12524] 329 0.228764 0.285234782 0.80202 MYCL1
LACTOYLGLUTATHIONE LYASE (EC 4.4.1.5) (METHYLGLYOXALASE) (ALDOKETOMUTASE) (GLYOXALASE I) (GLX I) (KETONE-ALDEHYDE MUTASE) (S-D-LACTOYLGLUTATHIONE METHYLGLYOXAL LYASE). [SWISSPROT;Acc:Q04760] 2770 0.570693 0.201400682 2.83362 GLO1
LAG1 LONGEVITY ASSURANCE HOMOLOG 2 ISOFORM 1; L3 PIGMENT; TUMOR METASTASIS-SUPPRESSOR. [RefSeq;Acc:NM_022075] 2922 0.172935 0.168005712 1.02934 LASS2
LAMIN A/C (70 KDA LAMIN). [SWISSPROT;Acc:P02545] 1592 0.175549 0.240258558 0.730667 LMNA
LAMIN B RECEPTOR (INTEGRAL NUCLEAR ENVELOPE INNER MEMBRANE PROTEIN) (LMN2R). [SWISSPROT;Acc:Q14739] 2713 0.0244747 0.207342426 0.11804 LBR
LAMIN B1. [SWISSPROT;Acc:P20700] 1596 0.210907 0.240252935 0.877854 LMNB1
LAMIN B2. [SWISSPROT;Acc:Q03252] 1264 0.481793 0.247040395 1.95026 no value
LAMININ GAMMA-1 CHAIN PRECURSOR (LAMININ B2 CHAIN). [SWISSPROT;Acc:P11047] 839 0.386694 0.260705473 1.48326 LAMC1
LANC LANTIBIOTIC SYNTHETASE COMPONENT C-LIKE 2; TESTIS-SPECIFIC ADRIAMYCIN SENSITIVITY PROTEIN; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT C)-LIKE 2; G PROTEIN-COUPLED RECEPTOR 69B. [RefSeq;Acc:NM_018697] 608 0.0958474 0.268952474 0.356373 LANCL2
LANTHIONINE SYNTHETASE C-LIKE PROTEIN 1; G PROTEIN-COUPLED RECEPTOR 69A; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT C)-LIKE 1; LANC (BACTERIAL LANTIBIOTIC SYNTHETASE COMPONENT). [RefSeq;Acc:NM_006055] 607 0.0803201 0.26895292 0.29864 LANCL1
LAP (LEUCINE-RICH REPEATS AND PDZ) AND NO PDZ PROTEIN. [RefSeq;Acc:NM_018214] 885 0.122677 0.259992625 0.471848 LRRC1
LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 2446 0.109079 0.217096399 0.502445 no value
LATS HOMOLOG 1. [RefSeq;Acc:NM_004690] 550 0.046789 0.271000214 0.172653 LATS1
LBP-9. [RefSeq;Acc:NM_014553] 641 0.198895 0.268222097 0.741531 TFCP2L1
LENG5 PROTEIN. [RefSeq;Acc:NM_024075] 2373 0.0517945 0.220049113 0.235377 TSEN34
LENS FIBER MAJOR INTRINSIC PROTEIN (MIP26) (MP26) (AQUAPORIN 0). [SWISSPROT;Acc:P30301] 2840 0.0610425 0.192747326 0.316697 MIP
LEUCINE-RICH REPEAT PROTEIN LRRC3 PRECURSOR. [SWISSPROT;Acc:Q9BY71] 841 0.0837034 0.260704653 0.321066 LRRC3
LEUCINE-RICH REPEAT PROTEIN SHOC-2 (RAS-BINDING PROTEIN SUR-8). [SWISSPROT;Acc:Q9UQ13] 2958 0.100774 0.146165148 0.689453 SHOC2
LEUCINE-RICH REPEAT-CONTAINING PROTEIN 15 PRECURSOR (HLIB). [SWISSPROT;Acc:Q8TF66] 843 0.0992922 0.260704562 0.380861 LRRC15
LEUCYL-TRNA SYNTHETASE. [RefSeq;Acc:NM_020117] 2155 0.159792 0.227259733 0.703125 LARS
LEUKOCYTE ELASTASE INHIBITOR (LEI) (MONOCYTE/NEUTROPHIL ELASTASE INHIBITOR) (M/NEI) (EI). [SWISSPROT;Acc:P30740] 2319 0.0244744 0.221796893 0.110346 SERPINB1
LEUKOTRIENE A-4 HYDROLASE (EC 3.3.2.6) (LTA-4 HYDROLASE) (LEUKOTRIENE A(4) HYDROLASE). [SWISSPROT;Acc:P09960] 2268 0.0297305 0.222740418 0.133476 LTA4H
LIFEGUARD; KIAA0950 PROTEIN. [RefSeq;Acc:NM_012306] 2150 0.0891166 0.227323188 0.392026 FAIM2
LIGATIN (HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 56). [SWISSPROT;Acc:P41214] 1920 0.495014 0.231969671 2.13396 LGTN
LIKELY ORTHOLOG OF MOUSE SHC SH2-DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_024745] 3118 0.0737653 0.088194123 0.836397 SHCBP1
LIKELY ORTHOLOG OF MOUSE VARIANT POLYADENYLATION PROTEIN CSTF-64. [RefSeq;Acc:NM_015235] 2075 0.388695 0.229175265 1.69606 CSTF2T
LIKELY ORTHOLOG OF RAT CYTOCHROME P450 4X1. [RefSeq;Acc:NM_178033] 629 0.0954996 0.26825881 0.355998 CYP4X1
LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 2; ILK-BINDING PROTEIN. [RefSeq;Acc:NM_017980] 2514 0.117844 0.214767107 0.548706 LIMS2

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/